Development, integration and benchmarking of algorithms and tools for analyzing large scale microbiome datasets A Simula­UiO­UCSD Research and PhD training collaboration (SUURPh) project proposal 

Project Scope

Relevance of the scientific problem within the biological and medical sciences We are constantly surrounded in our environment and even within our own bodies by large numbers of microorganisms including bacteria, fungi and viruses that are highly important for our lives but largely invisible to our eyes. The microbes in a niche form an ecosystem that is called a microbiome. These can be investigated using metagenomics, which is the study of the genetic material in a sample containing a mix of different microbial organisms. Samples may have been obtained from such diverse locations as the depths of the oceans (TARA Oceans) (Karsenti et al. 2011), the human body (Human Microbiome Project, HMP) (Human Microbiome Project Consortium, 2012), or anywhere on earth (Earth Microbiome Project, EMP) (Gilbert, Jansson and Knight, 2014).

Recent advances in DNA sequencing technologies have enabled very large amounts of such data to be obtained for analysis. Extracting biologically meaningful information from these huge datasets involves hard computational challenges. Interpreting the data correctly can advance science significantly by a better understanding of, for example, the diversity of ecosystems or how the human immune system responds to exposure to different microorganisms. In particular, we hope to build predictive models of disease and of environmental responses to perturbation including fire, climate change, and ocean acidification. The results are therefore very far-reaching.

The DNA sequence data must be carefully analyzed through many steps before a reliable estimate of diversity of the samples and an overview of the taxa present may be obtained. Several analysis pipelines have been established for this type of analysis, including QIIME (Quantitative Insights Into Microbial Ecology) (Caporaso et al., 2010). However, there is a need for computational tools that can analyze massive next-generation sequencing datasets (on the order of terabytes) with sufficient accuracy and speed. 

How computational approaches will be used to address this problem and extend prior work in this field An open-source clustering tool for microbiome data called SWARM that is based on single-linkage hierarchical clustering has recently been developed by Mahé, Rognes, Quince and collaborators (Mahé et al., 2014). The new version 2 offers fine-grained clustering with linear time complexity, and is now available (manuscript in prep.). This tool appears to be the only one that can analyze large EMP datasets containing several billion sequences in a matter of hours. Other tools have been estimated to require months of computation time for the same dataset. Rognes, Mahé and collaborators have also recently developed VSEARCH, a versatile open source tool for processing of metagenomics data (manuscript in prep.) that replaces many of the functionalities of the closed-source USEARCH tool (Edgar, 2010).

QIIME (www.qiime.org) is a widely used pipeline for microbiome data analysis that has been developed over several years by a large team led by Caporaso and Knight. The current version, 1.9 includes the ability to run several different tools including USEARCH and SWARM. However, QIIME version 2 will involve major changes and a different mechanism of integration.

The goal of this project is to add needed functionality and improve accuracy and speed of SWARM and VSEARCH, integrate them into QIIME, and perform extensive benchmarking against existing tools using several large datasets with real and synthetic data. The ability to handle huge datasets is of paramount importance, and this goal can only be reached by improved algorithms, clever use of data structures, and efficient parallelization.

Some of Knight’s San Diego Supercomputer Center (SDSC) allocation (500,000 core hours on the Gordon and Comet instruments) will be committed to benchmarking. The Abel cluster at the University of Oslo will also be used.

References Caporaso JG et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7,

335–336. doi:10.1038/nmeth.f.303 Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460-2461.

doi:10.1093/bioinformatics/btq461 Gilbert JA, Jansson JK, Knight R (2014) The Earth Microbiome project: successes and aspirations. BMC Biology, 12, 69.

doi:10.1186/s12915-014-0069-1

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Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature, 486, 207-214. doi:10.1038/nature11234

Karsenti E et al. (2011) A holistic approach to marine eco-systems biology. PLoS Biology, 9, e1001177. doi:10.1371/journal.pbio.1001177

Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M (2014) Swarm: robust and fast clustering method for amplicon-based studies. PeerJ 2, e593. doi:10.7717/peerj.593

Inter-Institutional Collaboration In Oslo, this project will be based primarily at UiO. Dr. Frédéric Mahé at CNRS and Sorbonne University, France, and the University of Kaiserslautern, Germany, will be advisor in addition to the faculty at UCSD and UiO.

Contributing faculty at UiO Primary advisor: Prof. Torbjørn Rognes, Dept. of Informatics. http://www.mn.uio.no/ifi/english/people/aca/torognes

Contributing faculty at UCSD Primary advisor: Prof. Rob Knight, Dept. of Pediatrics & Dept. of Computer Science. He is a member of the Steering Committee of the Earth Microbiome Project, and a co-founder of the American Gut Project. https://knightlab.ucsd.edu/ Secondary advisor: Postdoctoral research associate Evguenia Kopylova, Dept. of Pediatrics. Secondary advisor: Ph.D. candidate Jose A. Navas-Molina, Dept. of Pediatrics.

How the project will foster collaboration between the UCSD and Oslo groups, and how the major scientific and training objectives of the proposal will be distributed between Oslo and San Diego The project will bring together tool developers and members of the metagenomics community in Oslo with world leading metagenomics scientists and developers of the popular QIIME pipeline. This will be of mutual benefit as it will make state-of-the-art tools readily available to a large worldwide community. Specifications of integration into the QIIME pipeline will be provided by the group in San Diego, while most tool development and benchmarking will be carried out by the group in Oslo. Data sets from the large microbiome projects will be provided by the group in San Diego, or from public sources. Procedures for benchmarking will be developed together.

International and Local Training

Courses to be taken at UiO MNSES9100 - Science, ethics and society (mandatory, 5 credits) BIO9905MERG1 - Bioinformatics for Metagenomic Analyses and Environmental Sequencing (5 credits) INF9063 - Programming heterogeneous multi-core architectures (10 credits) STK9030 - Modern data analysis (10 credits)

Additional professional/research training activities at UiO The student will become a member of the Biomedical Informatics Research Group at the Department of Informatics and will work together with other PhD students as well as faculty and master students in the group. Several other people in the group will be working on very closely related projects. We collaborate closely also with the Department of Biosciences at UiO and the Department of Microbiology at Oslo University Hospital, and the student will also be involved these collaborations. Activities include seminars, journal clubs, etc.

Additional professional/research training activities at UCSD Training activities at UCSD would include working with the QIIME and QIITA developers, taking CSE courses as appropriate, working on real-world datasets of different kinds for sequence clustering and search, and interacting with the bioinformatics/systems biology community at UCSD including Trey Ideker, Pavel Pevzner, Bernhard Palsson, as well as researchers at the San Diego Supercomputing Center (SDSC) and the Qualcomm Institute (formerly CalIT2).

How advisors at both institutions will monitor the student’s progress and development The progress and development of the student will be monitored through weekly meetings with the supervisors at the local institution. In addition we will have monthly teleconference meetings with supervisors from all institutions. We plan physical meetings with all involved once per year. Mid-term evaluation will be carried out as usual at UiO.

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Curriculum Vitae for Torbjørn Rognes Personal information Birth: 20 July 1969 in Bergen, Norway Citizenship: Norwegian Marital status: Married, 1 child Address: Department of Informatics, University of Oslo, PO Box 1080 Blindern,

NO-0316 Oslo, Norway Phone numbers: Mobile: +47 90755587. Office +47 22844787. Fax +47 22852401 E-mail: torognes@ifi.uio.no Current positions Since Sep 2010 Professor, Department of Informatics, University of Oslo Since Jan 2004 Research scientist and group leader, Oslo University Hospital, Oslo Previous positions May 2003 – Oct 2013 Chief Executive Officer, Sencel Bioinformatics AS, Oslo Jun 2004 – Sep 2010 Associate professor, Department of Informatics, University of Oslo Jul 2001 – Dec 2004 Postdoc, University of Oslo / The Norwegian Cancer Society Jan 1995 – Jun 2001 PhD student, University of Oslo / Rikshospitalet / Medinnova Jan 1994 – Dec 1994 Programmer, MedProbe AS, Oslo Education Jan 1995 – Jun 2001 Ph.D. (Dr.philos), Bioinformatics, Faculty of Medicine, University of Oslo.

Thesis: ”Rapid and sensitive methods for protein sequence comparison and database searching”.

Sep 1988 – Jan 1994 M.Sc. (Sivilingeniør), Computer science, Institute of Computer Science and Telematics, Norwegian Institute of Technology (NTH), University of Trondheim. Thesis: "Vector Quantization with a Digital Data Filter".

Major grants • Eureka / EU: Eurostars project, 2010-2013, project leader • Research Council of Norway: Centre of Excellence grant 2003-2012 (CMBN), partner. • European Commission: 6FP Integrated Project: DNA damage response and repair mechanisms,

2005-2008, partner. • Research Council of Norway: FUGE career grant 2003-2007. • Research Council of Norway: Medicine and Health (MH) group grant, 2001-2005, partner. Research group / research leadership experience Since Jan 2015, leader of the Research Group for Biomedical Informatics (BMI) at Dept. of Informatics, UiO. Since 2002, group leader of the OUS Bioinformatics research group (one of the thirteen research groups in CMBN 2003-2012). For further information, please visit www.mn.uio.no/ifi/english/research/groups/bmi and www.ous-research.no/rognes. Student supervision • 7 Ph.D. students. Main supervisor of 4 students at University of Oslo (Lagesen, Thomassen and

Nakken have successfully defended their theses, 1 current), co-supervisor of 4 students (Razick and Aanes successfully defended, 2 current).

• 21 M.Sc. (cand.scient or master of science) students at Department of Informatics, University of Oslo (12 completed, 9 current)

• 3 M.Sc. (sivilingeniør) students at Department of Computer and Information Science, Norwegian University of Science and Technology (NTNU), Trondheim.

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Teaching Main responsible for INF4350 – Introduction to bioinformatics, fall 2008-2010 and spring 2013-2015 at the Department of Informatics, University of Oslo. Responsible for INF5340 – Algorithms in bioinformatics, spring 2005-2007. Participated in numerous other courses over several years at UiO (BIO9905MERG1, INF2300, INF3350, INF4130, INF5330, KJB492, MBV4010, MBV-INF4410, MF9210, MNBTS400, MNBTS9000) and Oslo College (HiO). Completed all courses required for basic pedagogical competence at the University of Oslo. Patents Inventor on 3 patent families, of which one is granted in US and Norway Research residency Center for Biological Sequence analysis (CBS), Technical University of Denmark, Lyngby, Denmark, March 2003 – March 2004. Boards and committees • Steering group for research in molecular biology, biotechnology and bioinformatics (EMBIO),

University of Oslo, deputy member, August 2004-August 2007. • Society for Bioinformatics in the Nordic countries, board member 2005-2008. Conference organization • Erling Seeberg Symposium on DNA Repair, Lofoten, Norway, 28 May – 2 June 2006 • Third-Seventh CMBN conference, Hafjell / Geilo, Norway, 2006-2010 • Fourth Norwegian Bioinformatics Forum, Oslo, 18-19 November 2010 • Norwegian Biochemical Society Contact Meeting 2013, Lillehammer, Norway, 30 January – 2

February 2013 (national meeting, 350 participants) • Bioinformatics 2014 (Annual SocBiN conference), June 11-13, Oslo, Norway Journal referee Bioinformatics, BMC Bioinformatics, BMC Microbiology, BMC Genomics, PeerJ, PLOS One, IEEE/ACM Trans. on Comp. Biology and Bioinformatics, Journal of Bioinformatics and Computational Biology, Journal of Parallel and Distributed Computing, BioSilico Evaluation of PhD thesis Opponent and member of the evaluation committee for the PhD theses of • Tony Håndstad, Dept. of Cancer Research and Molecular Medicine, NTNU, Norway (2014) • Kjetil Klepper, Dept. of Cancer Research and Molecular Medicine, NTNU, Norway (2013) • Pankaj Barah, Dept. of Biology, NTNU, Norway (2013) • Todd J. Treangen, Dept. of Computer Sci., Techn. Univ. of Catalonia, Barcelona, Spain (2008) Member of the evaluation committee for the PhD thesis of • Antonio C. Mora Ortiz, The Biotechnology Centre, University of Oslo, Norway (2012) Prizes • Bronze medal in the 20th International Chemistry Olympiad, Espoo, Finland, 1988. • Best poster prize, Norwegian Biochemical Society, Contact Meeting, Tromsø, 1999. Publication statistics Published 35 original journal articles, 6 reviews, 2 proceedings papers, 1 book chapter. According to Google Scholar, Apr 2015: 3363 total citations. H-index: 20

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Publication list for Torbjørn Rognes

Original articles in peer-reviewed journals 1. Bjørås M, Luna L, Johnsen B, Hoff E, Haug T, Rognes T and Seeberg E (1997)

Opposite base-dependent reactions of a human base excision repair enzyme on DNA containing 7,8-dihydro-8-oxoguanine in DNA and abasic sites EMBO J, 16 (20), 6314-6322. DOI 10.1093/emboj/16.20.6314 (289 citations*)

2. Rognes T and Seeberg E (1998) SALSA: improved protein database searching by a new algorithm for assembly of sequence fragments into gapped alignments Bioinformatics, 14 (10), 839-845. DOI 10.1093/bioinformatics/14.10.839 (18 citations)

3. Alseth I, Eide L, Pirovano M, Rognes T, Seeberg E and Bjørås M (1999) The Saccharomyces cerevisiae homologues of endonuclease III from Escherichia coli, Ntg1 and Ntg2, are both required for efficient repair of spontaneous and induced oxidative DNA damage in yeast Mol Cell Biol, 19 (5), 3779-3787. URL: http://mcb.asm.org/content/19/5/3779.full (131 citations)

4. Luna L, Bjørås M, Hoff E, Rognes T and Seeberg E (2000) Cell-cycle regulation, intracellular sorting and induced overexpression of the human NTH1 DNA glycosylase involved in removal of formamidopyrimidine residues from DNA Mutat Res, 460 (2), 95-104. DOI 10.1016/S0921-8777(00)00015-X (63 citations)

5. Rognes T and Seeberg E (2000) Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors Bioinformatics, 16 (8), 699-706. DOI 10.1093/bioinformatics/16.8.699 (204 citations)

6. Rognes T (2001) ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches Nucleic Acids Res, 29 (7), 1647-1652. DOI 10.1093/nar/29.7.1647 (65 citations)

7. Morland I, Rolseth V, Luna L, Rognes T, Bjørås M and Seeberg E (2002) Human DNA glycosylases of the bacterial Fpg/MutM superfamily: An alternative pathway for the repair of 8-oxoguanine and other oxidation products in DNA Nucleic Acids Res, 30 (22), 4926-4936. DOI 10.1093/nar/gkf618 (213 citations)

8. Moe A, Ringvoll J, Nordstrand LM, Eide L, Bjørås M, Seeberg E, Rognes T and Klungland A (2003) Incision at hypoxanthine residues in DNA by a mammalian homologue of the Escherichia coli antimutator enzyme endonuclease V Nucleic Acids Res, 31 (14) 3893-3900. DOI 10.1093/nar/gkg472 (54 citations)

9. Davidsen T, Rødland EA, Lagesen K, Seeberg E, Rognes T and Tønjum T (2004) Biased distribution of DNA uptake sequences towards genome maintenance genes Nucleic Acids Res, 32 (3), 1050-1058. DOI 10.1093/nar/gkh255 (69 citations)

10. Sætrom P, Sneve R, Kristiansen K, Snøve O, Grünfeld T, Rognes T and Seeberg E (2005) Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming Nucleic Acids Res, 33 (10), 3263-3270. DOI 10.1093/nar/gki644 (48 citations)

11. Sæbø PE, Andersen SM, Myrseth J, Laerdahl JK and Rognes T (2005) PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology Nucleic Acids Res, 33 (Web server issue), W535-W539. DOI 10.1093/nar/gki423 (44 citations)

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12. Alseth I, Rognes T, Lindbäck T, Solberg I, Robertsen K, Kristiansen KI, Mainieri D, Lillehagen L, Kolstø AB and Bjørås M (2006) A new protein superfamily includes two novel 3-methyladenine DNA glycosylases from Bacillus cereus, AlkC and AlkD Mol Microbiol, 59 (5), 1602-9. DOI 10.1111/j.1365-2958.2006.05044.x (29 citations)

13. Dalhus B, Helle IH, Backe PH, Alseth I, Rognes T, Bjørås M and Lærdahl J (2007) Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats Nucleic Acids Res, 35 (7), 2451-2459. DOI 10.1093/nar/gkm039 (20 citations)

14. Lagesen K, Hallin PF, Rødland EA, Stærfeldt HH, Rognes T and Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes Nucleic Acids Res, 35 (9), 3100-3108. DOI 10.1093/nar/gkm160 (1362 citations)

15. Cameron J, Holla ØL, Lærdahl JK, Kulseth MA, Ranheim T, Rognes T, Berge KE and Leren TP (2008) Characterization of novel mutations in the catalytic domain of the PCSK9 gene J Int Medicine, 263 (4), 420-431. DOI 10.1111/j.1365-2796.2007.01915.x (37 citations)

16. Skotheim RI, Thomassen GO, Eken M, Lind GE, Micci F, Ribeiro FR, Cerveira N, Teixeira MR, Heim S, Rognes T and Lothe RA (2009) A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis Mol Cancer, 8, 5. DOI 10.1186/1476-4598-8-5 (25 citations)

17. Nakken S, Rødland EA, Rognes T and Hovig E (2009) Large-scale inference of the point mutational spectrum in human segmental duplications BMC Genomics, 10, 43. DOI 10.1186/1471-2164-10-43 (4 citations)

18. Thomassen GOS, Rowe AD, Lagesen K, Lindvall JM and Rognes T (2009) Custom Design and Analysis of High-density Oligonucleotide Bacterial Tiling Microarrays PLOS One, 4 (6), e5943. DOI 10.1371/journal.pone.0005943 (16 citations)

19. Nakken S, Rognes T and Hovig E (2009) The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts Nucleic Acids Res, 37 (17), 5749-5756. DOI 10.1093/nar/gkp590 (16 citations)

20. Fensgård Ø, Kassahun H, Bombik I, Rognes T, Lindvall JM and Nilsen H (2010) A two-tiered compensatory response to loss of DNA repair modulates aging and stress response pathways Aging (Albany NY), 2 (3), 133-59. URL: www.impactaging.com/papers/v2/n3/full/100127.html (17 citations)

21. Nordstrand LM, Svärd J, Larsen E, Nilsen A, Ougland R, Furu K, Lien GF, Rognes T, Namekawa SH, Lee JT and Klungland A (2010) Mice lacking the novel histone H2A dioxygenase Alkbh1 display sex-ratio distortion, asymmetric left–right eye development and increased expression of a piRNA cluster PLOS One, 5 (11), e13827. DOI 10.1371/journal.pone.0013827 (17 citations)

22. Møllersen L, Rowe AD, Larsen E, Rognes T and Klungland A (2010) Continuous and periodic expansion of CAG repeats in Huntington's disease R6/1 mice PLOS Genet, 6 (12), e1001242. DOI 10.1371/journal.pgen.1001242 (19 citations)

23. Thomassen GOS, Weel-Sneve R, Rowe AD, Booth JA, Lindvall JM, Lagesen K, Kristiansen KI, Bjørås M and Rognes T (2010) Tiling Array Analysis of UV Treated Escherichia coli Predicts Novel Differentially Expressed Small Peptides PLOS One, 5 (12), e15356. DOI 10.1371/journal.pone.0015356 (8 citations)

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24. Lærdahl JK, Korvald H, Nilsen L, Dahl-Michelsen K, Rognes T, Alseth I and Bjørås M (2011) Schizosaccharomyces pombe encodes a mutated AP endonuclease 1 DNA repair (Amst), 10 (3), 296-305. DOI 10.1016/j.dnarep.2010.11.014 (4 citations)

25. Rognes T (2011) Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation BMC Bioinformatics, 12, 221. DOI 10.1186/1471-2105-12-221 (69 citations)

26. Yang M, Aamodt R, Dalhus B, Balasingham S, Helle I, Andersen P, Tønjum T, Alseth I, Rognes T and Bjørås M (2011) The ada operon of Mycobacterium tuberculosis encodes two DNA methyltransferases for inducible repair of DNA alkylation damage DNA repair (Amst), 10 (6), 595-602. DOI 10.1016/j.dnarep.2011.03.007 (10 citations)

27. Søberg K, Larsen ACV, Diskar M, Backe PH, Bjørås M, Jahnsen T, Laerdahl JK, Rognes T, Herberg FW and Skålhegg BS (2012) Identification and Characterization of Novel Mutations in the Human Gene Encoding the Catalytic Subunit Calpha of Protein Kinase A (PKA) PLOS One, 7 (4), e34838. DOI 10.1371/journal.pone.0034838 (1 citation)

28. Nordstrand LM, Furu K, Paulsen J, Rognes T and Klungland A (2012) Alkbh1/Tzfp Repress a Non-Repeat piRNA Cluster in Pachytene Spermatocytes Nucleic Acids Res, 40 (21), 10950-10963. DOI 10.1093/nar/gks839 (7 citations)

29. Ougland R, Lando D, Jonson I, Dahl JA, Nordstrand LM, Rognes T, Lee JT, Klungland A, Kouzarides T and Larsen E (2012) ALKBH1 is a Histone H2A Dioxygenase Involved in Neural Differentiation Stem Cells, 30 (12), 2672-2682. DOI 10.1002/stem.1228 (12 citations)

30. Weel-Sneve R, Kristiansen KI, Odsbu I, Dalhus B, Booth J, Rognes T, Skarstad K and Bjørås M (2013) Single Transmembrane Peptide DinQ Modulates Membrane Dependent Activities PLOS Genet, 9 (2), e1003260. DOI 10.1371/journal.pgen.1003260 (6 citations)

31. Søberg K, Jahnsen T, Rognes T, Skålhegg BS and Lærdahl JK (2013) Evolutionary paths of the cAMP-dependent protein kinase (PKA) catalytic subunits PLOS One, 8 (4), e60935. DOI 10.1371/journal.pone.0060935 (6 citations)

32. Backe PH, Simm R, Lærdahl JK, Dalhus B, Fagerlund A, Økstad OA, Rognes T, Alseth I, Kolstø AB and Bjørås M (2013) A new familiy of proteins related to the HEAT-like repeat DNA glycosylases with affinities for branched DNA structures J Struct Biol, 183 (1), 66-75. DOI 10.1016/j.jsb.2013.04.007

33. Thomassen GOS, Booth JA, Rowe AD, Weel-Sneve R, Lagesen K, Kristiansen KI, Bjørås M, Rognes T and Lindvall JM (2013) Tiling array study of MNNG treated Escherichia coli reveals a widespread transcriptional response Sci Rep, 3, 3053. DOI 10.1038/srep03053 (1 citation)

34. Aanes H, Winata C, Moen LF, Østrup O, Mathavan S, Collas P, Rognes T, Aleström P (2014) Normalization of RNA-sequencing data from samples with varying mRNA levels PLOS One, 9 (2), e89158. DOI 10.1371/journal.pone.0089158 (2 citations)

35. Mahé F, Rognes T, Quince C., de Vargas C, Dunthorn M (2014) Swarm: robust and fast clustering method for amplicon-based studies PeerJ, 2, e593. DOI 10.7717/peerj.593 (4 citations)

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Preprints

1. Mahé F, Rognes T, Quince C., de Vargas C, Dunthorn M (2014) Swarm: robust and fast clustering method for amplicon-based studies PeerJ PrePrints 2, e386v1. DOI 10.7287/peerj.preprints.386v1

Manuscripts 1. Kopylova E, Navas-Molina JA, Mercier C, Xu Z, Mahé F, Rognes T, Caporaso JG, Knight R

Open-source sequence clustering methods improve the state of the art (submitted)

2. Flouri T, Kobert K, Rognes T, Stamatakis A Are all global sequence alignment algorithms and implementations correct? (submitted)

3. Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M Swarm 2.0: highly scalable clustering (in preparation)

4. Rognes T, Mahé F, Flouri T, Nichols B, Ijaz UZ, Quince C VSEARCH: a versatile open source metagenomics tool (in preparation)

Reviews 1. Falnes PØ and Rognes T (2003)

DNA repair by bacterial AlkB proteins Res Microbiol, 154 (8), 531-538. DOI 10.1016/S0923-2508(03)00150-5 (41 citations)

2. Thomassen GOS, Røsok Ø and Rognes T (2006) Computational prediction of microRNAs encoded in viral and other genomes J Biomed Biotechnol, 2006 (4), 95270. DOI 10.1155/JBB/2006/95270 (6 citation)

3. Nakken S, Alseth I and Rognes T (2007) Computational prediction of the effects of non-synonymous single nucleotide polymorphisms in human DNA repair genes Neuroscience, 145, 1273-1279. DOI 10.1016/j.neuroscience.2006.09.004 (28 citations)

4. Røyrvik EC, Ahlquist T, Rognes T, Lothe RA (2007) Slip Slidin’ Away: A duodecennial review of targeted genes in mismatch repair deficient colorectal cancer Crit Rev Oncog, 13 (3), 229-257. DOI 10.1615/CritRevOncog.v13.i3.20 (16 citations)

5. Robertson AB, Klungland A, Rognes T, Leiros I (2009) DNA repair in mammalian cells: Base excision repair: the long and short of it Cell Mol Life Sci, 66 (6), 981-993. DOI 10.1007/s00018-009-8736-z (299 citations)

6. Ambur OH, Davidsen T, Frye SA, Balasingham SV, Lagesen K, Rognes T, Tønjum T (2009) Genome dynamics in major bacterial pathogens FEMS Microbiol Rev, 33 (3), 453-70. DOI 10.1111/j.1574-6976.2009.00173.x (59 citations)

Proceedings papers 1. Luna L, Bjørås M, Berdal KG, Alseth I, Eide L, Rognes T, Seeberg E (1999)

Genes and enzymes for the removal of oxidative DNA base damage In Molecular biology of aging, Alfred Benzon Symposium Series, 44, 272-283.

2. Seeberg E, Luna L, Morland I, Eide L, Johnsen B, Larsen E, Alseth I, Dantzer F, Baynton K, Aamodt R, Kristiansen KI, Rognes T, Klungland A, Bjørås M (2000)

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Base removers and strand scissors: Different strategies employed in base excision and strand incision at modified base residues in DNA Cold Spring Harb Symp Quant Biol, 65, 135-142. DOI 10.1101/sqb.2000.65.135 (9 citations)

Book chapters

1. Klungland A, Lærdahl JK, Rognes T (2007) OGG1: from structural analysis to the knockout mouse In Oxidative Damage to Nucleic Acids (Eds. Evans and Cooke), Landes Biosciences, 67-80. ISBN 978-0-387-72973-2. DOI 10.1007/978-0-387-72974-9_5 (2 citations)

Theses

1. Rognes T (1994) Vector Quantization with a Digital Data Filter Master thesis, Institute of Computer Science and Telematics, Norwegian Institute of Technology, University of Trondheim, Trondheim, Norway.

2. Rognes T (2000) Rapid and sensitive methods for protein sequence comparison and database searching Doctoral thesis, Institute of Medical Microbiology, University of Oslo.

Books 1. Rognes T, Seeberg E, Kvale D (1994)

SpeedGenie User’s guide MedProbe AS, Oslo, Norway, 89 pages.

2. Rognes T, Seeberg E, Kvale D (1994) SpeedGenie Demo Guide MedProbe AS, Oslo, Norway, 73 pages.

Patents 1. Rognes T. (Inventor) Rognes T. and Seeberg E. (Assignees)

Determination of optimal local sequence alignment similarity score US Patent No 7917302 issued 29 March 2011. Norwegian Patent No 324517 granted 5 November 2007. PCT/NO 01/00394. Patent pending in other countries.

2. Rognes T. (Inventor) Rognes T. and Seeberg E. (Assignees) Parallel biological sequence alignments US patent application 10/471,897. PCT/NO02/00041.

3. Lothe RA, Lind GE, Skotheim RI, Thomassen GOS, Rognes T (Inventors) Oslo Universitetssykehus HF (Assignee) Fusion Gene Microarray US Patent application 12/664,537. PCT/EP2008/058272.

Popular science publications

1. Rognes T (2004) Bedre søk i sekvensdatabaser NBS-nytt, Norwegian Biochemical Society, Oslo, Norway, 1, 2004.

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2. Rognes T (2007) Large-scale comparison of biological sequences META, The NOTUR project, Norway, 2, 2007.

3. Rognes T, Hovig E (2015) Bioinformatikk - å forstå teksten In Mendels arv - Genetikkens æra (Eds. Hessen, Lie and Stenseth), Gyldendal, 329-354. ISBN 978-82-05-45818-5.

* Citations according to Google Scholar as of April 2015.

Curriculum Vitae: Rob Knight Contact Details Address: University of California, San Diego 9500 Gilman Drive, MC 0763 La Jolla, CA 92093-0763 USA Phone: (858) 246-1184 Email: robknight@ucsd.edu Web: http://biomedsci.ucsd.edu/faculty/faculty_descrip.aspx?id=339 Biographical Details Date of birth: November 13, 1976 Place of birth: Dunedin, New Zealand Nationality: New Zealand Education: 2001 Ph.D., Princeton University (Ecology and Evolutionary Biology) Thesis topic: Origin and Evolution of the Genetic Code 1996 B.Sc., University of Otago (Biochemistry) Employment: 2015- Professor, Departments of Pediatrics and Computer Science &

Engineering, University of California at San Diego 2013-2014 Professor, Department of Chemistry and Biochemistry and BioFrontiers

Institute, University of Colorado, Boulder 2010-2013 Associate Professor, Department of Chemistry and Biochemistry,

University of Colorado, Boulder 2007-2014 Assistant Professor, Department of Computer Science, University of

Colorado, Boulder (courtesy appointment) 2004-2014 Assistant Professor, Computational Biosciences Program, University of

Colorado Health Sciences Center/University of Colorado, Denver

2004-2010 Assistant Professor, Department of Chemistry and Biochemistry, University of Colorado, Boulder. 2001-2004 Postdoctoral Research Assistant, University of Colorado Principal Investigator: Professor Michael Yarus

Research: sequence/function relationships in RNA; gene and genome evolution relevant to the evolution of the genetic code and the origin of life

1996-2001 Assistant in Instruction, Princeton University In addition to completing thesis research on the origin and evolution of the genetic code, worked with and directed undergraduate research assistants and graduate laboratory technicians; used standard protocols in molecular biology, and developed software in several languages for several platforms. Honors and Awards: 2014 Thomson Reuters Highly Cited Researcher 2013 Science Watch, Hottest Scientific Researchers and Research 2012 AAAS Fellow 2011 RGE Murray Lectureship 2011 Provost Faculty Achievement Award 2010 Kavli Fellow Award 2009 Howard Hughes Medical Institute Early Career Scientist Award 2008 Marinus Smith Parents Association Award “for making a difference in the lives of one or

more undergraduates”. 2006 BMC Top 100 contributor 2001 Council of Graduate Schools/ University Microfilms International Distinguished Dissertation Award (Biological and Life Sciences). 2001 Travel grant from NSF Incubation Activity/Biocomplexity grant to present thesis research at joint SSE/SSB/ASN meeting in Knoxville, TN, June 26-July 1 2000 Travel funding from Santa Fe Institute to visit September 6-9 and to present thesis research. 1996 Princeton University Merit Award 1995 Ministry of Research, Science and Technology Travel Award under the NZ-USA Collaborative Science Programme to visit Princeton University to investigate the feasibility of using meiotic drive genes to control mammalian pests 1993 NSEST Scholarship Exams: Ranked Top Scholar in New Zealand for aggregate of five subjects 1993 Bursary: received Scholarship grade in six subjects 1993 Reserve (5th in country), New Zealand Chemical Olympiad Team 1993 1993 First Equal in Fair, Otago Science Fair 1993 (also First Prize, Senior Experimental Research Section; NZ Statistical Association Prize; Division of Sciences—Otago University Prize) 1993 1st in New Zealand, National Bank Senior Science Competition 1993 1993 1st Equal, Canadian Institute of Chemistry Examination (with 100%) Publications from work prior to becoming an Assistant Professor: Research articles (peer-reviewed)

1. Freeland, S. J., Knight, R.D. and Landweber, L.F. (1999). "Do proteins predate DNA?" Science 286(5440): 690-2.

2. Freeland, S. J., Knight, R.D., Landweber, L.F. and Hurst, L.D. (2000). "Early Fixation of an Optimal Genetic Code." Mol Biol Evol 17(4): 511-518.

3. Knight, R. D. and Landweber, L.F. (2000). "Guilt by association: the arginine case revisited." RNA 6(4): 499-510.

4. Lozupone, C. A., Knight, R. D., and Landweber, L.F. (2001). "The Molecular Basis of Nuclear Genetic Code Changes in Ciliates." Current Biology 11:65-74.

5. Knight, R. D., Landweber, L. F., and Yarus, M. (2001). "How mitochondria redefine the code." J. Mol. Evol. 53:299-313

6. Knight, R. D., Freeland, S. J., and Landweber, L.F. (2001). "A Simple Model Based On Mutation and Selection Explains Compositional Trends Within and Across Genomes." GenomeBiology 2(4):research0010.1-0010.13.

7. Knight, R. and Yarus, M. (2003). "Finding specific RNA motifs: Function in a zeptomole world?" RNA 9:218-230.

8. Knight, R. and Yarus, M. (2003). "Analyzing partially randomized nucleic acid pools: straight dope on doping." Nucleic Acids Research 31:e30.

9. Resing, K.A., Meyer-Arendt, K.E., Alex M. Mendoza, A.M., Aveline-Wolf, L.D., Jonscher, K.R., Pierce, K.G., Old, W.M., Cheung, H.T., Russell, S., Wattawa, J.L., Goehle, G.R., Knight, R.D., and Ahn, N.G. (2004). “Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics.” Anal Chem. 76(13):3556-68.

10. Knight, R., Birmingham, A. E., and Yarus, M. (2004). “Bayesfold: Rational secondary folds that combine thermodynamic, covariation and chemical data for aligned RNA sequences”. RNA10(9):1323-36.

11. Stotz, K., Griffiths, P.E., and Knight, R (2004). “How biologists conceptualize genes: an empirical study.” Studies in History and Philosophy of Science Part C: Medical Sciences 35(4):647-73.

Reviews (peer-reviewed)

12. Knight, R. D. and Landweber, L.F. (1998). "Rhyme or reason: RNA-arginine interactions and the genetic code." Chem Biol 5(9): R215-20.

13. Knight, R. D. and Landweber, L.F. (1999). "Is the genetic code really a frozen accident? New evidence from in vitro selection." Ann N Y Acad Sci 870: 408-10.

14. Knight, R. D., Freeland, S.J. and Landweber, L.F. (1999). "Selection, history and chemistry: the three faces of the genetic code." Trends Biochem Sci 24(6):241-7.

15. Knight, R. D. and Landweber, L.F. (2000). "The Early Evolution of the Genetic Code" Cell 101(6): 569-572.

16. Knight, R. D., Freeland, S.J. and Landweber, L.F. (2001). "Rewiring the Keyboard: Evolvability of the Genetic Code" Nat Rev Genet 2:49-58.

17. Yarus, M., Caporaso, J.G., and Knight, R. (2005). “Experimental evidence for the escaped triplet theory of the genetic code”. Annual Review of Biochemistry 74:179-98.

Other articles (not peer-reviewed)

18. Griffiths, P. E. and Knight, R.D. (1998). “What is the Developmentalist Challenge?” Philosophy of Science 65:253-258

19. Freeland, S. J., Knight, R.D. and Landweber, L.F. (2000). "Measuring adaptation within the genetic code." Trends Biochem Sci 25(2): 44-5.

Book chapters (not peer reviewed)

20. Knight, R. D., Landweber, L.F. and Yarus, M. (2003). "Tests of a Stereochemical Genetic Code ". In "Translation Mechanisms", Landes Bioscience.

21. Yarus, M, and Knight, R. D. (2004). "The Scope of Selection". In "The Genetic Code and the Origin of Life", Landes Bioscience.

22. Knight, R. D., Freeland, S. J., and L. F. Landweber (2004) Adaptive Evolution of the Genetic Code. In “The Genetic Code and the Origin of Life”, Landes Bioscience.

Publications from work after becoming an Assistant Professor: Research articles (peer-reviewed)

23. Hamady, M., Cheung, T., Tufo, H. and Knight, R. (2005). “Using structural properties to predict behavior of related proteins: does protein structure influence trypsin miscleavage?” IEEE Engineering in Medicine and Biology Magazine 24(3):58-66.

24. Wolfson, A., and Knight, R. (2005). “Occurrence of mammalian AARS in high molecular weight complexes correlates with the size of substrate amino acids.” FEBS letters 579(17) 3467-72.

25. Ley, R.E., Backhed, F., Turnbaugh, P., Lozupone, C.A., Knight, R.D., and Gordon, J.I. (2005) "Obesity alters gut microbial ecology." Proceedings of the National Academy of Sciences. Volume 102. pp11070-11075.

26. *Knight, R., De Sterck, H., Markel, R., Smit, S., Oshmyansky, A., and Yarus, M. (2005) "Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids". Nucleic Acids Research 33:5924-35.

27. *Widmann, J., Di Giulio, M., Yarus, M., and Knight, R. (2005). “tRNA creation by hairpin duplication.” Journal of Molecular Evolution 61:524-30.

28. *Legiewicz, M., Lozupone, C., Knight, R. and Yarus, M. (2005). "Size and constant sequences alter selection". RNA 11:1701-9.

29. *Caporaso, J.G., Yarus, M., and Knight, R. (2005). “Error minimization and coding triplet/binding site associations are independent features of the canonical genetic code.” J Mol Evol 61:597-607.

30. Lozupone, C.A. and Knight, R. (2005). "Unifrac: A New Phylogenetic Method For Comparing Microbial Communities." Appl Envrionm Microbiol 71:8228-35.

31. Marquez, R., Smit, S., and Knight, R (2005). “Do universal codon usage patterns minimize the effects of mutation and translation error?” Genome Biol 6:R91.

32. Yarus, M., Caporaso, J.G., Knight, R. (2005). “Origins of the genetic code: the escaped triplet theory.” Annu Rev Biochem. 2005;74:179-98.

33. Hamady, M., Cheung, T.H., Tufo, H., Knight, R. (2005). “Does protein structure influence trypsin miscleavage? Using structural properties to predict the behavior of related proteins.” IEEE Eng Med Biol Mag. 2005 May-Jun;24(3):58-66.

34. Smit, S., Yarus, M, and Knight, R (2006). “Natural selection is not required to explain universal compositional patterns in rRNA structural categories.” RNA 12:1-14.

35. Hamady, M., Peden, E., Knight, R., and Singh, R. (2006) “Fast-Find: A novel computational approach to analyzing combinatorial motifs.” BMC Bioinformatics 7:1.

36. Ruth, M.C., Old, W.M., Emrick, M.A., Meyer-Arendt, K., Aveline-Wolf, L.D., Pierce, K.G., Mendoza, A.M., Sevinsky, J.R., Hamady, M., Knight, R.D., Resing, K.A., and Ahn, N.G. (2006) “Analysis of Membrane Proteins from Human Chronic Myelogenous Leukemia Cells: Comparison of Extraction Methods for Multidimensional LC-MS/MS.” Journal of Proteome Research 5:709-19.

37. Abascal, F., Posada, D., Knight, R.D., and Zardoya, R. (2006) “Parallel Evolution of the Genetic Code in Arthropod Mitochondrial Genomes.” PLoS Biology, 4:e127.

38. Lozupone, C., Hamady, M. and Knight, R. (2006). “UniFrac: An Online Tool for Comparing Microbial Community Diversity in a Phylogenetic Context”. BMC Bioinformatics. 2006 Aug 7;7:371.

39. Widmann, J., Hamady, M., and Knight, R. (2006). “DivergentSet: Picking non-redundant sequences from large sequence collections”. Mol Cell Proteomics 8:1520-1532.

40. Hamady, M., Betterton, M.D., and Knight, R. (2006). “Using the nucleotide substitution rate matrix to detect horizontal gene transfer”. BMC Bioinformatics. 2006 Oct 26;7:476.

41. Lozupone, C.A., Hamady, M., Kelley, S.T., and Knight, R. (2007) “Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities”. Appl Env Microbiol. 73:1576-85.

42. Smit, S., Widmann, J. and Knight, R. (2007) “Evolutionary rates vary among rRNA structural elements.” Nucleic Acids Res 35:3339-54.

43. Xu, J., Mahowald, M.A., Ley, R.E., Lozupone, C.A., Hamady, M., Martens, E.C., Henrissat, B., Coutinho, P.M., Minx, P., Latreille, P., Cordum, H., Van Brunt, A., Kim, K., Fulton, R.S., Fulton, L.A., Clifton, S.W., Wilson, R.K., Knight, R.D., Gordon, J.I. (2007). “Evolution of symbiotic bacteria in the distal human intestine”. PLoS Biology. 2007 Jul;5(7):e156.

44. Lozupone, C.A., and Knight, R. (2007) “Global patterns in bacterial diversity”. PNAS 104:11436-40.

45. Knight, R., Maxwell, P., Birmingham, A., Carnes, J., Caporaso, J.G., Easton, B.C., Hamady, M., Liu, Z., Lozupone, C., Sammut, R., Smit, S., Wakefield, M., Widmann, J., Wikman, S., Wilson, S., and Huttley, G.A.. (2007) “PyCogent: a toolkit for making sense from sequence”. Genome Biology. 2007;8(8):R171.

46. Liu, Z., Lozupone, C.A., Hamady, M., Bushman, F., and Knight, R. (2007) “Short pyrosequencing reads suffice for accurate microbial community analysis”. Nucleic Acids Research. 2007;35(18):e120.

47. Fierer, N., Brietbart, M., Nulton, J., Salamon, P., Lozupone, C., Jones, R., Robeson, M., Edwards, R.A., Felts, B., Rayhawk, S., Knight, R., Rowher, F., and Jackson, R.B. (2007) “Metagenomic and small-subunit rRNA analyses of the genetic diversity of bacteria, archaea, fungi, and viruses in soil”. Applied Environ Microbiol. 2007 Nov;73(21):1059-66.

48. Fierer, N., Liu, Z., Rodriguez, M. Knight, R., Henn, M., and Hernandez, M. (2008) “The short-term temporal variability of airborne bacterial and fungal populations in Boulder, Colorado.” Appl Env Microbiol. 2008 Jan;74(1):200-7.

49. McKenna, P., Hoffman, C., Aye, P.P., Lackner. A., Liu, Z., Lozupone, C.A., Hamady, M., Knight, R., and Bushman, F.D. (2008) “The Macaque Gut Microbiome in Health, Lentiviral Infection and Inflammatory Bowel Disease”. PLoS Pathogens. 2008 Feb 8;4(2):e20

50. Smit, S., Rother, C., Heringa, J., and Knight, R. (2008) “From knotted to nested RNA structures: a variety of computational methods to objectively untangle RNA pseudoknots”. RNA 14:410-6.

51. Hamady, M., Walker, J.J., Harris, J.K., Gold, N., and Knight, R. (2008) “Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex”. Nature Methods 5:235-7.

52. Nemergut, D.R., Robeson, M.S., Kysela, R.F., Martin, A.P., Schmidt, S.K., and Knight, R. (2008) “Insights and inferences about integron evolution from genomic data.” BMC Genomics 9:261.

53. Ley, R.E., Hamady, M., Lozupone, C., Turnbaugh, P.J., Ramey, R.R., Bircher, J.S., Schlegel, M.L., Tucker, T.A., Schrenzel, M.D., Knight, R., and Gordon, J.I. (2008) “Evolution of Mammals and their Gut Microbes”. Science 320:1647-51.

54. Kennedy, R., Lladser, M.E., Yarus, M., and Knight, R. (2008) “Information, probability, and the abundance of the simplest RNA active sites”. Frontiers in Bioscience 13:6060-71.

55. Hamady, M., Widmann, J., Copley, S.D., and Knight, R. (2008) “MotifCluster: An interactive online tool for clustering and visualizing sequences using shared motifs.” Genome Biol 9:R128.

56. Liu, Z., DeSantis, T.Z., Andersen, G.L., and Knight, R. (2008) “Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers.” Nucleic Acids Res 36:e120.

57. Lozupone, C.A., Hamady, M., Cantarel, B.L., Coutinho, P.M., Henrissat, B., Gordon, J.I., and Knight, R. (2008) “The convergence of carbohydrate active gene repertoires in human gut microbes.” PNAS 105:15076.

58. McDonald, D., Waterbury, L., Knight, R. and Betterton, M.D. (2008) “Activating and inhibiting connections in biological networks.” Biology Direct 3:49.

59. Fierer, N., Hamady, M., Lauber, C., and Knight, R. (2008) “The influence of sex, handedness, and washing on the diversity of hand surface bacteria.” PNAS 105:17994.

60. Caporaso, J.G., Smit, S., Easton, B.C., Hunter, L., Huttley, G.A., and Knight, R. (2008) “Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics.” BMC Evol Biol 8:327.

61. Oscamou, M., McDonald, D., Yap, V.B., Huttley, G.A., Lladser, M.E., and Knight, R. (2008) “Comparison of methods for estimating the nucleotide substitution matrix.” BMC Bioinformatics 9:511.

62. Yen, C.-Y., Meyer-Arendt, K., Eichelberger, B., Sun, S., Houel, S., Old, W.M., Knight, R., Ahn, N.G., Hunter, L.E., and Resing, K.A. (2008) A Simulated MS/MS Library for Spectrum-to-spectrum Searching in Large-scale Identification of Proteins. Mol Cell Proteomics. 2009 Apr;8(4):857-69.

63. Schranz, H.W., Yap, V.B., Easteal, S., Knight, R., and Huttley, G.A. (2008) “Pathological rate matrices: from primates to pathogens.” BMC Bioinformatics 9:550.

64. Turnbaugh, P.J., Hamady, M., Yatsunenko, T., Cantarel, B.L., Duncan, A., Ley, R.E., Sogin, M.L., Jones, W.J., Roe, B.A., Affourtit, J.P., Egholm, M., Henrissat, B., Heath, A.C., Knight, R., and Gordon, J.I. (2009) “A core gut microbiome in obese and lean twins.” Nature 457:480-4.

65. Smit, S., Knight, R. and Heringa, J. (2009) “RNA structure prediction from evolutionary patterns of nucleotide composition”. NAR 37:1378-86.

66. Jones, R.T., Robeson, M.S., Lauber, C.L., Hamady, M., Knight, R., and Fierer, N. (2009) “A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses.” ISME J. 3:442.

67. Hamady, M., Buvoli, M., Leinwand, L.A., and Knight, R. (2009) “Estimate of the Abundance and Distribution of Cardiomyopathic Mutations in the β-Myosin Gene.” International Journal of Cardiology. 2010 Sep 24;144(1):124-6.

68. Hamady M, Wilson S.A., Zaneveld J., Sueoka N., and Knight, R. (2009) “CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes.” Bioinformatics 25:1331.

69. Zaneveld J, Hamady M, Sueoka N, Knight R. (2009) “CodonExplorer: an interactive online database for the analysis of codon usage and sequence composition.” Methods Mol Biol 537:207.

70. Bowers, R.M., Lauber, C.L., Wiedenmyer, C., Hamady, M., Hallar, A.G., Fall, R., Knight, R., and Fierer, N. (2009) “Characterization of airborne microbial communities at a high-elevation site and their potential to act as atmospheric ice nuclei”. Appl Environ Microbiol 75:5121.

71. Lauber, C.L., Hamady, M., Knight, R., and Fierer, N. (2009) “Pyrosequencing-based assessment of soil pH as a predictor of bacterial community structure at the continental scale.” Appl Environ Microbiol 75:5111.

72. Crawford, P.A., Crowley, J.R., Sambandam, N., Muegge, B.D., Costello, E.K., Hamady, M., Knight, R., and Gordon, J.I. (2009) “Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation”. PNAS 106:11276.

73. Brown, J.W., Birmingham, A., Griffiths, P.E., Jossinet, F., Kachouri-Lafond, R., Knight, R., Lang, B.F., Leontis, N., Steger, G., Stombaugh, J., and Westhof, E. (2009) “The RNA structure alignment ontology.” RNA 15:1623.

74. Goodman, A.L., McNulty, N.P., Zhao, Y., Leip, D., Mitra, R.D., Lozupone, C.A., Knight, R., and Gordon, J.I. (2009) “Identifying genetic determinants needed to establish a human gut symbiont in its habitat”. Cell Host and Microbe 6:279.

75. Hildebrandt, M.A., Hoffman, C., Sherrill-Mix, S.A., Kellbaugh, S.A., Hamady, M., Chen, Y., Knight, R., Ahima, R.S., Bushman, F., and Wu, G.D. (2009) “High fat diet determines the composition of the murine gut microbiome independently of obesity”. Gastroenterology 137:1716.

76. Yarus, M., Widmann, J.J., and Knight, R. (2009) “RNA-amino acid binding: A stereochemical era for the genetic code”. J. Mol. Evol. 69:406.

77. Costello, E.K., Lauber, C.L., Hamady, M., Fierer, N., Gordon, J.I., and Knight, R. (2009) “Bacterial variation in human body habitats across space and time”. Science, 326:1694.

78. Faith, D.P., Lozupone, C.A., Nipperess, D., and Knight, R. (2009) “A general model linking evolutionary features and environmental gradients supports broad applications of microbial ecology’s phylogenetic beta diversity framework”. International Journal of Molecular Sciences 10:4723.

79. Turnbaugh, P.J., Ridaura, V., Faith, J., Rey, F.E., Knight, R., and Gordon, J.I. (2009) “The impact of diet on the human gut microbiome: a metagenomic clinical trial in humanized gnotobiotic mice”. Science Translational Medicine 2009 Nov 11;1(6):6ra14.

80. Caporaso, J.G., Bittinger, K., Bushman, F.D., DeSantis, T.Z., Andersen, G.L., and Knight, R. (2010). PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26:266.

81. Hamady, M., Lozupone, C.A., and Knight, R. (2010) “Fast Unifrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyroseqeuncing and PhyloChip data”. ISME J. 4:17.

82. Jones, R.T., Knight, R. and Martin, A.P. (2010). “Bacterial communities of disease vectors, sampled over space and time.” ISME J. 4:223.

83. Kennedy, R., Lladser, M.E., Wu, Z., Zhang, C., Yarus, M., De Sterck, H., and Knight, R. (2010) “Natural and artificial RNAs occupy the same restricted region of sequence space”. RNA 16:280.

84. Zaneveld, J.R., Lozupone, C., Gordon, J.I., and Knight, R. (2010) “Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives.” Nucleic Acids Res. 2010 Jul 1;38(12):3869-79.

85. Fierer, N., Lauber, C.L., Zhou, N., McDonald, D., Costello, E.K., and Knight, R. (2010) “Forensic identification using skin bacterial communities”. PNAS 107:6477.

86. Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Peña, A.G., Goodrich, J.K., Gordon, J.I., Huttley, G.A., Kelley, S.T., Knights, D., Koenig, J.E., Ley, R.E., Lozupone, C.A., McDonald, D., Muegge, B.D., Pirrung, M., Reeder, J., Sevinsky, J.R., Turnbaugh, P.J., Walters, W.A., Widmann, J., Yatsunenko, T., Zaneveld, J., Knight, R. (2010). “QIIME allows analysis of high-throughput community sequencing data”. Nat Meth. 2010 May;7(5):335-6.

87. Turnbaugh, P.J., Quince, C., Faith, J.J., McHardy, A.C., Yatsunenko, T., Niazi, F., Affourtit, J., Egholm, M., Henrissat, B., Knight, R., Gordon, J.I. (2010). “Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins.” PNAS 107:7502.

88. Lauber, C.L., Zhou, N., Gordon, J.I., Knight, R., and Fierer, N. (2010). “Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples.” FEMS Microbiol Lett. Jun;307(1):80-6.

89. Janas, T., Widmann, JJ, Knight, R., Yarus, M. (2010) “Simple, recurring RNA binding sites for L-arginine.” RNA. 2010 Apr;16(4):805-16.

*Includes mixture of work performed both before and after becoming and assistant professor. Reviews (peer-reviewed)

90. Hamady, M., Cheung, T., Resing, K, Cios, K, and Knight, R. (2005). “Key Challenges in Proteomics and Proteoinformatics”. IEEE Engineering in Medicine and Biology Magazine 24(3):34-40.

91. Ley, R.E., Knight, R. and Gordon, J.I. (2007) “The human microbiome: eliminating the biomedical/environmental dichotomy in microbial ecology.” Environ. Microbiol. 9:3-4

92. Turnbaugh, P.J, Hamady, M., Ley, R., Fraser, C., Knight, R., and Gordon, J.I. (2007) “The human microbiome project: exploring the microbial side of ourselves”. Nature 449:804.

93. Lladser, M.E., Betterton, M.D., and Knight, R. (2008) “Multiple pattern matching: a Markov chain approach.” J. Comput. Biol. 56:51.

94. Zaneveld, J., Turnbaugh, P.J., Lozupone, C., Ley, R.E., Hamady, M., Gordon, J.I., and Knight, R. (2008) “Host-bacterial coevolution and the search for new drug targets”. Curr Opin Chem Biol. 12:109-114.

95. Zaneveld, J., Nemergut, D., and Knight, R. (2008) “Not all horizontal gene transfers are created equal: Prospects for mechanism-based HGT detection.” Microbiology 154:1.

96. Lozupone, C.A., and Knight, R. (2008) “Species Divergence and the Measurement of Microbial Diversity”. FEMS Microbiology Reviews 32:557-78.

97. Buvoli. M., Hamady, M., Leinwand, L.A., and Knight, R. (2008) “Bioinformatics Assessment of β-Myosin Mutations.” Trends in Cardiovascular Medicine 18:141-9.

98. Ley, R.E., Lozupone, C.A., Hamady, M., Knight, R., and Gordon, J.I. (2008). “Worlds within worlds: evolution of the vertebrate gut microbiota.” Nature Reviews Microbiology 6:776.

99. Hamady M. and Knight, R. (2009). “Microbial community profiling for human microbiome projects: tools, techniques and challenges.” Genome Res 19:1141.

100. Singh, R. and Knight, R. (2009) “Systems Biology: Understanding Function from Genes to Networks”. Curr Proteomics 6:93-103.

101. Spath, S., O’Malley, M., Zaneveld, J., Knight, R. and Zimmer, C. (2009). “Life through a Microbial Lens”. Metascience 18:179

102. Kuczynski, J., Costello, E.K., Nemergut, D.R., Zaneveld, J., Lauber, C.L., Knights, D., Koren, O., Fierer, N., Kelley, S.T., Ley, R.E., Gordon, J.I., Knight, R. (2010) “Direct sequencing of the human microbiome readily reveals community differences.” Genome Biol. 2010 May 5;11(5):210.

Conference proceedings (peer reviewed)

103. Batchelor, C., Bittner, T., Eilbeck, K., Mungall, C., Richardson, J., Knight, R., Stombaugh, J., Zirbel, C., Westhof, E., and Leontis, N. (2009) The RNA Ontology

(RNAO): An Ontology for Integrating Sequence and Structure Data”. ICBO: International Conference on Biomedical Ontology, Jul 24-26, Buffalo, NY Pp 7-10.

Book chapters (not peer reviewed)

104. de Zwart, I., Lozupone, C., Knight, R., Birmingham, A., Illangasekare, M., Jadhav, V., Legiewicz, M., Majerfeld, I., Widmann, J., and Yarus, M. (2005). “Artificial Selection: Finding function amongst randomized sequences” in Handbook of RNA Biochemistry. Edited by R. K. Hartmann, A. Bindereif, A. Schon, E. Westhof. Chapter 47, p 783-806.

105. De Sterck, H., Markel, R., and Knight, R. (2006) “TaskSpaces: A Software Fremework for Parallel Bioinformatics on Computational Grids”. Chapter in “Parallel Computing for Bioinformatics and Computational Biology”, A. Y. Zomaya, ed., Wiley Series on Parallel and Distributed Computing, Wiley, Hoboken, NJ, pp. 651-670.

106. De Sterck, H., Papo, A., Zhang, C., Hamady, M., and Knight, R. (2008) “Database-driven grid computing and distributed web applications: a comparison.” Chapter in “Grid computing for bioinformatics and computational biology”, E. Talbi & A. Y. Zomaya, eds., Wiley, Hoboken, NJ, pp. 247-266.

107. Knight, R. (2008). “Disentangling the Genetic Code”. Chapter in “The Seventy Great Mysteries of the Natural World”, M. J. Benton ed., Thames & Hudson, London. Pp. 25-24.

Other articles (not peer reviewed)

108. Knight, R. (2007) “Reports of the death of the gene are greatly exaggerated”. Biology and Philosophy 22:293-306.

109. Reeder, J. and Knight, R. (2009) “The rare biosphere: a reality check”. Nature Methods 6:639.

Publications from work after promotion to Associate Professor: Research articles (peer-reviewed)

110. Rousk, J., Bååth, E., Brookes, P.C., Lauber, C.L., Lozupone, C., Caporaso, J.G., Knight, R., Fierer, N. (2010) “Soil bacterial and fungal communities across a pH gradient in an arable soil.” ISME J. 2010 Oct;4(10):1340-51.

111. Vijay-Kumar, M., Aitken, J.D., Carvalho, F.A., Cullender, T.C., Mwangi, S., Srinivasan, S., Sitaraman, S.V., Knight, R., Ley, R.E., Gewirtz, A.T. (2010). “Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5”. Science. 2010 Apr 9;328(5975):228-31.

112. Costello, E.K., Gordon, J.I., Secor, S.M., Knight, R. (2010)” Postprandial remodeling of the gut microbiota in Burmese pythons.” ISME J. 2010 Nov;4(11):1375-85.

113. Caporaso, J.G., Lauber, C.L., Walters, W.A., Berg-Lyons, D., Lozupone, C.A., Turnbaugh, P.J., Fierer, N., Knight, R. (2010) “Microbes and Health Sackler Colloquium: Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.” Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4516-22.

114. Redford, A.J., Bowers, R.M., Knight, R., Linhart, Y., Fierer, N. (2010) “The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves.” Environ Microbiol. 2010 Nov;12(11):2885-93.

115. Widmann, J., Harris, J.K., Lozupone, C., Wolfson, A., Knight, R. (2010) “Stable tRNA-based phylogenies using only 76 nucleotides.” RNA. 2010 Aug;16(8):1469-77.

116. Chu, H., Fierer, N., Lauber, C.L., Caporaso, J.G., Knight, R., Grogan, P. (2010) “Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes.” Environ Microbiol. 2010 Nov;12(11):2998-3006.

117. Dominguez-Bello, M.G., Costello, E.K., Contreras, M,, Magris, M., Hidalgo, G., Fierer, N., Knight, R. (2010) “Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns.” Proc Natl Acad Sci U S A. 2010 Jun 29;107(26):11971-5.

118. Koenig, J.E., Spor, A., Scalfone, N., Fricker, A.D., Stombaugh, J., Knight, R., Angenent, L.T., Ley, R.E. (2010) “Microbes and Health Sackler Colloquium: Succession of microbial consortia in the developing infant gut microbiome.” Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4578-85.

119. Wu, G.D., Lewis, J.D., Hoffmann, C., Chen, Y.Y., Knight, R., Bittinger, K., Hwang, J., Chen, J., Berkowsky, R., Nessel, L., Li, H., Bushman, F.D. (2010) “Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags.” BMC Microbiol. 2010 Jul 30;10:206.

120. Majerfeld, I., Chocholousova, J., Malaiya, V., Widmann, J., McDonald, D., Reeder, J., Iyer, M., Illangasekare, M., Yarus, M., Knight, R. (2010) “Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA.” RNA. 2010 Oct;16(10):1915-24.

121. Manichanh, C., Reeder, J., Gibert, P., Varela, E., Llopis, M., Antolin, M., Guigo, R., Knight, R., Guarner, F. (2010) “Reshaping the gut microbiome with bacterial transplantation and antibiotic intake.” Genome Res. 2010 Oct;20(10):1411-9.

122. Reeder, J., Knight, R. (2010) “Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions.” Nat Methods. 2010 Sep;7(9):668-9.

123. Kuczynski, J., Liu, Z., Lozupone, C., McDonald, D., Fierer, N., Knight, R. (2010) “Microbial community resemblance methods differ in their ability to detect biologically relevant patterns.” Nat Methods. 2010 Oct;7(10):813-9.

124. Lozupone, C., Lladser, M.E., Knights, D., Stombaugh, J., Knight, R. (2010) “UniFrac: an effective distance metric for microbial community comparison.” ISME J. 2011 Feb;5(2):169-72.

125. Contreras, M., Costello, E.K., Hidalgo, G., Magris, M., Knight, R., Dominguez-Bello, M.G. (2010) “The bacterial microbiota in the oral mucosa of rural Amerindians.” Microbiology. 2010 Nov;156(Pt 11):3282-7.

126. Knights, D., Kuczynski, J., Koren, O., Ley, R.E., Field, D., Knight, R., Desantis, T.Z., Kelley, S.T. (2010) “Supervised classification of microbiota mitigates mislabeling errors.” ISME J. 2011 Apr;5(4):570-3.

127. Koren, O., Spor, A., Felin, J., Fåk, F., Stombaugh, J., Tremaroli, V., Behre, C.J., Knight, R., Fagerberg, B., Ley, R.E., Bäckhed, F. (2010) “Microbes and Health Sackler Colloquium: Human oral, gut, and plaque microbiota in patients with atherosclerosis.” Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4592-8.

128. King, A.J., Freeman, K.R., McCormick, K.F., Lynch, R.C., Lozupone, C., Knight, R., Schmidt, S.K. (2010) “Biogeography and habitat modelling of high-alpine bacteria.” Nat Commun. 2010 Aug 10;1:53

129. Bowers, R.M., McLetchie, S., Knight, R., Fierer, N. (2010) “Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments.” ISME J. 2011 Apr;5(4):601-12.

130. Bates, S.T., Berg-Lyons, D., Caporaso, J.G., Walters, W.A., Knight, R., Fierer, N. (2010) “Examining the global distribution of dominant archaeal populations in soil.” ISME J. 2011 May;5(5):908-17.

131. Bates, S.T., Cropsey, G.W., Caporaso, J.G,, Knight, R., Fierer, N. (2010) “Bacterial communities associated with the lichen symbiosis.” Appl Environ Microbiol. 2011 Feb;77(4):1309-14.

132. Nemergut, D.R., Costello, E.K., Hamady, M., Lozupone, C., Jiang, L., Schmidt, S.K., Fierer, N., Townsend, A.R., Cleveland, C.C., Stanish, L., Knight, R. (2011) “Global patterns in the biogeography of bacterial taxa.” Environ Microbiol. 2011 Jan;13(1):135-144.

133. Haas, B.J., Gevers, D., Earl, A., Feldgarden, M., Ward, D.V., Giannokous, G., Ciulla, D., Tabbaa, D., Highlander, S.K., Sodergren, E., Methe, B., Desantis, T.Z., Petrosino, J.F., Knight, R., Birren, B.W. (2011) “Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.” Genome Res. 2011 Mar;21(3):494-504.

134. Ramirez, K.S., Lauber, C.L., Knight, R., Bradford, M.A., Fierer, N. (2010) ”Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems.” Ecology. 2010 Dec;91(12):3463-70; discussion 3503-14.

135. Hansen, E.E., Lozupone, C.A., Rey, F.E., Wu, M., Guruge, J.L., Narra, A., Goodfellow, J., Zaneveld, J.R., McDonald, D.T., Goodrich, J.A., Heath, A.C., Knight, R., Gordon, J.I. (2011) “Microbes and Health Sackler Colloquium: Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins.” Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4599-606.

136. Walters, W.A., Caporaso, J.G., Lauber, C.L., Berg-Lyons, D.L., Fierer, N., Knight, R. (2011) “PrimerProspector: de novo design and taxonomic analysis of barcoded PCR primers.” Bioinformatics. 2011 Apr 15;27(8):1159-61.

137. Werner, J.J., Knights, D., Garcia, M.L., Scalfone, N.B., Smith, S., Yarasheski, K., Cummings, T.A., Beers, A.R., Knight, R., Angenent, L.T. (2011) “Bacterial community structures are unique and resilient in full-scale bioenergy systems.” Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):4158-63.

138. Caporaso, J.G., Knight, R., Kelley, S.T. (2011) “Host-associated and free-living phage communities differ profoundly in phylogenetic composition.” PLoS One. 2011 Feb 24;6(2):e16900.

139. Sun, Y., Cai, Y., Huse, S.M., Knight, R., Farmerie, W.G., Wang, X., Mai, V. (2011) “A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis.” Brief Bioinform. 2012 Jan;13(1):107-21.

140. Stombaugh, J., Widmann, J., McDonald, D., Knight, R. (2011) “Boulder ALignment Editor (ALE): a web-based RNA alignment tool.” Bioinformatics. 2011 Jun 15;27(12):1706-7.

141. Yilmaz, P., Kottmann, R., Field, D., Knight, R., Cole, J.R., Amaral-Zettler, L., Gilbert, J.A., Karsch-Mizrachi, I., Johnston, A., Cochrane, G., Vaughan, R., Hunter, C., Park, J., Morrison, N., Rocca-Serra, P., Sterk, P., Arumugam, M., Bailey, M., Baumgartner, L., Birren, B.W., Blaser, M.J., Bonazzi, V., Booth, T., Bork, P., Bushman, F.D., Buttigieg, P.L., Chain, P.S., Charlson, E., Costello, E.K., Huot-Creasy, H., Dawyndt, P., Desantis, T., Fierer, N., Fuhrman, J.A., Gallery, R.E., Gevers, D., Gibbs, R.A., Gil, I.S., Gonzalez, A., Gordon, J.I., Guralnick, R., Hankeln, W., Highlander, S., Hugenholtz, P., Jansson, J., Kau, A.L., Kelley, S.T., Kennedy, J., Knights, D., Koren, O., Kuczynski, J., Kyrpides, N., Larsen, R., Lauber, C.L., Legg, T., Ley, R.E., Lozupone, C.A., Ludwig, W., Lyons, D., Maguire, E., Methé, B.A., Meyer, F., Muegge, B., Nakielny, S., Nelson, K.E., Nemergut, D., Neufeld, J.D., Newbold, L.K., Oliver, A.E., Pace, N.R., Palanisamy, G., Peplies, J., Petrosino, J., Proctor, L., Pruesse, E., Quast, C., Raes, J.,

Ratnasingham, S., Ravel, J., Relman, D.A., Assunta-Sansone, S., Schloss, P.D., Schriml, L., Sinha, R., Smith, M.I., Sodergren, E., Spor, A., Stombaugh, J., Tiedje, J.M., Ward, D.V., Weinstock, G.M., Wendel, D., White, O., Whiteley, A., Wilke, A., Wortman, J.R., Yatsunenko, T., Glöckner, F.O. (2011) “Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.” Nat Biotechnol. 2011 May 6;29(5):415-420.

142. Ravussin, Y., Koren, O., Spor, A., Leduc, C., Gutman, R., Stombaugh, J., Knight, R., Ley, R.E., Leibel, R.L. (2011) “Responses of Gut Microbiota to Diet Composition and Weight Loss in Lean and Obese Mice.” Obesity (Silver Spring). 2012 Apr;20(4):738-47.

143. Muegge, B.D., Kuczynski, J., Knights, D., Clemente, J.C., González, A., Fontana, L., Henrissat, B., Knight, R., Gordon, J.I. (2011) “Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans.” Science. 2011 May 20;332(6032):970-4.

144. Rocca-Serra, P., Bellaousov, S., Birmingham, A., Chen, C., Cordero, P., Das, R., Davis-Neulander, L., Duncan, C.D., Halvorsen, M., Knight, R., Leontis, N.B., Mathews, D.H., Ritz, J., Stombaugh, J., Weeks, K.M., Zirbel, C.L., Laederach, A. (2011) “Sharing and archiving nucleic acid structure mapping data.” RNA. 2011 Jul;17(7):1204-12.

145. Caporaso, J.G., Lauber, C.L., Costello, E.K., Berg-Lyons, D., Gonzalez, A., Stombaugh, J., Knights, D., Gajer, P., Ravel, J., Fierer, N., Gordon, J.I., Knight, R. (2011) “Moving pictures of the human microbiome.” Genome Biol. 2011 May 30;12(5):R50.

146. Carvalho, F.A., Nalbantoglu, I., Ortega-Fernandez, S., Aitken, J.D., Su, Y., Koren, O., Walters, W.A., Knight, R., Ley, R.E., Vijay-Kumar, M., Gewirtz, A.T. (2011) “Interleukin-1{beta} (IL-1{beta}) promotes susceptibility of Toll-like receptor 5 (TLR5) deficient mice to colitis.” Gut. 2012 Mar;61(3):373-84.

147. Fierer, N., McCain, C., Meir, P., Zimmermann, M., Rapp, J., Silman, M., Knight, R. In Press. “Microbes do not follow the elevational diversity patterns of plants and animals.” Ecology. 2011 Apr;92(4):797-804.

148. Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C., Knight, R. (2011) “UCHIME improves sensitivity and speed of chimera detection.” Bioinformatics. 2011 Aug 15;27(16):2194-200.

149. Werner, J.J., Koren, O., Hugenholtz, P., Desantis, T.Z., Walters, W.A., Caporaso, J.G., Angenent, L.T., Knight, R., Ley, R.E. (2011) “Impact of training sets on classification of high-throughput bacterial 16S rRNA gene surveys.” ISME J. 2012 Jan;6(1):94-103.

150. Knights, D., Kuczynski, J., Charlson, E.S., Zaneveld, J., Mozer, M.C., Collman, R.G., Bushman, F.D., Knight, R., Kelley, S.T. (2011) “Bayesian community-wide culture-independent microbial source tracking.” Nat Methods. 2011 Jul 17;8(9):761-3.

151. Bowers, R.M., Sullivan, A.P., Costello, E.K., Collett, J.L., Knight, R., Fierer, N. (2011) “Sources of bacteria in outdoor air across cities in the midwestern United States.” Appl. Environ. Microbiol. 2011 Sep;77(18):6350-6.

152. Gilbert, J.A., Steele, J.A., Caporaso, J.G., Steinbrück, L., Reeder, J., Temperton, B., Huse, S., McHardy, A.C., Knight, R., Joint, I., Somerfield, P., Fuhrman, J.A., Field, D. (2011) “Defining seasonal marine microbial community dynamics”. ISME J. 2012 Feb;6(2):298-308.

153. Wu, G.D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y., Keilbaugh, S.A., Bewtra, M., Knights, D., Walters, W.A., Knight, R., Sinha, R., Gilroy, E., Gupta, K., Baldassano, R., Nessel, L., Li, H., Bushman, F.D., Lewis, J.D. (2011) “Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes”. Science. 2011 Oct 7;334(6052):105-8.

154. Pirrung, M., Kennedy, R., Caporaso, J.G., Stombaugh, J., Wendel, D., Knight, R. (2011) “TopiaryExplorer: Visualizing large phylogenetic trees with environmental metadata.” Bioinformatics. 2011 Nov 1;27(21):3067-9.

155. McKenzie, V.J., Bowers, R.M., Fierer, N., Knight, R., Lauber, C.L. (2011) “Co-habiting amphibian species harbor unique skin bacterial communities in wild populations.” ISME J. 2012 Mar;6(3):588-96.

156. Knights, D., Parfrey. L.W., Zaneveld, J., Lozupone, C., Knight, R. (2011) “Human-associated microbial signatures: examining their predictive value.” Cell Host Microbe. 2011 Oct 4;10(4):292-6.

157. McNulty, N.P., Yatsunenko, T., Hsiao, A., Faith, J.J., Muegge, B.D., Goodman, A.L., Henrissat, B., Oozeer, R., Cools-Portier, S., Gobert, G., Chervaux, C., Knights, D., Lozupone, C.A., Knight, R., Duncan, A.E., Bain, J.R., Muehlbauer, M.J., Newgard, C.B., Heath, A.C., Gordon, J.I. (2011) “The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins.” Sci Transl Med. 2011 Oct 26;3(106):106ra106.

158. Almodovar, S., Knight, R., Allshouse, A.A., Roemer, S., Lozupone, C., McDonald, D., Widmann, J.J., Voelkel, N., Shelton, R.J., Suarez-Martinez, E.B., Hammer, K., Goujard, C.M., Petrosillo, N., Simonneau, G., Hsue, P.Y., Humbert, M., Flores, S.C. (2011) “Human Immunodeficiency Virus nef Signature Sequences are Associated with Pulmonary Hypertension.” AIDS Res Hum Retroviruses. 2012 Jun;28(6):607-18.

159. Caporaso, J.G., Paszkiewicz, K., Field, D., Knight, R., Gilbert, J.A. (2011) “The Western English Channel contains a persistent microbial seed bank.” ISME J. 2012 Jun;6(6):1089-93.

160. Flores, G.E., Bates, S.T., Knights, D., Lauber, C.L., Stombaugh, J., Knight, R., Fierer, N. (2011) “Microbial biogeography of public restroom surfaces.” PLoS One. 2011;6(11):e28132.

161. Fierer, N., Lauber, C.L., Ramirez, K.S., Zaneveld, J., Bradford, M.A., Knight, R. (2011) “Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients.” ISME J. 2012 May;6(5):1007-17.

162. McDonald, D., Price, M.N., Goodrich, J., Nawrocki, E.P., Desantis, T.Z., Probst, A., Andersen, G.L., Knight, R., Hugenholtz, P. (2011) “An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.” ISME J. 2012 Mar;6(3):610-8.

163. Bergmann, G.T., Bates, S.T., Eilers, K.G., Lauber, C.L., Caporaso, J.G., Walters, W.A., Knight, R., Fierer, N. (2011) “The under-recognized dominance of Verrucomicrobia in soil bacterial communities.” Soil Biology and Biochemistry, Volume 43, Issue 7, Pages 1450-1455.

164. Werner, J.J., Zhou, D., Caporaso, J.G., Knight, R., Angenent, L.T. (2011) “Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys.” ISME J. 2012 Jul;6(7):1273-6.

165. Wang, X., Cai, Y., Sun, Y., Knight, R., Mai, V. (2011) “Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences.” ISME J. 2012 Jul;6(7):1277-80.

166. Gonzalez, A., Stombaugh, J., Lauber, C.L., Fierer, N., Knight, R. (2011) “SitePainter: A tool for exploring biogeographical patterns.” Bioinformatics. 2012 Feb 1;28(3):436-8.

167. Bates, S.T., Berg-Lyons, D., Lauber, C.L., Walters, W.A., Knight, R., Fierer, N. (2011) “A preliminary survey of lichen associated eukaryotes using pyrosequencing.” The Lichenologist, volume 44, issue 01, pp. 137-146.

168. Verhulst, N.O., Qiu, Y.T., Beijleveld, H., Maliepaard, C., Knights, D., Schulz, S., Berg-Lyons, D., Lauber, C.L., Verduijn, W., Haasnoot, G.W., Mumm, R., Bouwmeester, H.J., Claas, F.H., Dicke, M., van Loon, J.J., Takken, W., Knight, R., Smallegange, R.C. (2011) “Composition of human skin microbiota affects attractiveness to malaria mosquitoes.” PLoS One. 2011;6(12):e28991.

169. Soergel, D.A., Dey, N., Knight, R., Brenner, S.E. (2012) “Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences.” ISME J. 2012 Jul;6(7):1440-4.

170. Caporaso, J.G., Lauber, C.L., Walters, W.A., Berg-Lyons, D., Huntley, J., Fierer, N., Owens, S.M., Betley, J., Fraser, L., Bauer, M., Gormley, N., Gilbert, J.A., Smith, G., Knight, R. (2012) “Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms.” ISME J. 2012 Aug;6(8):1621-4.

171. Lin, X., McKinley, J., Resch, C.T., Kaluzny, R., Lauber, C.L., Fredrickson, J., Knight, R., Konopka, A. (2012) “Spatial and temporal dynamics of the microbial community in the Hanford unconfined aquifer”. ISME J. 2012 Sep;6(9):1665-76.

172. Yatsunenko, T., Rey, F.E., Manary, M.J., Trehan, I., Dominguez-Bello, M.G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R.N., Anokhin, A.P., Heath, A.C., Warner, B., Reeder, J., Kuczynski, J., Caporaso, J.G., Lozupone, C.A., Lauber, C., Clemente, J.C., Knights, D., Knight, R., Gordon, J.I. (2012) “Human gut microbiome viewed across age and geography”. Nature. 2012 May 9;486(7402):222-7.

173. Widmann, J., Stombaugh, J., McDonald, D., Chocholousova, J., Gardner, P., Iyer, M.K., Liu, Z., Lozupone, C.A., Quinn, J., Smit, S., Wikman, S., Zaneveld, J.R., Knight, R. (2012) “RNASTAR: An RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs”. RNA. 2012 Jul;18(7):1319-27.

174. Lozupone, C., Faust, K., Raes, J., Faith, J.J., Frank, D.N., Zaneveld, J., Gordon, J.I., Knight, R. (2012) “Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts.” Genome Res. 2012 Oct;22(10):1974-84.

175. Xiong, J., Liu, Y., Lin, X., Zhang, H., Zeng, J., Hou, J., Yang, Y., Yao, T., Knight, R., Chu, H. (2012) “Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau”. Environ Microbiol. 2012 Sep;14(9):2457-66.

176. Human Microbiome Project Consortium. "Structure, Function and Diversity of the Human Microbiome in an Adult Reference Population". Nature. 2012 Jun 13;486(7402):207-14.

177. Human Microbiome Project Consortium. "A framework for human microbiome research”. Nature. 2012 Jun 13;486(7402):215-21.

178. Shade, A., Read, J.S., Youngblut, N.D., Fierer, N., Knight, R., Kratz, T.K., Lottig, N.R., Roden, E.E., Stanley, E.H., Stombaugh, J., Whitaker, R.J., Wu, C.H., McMahon, K.D. (2012) “Lake microbial communities are resilient after a whole-ecosystem disturbance.” ISME J. 2012 Dec;6(12):2153-67.

179. Koren, O., Goodrich, J.K., Cullender, T.C., Spor, A., Laitinen, K., Kling Bäckhed, H., Gonzalez, A., Werner, J.J., Angenent, L.T., Knight, R., Bäckhed, F., Isolauri, E., Salminen, S., Ley, R.E. (2012) “Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy.” Cell. 2012 Aug 3;150(3):470-80.

180. Carvalho, F.A., Koren, O., Goodrich, J.K., Johansson, M.E., Nalbantoglu, I., Aitken, J.D., Su, Y., Chassaing, B., Walters, W.A., González, A., Clemente, J.C., Cullender, T.C., Barnich, N., Darfeuille-Michaud, A., Vijay-Kumar, M., Knight, R., Ley, R.E., Gewirtz, A.T. (2012) “Transient Inability to Manage Proteobacteria Promotes Chronic Gut Inflammation in TLR5-Deficient Mice.” Cell Host Microbe. 2012

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181. Blaser, M.J., Dominguez-Bello, M.G., Contreras, M., Magris, M., Hidalgo, G., Estrada, I., Gao, Z., Clemente, J.C., Costello, E.K., Knight, R. (2012) “Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents.” ISME J. 2013 Jan;7(1):85-95.

182. Gevers, D., Knight, R., Petrosino, J.F., Huang, K., McGuire, A.L., Birren, B.W., Nelson, K.E., White, O., Methé, B.A., Huttenhower, C. (2012) “The human microbiome project: a community resource for the healthy human microbiome.” PLoS Biol. 2012 Aug;10(8):e1001377.

183. Zupancic, M.L., Cantarel, B.L., Liu, Z., Drabek, E.F., Ryan, K.A., Cirimotich, S., Jones, C., Knight, R., Walters, W.A., Knights, D., Mongodin, E.F., Horenstein, R.B., Mitchell, B.D., Steinle, N., Snitker, S., Shuldiner, A.R., Fraser, C.M. (2012) “Analysis of the gut microbiota in the old order amish and its relation to the metabolic syndrome.” PLoS One. 2012;7(8):e43052.

184. Semova, I., Carten, J.D., Stombaugh, J., Mackey, L.C., Knight, R., Farber, S.A., Rawls, J.F. (2012) “Microbiota regulate intestinal absorption and metabolism of Fatty acids in the zebrafish.” Cell Host Microbe. 2012 Sep 13;12(3):277-88.

185. Harris, J.K., Caporaso, J.G., Walker, J.J., Spear, J.R., Gold N,J., Robertson, C.E., Hugenholtz, P., Goodrich, J., McDonald, D., Knights, D., Marshall, P., Tufo, H., Knight, R., Pace, N.R. (2012) “Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat” ISME J. 2013 Jan;7(1):50-60.

186. Stahringer, S.S., Clemente, J.C., Corley, R.P., Hewitt, J., Knights, D., Walters, W.A., Knight, R., Krauter, K.S. (2012) “Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood.” Genome Res. 2012 Nov;22(11):2146-52.

187. Ragan-Kelley, B., Walters, W.A., McDonald, D., Riley, J., Granger, B.E., Gonzalez, A., Knight, R., Perez, F., Caporaso, J.G. (2012) “Collaborative cloud-enabled tools allow rapid, reproducible biological insights.” ISME J. 2012 Oct 25.

188. Carey, H.V., Walters, W.A., Knight, R. (2012) “Seasonal Restructuring of the Ground Squirrel Gut Microbiota Over the Annual Hibernation Cycle.” Am J Physiol Regul Integr Comp Physiol. 2013 Jan;304(1):R33-42.

189. Flores, G.E., Bates, S.T., Caporaso, J.G., Lauber, C.L., Leff, J.W., Knight, R., Fierer, N. (2012) “Diversity, distribution and sources of bacteria in residential kitchens.” Environ Microbiol. 2012 Nov 5.

190. Kuczynski, J., Stombaugh, J., Walters, W.A., González, A., Caporaso, J.G., Knight, R. (2012) “Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities.” Curr Protoc Microbiol. 2012 Nov;Chapter 1:Unit1E.5.

191. Bokulich, N.A., Subramanian, S., Faith, J.J., Gevers, D., Gordon, J.I., Knight, R., Mills, D.A., Caporaso, J.G. (2012) “Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.” Nat Methods. 2013 Jan;10(1):57-9.

192. Bates, S.T., Clemente, J.C., Flores, G.E., Walters, W.A., Parfrey, L.W., Knight, R., Fierer, N. (2012) “Global biogeography of highly diverse protistan communities in soil.” ISME J. 2012 Dec 13.

193. Maslanik, T., Tannura, K., Mahaffey, L., Loughridge, A.B., Benninson, L., Ursell, L., Greenwood, B.N., Knight, R., Fleshner, M. (2012) “Commensal Bacteria and MAMPs

Are Necessary for Stress-Induced Increases in IL-1β and IL-18 but Not IL-6, IL-10 or MCP-1.” PLoS One. 2012;7(12):e50636.

194. Tito, R.Y., Knights, D., Metcalf, J., Obregon-Tito, A.J., Cleeland, L., Najar, F., Roe, B., Reinhard, K., Sobolik, K., Belknap, S., Foster, M., Spicer, P., Knight, R., Lewis, C.M. Jr. (2012) “Insights from characterizing extinct human gut microbiomes.” PLoS One. 2012;7(12):e51146.

195. Parks, B.W., Nam, E., Org, E., Kostem, E., Norheim, F., Hui, S.T., Pan, C., Civelek, M., Rau, C.D., Bennett, B.J., Mehrabian, M., Ursell, L.K., He, A., Castellani, L.W., Zinker, B., Kirby, M., Drake, T.A., Drevon, C.A., Knight, R., Gargalovic, P., Kirchgessner, T., Eskin, E., Lusis, A.J. (2013) “Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice.” Cell Metab. 2013 Jan 8;17(1):141-52.

196. Koren, O., Knights, D., Gonzalez, A., Waldron, L., Segata, N., Knight, R., Huttenhower, C., Ley, R.E. (2013) “A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets.” PLoS Comput Biol. 2013 Jan;9(1):e1002863.

197. Smith, M.I., Yatsunenko, T., Manary, M.J., Trehan, I., Mkakosya, R., Cheng, J., Kau, A.L., Rich, S.S., Concannon, P., Mychaleckyj, J.C., Liu, J., Houpt, E., Li, J.V., Holmes, E., Nicholson, J., Knights, D., Ursell, L.K., Knight, R., Gordon, J.I. (2013) “Gut microbiomes of Malawian twin pairs discordant for kwashiorkor.” Science. 2013 Feb 1;339(6119):548-54.

198. Hewitt, K.M., Mannino, F.L., Gonzalez, A., Chase, J.H., Caporaso, J.G., Knight, R., Kelley, S.T. (2013) “Bacterial Diversity in Two Neonatal Intensive Care Units (NICUs).” PLoS One. 2013;8(1):e54703.

199. Blaser, M., Bork, P., Fraser, C., Knight, R., Wang, J. (2013) “The microbiome explored: recent insights and future challenges.” Nat Rev Microbiol. 2013 Mar;11(3):213-7.

200. Kashyap, P.C., Marcobal, A., Ursell, L.K., Larauche, M., Duboc, H., Earle, K.A., Sonnenburg, E.D., Ferreyra, J.A., Higginbottom, S.K., Million, M., Tache, Y., Pasricha, P.J., Knight, R., Farrugia, G., Sonnenburg, J.L. (2013) “Complex Interactions Among Diet, Gastrointestinal Transit, and Gut Microbiota in Humanized Mice.” Gastroenterology. 2013 Feb 1.

201. Lozupone, C., Cota-Gomez, A., Palmer, B.E., Linderman, D.J., Charlson, E.S., Sodergren, E., Mitreva, M., Abubucker, S., Martin, J., Yao, G., Campbell, T.B., Flores, S.C., Ackerman, G., Stombaugh, J., Ursell, L., Beck, J.M., Curtis, J.L., Young, V.B., Lynch, S.V., Huang, L., Weinstock, G.M., Knox, K.S., Twigg, H., Morris, A., Ghedin, E., Bushman, F.D., Collman, R.G., Knight, R., Fontenot, A.P.; for the Lung HIV Microbiome Project. (2013) “Widespread Colonization of the Lung by Tropheryma whipplei in HIV Infection.” Am J Respir Crit Care Med. 2013 Feb 7.

202. Song, S.J., Dominguez-Bello, M.G., Knight, R. (2013) “How delivery mode and feeding can shape the bacterial community in the infant gut.” CMAJ. 2013 Feb 11.

203. Kittelmann, S., Seedorf, H., Walters, W.A., Clemente, J.C., Knight, R., Gordon, J.I., Janssen, P.H. (2013) “Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities.” PLoS One. 2013;8(2):e47879.

204. Ursell, L.K., Knight, R. (2013) “Xenobiotics and the human gut microbiome: metatranscriptomics reveal the active players.” Cell Metab. 2013 Mar 5;17(3):317-8.

205. Stoddard, C.D., Widmann, J., Trausch, J.J., Marcano-Velázquez, J.G., Knight, R., Batey, R.T. (2013) “Nucleotides Adjacent to the Ligand-Binding Pocket are Linked to Activity Tuning in the Purine Riboswitch.” J Mol Biol. 2013 May 27;425(10):1596-611.

206. Gibbons, S.M., Caporaso, J.G., Pirrung, M., Field, D., Knight, R., Gilbert, J.A.

(2013) “Evidence for a persistent microbial seed bank throughout the global ocean.” Proc Natl Acad Sci U S A. 2013 Mar 19;110(12):4651-5.

207. Morris, A., Beck, J.M., Schloss, P.D., Campbell, T.B., Crothers, K., Curtis, J.L., Flores, S.C., Fontenot, A.P., Ghedin, E., Huang, L., Jablonski, K., Kleerup, E., Lynch, S.V., Sodergren, E., Twigg, H., Young, V.B., Bassis, C.M., Venkataraman, A., Schmidt, T.M., Weinstock, G.M.; Lung HIV Microbiome Project. (2013) “Comparison of the respiratory microbiome in healthy nonsmokers and smokers.” Am J Respir Crit Care Med. 2013 May 15;187(10):1067-75.

208. Pantoja-Feliciano, I.G., Clemente, J.C., Costello, E.K., Perez, M.E., Blaser, M.J., Knight, R., Dominguez-Bello, M.G. (2013) “Biphasic assembly of the murine intestinal microbiota during early development.” ISME J. 2013 Mar 28.

209. Shade, A., Caporaso, J.G., Handelsman, J., Knight, R., Fierer, N. (2013) “A meta-analysis of changes in bacterial and archaeal communities with time.” ISME J. 2013 Apr 11.

210. Song, S.J., Lauber, C., Costello, E.K., Lozupone, C.A., Humphrey, G., Berg-Lyons, D., Caporaso, J.G., Knights, D., Clemente, J.C., Nakielny, S., Gordon, J.I., Fierer, N., Knight, R. (2013) “Cohabiting family members share microbiota with one another and with their dogs.” Elife. 2013 Apr 16;2:e00458.

211. Ottesen, A.R., González Peña, A., White, J.R., Pettengill, J.B., Li, C., Allard, S., Rideout, S., Allard, M., Hill, T., Evans, P., Strain, E., Musser, S., Knight, R., Brown, E. (2013) “Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato).” BMC Microbiol. 2013 May 24;13:114.

212. Manichanh, C., Eck, A., Varela, E., Roca, J., Clemente, J.C., González, A., Knights, D., Knight, R., Estrella, S., Hernandez, C., Guyonnet, D., Accarino, A., Santos, J., Malagelada, J.R., Guarner, F., Azpiroz, F. (2013) “Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet.” Gut. 2013 Jun 13.

213. Faith, J.J., Guruge, J.L., Charbonneau, M., Subramanian, S., Seedorf, H., Goodman, A.L., Clemente, J.C., Knight, R., Heath, A.C., Leibel, R.L., Rosenbaum, M., Gordon, J.I. (2013) “The Long-Term Stability of the Human Gut Microbiota” Science 5 July 2013.

214. Michelou, V.K., Caporaso, J.G., Knight, R., Palumbi, S.R. (2013) “The Ecology of Microbial Communities Associated with Macrocystis pyrifera.” PLoS One. 2013 Jun 19;8(6):e67480.

215. Lozupone, C., Stombaugh, J., Gonzalez, A., Ackermann, G., Wendel, D., Vazquez-Baeza, Y., Jansson, J.K., Gordon, J.I., Knight, R. (2013) “Meta-analyses of studies of the human microbiota.” Genome Res. 2013 Jul 16.

216. Langille, M.G., Zaneveld, J., Caporaso, J.G., McDonald, D., Knights, D., Reyes, J.A., Clemente, J.C., Burkepile, D.E., Vega Thurber, R.L., Knight, R., Beiko, R.G., Huttenhower, C. (2013) “Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.” Nat Biotechnol. 2013 Aug 25.

217. Ridaura, V.K., Faith, J.J., Rey, F.E., Cheng, J., Duncan, A.E., Kau, A.L., Griffin, N.W., Lombard, V., Henrissat, B., Bain, J.R., Muehlbauer, M.J., Ilkayeva, O., Semenkovich, C.F., Funai, K., Hayashi, D.K., Lyle, B.J., Martini, M.C., Ursell, L.K., Clemente, J.C., Van Treuren, W., Walters, W.A., Knight, R., Newgard, C.B., Heath, A.C., Gordon, J.I. (2013) “Gut microbiota from twins discordant for obesity modulate metabolism in mice.” Science. 2013 Sep 6;341(6150):1241214.

218. Devine, A.A., Gonzalez, A., Speck, K.E., Knight, R., Helmrath, M., Lund, P.K., Azcarate-Peril, M.A. (2013) “Impact of ileocecal resection and concomitant antibiotics on the microbiome of the murine jejunum and colon.” PLoS One. 2013 Aug 27;8(8):e73140.

219. Lozupone, C.A., Li, M., Campbell, T.B., Flores, S.C., Linderman, D., Gebert, M.J., Knight, R., Fontenot, A.P., Palmer, B.E. (2013) “Alterations in the Gut Microbiota

Associated with HIV-1 Infection.” Cell Host Microbe. 2013 Sep 11;14(3):329-39. 220. Ottesen, A.R., Gonzalez, A., Bell, R., Arce, C., Rideout, S., Allard, M., Evans, P.,

Strain, E., Musser, S., Knight, R., Brown, E., Pettengill, J.B. (2013) “Co-enriching microflora associated with culture based methods to detect salmonella from tomato phyllosphere.” PLoS One. 2013 Sep 9;8(9):e73079.

221. Kashyap, P.C., Marcobal, A., Ursell, L.K., Smits, S.A., Sonnenburg, E.D., Costello, E.K., Higginbottom, S.K., Domino, S.E., Holmes, S.P., Relman, D.A., Knight, R., Gordon, J.I., Sonnenburg, J.L. (2013) “Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota.” Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):17059-64.

222. Delsuc, F., Metcalf, J.L., Wegener Parfrey, L., Song, S.J., González, A., Knight, R. (2013) “Convergence of gut microbiomes in myrmecophagous mammals.” Mol Ecol. 2013 Aug 29

Reviews (peer-reviewed)

223. Knights, D., Costello, E.K., Knight, R. (2010) “Supervised classification of human microbiota.” FEMS Microbiol Rev. 2011 Mar;35(2):343-59.

224. Fierer, N., Nemergut, D., Knight, R., Craine, J.M. (2010) “Changes through time: integrating microorganisms into the study of succession.” Res Microbiol. 2010 Oct;161(8):635-42.

225. Reid, G., Younes, J.A., Van der Mei, H.C., Gloor, G.B., Knight, R., Busscher H.J. (2010) “Microbiota restoration: natural and supplemented recovery of human microbial communities.” Nat Rev Microbiol. 2011 Jan;9(1):27-38.

226. Gonzalez, A., Stombaugh, J., Lozupone, C., Turnbaugh, P.J., Gordon, J.I., Knight, R. (2011) “The mind-body-microbial continuum.” Dialogues Clin Neurosci. 2011;13(1):55-62.

227. Dominguez-Bello, M.G., Blaser, M.J., Ley, R.E., Knight, R. (2011) “Development of the human gastrointestinal microbiota and insights from high-throughput sequencing.” Gastroenterology. 2011 May;140(6):1713-9.

228. Field, D., Amaral-Zettler, L., Cochrane, G., Cole, J.R., Dawyndt, P., Garrity, G.M., Gilbert, J., Glöckner, F.O., Hirschman, L., Karsch-Mizrachi, I., Klenk, H.P., Knight, R., Kottmann, R., Kyrpides, N., Meyer, F., San, Gil. I., Sansone, S.A., Schriml, L.M., Sterk, P., Tatusova, T., Ussery, D.W., White, O., Wooley, J. (2011) “The genomic standards consortium.” PLoS Biol. 2011 Jun;9(6):e1001088.

229. Gonzalez, A., Clemente, J.C., Shade, A., Metcalf, J.L., Song, S., Prithiviraj, B., Palmer, B.E., Knight, R. (2011) “Our microbial selves: what ecology can teach us.” EMBO Rep. 2011 Jul 1;12(8):775-84.

230. Parfrey, L.W., Walters, W.A., Knight, R. (2011) “Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions.” Front Microbiol. 2011;2:153.

231. Zaneveld, J.R., Parfrey, L.W., Van Treuren, W., Lozupone, C., Clemente, J.C., Knights, D., Stombaugh, J., Kuczynski, J., Knight, R. (2011) “Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation”. Trends Microbiol. 2011 Oct;19(10):472-82.

232. Gonzalez, A., King, A., Robeson II, M.S., Song, S., Shade, A., Metcalf, J.L., Knight, R. (2011) “Characterizing microbial communities through space and time.” Curr Opin Biotechnol. 2012 Jun;23(3):431-6.

233. Gonzalez, A., Knight, R. (2011) “Advancing analytical algorithms and pipelines for billions of microbial sequences.” Curr Opin Biotechnol. 2012 Feb;23(1):64-71.

234. Kuczynski, J., Lauber, C.L., Walters, W.A., Parfrey, L.W., Clemente, J.C., Gevers, D., Knight, R. (2011) “Experimental and analytical tools for studying the human microbiome.” Nat Rev Genet. 2011 Dec 16;13(1):47-58.

235. Kuczynski, J., Stombaugh, J., Walters, W.A., González, A., Caporaso, J.G., Knight, R. (2011) “Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities.” Curr Protoc Bioinformatics. 2011 Dec;Chapter 10:Unit10.7.

236. Bik, H.M., Porazinska, D.L., Creer, S., Caporaso, J.G., Knight, R., Thomas, W.K. (2012) “Sequencing our way towards understanding global eukaryotic biodiversity.” Trends Ecol Evol. 2012 Apr;27(4):233-43.

237. Gilbert, J.A., Catlett, C., Desai, N., Knight, R., White, O., Robbins, R., Sankaran, R., Sansone, S.A., Field, D., Meyer, F. (2012) “Conceptualizing a Genomics Software Institute (GSI)” Stand Genomic Sci. 2012 Mar 19;6(1):136-44.

238. Clemente, J.C., Ursell, L.K., Parfrey, L.W., Knight, R. (2012) “The impact of the gut microbiota on human health: an integrative view.” Cell. 2012 Mar 16;148(6):1258-70.

239. Sullam, K.E., Essinger, S.D., Lozupone, C.A., O'Connor, M.P., Rosen, G.L., Knight, R., Kilham, S.S., Russell, J.A. (2012) “Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis.” Mol Ecol. 2012 Jul;21(13):3363-78.

240. Ursell, L.K., Clemente, J.C., Rideout, J.R., Gevers, D., Caporaso, J.G., Knight, R. (2012) “The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites.” J Allergy Clin Immunol. 2012 May;129(5):1204-8.

241. Ursell, L.K., Metcalf, J.L., Parfrey, L.W., Knight, R. (2012) “Defining the human microbiome.” Nutr Rev. 2012 Aug;70 Suppl 1:S38-44.

242. Parfrey, L.W., Knight, R. (2012) “Spatial and temporal variability of the human microbiota.” Clin Microbiol Infect. 2012 Jul;18 Suppl 4:8-11.

243. Knight, R., Jansson, J., Field, D., Fierer, N., Desai, N., Fuhrman, J.A., Hugenholtz, P., van der Lelie, D., Meyer, F., Stevens, R., Bailey, M.J., Gordon, J.I., Kowalchuk, G.A., Gilbert, J.A. (2012) “Unlocking the potential of metagenomics through replicated experimental design.” Nat Biotechnol. 2012 Jun 7;30(6):513-20.

244. Lozupone, C.A., Stombaugh, J.I., Gordon, J.I., Jansson, J.K., Knight, R. (2012) “Diversity, stability and resilience of the human gut microbiota.” Nature. 2012 Sep 13;489(7415):220-30.

245. McDonald, D., Vazquez-Baeza, Y., Walters, W.A., Caporaso, J.G., Knight, R. (2013) “From molecules to dynamic biological communities.” Biology & Philosophy. Volume 28, Issue 2 (2013), pp 241-259.

246. Curtis, T., Daran, J.M., Pronk, J.T., Frey, J., Jansson, J.K., Robbins-Pianka, A., Knight, R., Schnürer, A., Smets, B.F., Smid, E.J., Abee, T., Vicente, M., Zengler, K. (2013) “Crystal ball-2013.” Microbial Biotechnology. Volume 6, Issue 1, p 3-16.

247. Ursell, L.K., Treuren, W.V., Metcalf, J.L., Pirrung, M., Gewirtz, A., Knight, R. (2013) “Replenishing our defensive microbes.” Bioessays. 2013 Jul 8.

Book chapters (not peer reviewed)

248. Lladser, M. E. and Knight, R. (2013) “Mathematical Approaches for Describing Microbial Populations: Practice and Theory for Extrapolation of Rich Environments”, in The Human Microbiota: How Microbial Communities Affect Health and Disease (ed D. N. Fredricks), John Wiley & Sons, Inc., Hoboken, NJ, USA.

Other articles (not peer reviewed)

249. Gilbert, J., Meyer, F., Knight, R., Field, D., Kyrpides, N.C., Yilmaz, P., Wooley, J. (2010) “Meeting Report: GSC M5 Roundtable at the 13th International Society for Microbial Ecology Meeting in Seattle, WA, USA August 22-27, 2010.“ Stand Genomic Sci. 2010 Dec 15;3(3):235-9.

250. Gilbert, J., Meyer, F., Antonopoulos, D., Balaji, P., Brown, C.T., Brown, C.T., Desai, N., Eisen, J.A., Evers, D., Field, D., Feng, W., Huson, D., Jansson, J., Knight, R., Knight, J., Kolker, E., Konstantindis, K., Kostka, J., Kyrpides, N.C., Mackelprang, R., McHardy, A., Quince, C., Raes, J., Sczyrba, A., Shade, A., Stevens, R. (2010) “Meeting Report. The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project.” Stand Genomic Sci. 2010 Dec 25;3(3):243-8.

251. Gilbert, J., Meyer, F., Jansson, J., Gordon, J., Pace, N., Tiedje, J., Ley, R., Fierer, N., Field, D., Kyrpides, N.C., Glöckner, F.O., Klenk, H., Wommack, K.E., Glass, E., Docherty, K., Gallery, R., Stevens, R., Knight, R. (2010) “The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010.” Stand Genomic Sci. 2010 Dec 25;3(3):249-53.

252. Caporaso, J.G., Knight, R. (2011) “New Insight into the Diversity of Life's Building Blocks: Evenness, Not Variance.” Astrobiology. 2011 Apr;11(3):197-8.

253. Yilmaz, P., Gilbert, J.A., Knight, R., Amaral-Zettler, L., Karsch-Mizrachi, I., Cochrane, G., Nakamura, Y., Sansone, S.A., Glöckner, F.O., Field, D. (2011) “The genomic standards consortium: bringing standards to life for microbial ecology.” ISME J. 2011 Oct;5(10):1565-7.

254. Birmingham, A., Clemente, J.C., Desai, N., Gilbert, J., Gonzalez, A., Kyrpides, N., Meyer, F., Nawrocki, E., Sterk, P., Stombaugh, J., Weinberg, Z., Wendel, D., Leontis, N.B., Zirbel, C., Knight, R., Laederach, A. (2011) “Meeting report of the RNA Ontology Consortium January 8-9, 2011.” Stand Genomic Sci. 2011 Apr 29;4(2):252-6.

255. Brown, J., de Vos, W.M., Distefano, P.S., Doré, J., Huttenhower, C., Knight, R., Lawley, T.D., Raes, J., Turnbaugh, P. (2013) “Translating the human microbiome.” Nat Biotechnol. 2013 Apr;31(4):304-8.

256. Smith, D., Alverdy, J., An, G., Coleman, M., Garcia-Houchins, S., Green, J., Keegan, K., Kelley, S.T., Kirkup, B.C., Kociolek, L., Levin, H., Landon, E., Olsiewski, P., Knight, R., Siegel, J., Weber, S., Gilbert, J. (2013) “The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012.“ Stand Genomic Sci. 2013 Apr 15;8(1):112-7.

257. Bates, S.T., Ahrendt, S., Bik, H.M., Bruns, T.D., Caporaso, J.G., Cole, J., Dwan, M., Fierer, N., Gu, D., Houston, S., Knight, R., Leff, J., Lewis, C., Maestre, J.P., McDonald, D., Nilsson, R.H., Porras-Alfaro, A., Robert, V., Schoch, C., Scott, J., Taylor, D.L., Parfrey, L.W., Stajich, J.E. (2013) “Meeting report: fungal its workshop (october 2012).“ Stand Genomic Sci. 2013 Apr 15;8(1):118-23.

258. Schriml, L., Mizrachi, I., Sterl, P., Field, D., Hirschman, L., Tatusova, T., Sansone, S., Gilbert, J., Schindel, D., Davies, N., Meyer, C., Meyer, F., Garrity, G., Proctor, L., Medema, M., Lan, Y., Klindworth, A., Glöckner, F.O., Korves, T., Gonzalez, A., Dwayndt, P., Göker, M., Johnston, A., Pafilis, E., Schneider, S., Baker, K., Parr, C., Sutton, G., Creasy, H., Kyrpides, N., Wommack, K.E., Whetzel, P.L., Nasko, D., Lapp, H., Fujisawa, T., Phillippy, A.M., Kottman, R., Blake, J.A., Li, J., Glass, E.M., ten Hoopen, P., Knight, R., Holmes, S., Huttenhower, C., Salzberg, S.L., Ma, B., White, O. (2013) “The 15th Genomic Standards Consortium meeting” Standards in Genomic Sciences 8 (1).

259. Hecht, G.A., Blaser, M.J., Gordon, J., Kaplan, L.M., Knight, R., Laine, L., Peek, R., Sanders, M.E., Sartor, B., Wu, G.D., Yang, V.W. (2013) “What's the Value of an FDA

IND for Fecal Microbiota Transplantation in Clostridium difficile Infection?” Clin Gastroenterol Hepatol. 2013 Oct 19.

Publications from work after promotion to Full Professor: Research articles (peer-reviewed)

260. Metcalf, J.L., Wegener Parfrey, L., Gonzalez, A., Lauber, C.L., Knights, D., Ackermann, G., Humphrey, G.C., Gebert, M.J., Van Treuren, W., Berg-Lyons, D., Keepers, K., Guo, Y., Bullard, J., Fierer, N., Carter, D.O., Knight, R. (2013) “A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system.” Elife. 2013 Oct 15;2:e01104.

261. Glass, E.M., Dribinsky, Y., Yilmaz, P., Levin, H., Van Pelt, R., Wendel, D., Wilke, A., Eisen, J.A., Huse, S., Shipanova, A., Sogin, M., Stajich, J., Knight, R., Meyer, F., Schriml, L.M. (2013) “MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment.” ISME J. 2013 Oct 24.

262. Ponnusamy, L., Gonzalez, A., Van Treuren, W., Weiss, S., Parobek, C.M., Juliano, J.J., Knight, R., Roe, R.M., Apperson, C.S., Meshnick, S.R. (2013) “Diversity of Rickettsiales in the Microbiome of the Lone Star Tick, Amblyomma americanum.” Appl Environ Microbiol. 2013 Oct 25.

263. Kueneman, J.G., Parfrey, L.W., Woodhams, D.C., Archer, H.M., Knight, R., McKenzie, V.J. (2013) “The amphibian skin-associated microbiome across species, space and life history stages.” Mol Ecol. 2013 Sep 11.

264. Fierer, N., Ladau, J., Clemente, J.C., Leff, J.W., Owens, S.M., Pollard, K.S., Knight, R., Gilbert, J.A., McCulley, R.L. (2013) “Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States.” Science. 2013 Nov 1;342(6158):621-4.

265. Vázquez-Baeza, Y., Pirrung, M., Gonzalez, A., Knight, R. (2013) “EMPeror: a tool for visualizing high-throughput microbial community data.” Gigascience. 2013 Nov 26;2(1):16.

266. Peralta-Sánchez, J.M., Soler, J.J., Martín-Platero, A.M., Knight, R., Martínez-Bueno, M., Møller, A.P. (2013) “Eggshell bacterial load is related to antimicrobial properties of feathers lining barn swallow nests.” Microb Ecol. 2014 Feb;67(2):480-7.

267. Loudon, A.H., Woodhams, D.C., Parfrey, L.W., Archer, H., Knight, R., McKenzie, V., Harris, R.N. (2013) “Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus).” ISME J. 2013 Dec 12.

268. Ursell, L.K., Gunawardana, M., Chang, S., Mullen, M., Moss, J.A., Herold, B.C., Keller, M.J., McDonald, D., González, A., Knight, R., Baum, M.M. (2013) “Comparison of the vaginal microbial communities in women with recurrent genital HSV receiving acyclovir intravaginal rings.” Antiviral Res. 2013 Dec 19;102C:87-94.

269. Walters, W.A., Knight, R. (2014) “Technology and Techniques for Microbial Ecology via DNA Sequencing.” Ann Am Thorac Soc. 2014 Jan;11 Suppl 1:S16-20.

270. Mason, O.U., Scott, N.M., Gonzalez, A., Robbins-Pianka, A., Bælum, J., Kimbrel, J., Bouskill, N.J., Prestat, E., Borglin, S., Joyner, D.C., Fortney, J.L., Jurelevicius, D., Stringfellow, W.T., Alvarez-Cohen, L., Hazen, T.C., Knight, R., Gilbert, J.A., Jansson, J.K. (2014) “Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill.” ISME J. 2014 Jan 23.

271. Green, H.C., Haugland, R.A., Varma, M., Millen, H.T., Borchardt, M.A., Field, K.G., Walters, W.A., Knight, R., Sivaganesan, M., Kelty, C.A., Shanks, O.C. (2014)

“Improved HF183 Quantitative Real-Time PCR Assay for Characterization of Human Fecal Pollution in Ambient Surface Water Samples.” Appl Environ Microbiol. 2014 May;80(10):3086-94.

272. Gevers, D., Kugathasan, S., Denson, L.A., Vázquez-Baeza, Y., Van Treuren, W., Ren, B., Schwager, E., Knights, D., Song, S.J., Yassour, M., Morgan, X.C., Kostic, A.D., Luo, C., González, A., McDonald, D., Haberman, Y., Walters, T., Baker, S., Rosh, J., Stephens, M., Heyman, M., Markowitz, J., Baldassano, R., Griffiths, A., Sylvester, F., Mack, D., Kim, S., Crandall, W., Hyams, J., Huttenhower, C., Knight, R., Xavier, R.J. (2014) “The treatment-naive microbiome in new-onset Crohn's disease.” Cell Host Microbe. 2014 Mar 12;15(3):382-92.

273. Huang, S., Li, R., Zeng, X., He, T., Zhao, H., Chang, A., Bo, C., Chen, J., Yang, F., Knight, R., Liu, J., Davis, C., Xu, J. (2014) “Predictive modeling of gingivitis severity and susceptibility via oral microbiota” ISME J. 2014 Mar 20.

274. Metcalf, J.L., Ursell, L.K., Knight, R. (2014) “Ancient human oral plaque preserves a wealth of biological data.” Nat Genet. 2014 Mar 27;46(4):321-3.

275. Taş, N., Prestat, E., McFarland, J.W., Wickland, K.P., Knight, R., Berhe, A.A., Jorgenson, T., Waldrop, M.P., Jansson, J.K. (2014) “Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest.” ISME J. 2014 Apr 10.

276. Trausch, J.J., Xu, Z., Edwards, A.L., Reyes, F.E., Ross, P.E., Knight, R., Batey, R.T. (2014) “Structural basis for diversity in the SAM clan of riboswitches.” Proc Natl Acad Sci U S A. 2014 May 6;111(18):6624-9.

277. Woodhams, D.C., Brandt, H., Baumgartner, S., Kielgast, J., Küpfer, E., Tobler, U., Davis, L.R., Schmidt, B.R., Bel, C., Hodel, S., Knight, R., McKenzie, V. (2014) “Interacting symbionts and immunity in the amphibian skin mucosome predict disease risk and probiotic effectiveness.” PLoS One. 2014 Apr 30;9(4):e96375.

278. Bolnick, D.I., Snowberg, L.K., Hirsch, P.E., Lauber, C.L., Knight, R., Caporaso, J.G., Svanbäck, R. (2014) “Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch).” Ecol Lett. 2014 May 22.

279. Forsberg, K.J., Patel, S., Gibson, M.K., Lauber, C.L., Knight, R., Fierer, N., Dantas, G. (2014) “Bacterial phylogeny structures soil resistomes across habitats.” Nature. 2014 May 29;509(7502):612-6.

280. Lauber, C.L., Metcalf, J.L., Keepers, K., Ackermann, G., Carter, D.O., Knight, R. (2014) “Vertebrate Decomposition is Accelerated by Soil Microbes.” Appl Environ Microbiol. 2014 Aug;80(16):4920-9.

281. Macdonald, C.A., Crawley, M.J., Wright, D.J., Kuczynski, J., Robinson, L., Knight, R., Al-Soud, W.A., Sørensen, S.J., Deng, Y., Zhou, J., Singh, B.K. (2014) “Identifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experiment.” Environ Microbiol. 2014 Jun 16.

282. Bolnick, D.I., Snowberg, L.K., Caporaso, J.G., Lauber, C., Knight, R., Stutz, W.E. (2014) “Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity.” Mol Ecol. 2014 Jun 27.

283. Parfrey, L.W., Walters, W.A., Lauber, C.L., Clemente, J.C., Berg-Lyons, D., Teiling, C., Kodira, C., Mohiuddin, M., Brunelle, J., Driscoll, M., Fierer, N., Gilbert, J.A., Knight, R. (2014) “Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity.” Front Microbiol. 2014 Jun 19;5:298.

284. Shade, A., Jones, S.E., Caporaso, J.G., Handelsman, J., Knight, R., Fierer, N., Gilbert, J.A. (2014) “Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity.” MBio. 2014 Jul 15;5(4):e01371-14.

285. Bolnick, D.I., Snowberg, L.K., Hirsch, P.E., Lauber, C.L., Org, E., Parks, B., Lusis, A.J., Knight, R., Caporaso, J.G., Svanbäck, R. (2014) “Individual diet has sex-dependent effects on vertebrate gut microbiota.” Nat Commun. 2014 Jul 29;5:4500.

286. Larsen, P.E., Scott, N., Post, A.F., Field, D., Knight, R., Hamada, Y., Gilbert, J.A. (2014) “Satellite remote sensing data can be used to model marine microbial metabolite turnover.” ISME J. 2014 Jul 29.

287. Eilam, O., Zarecki, R., Oberhardt, M., Ursell, L.K., Kupiec, M., Knight, R., Gophna, U., Ruppin, E. (2014) “Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations.” MBio. 2014 Aug 12;5(4). pii: e01526-14.

288. Lin, P., Bach, M., Asquith, M., Lee, A.Y., Akileswaran, L., Stauffer, P., Davin, S., Pan, Y., Cambronne, E.D., Dorris, M., Debelius, J.W., Lauber, C.L., Ackermann, G., Baeza, Y.V., Gill, T., Knight, R., Colbert, R.A., Taurog, J.D., Van Gelder, R.N., Rosenbaum, J.T. (2014) “HLA-B27 and Human β2-Microglobulin Affect the Gut Microbiota of Transgenic Rats.” PLoS One. 2014 Aug 20;9(8):e105684.

289. Lax, S., Smith, D.P., Hampton-Marcell, J., Owens, S.M., Handley, K.M., Scott, N.M., Gibbons, S.M., Larsen, P., Shogan, B.D., Weiss, S., Metcalf, J.L., Ursell, L.K., Vázquez-Baeza, Y., Van Treuren, W., Hasan, N.A., Gibson, M.K., Colwell, R., Dantas, G., Knight, R., Gilbert, J.A. (2014) “Longitudinal analysis of microbial interaction between humans and the indoor environment.” Science. 2014 Aug 29;345(6200):1048-52.

290. Xu, Z., Malmer, D., Langille, M.G., Way, S.F., Knight, R. “Which is more important for classifying microbial communities: who's there or what they can do?” (2014) ISME J. 2014 Aug 29.

291. Rideout, J.R., He, Y., Navas-Molina, J.A., Walters, W.A., Ursell, L.K., Gibbons, S.M., Chase, J., McDonald, D., Gonzalez, A., Robbins-Pianka, A., Clemente, J.C., Gilbert, J.A., Huse, S.M., Zhou, H.W., Knight, R., Caporaso, J.G. (2014) “Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.” PeerJ. 2014 Aug 21;2:e545.

292. Seedorf, H., Griffin, N.W., Ridaura, V.K., Reyes, A., Cheng, J., Rey, F.E., Smith, M.I., Simon, G.M., Scheffrahn, R.H., Woebken, D., Spormann, A.M., Van Treuren, W., Ursell, L.K., Pirrung, M., Robbins-Pianka, A., Cantarel, B.L., Lombard, V., Henrissat, B., Knight, R., Gordon, J.I. (2014) “Bacteria from diverse habitats colonize and compete in the mouse gut.” Cell. 2014 Oct 9;159(2):253-66.

293. Knights, D., Ward, T.L., McKinlay, C.E., Miller, H., Gonzalez, A., McDonald, D., Knight, R. (2014) “Rethinking "enterotypes".” Cell Host Microbe. 2014 Oct 8;16(4):433-7.

294. Walters, W.A., Xu, Z., Knight, R. (2014) “Meta-analyses of human gut microbes associated with obesity and IBD.” FEBS Lett. 2014 Oct 10. pii: S0014-5793(14)00717-0.

295. Mayer, E.A., Knight, R., Mazmanian, S.K., Cryan, J.F., Tillisch, K. (2014) “Gut microbes and the brain: paradigm shift in neuroscience.” J Neurosci. 2014 Nov 12;34(46):15490-6.

296. Goodrich, J.K., Waters, J.L., Poole, A.C., Sutter, J.L., Koren, O., Blekhman, R., Beaumont, M., Van Treuren, W., Knight, R., Bell, J.T., Spector, T.D., Clark, A.G., Ley, R.E. (2014) “Human genetics shape the gut microbiome.” Cell. 2014 Nov 6;159(4):789-799.

297. Sharon, G., Garg, N., Debelius, J., Knight, R., Dorrestein, P.C., Mazmanian, S.K. (2014) “Specialized metabolites from the microbiome in health and disease.” Cell Metab. 2014 Nov 4;20(5):719-30.

298. Korajkic, A., Parfrey, L.W., McMinn, B.R., Baeza, Y.V., VanTeuren, W.,

Knight, R., Shanks, O.C. (2014) “Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water.” Water Res. 2014 Nov 13;69C:30-39.

299. Xu, Z., Knight, R. (2015) “Dietary effects on human gut microbiome diversity.” Br J Nutr. 2015 Jan;113 Suppl:S1-5.

300. Flores, G.E., Caporaso, J.G., Henley, J.B., Rideout, J.R., Domogala, D., Chase, J., Leff, J.W., Vázquez-Baeza, Y., Gonzalez, A., Knight, R., Dunn, R.R., Fierer, N. (2014) “Temporal variability is a personalized feature of the human microbiome.” Genome Biol. 2014 Dec 3;15(12):531.

301. Weiss, S., Amir, A., Hyde, E.R., Metcalf, J.L., Song, S.J., Knight, R. (2014) “Tracking down the sources of experimental contamination in microbiome studies.” Genome Biol. 2014 Dec 17;15(12):564.

302. Neuman, H., Debelius, J.W., Knight, R., Koren, O. (2015) “Microbial endocrinology: the interplay between the microbiota and the endocrine system.” FEMS Microbiol Rev. 2015 Feb 19. pii: fuu010.

303. Knight, R. (2015) “Why microbiome treatments could pay off soon.” Nature. 2015 Feb 26;518(7540):S5.

304. Carter, D.O., Metcalf, J.L., Bibat, A., Knight, R. (2015) “ Seasonal variation of postmortem microbial communities.” Forensic Sci Med Pathol. 2015 Mar 4.

Reviews (peer-reviewed)

305. Navas-Molina, J.A., Peralta-Sánchez, J.M., González, A., McMurdie, P.J., Vázquez-Baeza, Y., Xu, Z., Ursell, L.K., Lauber, C., Zhou, H., Song, S.J., Huntley, J., Ackermann, G.L., Berg-Lyons, D., Holmes, S., Caporaso, J.G., Knight, R. (2013) “Advancing Our Understanding of the Human Microbiome Using QIIME.” Methods Enzymol. 2013;531:371-444.

306. Gilbert, J.A., Krajmalnik-Brown, R., Porazinska, D.L., Weiss, S.J., Knight, R. (2013) “Toward effective probiotics for autism and other neurodevelopmental disorders.” Cell. 2013 Dec 19;155(7):1446-8.

307. Davies, N., Field, D., Amaral-Zettler, L., Clark, M.S., Deck, J., Drummond, A., Faith, D.P., Geller, J., Gilbert, J., Glöckner, F.O., Hirsch, P.R., Leong, J.A., Meyer, C., Obst, M., Planes, S., Scholin, C., Vogler, A.P., Gates, R.D., Toonen, R., Berteaux-Lecellier, V., Barbier, M., Barker, K., Bertilsson, S., Bicak, M., Bietz, M.J., Bobe, J., Bodrossy, L., Borja, A., Coddington, J., Fuhrman, J., Gerdts, G., Gillespie, R., Goodwin, K., Hanson, P.C., Hero, J.M., Hoekman, D., Jansson, J., Jeanthon, C., Kao, R., Klindworth, A., Knight, R., Kottmann, R., Koo, M.S., Kotoulas, G., Lowe, A.J., Marteinsson, V.T., Meyer, F., Morrison, N., Myrold, D.D., Pafilis, E., Parker, S., Parnell, J.J., Polymenakou, P.N., Ratnasingham, S., Roderick, G.K., Rodriguez-Ezpeleta, N., Schonrogge, K., Simon, N., Valette-Silver, N.J., Springer, Y.P., Stone, G.N., Stones-Havas, S., Sansone, S.A., Thibault, K.M., Wecker, P., Wichels, A., Wooley, J.C., Yahara, T., Zingone, A.; GOs-COS. (2014) “The founding charter of the Genomic Observatories Network.” Gigascience. 2014 Mar 7;3(1):2.

308. Ursell, L.K., Haiser, H.J., Van Treuren, W., Garg, N., Reddivari, L., Vanamala, J., Dorrestein, P.C., Turnbaugh, P.J., Knight, R. (2014) “The intestinal metabolome: an intersection between microbiota and host.” Gastroenterology. 2014 May;146(6):1470-6.

309. Dorrestein, P.C., Mazmanian, S.K., Knight, R. (2014) “Finding the Missing Links among Metabolites, Microbes, and the Host.” Immunity. 2014 Jun 19;40(6):824-32.

310. Goodrich, J.K., Di Rienzi, S.C., Poole, A.C., Koren, O., Walters, W.A., Caporaso, J.G., Knight, R., Ley, R.E. (2014) “Conducting a Microbiome Study.” Cell.

2014 Jul 17;158(2):250-62. 311. Gilbert, J.A., Jansson, J.K., Knight, R. (2014) “The Earth Microbiome project:

successes and aspirations.” BMC Biol. 2014 Aug 22;12(1):69. Other articles (not peer reviewed)

312. Field, D., Sterk, P., Kottmann, R., De Smet, J.W., Amaral-Zettler, L., Cochrane, G., Cole, J.R., Davies, N., Dawyndt, P., Garrity, G.M., Gilbert, J.A., Glöckner, F.O., Hirschman, L., Klenk, H.P., Knight, R., Kyrpides, N., Meyer, F., Karsch-Mizrachi, I., Morrison, N., Robbins, R., San Gil, I., Sansone, S., Schriml, L., Tatusova, T., Ussery, D., Yilmaz, P., White, O., Wooley, J., Caporaso, G. (2014) “Genomic standards consortium projects.” Stand Genomic Sci. 2014 Feb 15;9(3):599-601.

313. Kyrpides, N.C., Hugenholtz, P., Eisen, J.A., Woyke, T., Göker, M., Parker, C.T., Amann, R., Beck, B.J., Chain, P.S., Chun, J., Colwell, R.R., Danchin, A., Dawyndt, P., Dedeurwaerdere, T., DeLong, E.F., Detter, J.C., De Vos, P., Donohue, T.J., Dong, X.Z., Ehrlich, D.S., Fraser, C., Gibbs, R., Gilbert, J., Gilna, P., Glöckner, F.O., Jansson, J.K., Keasling, J.D., Knight, R., Labeda, D., Lapidus, A., Lee, J.S., Li, W.J., Ma, J., Markowitz, V., Moore, E.R., Morrison, M., Meyer, F., Nelson, K.E., Ohkuma, M., Ouzounis, C.A., Pace, N., Parkhill, J., Qin, N., Rossello-Mora, R., Sikorski, J., Smith, D., Sogin, M., Stevens, R., Stingl, U., Suzuki, K., Taylor, D., Tiedje, J.M., Tindall, B., Wagner, M., Weinstock, G., Weissenbach, J., White, O., Wang, J., Zhang, L., Zhou, Y.G., Field, D., Whitman, W.B., Garrity, G.M., Klenk, H.P. (2014) “Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.” PLoS Biol. 2014 Aug 5;12(8):e1001920.

314. González, A., Vázquez-Baeza, Y., Knight, R. (2014) “SnapShot: The Human Microbiome.” Cell. 2014 Jul 31;158(3):690-690.e1.

315. Huttenhower, C., Knight, R., Brown, C.T., Caporaso, J.G., Clemente, J.C., Gevers, D., Franzosa, E.A., Kelley, S.T., Knights, D., Ley, R.E., Mahurkar, A., Ravel, J.; Scientists for Advancement of Microbiome Research, White, O. (2014) “Advancing the microbiome research community.” Cell. 2014 Oct 9;159(2):227-30.

Presentations at Professional Meetings 2015 American Society of Clinical Pharmacology and Therapeutics (ASCPT), New Orleans,

LA, Mar 3-7. “The Role of the Gut Microbiota in the Pathogenesis of Disease”. Oral, invited speaker.

2015 Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, FL, Feb 25-28. “Dynamics of the human microbiome and its evolving genomes”. Oral, invited speaker.

2014 West Coast Bacterial Physiologist's Meeting, Asilomar, CA, Dec 13-15. “Tracking the human microbiome from birth to death (and beyond)”. Oral, invited speaker.

2014 Imperial College London Neonatal Update, London, UK, Dec 1-5. “Faecal transplantation: a new therapeutic horizon”. Oral, invited speaker.

2014 Neuroscience 2014 Symposium, Washington, DC, Nov 19. "Crowdsourcing microbe-brain connections through American Gut." Oral, invited speaker.

2014 Consortium for Functional Glycomics (CFG) satellite meeting, by video conference, Nov 16. “Dynamics of the Human Microbiome”. Oral, invited speaker.

2014 American College of Rheumatology (ACR) Annual Meeting, Boston, MA, Nov 14-19. “Culture Independent Surveys of Microbiomes”. Oral, invited speaker.

2014 11th Nestlé International Nutrition Symposium on “Nutrition and the Human Gut Microbiome” , Lausanne, Switzerland, Oct 23-24. “Gut Microbes and their Role in Malnutrition and Obesity”. Oral, invited keynote speaker.

2014 Disruptive Innovation in Boulder, CO, Oct 9-10. “The New Health Frontier: What the Human Microbiome Project is Teaching Us About Ourselves”. Oral, invited speaker.

2014 2nd Microbiome/Microbiota R&D and Business Collaboration Forum USA, San Diego, CA, Oct 2-3. “Dynamics of the human microbiome”. Oral, invited speaker.

2014 ISME (International Society for Microbial Ecology), Seoul, South Korea, August 24-29. “The American Gut Project”. Oral, invited speaker.

2014 International Society of Anthrozoology (ISAZ) meeting, Vienna, Austria, July 19-22. “How the microbiome links us and our companion animals.” Oral, invited speaker.

2014 Kenneth Rainin Foundation Symposium, San Francisco, CA, July 15-16. “Meta-analyses and cross-cohort studies of the human gut microbiome with application to IBD”. Oral, invited speaker.

2014 International Probiotics Association World Congress, Athens, Greece, May 10-11. “American Gut project.” Oral, invited speaker.

2014 Digestive Disease Week, Chicago, May 3-5. “Understanding Available Platforms for Characterization of the Microbiome - From 16S to the Metagenome.” and “Basic Principles in the Dynamics of Defined Microbial Consortia in the Gut.” Oral, invited speaker.

2014 PSC Partners Meeting, Denver, Apr 26. “Towards a pipeline for personalized medicine based on the human microbiome.” Oral, invited speaker.

2014 2014 Meetings of the Human Biology Association, Calgary, Canada, Apr 9. “Ecology and demography of the human microbiome.” Oral, invited speaker.

2014 Health Journalism 2014, Denver, CO, Mar 28. “Mapping bacteria in the body”. Panelist. 2014 TED 2014, Vancouver, Canada, Mar 17–21. “Our remarkable microbial journeys and

their implications for health and disease.“ Oral, invited speaker. 2013 11th Annual Ecological Genomics Symposium, Kansas State University, Kansas City,

KS, Nov 1-3. “The Earth Microbiome Project”. Oral, invited speaker. 2013 29th Boulder Conference on the History and Philosophy of Science, University of

Colorado at Boulder, CO, Nov 1-3. “Measuring the kinds of microbes, and the microbial communities they form”. Oral, invited speaker.

2013 HHMI science meeting, Janelia Farm Research Campus, Ashburn, VA, Oct 8-10. “Gut microbes and their role in nutrition and obesity”. Oral, invited speaker.

2013 Waltham International Nutritional Sciences Symposium 2013, Portland, OR, Oct 2-4. “Role of the oral and gut microbiome on health: dietary implications”. Oral, plenary speaker.

2013 International Human Microbiome Congress, Hangzhou, China, Sep 13-15. “Crowdsourced Science: The Earth Microbiome Project and American Gut”. Oral, invited speaker.

2013 Office of Science and Technology Policy under the Executive Office of the President, brown bag seminar on the microbiome, Washington, DC, July 25. “Microbial communities as a unifying principle for human, animal and environmental health: crowdsourcing and crowdfunding as approaches to large-scale projects”. Oral, invited speaker.

2013 Human Microbiome Science: Vision for the Future, Bethesda, MD, July 24-26. “From correlation to causation in human microbiome studies”. Oral, invited speaker.

2013 Gordon Research Conference (GRC) Applied & Environmental Microbiology, South Hadley, MA, July 7-12. Introduction to the session Is everything everywhere or does the environment select?. Oral, invited speaker and discussion leader.

2013 2013 International Conference on Genomics in Europe, Ghent, Belgium, June 25-28. “Characterizing microbial effects of family structure, including our furry family members?” Oral, invited speaker.

2013 Probiotics, Prebiotics, and the Host Microbiome: The Science of Translation, New York City, NY, June 12-14. Scientific organizing committee member.

2013 JDRF Probiotics, Prebiotics, and the Host Microbiome workshop, NewYork City, NY, June 11. “Bioinformatics techniques for combining large datasets: the HMP, American Gut, and TEDDY”. Oral, invited speaker.

2013 The Thomas L. Petty Aspen Lung Conference, Aspen, CO, Jun 5. “Technologies and Techniques: Old and New”. Oral, invited speaker.

2013 2nd Conference on the Microbiology of the Built Environment, Boulder, CO, May 23-24. “Upgrading and Updating Primer on Translational Progress on Bioinformatics Processing”. Oral, invited speaker.

2013 ASM 2013, Denver, CO, May 18-21. Workshop “Metagenomic Approaches: Frontiers of Annotation and Assembly, Networking and Discovery”. Keynote speaker, invited participant.

2013 Illumina Discovery Symposium at ASM 2013, Denver, CO, May 17. “Using the Illumina platform to reveal the human and earth microbiome”. Oral, invited speaker.

2013 Gordon Research Conference (GRC) Epithelial Differentiation & Keratinization, Lucca, Italy, May 12–17. “Distribution of microbes on the skin of humans and other vertebrates”. Oral, invited speaker.

2013 Cell Symposia: Microbiome and Host Health 2013, Lisbon, Portugal, May 12-14. “Effect size and cross-species translatability of microbiome studies”. Oral, invited speaker.

2013 Molecular Pathogenesis of Infectious Diseases (MPID) Mini-Symposium, Denver, CO, May 3. “Making the Human Microbiome Project data work for you”. Oral, invited speaker.

2013 Genomes Environments Traits (GET) conference, Boston, MA, Apr 26. “Human Microbiome”. Oral, invited speaker.

2013 NIMH Director's Innovation Speaker Series, Bethesda, MD, Apr 25. “Trillions of tiny voices: how does gut microbes speak to the brain, and what are they saying?”. Oral, invited speaker.

2013 Genomic Standards Consortium (GSC) meeting, Washington, DC, Apr 22-24. Main meeting: “Using standards-compliant metadata to combine human microbiome studies”. Working group Genomic Observatories: ”American Gut: crowdfunding microbiome science”. Oral, invited speaker, chair.

2013 NIJ Forensic Research and Development Grantees Meeting, Washington, DC, Feb 19. “Microbial Community Change Associated with Decomposing Corpses”. Oral, invited speaker.

2013 Museum of Science, Boston, MA, Feb 6. Title of the program: “Friends with Benefits: The Human Microbiome". Oral, invited speaker.

2013 National Academies Keck Future Initiative (NAKFI) Microbial Ecosystem Services workshop at SESYNC, Annapolis, MD, Jan 7-9.

2012 Institute of Medicine (IOM) Forum on Microbial Threats, Washington, DC, Dec 11-12. “Bacterial communities as a theme unifying human, animal and environmental health”. Oral, invited speaker.

2012 Genetics Otago (GO) symposium, University of Otago, Dunedin, New Zealand, Nov 29. “Making the HMP Data Work For You”. Oral, invited speaker.

2012 New Zealand Society for Microbiology Annual Meeting, Dunedin, New Zealand, Nov 26-29. “Microbial genomics and the human microbiome”. Oral, keynote speaker.

2012 Philosophy of Science Association (PSA) Biennial Meeting, San Diego, CA, Nov 17. “From Molecules to Dynamic Biological Communities”. Oral, invited speaker.

2012 UAB Comprehensive Cancer Center Scientific Retreat, Birmingham, AL, Oct 29. “Spatial

and temporal variability in the human microbiome”. Oral, keynote speaker. 2012 ASM Conference on Beneficial Microbes, San Antonio, TX, Oct 22-26. “Placing the

human microbiome in context”. Oral, invited speaker. 2012 Host-associated Microbiota workshop 2012, Basel, Switzerland, Sep 12-14.

“Quantitative Insights Into Microbial Ecology” and “Using QIIME to understand the evolution of mammals and their microbes”. Oral, invited speaker.

2012 ISME (International Society for Microbial Ecology), Copenhagen, Denmark, Aug 19-24. " From the HMP to the EMP: deriving insight from large-scale sequencing projects". Oral, invited speaker.

2012 Benasque RNA Bioinformatics Workshop, Benasque, Spain. “Homology vs Analogy via Motifs”, Jul 24, and “RNASTAR, Greengenes and QIIMEdb”, Jul 30. Oral, invited.

2012 ASM general meeting, San Francisco, CA, Jun 16-19. Program committee member, session co-chair, “Evolution of Mammals and their Gut Microbes”, Jun 18, and “Integrating the HMP Healthy Cohort with Other Populatinos to Gain Insight Into Health, Disease and Technical Variation”. Oral, invited.

2012 GlaxoSmithKline, Collegeville, PA, May 2. “Towards a pipeline for microbiome-based personalized medicine”. Oral, invited speaker.

2012 International Human Microbiome Congress (IHMC), Paris, France, Mar 19-21. “Sources of variation in the human microbiome”. Oral, invited speaker.

2012 Keystone Symposia, Keystone, CO, Mar 4–6. "Defining an aberrant microbiota". Oral, invited speaker.

2012 Advancing Science, Serving Society (AAAS) Annual Meeting, Vancouver, Canada, Feb 17-19. “Exploring the Microbial World - why should humanity care?”. Oral, invited speaker.

2012 Annual Meeting of the Israeli Society of Microbiology (ISM), Ramat Gan, Israel, Feb 13-14. “Bioinformatics for the Human Microbiome and Beyond”. Oral, invited speaker.

2011 Science writers 2011 meeting, Flagstaff, AZ, Oct 17. “Human microbiomes: How bacteria affect our behavior, our weight and our brains.”. Oral, invited speaker.

2011 Argonne Soil Metagenomics Workshop, Indian Lakes Resort, IL, Oct 5-7. “Analysis and visualization of community structure (16S) data”. Oral, invited speaker.

2011 Montreal Bioinformatics Users Group (MonBUG) Bioinformatics Symposium 2011, Montreal, Canada, Sep 23. “Bioinformatics for the Human Microbiome and Beyond”. Oral, invited speaker.

2011 Federation of American Societies for Experimental Biology (FASEB) Summer Research Conference, Steamboat, CO, Aug 17. “Microbial Ecology in the Gut”. Oral, invited speaker.

2011 Marine Biology Lab, Woods Hole, MA, Aug 3-13. Course: Strategies and Techniques for Analyzing Microbial Population Structures. “Quantitative Insights Into Microbial Ecology”. Oral, invited speaker, faculty member.

2011 Workshop on Comparative Genomics, Fort Collins, CO, July 19-20. “QIIME: Quantitative Insights Into Microbial Ecology”. Oral, invited speaker, faculty member.

2011 Gordon Research Conference (GRC) Applied & Environmental Microbiology, South Hadley, MA, July 10-15. Introduction to the session Evolution of Bacterial Species and their Genomes. Oral, invited speaker and discussion leader.

2011 International Society for Exercise Immunology (ISEI), Oxford, UK, July 11. “Diet, genetics, and the mammalian microbiome”. Oral, invited speaker, keynote speaker.

2011 The First International EMP Workshop, Shenzhen, China, Jun 13-15. “Lessons learned from Massive Datasets”. Oral, invited speaker, session chair.

2011 Marabou Nutrition Symposium, Stockholm, Sweden, Jun 10-12. “Defining the human microbiome”. Oral, invited.

2011 Conference on Bacterial Genetics and Ecology (BAGECO11), Corfu, Greece, May 29 –

Jun 2. “Spatial and temporal patterning of the human microbiome”. Oral, invited speaker.

2011 Keystone Symposia, Breckenridge, CO, Mar 25-29. ”Quantitative Insights into Microbial Ecology”. Oral, invited speaker, plenary session chair.

2011 ASM general meeting, New Orleans, LA, May 21-24. “Spatially and Temporally Resolved Studies of the Human Microbiome”. Oral, invited speaker, covener along with Lita Proctor.

2011 JGI Genomics of Energy and Environment, San Francisco, CA, Mar 22-24.” Spatially and Temporally Resolved Studies of the Human Microbiome”. Oral, invited speaker.

2011 Annual R.G.E. Murray Lectureship, University of Western Ontario, London, Canada, Mar 21. “Variation in the human microbiome across space in time”. Oral, invited speaker.

2011 International Human Microbiome Congress (IHMC), Vancouver, Canada, Mar 9-11. “I Believe The Robots Are Our Future: Automation, Machine Learning, and 10,000 Samples Per Study”. Oral, invited.

2011 Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, FL, Feb 2-5. “Spatially and temporally explicit studies of the human microbiome”. Oral, invited, plenary speaker.

2011 Pacific Symposia in Biocomputing, Kohala Coast, Hawaii, Jan 3-7. “Spatial and Temporal Diversity of the Human Microbome”. Oral, invited.

2010 Microbiota, Paris, France, Dec 14-15. "Defining a core human microbiome". Oral, invited.

2010 American College of Neuropsychopharmacology (ACNP) annual meeting, Miami, FL, Dec 5-9, Presidential Plenary. "Variation in Human and Mouse Microbiomes Over Space, Time and Pathological Status". Oral, invited.

2010 Eli Lilly Foundation "Microbiota" meeting, Madrid, Spain, Nov 18-19. "Spatial and temporal variability in the human microbiota". Oral, invited.

2010 22nd Annual Kavli Frontiers of Science Symposium, Beckman Center, Irvine, CA, Nov 4-6. "Spatially and temporally explicit studies of the human microbiome". Oral, invited. Acted as session chair.

2010 Beneficial Microbes, Miami, FL, Oct 25-29. "Spatial and temporal variability of the human skin microbiome". Oral, invited.

2010 Forward Look Genes Environment, Barcelona, Spain, Oct 20-21. "Microbiota of Surfaces and Disease". Oral, invited.

2010 Genome Biology "Beyond the Genome", Harvard Medical School, Cambridge, MA, Oct 11-13. "Translational medicine and the human microbiome". Oral, invited.

2010 Upstate New York RNA meeting, Rensselaerville, NY, Oct 8-9. "Nucleotides that are essential but not conserved". Oral, invited.

2010 Genomic Standards Consortium meeting, Argonne National Labs, Chicago, IL, Oct 6. "The importance of metadata for science". Oral, invited.

2010 Pfizer Research Symposium, Long Island, NY, Sep 3-5. "Diversity of the Human Microbiome Across Spatial and Temporal Scales". Oral, invited.

2010 Human Microbiome Project Research Network Meeting, St. Louis, MO, Aug 31-Sep 2. "Spatially and temporally explicit studies of the human microbiome". Oral, invited.

2010 ISME (International Society for Microbial Ecology), Seattle, WA, Aug 22-27. "Genomic Standards Consortium M5 Roundtable". Oral, invited, co-chair of session (with Jack Gilbert, Argonne National Lab).

2010 ICIS (Institute for Computing in Science) Terabase Metagenomics meeting, Snowbird, UT, Jul 17-24. "Shallow Sequencing: Modeling the Microbial Climate" and "Single-copy marker genes & a terabase of sequence". Oral, invited.

2010 Cambridge Healthtech Beyond Sequencing meeting, San Francisco, CA, Jun 22-23.

"Relating microbial communities to function: insights from high-throughput sequencing". Oral, invited.

2010 Sloan Indoor Environment workshop, Chicago, IL, Jun 15. "QIIME: Quantitative Insights Into Microbial Ecology". Oral, invited.

2010 Canadian Society of Microbiologists 60th annual meeting, McMaster University, Hamilton, ON, Canada, Jun 14-17. "Diversity of the Human Microbiome Across Spatial and Temporal Scales". Oral, invited.

2010 ASMCUE (American Society for Microbiology Conference on Undergraduate Education), San Diego, CA, May 20-22. "They have us surrounded and we're outnumbered: the microbiome project." Oral, invited.

2010 GET (Genes, Environment, Technology) meeting, Boston, MA, Apr 27. "Visions of the Future: The Bio Weather Map". Oral, invited.

2010 University of Colorado Anschutz Medical Campus Molecular Biology Graduate Student Symposium, Denver, CO, Apr 22-23. "From the 16S rRNA renaissance to the 16S rRNA enlightenment: computational and experimental perspectives." Oral, invited.

2010 MSI (Microbial Science Initiative), Harvard University, Cambridge, MA, Apr 17. "Diversity of the Human Microbiome Across Spatial and Temporal Scales". Oral, invited.

2010 NCAS (North Carolina Academy of Sciences) Annual Meeting, Guilford College, Greensboro, NC, Mar 26-27. "The Human Microbiome". Oral, invited.

2010 ABRF (Association of Biomolecular Resource Facilities), Sacramento, CA, Mar 21-23. "From sequences to insight in microbial ecology". Oral, invited.

2010 HUPO (Human Proteomics Organization), Denver, CO, Mar 7-10. "Bacterial community variation in human body habitats across space and time". Oral, invited.

2010 Meta-HIT, Shenzhen, China, Mar 1-3. "Defining a core human gut microbiome". Oral, invited.

2010 ICoMM (International Census of Marine Microbes) Working Group on Alpha Diversity, Max Planck Institute-Bremen (participated by teleconference), Jan 25. "Metrics for comparing microbial communities". Oral, invited.

2010 Human Microbiome Project Research Network Meeting, Houston, TX, Jan 19-21. “16S rRNA Data Management and Analysis at the DACC”. Poster, invited.

2010 RNA Ontology Consortium Structure Mapping Group Meeting, Kona, HI, Jan 8-10. Workshop organizer.

2010 Pacific Symposia in Quantitative Biology, Kona, HI, Jan 4-8. Invited participant at Genomics Standards Consortium session Jan 4.

2009 National Academy Keck Futures Initiative, Nov 19-22. “Group 8: Determine the context in and extent to which evolution can be exploited in synthetic biology”. Oral, chosen by working group to present findings.

2009 Howard Hughes Medical Institute Early Career Scientists Meeting, Janelia Farm Research Campus, Ashburn, VA, Nov 15-18. “Development of the Human Microbiome”. Oral, invited.

2009 National Association of Biology Teachers, Denver, CO, Nov 11-14. “They have us SURROUNDED and we’re OUTNUMBERED: the Microbiome Project”. Oral, invited.

2009 National Academy of Sciences Sackler Symposium, Irvine, CA, Nov 1-3. “From the 16S rRNA renaissance to the 16S rRNA enlightenment: computational and experimental perspectives”. Oral, invited.

2009 CSIRO Genes in Ecology Workshop, Brisbane, Australia, Oct 26-27. “Tools and strategies for understanding microbial communities”. Oral, invited.

2009 Smith College Darwin Symposium, Smith College, Northampton, MA, Oct 2-3. “Evolution of the Human Microbiome”. Oral, invited.

2009 Cambridge HealthTech Next-Generation Sequencing Meeting, Providence, RI, Sep 21-23. “Sequencing application: obesity and the gut microbiome”. Oral, invited.

2009 Cambridge HealthTech Next-Generation Sequencing Meeting, Providence, RI, Sep 21-23. “Exploring the human microbiome with next-gen sequencing”. Oral, invited.

2009 Joint Genome Institute Microbial Genomics and Metagenomics Workshop, Walnut Creek, CA, Sep 14-18. “Defining a core human gut microbiome”. Oral, invited.

2009 Interscience Conference on Antimicrobial Agents and Chemotherapy, San Francisco, CA, Sep 12-15. “Strategies and tools for understanding the human microbiome”. Oral, invited.

2009 Evolution Symposium, University of Nebraska at Kearney, Kearney, NE, Sep 3-4. “Evolution of the Genetic Code”. Oral, invited.

2009 Computational methods for RNA analysis meeting, Benasque, Spain, Jul 26-Aug 8. “Evolution of the Human Microbiome”. Oral, invited.

2009 Human Microbiome Project Research Network Meeting, Jun 9-10, Washington, DC. “To Tree or Not To Tree: Phylogeny and Microbial Community Comparisons”. Invited, Poster; “New Tools for Computational Analysis: Tools for understanding microbial communities & diversity in human body habitats”, Invited, Poster.

2009 RNA Society Meeting, May 26-Jun 1, Madison, WI. “Active site specifications and self-organization drive universal compositional biases in natural and artificial RNA sequences”. Poster.

2009 RNA Ontology Consortium Meeting, May 24-25, Madison, WI. “Proposal for the RNA Alignment Ontology”. Oral, invited.

2009 American Society for Microbiology General Meeting, May 17-21, Philadelphia, PA. “Using pyrosequencing to explore the human microbiome”. Oral, invited.

2009 Department of Energy “New Frontiers in Characterizing Biological Systems” panel, May 13-14, Washington, DC, invited participant.

2009 Human Microbiome Project Jumpstart Meeting, Cold Spring Harbor Laboratories, May 5. “What community analysis with 454 can and can’t do for you”. Oral, invited.

2009 Association of Biomolecular Resource Facilities, Memphis, TN Feb 9-10. “Massively Parallel Barcoded Pyroseqeuncing Reveals Unexpected Diversity in the Human microbiome”. Oral, invited.

2009 RNA Ontology Consortium Meeting, Cambridge, UK Jan 4-6. “Initial Proposal for the RNA Alignment Ontology”. Oral, invited.

2008 International Society for Microbial Ecology, Cairns, Australia, Aug 17-22. “Evolution of the human microbiome.” Oral, invited.

2008 RNA Society Meeting, Berlin, Germany, Jul 28-Aug 3. “Error-correcting barcoded pyrosequencing allows simultaneous analysis of hundreds of microbial communities.” Oral.

2008 RNA Ontology Consortium Meeting. Berlin, Germany, Jul 26-27. “Explicit representation of RNA correspondences”. Oral, invited.

2008 Society for Molecular Biology and Evolution, Barcelona, Spain, Jun 5-8. “Novel approaches for comparing microbial communities.” Poster.

2008 Living on Human Beings: Metagenomic Approaches and Challenges, Banbury Centre, Cold Spring Harbor Laboratories, NY, Mar 2-5. “Is there a core human microbiome?” Oral, invited.

2007 American Geophysical Union General Meeting, San Francisco, CA, Dec 10-14. “New tools for understanding microbial diversity using high-throughput sequence data”. Oral, invited.

2007 RNA Ontology Consortium Structure Mapping Working Group. Montreal, Canada, Sep 4-6. “Connecting mapping data to RNA alignments”. Oral, invited.

2007 NSF Frontiers in Integrative Biological Research (FIBR) workshop: “Do Species Matter in Microbial Ecology?” Bozeman, Montana, USA, Jul 30-Aug 1. “New insights into tRNA pool evolution and environmental distribution of microbes using UniFrac.” Poster.

2007 Evolution Meeting, Christchurch, New Zealand, June 16-20. “Mapping microbial communities using 16S rRNA.” Oral.

2007 RNA Society Meeting, Madison, Wisconsin, USA, May 29-Jun 3. “New insights into tRNA pool evolution and environmental distribution of microbes using UniFrac.” Poster.

2007 RNA Ontology Consortium Meeting, Madison, Wisconsin, USA, May 28-29. “Data representation: techniques and trade-offs.” Oral, invited.

2006 Benasque RNA Bioinformatics Workshop, Benasque, Spain, July 16-July 28. “Mapping Microbial Communities Using 16S rRNA”. Oral, invited.

2005 National Academy Keck Futures Initiative Workshop, Irvine, California, USA, November 10-13. “Novel methods for detecting horizontal gene transfer.” Poster, invited.

2005 Society for Molecular Biology and Evolution, Auckland, New Zealand, June 19-23. “The Scope of Selection: Finding Correctly Folded RNA Molecules”. Oral, invited. 2004 Evolution, Ft. Collins, CO, June 26-30. “Bayesian Methods for RNA Secondary Structure Prediction”. Oral. 2003 RNA, Vienna, Austria, July 1-6. “Finding correctly folded active RNA motifs” and “BayesFold: Rational 2° folds combining chemical, thermodynamic, and sequence information.” Posters. 2002 RNA, Madison, WI, May 28-Jun 2. “A Bayesian method for RNA folding that combines multiple forms of information”. Poster. 2001 Evolution 2001 (joint meeting of the Society for the Study of Evolution, the Society of Systematic Biologists, and the American Society of Naturalists), Knoxville, TN June 26- July 1. “Nonadaptive Molecular Evolution: Are Amino Acid and Codon Usage Spandrels?” Oral. 2001 DIMACS Workshop on Whole-Genome Comparisons, New Brunswick, NJ February 28- March 2. “Have functional nucleic acid sequences evolved characteristic base composition biases? A comparative study of genes and genomes”. Research in collaboration with Dr. Erik Schultes (Whitehead Institute, MIT). Oral. 2000 Artificial Life VII, Portland, OR, August 1-6. “From Chemistry to Information: Emergence of the Genetic Code”. Travel funding from NASA; presented in Astrobiology session. Oral. 2000 SMBE, New Haven, CT, June 17-20. “Can Genome Composition Explain Codon Bias? Insights from a Null Hypothesis” and “Evolution of the Genetic Code: Rewiring the Keyboard in an Inconstant World”. Oral. 2000 RNA Society, Madison, WI, May 30-June 4. “Rewiring the Keyboard: Quantitative Tests of Genetic Code Evolution”. Poster. 1998 SMBE/GSA, Brisbane, Australia, July 11-14. “Adaptation, Chemistry, and History: Three Faces of Genetic Code Evolution”. Oral. 1999 DIMACS Workshop on Evolution as Computation, January 11-12, Princeton, NJ. “Genetic Code Evolution in the RNA World and Beyond”. Oral. 1998 NEMEB, New York, NY, October 31. “Evolution of the Genetic Code: New Evidence from In Vitro Selection”. Poster. 1998 New York Academy of Sciences workshop, “Molecular Strategies in Biological

Evolution”, New York, NY, June 27-29. “Evolution of the Genetic Code: New Evidence from In Vitro Selection”. Poster.

1998 DIMACS Workshop on Nucleic Acid Selection and Computing, Princeton, NJ, March 15-17. “Arginine Codon/Binding Site Associations and the Origin of the Genetic Code”. Poster.

Research Seminars 2015 Georgia State University, Atlanta, GA, Mar 6. “Ecology and evolution of the human

microbiome in health and disease”. Oral, invited speaker. 2015 University of Georgia, Athens, GA, Mar 5. “Microbes and their role in obesity and

malnutrition”. Oral, invited speaker. 2015 University of North Carolina, Chapel Hill, NC, Mar 4. “Microbes and their role in obesity

and malnutrition”. Oral, invited speaker. 2015 Duke University, Durham, NC, Mar 3. “Ecology and evolution of the human microbiome

in health and disease”. Oral, invited speaker. 2015 San Diego State University, San Diego, CA, Feb 26. “Dynamics of the Human

Microbiome”. Oral, invited speaker. 2015 CHLA Annual Symposium, Los Angeles, CA, Jan 15. “Dynamics of the human gut

microbiome”. Oral, invited speaker. 2015 Hurley Distinguished Lecture at UC Davis, Davis, CA, Jan 5. “Dynamics of the Human

Microbiome”. Oral, invited speaker. 2014 Columbia University, New York, NY, Dec 3. “Dynamics of the human microbiota”. Oral,

invited speaker. 2014 University of Colorado, CHPS (The Committee on the History and Philosophie of

Science) Coffee Talk, Boulder, CO, Nov 11. “The human microbiome: concepts, technologies, and inferences”. Oral, invited speaker.

2014 University of Colorado, IPHY colloquium, Boulder, CO, Nov 10. “The human microbiome and its variation, development, and effects on health”. Oral, invited speaker.

2014 UCSD/Rady Children’s Hospital Grand Rounds, San Diego, CA, Nov 7. “Human and environmental microbiomes, and their connections to health”. Oral, invited speaker.

2014 University of Bari, Bari, Italy, Oct 21. “Dynamics of the human microbiome”. Oral, invited speaker.

2014 University of Colorado, CU on the Weekend Program, Boulder, CO, Oct 18. “Introduction to Your Human Microbiome”. Oral, invited speaker.

2014 University of Maryland School of Medicine, Institute for Genome Sciences (IGS) Seminar Series, Baltimore, MD, Sep 25. “Connecting human and environmental microbiomes” . Oral, invited speaker.

2014 NIST, Rockville MD, Sep 26. “Measuring our microbial communities and their dynamics”. Oral, invited speaker.

2014 Woods Hole Oceanographic Institution, Woods Hole, MA, Aug 8-12. “Tools for understanding human microbiome dynamics” (Departmental), “From open-source software to crowdfunding and crowdsourcing: leveraging a broader community for large-scale scientific efforts” (Student lunch and discussion), “From the human microbiome to the earth microbiome: understanding global microbial patterns and processes” (Institutional). Oral, invited speaker, Biology Steinbach Scholar.

2014 Marine Biology Lab, Woods Hole, MA, Aug 9. Course: Strategies and Techniques for Analyzing Microbial Population Structures. “Quantitative Insights Into Microbial Ecology”. Oral, invited speaker, faculty member.

2014 Science webinar live online, July 15. “Microbiomes in obesity and malnutrition”. Oral. 2014 Stanford University, Stanford, CA, June 26-27. “Tracking the human microbiome from

birth to death (and beyond)”. Oral, invited speaker. 2014 Colorado Sleep and Circadian Research Symposia, Boulder, CO, June 10. “Microbiota”.

Oral, invited speaker. 2014 Smith Conference, Colorado State University CSU, Fort Collins, CO, June 5. “The

Human Gut Microbiome”. Oral, invited speaker.

2014 University of California, San Diego, CA, Apr 9. “Coevolution of computational tools and next-generation sequencing methods for microbiome studies.” Oral, invited speaker.

2014 Keystone symposium, Big Sky, Montana, Apr 1-6. “Microbial Communities Viewed Over Time and Space”. Oral, invited speaker.

2014 University of British Columbia, Vancouver, Canada, Mar 16. “Spatial and temporal patterning in microbial communities, including the human microbiome.” Oral, invited speaker.

2014 University of California, Los Angeles, CA, Mar 6. “Gut microbes and their role in malnutrition in obesity.” Oral, invited speaker.

2014 University Montreal, Montreal, Canada, Feb 7. “Microbial Communities and their Implications for Human and Environmental Health.” Oral, invited speaker.

2014 McGill University, Montreal, Canada, Feb 6. “Gut Microbes and their Role in Obesity and Malnutrition.” Oral, invited speaker.

2014 University of California, San Diego, CA, Jan 30. “Towards a pipeline for personalized medicine based on the human microbiome.” Oral, invited speaker.

2014 University of Colorado at Colorado Springs, Center for Biofrontiers, Colorado Springs, CO, Jan 24. “Gut Microbes and their Role in Malnutrition and Obesity.” Oral, invited speaker.

2014 Workshop on Genomics, Cesky Krumlov, Czech Republic, Jan 18. Faculty. 2014 Institute of Organic Chemistry and Biochemistry (IOCB), Prague, Czech Republic, Jan

17. “Microbial Communities and their Implications for Human and Environmental Health.” Oral, invited speaker.

2014 ARO, Volcani Research Center, Bet Dagan, Israel, Jan 16. “Gut Microbes and their Role in Malnutrition and Obesity”. Oral, invited speaker.

2014 Weizmann Institute of Science, Revohot, Israel, Jan 13-14. Course lecture for Contemporary Systems Biology “QIIME: Quantitative Insights Into Microbial Ecology” and seminar “Gut microbes and their role in obesity and malnutrition.” Oral, invited speaker.

2013 Arizona State University, The Biodesign Institute, Tempe, AZ, Dec 9. “Gut microbes and their role in obesity and malnutrition.” Oral, invited speaker.

2013 University of Adelaide, Australian Centre for Ancient DNA, Advanced Bioinformatics Workshop for Early Career Researchers, Adelaide, Australia, Nov 11-15. “Microbial Diversity Analyses with the QIIME pipeline” and “From the Human Microbiome Project to the Earth Microbiome Project: Integrating Vast Microbial Datasets”. Oral, invited speaker.

2013 University of Chicago, Chicago, IL, Nov 7–8. “Gut microbes and their role in nutrition and obesity”. Oral, invited speaker.

2013 The Rockefeller University, New York, NY, Oct 30. “Gut microbes and their role in nutrition and obesity”. Oral, invited speaker.

2013 University of Minnesota, Minneapolis, MN, Oct 24. “Combining large microbial datasets to asses the diversity, stability, and major features of the human microbiome” Oral, invited speaker.

2013 Mayo Clinic, Rochester, MN, Oct 23. “Gut microbes and their role in malnutrition and obesity”. Oral, invited speaker.

2013 University of Colorado, DOM Grand Rounds, Denver, CO, Oct 16. “Microbial Readouts Of and Effects On Host Behavior”. Oral, invited speaker.

2013 Stanford University, Stanford, CA, Oct 7. “The Earth Microbiome Project and American Gut: using crowd sourcing to unify human, animal and environmental health through microbes”. Oral, invited speaker.

2013 Oregon Health & Science University, Portland, OR, Oct 3. “Towards a pipeline for microbiome-based personalized medicine”. Oral, invited speaker.

2013 California Institute of Technology, Pasadena, CA, Sep 30 – Oct 1. “Gut microbes and their role in obesity and malnutrition”. Oral, invited speaker.

2013 The Salk Institute for Biological Studies, La Jolla, CA, Sep 17-18. “Gut microbes and their role in obesity and malnutrition”. Oral, invited speaker.

2013 California Institute of Technology, Microbiology Bioinformatics Workshop, Pasadena, CA, Sep 16-20. Oral invited.

2013 Marine Biology Lab, Woods Hole, MA, Aug 2. Course: Strategies and Techniques for Analyzing Microbial Population Structures. “Microbial Community Analysis.” Oral, invited speaker.

2013 University of Pennsylvania, Philadelphia, PA, July 22. “Towards a pipeline for microbiome-based personalized medicine.” Oral, invited speaker.

2013 Hopkins Marine Station, Stanford University, Pacific Grove, CA. July 12, “Microbial Community Analysis”, and July 13, “Gut Microbes and their Role in Obesity and Malnutrition”. Oral, invited speaker.

2013 Yale University, New Haven, CT, MCDB Special Seminar, July 9. “Gut microbes and their role in obesity and malnutrition”. Oral, invited speaker.

2013 Barbara Davis Center for Diabetes, Aurora, CO, June 18. “Predictive models for the human microbiome”. Oral, invited speaker.

2013 University of Colorado, Denver, CO, Infectious Disease Symposium, May 3. “Making the Human Microbiome Project data work for you”. Oral, invited speaker.

2013 Harvard FAS Center for Systems Biology, Cambridge, MA, Mar 7. “Sources of variation and lack of enterotypes in the human microbiome”. Oral, invited speaker.

2013 University of Colorado, JILA colloquium, Boulder, CO, Mar 5. “What affects the human microbiome?” Oral, invited speaker.

2013 Yale University, Microbiology Graduate Program Seminar Series, New Haven, CT, Feb 21. “Making the Human Microbiome Project data work for you”. Oral, invited speaker.

2013 Colorado State University, CMB Seminar Series, Fort Collins, CO, Feb 8. “Profiling microbial community composition dynamics across ecosystems, including the human microbiome”. Oral, invited speaker.

2013 University of Oklahoma, Presidential Dream Course in Microbiology, Norman, OK, Feb 5. “Using QIIME to reveal spatial and temporal patterns in the human microbiome”. Oral, invited speaker.

2012 University of Toronto, Toronto, Canada, Department of Molecular Genetics, Oct 1. “Spatial and temporal variability in the human microbiome”.

2012 Marine Biology Lab, Woods Hole, MA, Aug 3. Course: Strategies and Techniques for Analyzing Microbial Population Structures. “Microbial Community Analysis.” Oral, invited speaker.

2012 Hopkins Marine Station, Stanford University, Pacific Grove, CA, July 13. “Microbial Community Analysis”, and July 14, “Spatial and Temporal Diversity of the Human Microbiome”.

2012 Northwestern University, Chicago, IL, Microbiology-Immunology Seminar, May 22. “Spatial and temporal variability in the human microbiome”.

2012 Baylor College of Medicine, Houston, TX, Molecular Virology and Microbiology Seminar, May 3. “Spatial and temporal variability in the human microbiome”.

2012 Stanford University, Stanford, CA, Frontiers in Quantitative Biology seminar, Apr 5. “Towards a pipeline for microbiome-based personalized medicine”.

2012 Institut Pasteur, Paris, France, Mar 22. “Spatial and temporal variability in the human microbiome”.

2012 Michigan State University, Microbiology & Molecular Genetics Seminar, East Lansing, MI, Feb 21. Spatial and temporal variability in the human microbiome”.

2012 University of Michigan, Human Genetics Seminar, Ann Arbor, MI, Feb 20. “Spatial and temporal variability in the human microbiome”.

2011 Memorial Sloan-Kettering Cancer Center, New York, NY, Oct 27. “Tools for understanding the human microbiome”.

2011 Rockefeller University, New York, NY, Oct 28. “Tools for understanding the human microbiome”.

2011 University of Georgia, Microbiology seminar, Athens, GA, Oct 6. “Spatially and temporally explicit studies of the human microbiome”.

2011 University of Chicago, Ecology & Evolution Weekly Seminar, Chicago, IL, Oct 4. “Tools for understanding the human microbiome”.

2011 Dalhousie University, Centre for Comparative Genomics & Evolutionary Bioinformatics Seminar, Halifax, Canada. Sep 22. “Spatial and temporal variability in the human microbiome”.

2011 Stanford University, Hopkins Marine Station, Pacific Grove, CA, July 8. “Spatially and Temporally Resolved Studies of the Human Microbiome”.

2011 University of Puerto Rico, San Juan, Puerto Rico, Jan 25-27. “Spatial and Temporal Diversity of the Human Microbiome” and “QIIME: Quantitative Insights into Microbial Ecology”.

2011 University of California Los Angeles, (UCLA), Jan 21. “Spatial and Temporal Variation in the Human Microbiome”.

2011 San Diego Zoo, San Diego, CA, Jan 20. “Microbes in Humans and Other Animals”. 2010 University of North Carolina, Department of Microbiology, Chapel Hill, NC, Oct 18.

"Translational medicine and the human microbiome". 2010 Wadsworth Center, Albany, NY, Oct 7. " Open-Source Software Tools for Quantitative

Insights into the Human Microbiome". 2010 Wadsworth Center, Albany, NY, Oct 7. "Biogeography of the Human Microbiome". 2010 Frontiers in Genomics, UNAM, Cuernavaca, Mexico, Sep 7-8. "Tools for Understanding

the Human Microbiome". 2010 Proctor & Gamble, Cincinnati, OH, Aug 12. "High-Throughput Microbial Ecology (HiT-

ME): Biogeography of the Human Microbiome". 2010 Department of Biology, San Diego State University, San Diego, CA, May 20. "Diversity

of the Human Microbiome Across Spatial and Temporal Scales". 2010 Genentech, Inc., South San Francisco, CA, May 13. "Diversity of the Human

Microbiome Across Spatial and Temporal Scales". 2010 Department of Microbiology, Karolinska Institute, Stockholm, Sweden, May 11. "This

mouse is fat: who did it?" 2010 "What is Life" seminar series, Karolinska Institute, Stockholm, Sweden, May 10. "Tools

and Techniques for Understanding the Human Microbiome". 2010 NCSU (North Carolina State University), Department of Microbiology, Raleigh, NC, Mar

26. "Your microbes and you: viewing the human microbiome through an RNA lens". 2009 University of Puerto Rico, RISE Program, San Juan, PR, Dec 4. “Your microbes and

you: viewing the human microbiome through an RNA lens”. 2009 Colorado State University, Department of Statistics, Ft. Collins, CO, Nov 30. “To Tree

or Not To Tree: Phylogeny and Microbial Community Comparisons”. 2009 University of Colorado, CU Parents’ Association, Boulder, CO, Oct 16. “Your microbes

and you: viewing the human microbiome through an RNA lens”. 2009 University of Colorado, Department of Chemistry and Biochemistry, Boulder, CO, Oct

14. “Your microbes and you: viewing the human microbiome through an RNA lens”. 2009 University of Glasgow, Department of Civil Engineering, Glasgow, Scotland, UK, Sep

30. “Defining a core human gut microbiome”.

2009 Cornell University, Department of Microbiology, Ithaca, NY, Sep 17. “Defining a core human gut microbiome”.

2009 Hopkins Marine Station, Stanford University, Pacific Grove, CA. “”Tools for understanding the core human gut microbiome”. Presented as part of Alfred Spormann’s course BIOHOPK274 “Microbiology”.

2009 The Penn/CHOP Center for Digestive, Liver and Pancreatic Medicine and the NIH Center for Molecular Studies in Digestive and Liver Disease, Division of Gastroenterology, University of Pennsylvania, 10th annual retreat “Intestinal Microbiota in Health and Diseases”. “Biogeography of Human Body Habitats”. Jun 8.

2009 Department of Ecology and Evolutionary Biology, University of Chicago, Chicago, IL, Jun 1. “Evolution of the Human Microbiome”.

2009 SomaLogic, Boulder, CO, Apr 16. “Defining a Core Human Microbiome”. 2009 Pacific Northwest National Laboratory, Richland, WA, Feb 25. “Error-correcting

barcoded pyrosequencing allows simultaneous analysis of hundreds of microbial communities”.

2009 Luca Technologies, Golden, CO, Jan 26. “Microbial community analysis”. 2008 Department of Microbiology, Columbia University Medical School, New York, NY, Dec

10. “Mapping the Human Microbiome.” 2008 Department of Chemistry, Brandeis University, Boston, MA, Nov 5. “Defining a core

human microbiome”. 2008 RNA Biology Seminar Series, University of California at Merced, Merced, CA, Oct 31.

“The scope of selection: defining the abundance of the simplest RNA active sites.” 2008 Quantitative and Systems Biology Seminar Series, University of California at Merced,

Merced, CA, Oct 21. “Defining a core human microbiome.” 2008 Department of Microbiology, University of Pennsylvania, Philadelphia, PA, Oct 29.

“Defining a core human microbiome.” 2008 Institute for Thermal Biology, Montana State University, Bozeman, MO, Oct 27.

“Defining a core human microbiome”. 2008 Free University Amsterdam, Holland, Bioinformatics section, Department of Earth and

Life Sciences, Sep 29. “Computational aspects of RNA Evolution.” 2008 Department of Microbiology and Immunology University of Michigan, Ann Arbor, MI,

Sep 11. “Defining a core human microbiome.” 2008 Department of Microbiology and Molecular Genetics, Michigan State University,

Lansing, MI, Sep 10. “Defining a core human microbiome.” 2008 Alan Wilson Center, Massey University, Palmerston North, New Zealand, Aug 27. “Is

there a core human microbiome?” 2008 Department of Biochemistry, University of Otago, Dunedin, New Zealand, Aug 26. “Is

there a core human microbiome?” 2008 John Curtin School of Medical research, Australian National University, Canberra,

Australia, Aug 14. “Is there a core human microbiome?” 2008 Department of Chemistry, Czech Republic Academy of Sciences, Prague, Czech

Republic, Aug 5. “The Scope of Selection: Abundance of the Simplest RNA Active Sites.”

2008 Center for Genomic Sciences, Alleghany Medical Center, Pittsburgh, PA, May 12. “Is there a core human gut microbiome?”

2008 LUCA Technologies, Golden, CO, Mar 24. “Tools for Comparing Microbial Communities”.

2008 Department of Microbiology, University of Florida, Gainesville, FL, Jan 9. “To Tree or Not To Tree: Phylogeny and Microbial Community Comparisons”.

2007 Statistics and Genomics Graduate Seminar Series, Department of Statistics, University of California at Berkeley, Berkeley, CA, Dec. 13. “To Tree or Not To Tree: Phylogeny and Microbial Community Comparisons”.

2007 Washington University, St. Louis, Missouri, April 6. Genome Sciences Center. “Mapping Microbial Communities Using 16S rRNA.”

2007 Australian National University, Canberra, Australia, Mar 28. John Curtin School of Medical Research. “Mapping Microbial Communities Using 16S rRNA.”

2007 University of Colorado Health Science Center, Denver, Colorado, Jan 17. Colorado Center for AIDS Research. “Using UniFrac to explore sequence changes associated with gut microbial communities during SIV infection, and prospects for applications to understanding HIV setpoint”.

2007 Bowling Green State University, Bowling Green, Ohio, Jan 10. Department of Biology. “Mapping Microbial Communities Using 16S rRNA”.

2006 Free University, Amsterdam, Holland, Sep 27. Bioinformatics Section, Department of Earth and Life Sciences. “Defining the Abundance of Functional RNAs in Sequence Space.”

2006 University of Pennsylvania, Philadelphia, PA, Jun 14. Department of Microbiology. “UniFrac: A New Way of Mapping Microbial Communities.”

2006 Somalogic, Inc., Boulder, CO, May 16. “Comparing Communities of RNA Sequences.” 2005 University of Waterloo, Waterloo, Canada. Department of Applied Mathematics. Aug

18. “Finding correlated, modular patterns in random sequences: A new Markovian approach with applications to RNA structure.”

2004 Ji Lin University, Changchun, China. Department of Biological Sciences, Dec 28. “The Scope of Selection: Abundance of Functional RNA Motifs in Random-Sequence Pools.”

2004 Somalogic, Inc., Boulder, CO, July 7. “Bayesian Methods for finding Patterns in RNA.” 2004 University of Colorado, Boulder, CO, Mar 4. “Markov Models in Molecular Evolution.” 2003 American Mathematical Society, University of Colorado, Boulder, CO, Oct 3. “Finding

Functional RNAs in Sequence Space.” 2002 University of Colorado, Boulder, CO, Oct 4. Department of Applied Mathematics. “How Does Mutation Affect Genomes?” 2002 University of Texas, Austin, TX, Aug 8. Institute for Cellular and Molecular Biology.

“The Scope of Selection: Combinatorial analysis of modular sequences suggests a zeptomole RNA world.” Also presented Mar 6 at RNA Club, University of Colorado, Boulder, CO.

2002 University of Colorado, Boulder, CO, Feb 25. Bioinformatics Supergroup. “Information Loss in Mitochondria: Are Mutation Biases to Blame?” Also presented Apr 19 in the Department of Ecology, Population and Organismal Biology Seminar Series.

2002 University of Maryland at Baltimore County, Baltimore, MD, Jan 17. Bioinformatics seminar series. “Codon assignments as molecular fossils: Did ancient amino acid binding sites shape the modern genetic code?” 2001 Carnegie Mellon University, Pittsburgh, PA, March 23. “Have functional nucleic acid

sequences evolved characteristic base composition biases? A comparative study of genes and genomes”.

2001 Pittsburgh University, Pittsburgh, PA, March 22. Program in History and Philosophy of Science. “From Chemistry to Information: Emergence of the Genetic Code”. 2000 University of Colorado RNA Club, Boulder, CO September 27. “Genetic Code Evolution in Mitochondria: Testing Hypotheses by Genome Analysis”. 1999 Santa Fe Institute, Santa Fe, NM, September 8. “From Chemistry to Information: Emergence of the Genetic Code”. 1999 Institute for Advanced Study, Biology Group, Princeton, NJ, October 26. “Aminoacyl-

tRNA Synthetases and the History of the Genetic Code”.

1999 University of Otago, Department of Biochemistry, Dunedin, New Zealand. July. “Adaptation, Chemistry, and History: Three Faces of Genetic Code Evolution”. Other Meeting Participation 2015 World Economic Forum Annual Meeting, Davos, Switzerland, Jan 21-24. 2014 American Society for Microbiology (ASM) general meeting, Boston, May 17-20.

Convener. 2013 NIH “Human Microbiome Science: Vision for the Future”, Bethesda, MD July 24-26.

Meeting scientific advisor. 2012 Sloan Foundation, Sloan 16S/18S/ITS workshop, Boulder, CO, Oct 17-18. Workshop

organizer. 2012 Department of the Army, Skin Microbiota Workshop: Multidisciplinary Perspectives,

Challenges and Opportunities, Boulder, CO, Oct 15-16. Workshop organizer. 2012 King Abdullah University of Science and Technology (KAUST), American University in

Cairo (AUC) Red Sea Marine Genomics project, Jeddah, Saudi Arabia and Cairo, Egypt, Oct 6-8. Panelist.

2012 University of Colorado at Boulder, Cloud Computing for the Microbiome Workshop, Apr 2-4. Workshop organizer.

2012 ICDDR,B, Dhaka, Bangladesh, Microbial Ecology and the Human Body Workshop, Feb 6-10. Workshop organizer.

2011 Walter Reed Army Institute of Research (WRAIR) wound microbiome meeting, Forest Glen, MD, May 9-10. Discussion leader along with Owen White and Lance Price.

2011 Association of Biomolecular Resource Facilities (ABRF), San Antonio, TX, Feb 19-22. Session organizer.

2011 RNA Ontology Consortium –Genomic Standards Consortium meeting, Kohala Coast, Hawaii, Jan7-9. Organized meeting (with Alain Laederach).

2010 PyCogent/QIIME Workshop, National University of Singapore, Singapore, Nov 29-Dec 1. Co-organized meeting (with Von Bing Yap and Gavin Huttley), presented on KEGG database interaction with PyCogent and on QIIME.

2010 RNA Ontology Consortium Alignment Working Group meeting, Strasbourg, France, Nov 14-16. Organized meeting.

2010 Beneficial Microbes, Miami, FL, Oct 25-29. Session chair for metabolomics. 2010 Genome Biology "Beyond the Genome" cloud computing workshop, Harvard Medical

School, Cambridge, MA, Oct 11-13. "Translational medicine and the human microbiome". Invited participant for panel discussion.

2010 EMP (Earth Microbiome Project) meeting Argonne National Labs, Chicago, IL, Oct 6. Workshop organizer.

2010 JGI Community Sequencing Program (CSP) review panel, Walnut Creek, CA, Aug 5. Invited participant.

2010 RNA Ontology consortium meeting, Seattle, WA, Jun 20-21. Invited participant. 2010 Lung HIV Microbiome Project Steering Committee Meeting, Bethesda, MD, Jun 14-15.

Invited participant. 2010 HHMI science meeting, Janelia Farm Research Campus, Ashburn, VA, Jun 6-9. Invited

participant. 2010 Genomic Standards Consortium meeting, J. Craig Venter Institute, Rockville, MD.

Invited participant in MIENS session (teleconference). 2010 Archemix Inc., Science Advisory Board Meeting, Cambridge, MA, Mar 24. 2010 American Society for Microbiology Colloquium Advisory Committee, Chicago, IL, Feb

13-14. Invited participant.

2010 NIH Human Microbiome Project New Tools grant review panel, Bethesda, MD, Jan 25. Invited participant.

2010 RNA Ontology Consortium Alignment Group Meeting, Kona, HI, Jan 8-10. Workshop organizer.

2010 Pacific Symposium on Biocomputing, Kona, HI, Jan 3-8. Invited participant in Genomic Standards Consortium session.

2009 Genomic Standards Consortium workshop, Joint Genome Institute, Walnut Creek, CA, Sep 9-11. Invited participant, MIENS standards discussion.

2009 MAL-ED Network Meeting, Washington, DC, Feb 16-18. Invited workshop participant. 2008 National Academy Keck Futures Initiative, Irvine, CA, Nov 12-15. Invited workshop

participant; selected to present for Task Group 8, “Is The Biosphere Sustainable?” Oral. 2008 Integrating NEON and Microbial Ecology. Baton Rouge, LA, Feb 14-17. Invited

workshop participant. 2007 UMN-IMA special workshop on RNA in Biology, Bioengineering and Nanotechnology,

Minneapolis, MN, Oct 29-Nov 2, “Finding correctly folded active RNA motifs”. Poster, invited participant.

Grant Support: Completed Research Support Butcher Foundation 9/1/05 – 8/31/06 Role: Co-PI $95,000 direct costs Identifying Secreted Bacterial Proteins that Act on Host Cells with Bioinformatics and Genetics The goal of this project is to develop novel methods for identifying Type III secreted effectors in Salmonella, and to test these predictions in vitro. Keck RNA Bioinformatics Initiative 7/1/04 – 6/30/06 Role: PI $62,500 direct costs W. M. Keck Foundation Improving motif-based alignment strategies The goal of this project is to develop better methods for aligning unaligned RNA sequences, based on alignment ‘seeds’. National Academy Keck Futures Initiative 4/30/06-4/30/07 Role: Co-PI (with F. Bushman, Penn, PI) $75,000 direct costs for one year Human Intestinal Flora The goal of this project is to characterize the response of the human intestinal flora to antibiotics. Colorado Center for Aids Research 8/1/06-7/31/07 Role: PI $30,000 direct costs for one year Using UniFrac to investigate HIV setpoint The goal of this project is to apply UniFrac to studies of HIV, testing whether very large sequence data sets from pyrosequencing can inform us about sequence features diagnostic for different traits. DOD Air Force Office of Sponsored Research, 2006-2008 Role: Co-PI (with S. Copley, PI)

FA9550-06-1-0014 $554,062 total costs for 2/1/06-11/30/08 Exploring Convergent Evolution to Provide a Foundation for Protein Engineering #0705.01.1102b. The goal of this project is to identify groups of nonhomologous proteins that perform the same function, and to test how many different ways there are to construct a particular molecular function. Colorado Renewable Energy 1/1/09 – 12/31/10 Role: PI OCG5138B Bioinformatic Tools for the Parallel Assessment of Genomic and Meta-genomic data $50,000 total costs The goal of this project is to develop software to analyze microbial communities involved in fermentation of biofuels. HHS NHGRI 8/1/09 – 7/31/11 Role: PI $326,024 total costs over two years New Tools for Understanding microbial communities & diversity in human body habitats The goal of this project is to develop enriched descriptors of microbial community composition and timeseries methods for analyzing microbial diversity. National Science Foundation 8/1/08-7/31/11 Role: Senior Personnel, 0 time commitment (Henry Tufo, PI) CNS 0821794 $2,796,500 total costs over three years MRI-Consortium: Acquisition of a Supercomputer by the Front Range Computing Consortium The goal of this project is to acquire, maintain and support a supercomputer for many tasks, including 454 data analysis. NASA 5/1/08-8/12/11 Role: PI NNX08AP60G $549,614 over three years Measuring the abundance of the simplest functional RNAs The goal of this project is to understand how abundant simple aptamers and ribozymes are in random-sequence pools, with implications for SELEX and the origin of life. Crohn’s and Colitis Foundation of America 4/1/08-9/30/13 Role: subcontract PI (Jeff Gordon PI) WU-09-72 / 2905035N $887,427 total costs over five years Metagenomic Studies of the Human Gut Microbiome: An Initial Pilot Study The goal of this project is to understand how microbial communities change with Crohn’s disease and colitis, beginning with a sample of healthy individuals. National Science Foundation/Agriculture CSREES 6/1/08-5/31/12 Role: co-PI (with Noah Fierer, PI) 2008-34158-04713 $561,999 total costs over four years Collaborative Research: How are archaeal diversity, abundance, and function regulated in agroecosystems?

The goal of this project is to understand how land use affects the types of archaea present in soils. Battelle (PNNL) 12/2/08 – 9/30/12 Role: subcontract PI (Konopka, PI) DE-AC05-76RL01830 Role of Microenvironments and Transition Zones in Subsurface Reactive Contaminant Transport Research $271,780 total costs over three years The goal of this project is to explore the role of subsurface microbial communities in mobilization and demobilization of radioisotopes at the Hanford nuclear contaminated site. NIH NHLBI 7/1/08 – 6/30/12 Role: subcontract PI (Flores, PI) 5 R01 HL0090480 Longitudinal Studies of HIV-1 Nef in Pulmonary Hypertension $200,000 total costs over four years The goal of this project is to test whether the Nef protein in HIV is associated with heart disease: our role is to apply bioinformatics methods to the sequence datasets collected by the Flores lab. Bill and Melinda Gates Foundation 10/1/08-10/31/12 Role: subcontract PI (Bill Petri PI of

overall Project) WU-09-187/51678 $1,593,597 total costs over 3 years Study of Risk Factors for Malnutrition Using Molecular and Genomic Tools The goal of this project is to understand risk factors for malnutrition, focusing on microbial community composition. NIH 5/15/12-4/30/13 Role: subcontract PI (Owen White, PI) U01 HG006537 Open Data Framework (OSDF): Support Infrastructure for Next Generation Sequence Data Storage. Analysis and Management $144,561 total costs for 1 year (for the University of Colorado-Boulder subcontract) The goal of the project is to make the HMP dataset and demonstration projects cloud-accessible to a broader user community. NIH NHGRI 9/30/08-7/31/13 Role: PI (with Steven Brenner, Andrew Martin, Manuel Lladser co-PIs) 5 R01 HG004872-02 $762,036 total costs over 5 years (for the University of Calif.-Berkeley subcontract) Tools for Understanding microbial communities & diversity in human body habitats The goal of this project is to develop enriched descriptors of microbial community composition and timeseries methods for analyzing microbial diversity. NIH NHGRI 8/1/12 - 7/31/13 Role: supplement PI 3 R01 HG004872-03S2 New Tools for Understanding the Composition and Dynamics of Microbial Communities $199,774 total cost over one year The goal of this project is the application of the tools developed in the parent grant (R01 HG004872) to the HMP dataset itself. In addition, we will be integrating datasets produced using different technology (Sanger, 454, Illumina, Ion Torrent, PacBio, etc.) and observing different phenomena (e.g. 16S, metagenomic and metatranscriptomic data) into one single framework.

NIH NHGRI 9/30/08-9/29/13 Role: subcontract PI (Owen White, PI; numerous other co-PIs) 1 U01 HG004866 $885,473 total costs over 5 years (for the University of Colorado-Boulder subcontract) Data Analysis and Coordination Center for the Human Microbiome Project The goal of this project is to develop a data analysis and coordination center for the Human Microbiome Project. My lab’s component is to integrate UniFrac into the DACC. University of North Carolina at Chapel Hill 1/1/2013-12/31/2013 Role: subcontract PI (Balfour Sartor, PI) 5-46900/3375 Phase 3B microbiome clinical and data management application and Microbiome Consortium $246,789 total cost The goal is provide IBD investigators the ability to see their sequences and samples in the context of all other samples collected, or in specific subsets of that universe, and to identify organisms of interest that recur in many patient populations and experiments. DEPARTMENT OF JUSTICE 1/1/2012 – 3/31/2014 Role: PI 2011-DN-BX-K533 Characterization of Bacterial and Fungal Communities Associated with Corpse Decomposition Using Next Generation Sequencing $894,629 total costs over two years The goal of this project is to understand whether the succession of microbial communities can be exploited for forensic investigations. NIH NIDDK P01DK078669 7/1/07-6/30/14 Role: subcontract PI (J. Gordon PI) 1 P01 DK078669 $1,082,294 over six years Metagenomic Studies of the Gut Microbiomes of Obese and Lean Twins The goal of this project is to develop new methods for detecting lateral gene transfer and for comparing gut microbial communities. NIH NHLBI 9/23/09 – 7/31/14 Role: subcontract PI (Fontenot, PI) 1 U01 HL098996 Alterations in Lung Microbiome in Acute and Chronic HIV Infection $452,000 total costs over five years The goal of this project is to characterize changes in bacterial communities in the lung associated with HIV infection and attendant morbidity. DEPARTMENT OF THE ARMY 9/10/12–9/9/14 Role: PI W911NF-12-1-0513 Skin Microbiota Workshop: Multidisciplinary Perspectives, Challenges and Opportunities $10,000 Presented and co-chaired 2 day workshop October 16-17, 2012 in Boulder for Army research personnel and other researchers. Baylor College of Medicine 9/1/2012-8/31/2014 Role: subcontract PI (Petrosino, PI) 101743924 /HHSN267200700014C The Environmental Determinants of Diabetes in the Young (TEDDY) Virome and Microbiome Consortium $315,000 total cost

The goal of this project is to analyze bacterial and viral data, develop and apply new algorithms for multi-omics analysis and predictive modeling of diabetes and insulin resistance and relating such to host genomic features. ALFRED P. SLOAN FOUNDATION 4/1/2012 – 11/1/2014 Role: PI 2012-03-02 The Microbially Visible Home $187,154 total cost over one year The goal of this project is to use dense sampling (1000 samples) of environments in a single house with architecturally informed sampling, allowing links between visualization technologies, microbes, and architectural features. Northern Arizona University 10/1/2012-9/30/2014 Role: subcontract PI (Caporaso, PI) 1001980-02/2012-5-42 MBRP Microbial succession on common office surfaces $29,792 total cost over 2 years The goal of this project is to systematically analyze the establishment of microbial communities over time on different office surface materials in different climates to improve our ability to predict microbial community composition in the indoor environment based on environmental metadata. University of Chicago 4/1/2013-10/31/2014 Role: co-PI (Kirkup, Jr., PI) FP053235-B Hospital Microbiome Project $28,465 total cost The goal is to provide consultation on sample preparation and DNA sequencing methods, then process and assist with sample data analysis via the QIIME pipeline. ALFRED P. SLOAN FOUNDATION 1/1/2011-12/31/2014 Role: subcontract PI (Meyer, PI) 2010-12-04 MoBe DAC-- A data analysis core for the Indoor Environment Microbiology Program $450,000 total costs over three years The goal of this project is to develop new standards and software to facilitate interoperability between QIIME, VAMPS and MG-RAST, allowing users to conveniently visualize their 16S rRNA data and metagenomic data using a range of tools. UNIVERSITY OF CHICAGO 10/1/12-1/1/15 Role: co-PI (Folker Meyer, PI) 47325-B MoBe DAC: A Data Analysis Core for the Indoor Environment Microbiology $115,000 total cost over one and a half years The goal of the project is to integrate and support marker gene studies from investigations of the Microbiology of the Built Environment (microBE) using the analytical tools of QIIME and VAMPS. Current Research Support BINATIONAL SCIENCE FOUNDATION (BSF) - United States-Israel 10/1/2011-9/31/2016 Role: co-PI (Ruppin, co-PI) 2010287

An integrated computational and experimental investigation of microbial communities in the human gut $57,504 total costs over four years The goal of this project is to foster a collaboration with the Ruppin group in Israel, examining microbial and metabolite networks. BILL AND MELINDA GATES FOUNDATION 11/1/11 – 2/29/2016 Role: subcontract PI (Gordon, PI) WU-12-170/OPP1033518 Breast Milk, Gut Microbiome and Immunity (BMMI) Project $1,239,360 over two years The goal of this project is to improve the healthy growth of infants and children by identifying and validating new pre- and probiotics that support, repair, or recapitulate metabolic functions carried out by the gut microbiomes of individuals at risk for, or with already manifest malnutrition and associated immunologic disorders. Univ. of Wisconsin, Madison - Moore Foundation 2/14/13-3/1/16 Role: co-PI (Ned Ruby, PI) MSN156910 $155,447 total cost over 3 years Tracking microbial habitat transitions using single-cell transcriptomics The goal is develop and apply timeseries analyses for the metatranscriptomics data. NIH OD 4/22/2013-4/22/2015 Role: PI 1 S10 OD012300-01 A High-memory Supercomputer for Proteomics, Text Mining and Microbiome Research $1,900,000 total cost The goal is to support NIH investigators in acquiring, analyzing, displaying, and understanding research data by providing access and use of a new generation computational instrument. Keck Foundation 7/1/13 – 6/30/15 Role: PI DT061413 The Earth Microbiome Project $1,000,000 total cost over 2 years The goal of the project is to develop innovative research strategies in microbial ecology to understand existing microbial communities by analyzing gene and species dynamics in tens of thousands of communities spanning the planet. Templeton 9/1/2013 - 8/31/2016 Role: PI 44000 Convergent Evolution of the Vertebrate Microbiome $977,501 The goal of the project is to elucidate evolutionary processes governing vertebrate microbiome assembly, and the microbiome’s role in enabling new functions. University of Maryland – NIH 5/1/2013 - 4/30/2015 Role: co-PI (White, PI) HHS NHLBI U01 HG006537 / SR00002982 Open Data Framework (OSDF): Support Infrastructure for Next Generation Sequence Data Storage, Analysis and Management $138,128 The goal of the project is to make the HMP dataset and demonstration projects cloud-accessible to a broader user community.

Harvard-Broad 9/6/2013 - 8/31/2016 Role: co-PI (Xavier, PI) NIH 1U54DE023789-01 / 5230121-5500000604 Characterizing the gut microbial ecosystem for diagnosis and therapy in IBD $75,000 The goal of the project is the development of data analysis software, user interface design, database schema and multi-omics project data storage in the QIIME database (QIIMEdb). ALFRED P. SLOAN FOUNDATION 4/1/14 – 4/1/16 Role: PI 2014-3-04 An integrated data platform for democratized sequencing $1,000,000 The project goal is to build key infrastructure for adoption of indoor environment research by broader community as sequencing continues to become more accessible at lower cost by using improved user interfaces, protocols and standards. Ludwig Maximilian Universitat Munchen 1/1/2015 - 6/30/2016 Role: PI GABRIEL study: Potential effects of microorganisms on asthma $150,000 The aim of the Project will be to describe microbial exposure and colonization of the upper airways during childhood and how these factors affect the development of asthma. HHMI Early Career Scientist 9/1/09-3/31/15 12 calendar $1,500,000 direct costs over 6 years, no indirect This award provides unrestricted funding to pursue new research directions. Research Group Members, Past and Present: Graduate Students: Justine Debelius (Chemistry & Biochemistry, 2013-present) Samuel Way (Computer Science, 2013-present) Sophie Weiss (Chemical and Biochemical Engineering, 2013-present) Yoshiki Vázquez Baeza (Computer Science, 2013-present) Jose Navas (Computer Science, 2012-present) Josh Shorenstein (Chemistry & Biochemistry, 2012-present) Daniel McDonald (IQBio/Computer Science, 2011-present) Luke Ursell (Chemistry & Biochemistry, 2011-2014, graduated Ph.D. fall 2014, thesis title “The human microbiome and interactions with disease states, medical interventions, and the metabolome”) Nigel Cook (Computer Science, 2010-2011) Meg Pirrung (Chemistry & Biochemistry, 2009-2013) Tony Walters (MCDB, 2009-2014, graduated Ph.D. spring 2014, thesis title “Taxonomic Signatures of Human Gut Microbiota across Body Mass Index and Inflammatory Bowel Disease States as Revealed by Meta-analyses of High-Throughput Sequencing Surveys”) Antonio Gonzalez-Peña (Computer Science, 2010-2012, graduated Ph.D. fall 2012, thesis title “Tools, Methods and Visualizations to Elucidate Spatial and Temporal Patterns in Microbial Community Studies with Billions of Sequences”) Jeremy Widmann (Chemistry & Biochemistry, 2008-2012, graduated Ph.D. fall 2012, thesis title “Studying trends of non-coding RNA function and evolution”) (formerly PRA in the lab)

Dan Knights (Computer Science, 2009-2012, graduated Ph.D. spring 2012, “Predictive Modeling of Metagenomes”, College of Engineering's Outstanding Dissertation Award) Justin Kuczynski (MCDB, 2008--2011, graduated Ph.D. summer 2011, thesis title “Improved Analysis Methods for Sequenced-Based Microbial Community Ecology”) Jesse Zaneveld (MCDB, 2006-2011, graduated Ph.D. summer 2011, thesis title “Habitat Adaptation and Genome Evolution in the Gut Microbiome”) Micah Hamady (Computer Science, 2004-2009) (won EAPSI travel award from NSF to travel to Australia, summer 2008, graduated Ph.D. summer 2009, thesis title “Exploring Microbial Sequence and Community Diversity on an Unprecedented Scale”) Sandra Smit (formerly PRA, 2004-2008, graduated Ph.D. Fall 2008 via Amsterdam Free University, thesis title “RNA in Formation: Computational Studies on RNA Structure and Evolution”). Catherine Lozupone (MCDB, 2004-2007, graduated Ph.D. Summer 2007, thesis title “Global Patterns of Bacterial Diversity”) Shandy Wikmann (Umea University, Sweden, Masters student, 2004-2006) Postdocs: Embriette Hyde (2014-present) Evguenia Kopylova (2014-present) Se Jin Song (2014-present) Katie Amato (2013-present) Luke Thompson (2013-present) Amnon Amir (2013-present) Dorota Porazinska (2013-present) Antonio Gonzalez-Peña (2012-present, formerly graduate student in my lab) Zhenjiang Xu (2012-present) Jessica Metcalf (2011-present) Tony Walters (2014, formerly graduate student in my lab) Douglas Woodhams (2012-2014) Christian Lauber (2008-2014) Laura Parfrey (2011-2013) Jose Carlos Clemente Litran (2010-2013) Catherine Lozupone (2007-2013, formerly graduate student in my lab) Jesse Stombaugh (2009-2012) Bharath Prithiviraj (2011) Gregory Caporaso (2009-2011) Jens Reeder (2008-2010) Sara Nakielny (2009-2010) Elizabeth Costello (2008-2009) Zongzhi Liu (2006-2008) Jana Chocholousova (2006) Research Assistants: Grant Gogul (2013-present) James Gaffney (2013-present) Gail Ackermann (2011-present) Greg Humphrey (2010-present) Jerry Kennedy (2009-present) Emily TerAvest (2013-2014) Will van Treuren (2012-2014) Michael Oberg (2013-2014)

Donna Berg-Lyons (2008-2014) Juanma Peralta (2013-2013) Doug Wendel (2009-2013) Daniel McDonald (2008-2011, now graduate student in IQBio/Compter Science) Bill Shaffer (2009-2010) Bob Larsen (2009-2010) John Hayes (2009) Jeremy Widmann (2005-2007) Undergraduates: Kumar Thurimella (2012-2013, Computer Science) Will van Treuren (2009-2012, Chemistry & Biochemistry. Now research assistant in lab.) Becky Paulson (2009-2010, Integrative Physiology) Greg Humphrey (2009-2010, Chemistry & Biochemistry. Now technician in lab.) Reece Gesumaria (2009-2010, MCDB/Integrative Physiology) Ryan Kennedy (2007-2009 Computer Science) (won 2008 Astronaut Scholarship, $10,000; senior thesis with honors (Engineering), matriculated Penn PhD program) Julia Goodrich (2008-2010 Computer Science) (won 2009 Goldwater Scholarship, $7500, matriculated Cornell PhD program) Daniel McDonald (2004-2008 Computer Science) [Note: now research assistant] Anh Vu (2007-2009, Chemistry & Biochemistry, senior thesis cum laude) Jonathan Griego (2008, Chemistry & Biochemistry) Jason Forbes (2006-2007, Computer Science) Hazel Ozuna (summer 2007, SMART program) Nick Zhou (summer 2007, SURE program) Vikas Malaiya (2005-2007, MCDB, senior thesis cum laude) Stephanie Wilson (2005-2007, Computer Science, senior thesis with honors (Engineering)) Matthew Iyer (2006-2007, MCDB, independent study) John Quinn (2005-2006, MCDB) Preston Galais (2006, Chemistry & Biochemistry, independent study) Ian Sharp (2006, Computer Science, independent study) Johnross Ford (2005, NIH-HHMI Scholars program) Ravi Kumar (2005, MCDB, independent study) Michael Eaton (2004, Chemistry & Biochemistry, independent study) Roberto Marquez (summer 2004, SMART program) Interns: Timothy Vigers (2013) Kathryn Holt (2012-2013) Catherine Nicholas (2012-2013) Daniel Mayer (2012-2013) Yoshiki Vázquez Baeza (2012) An Tuong Le (2012) Michael Kalinger (2012) Martha Bawn (summer 2012) Ryan Bernstein (summer 2012) Abhisaar Yadav (summer 2012) Rima Kharbush (summer 2010) Visitors: Eva Novakova (University of South Bohemia, Czech Republic), 2014

Sonia Rodriguez Ruano (University of Grenada, Spain), 2014 Merete Eggesbo (Norwegian Institute of Public Health, Norway), 2013 Fred Delsuc (University of Montpelier, France, Fulbright scholar), 2012 Juanma Peralta (University of Grenada, Spain), 2012 Hongwei Zhou (Southern Medical University, China), 2012 Professional Affiliations Member: American Society for Microbiology (ASM) (2005-present, General Meeting Planning Committee 2010-present, Junior Advisory Group chair 2011-present) Member: International Society for Microbial Ecology (ISME) (2009- present) Member: RNA Society (2011- present) Member: Society for Applied Microbiology (SfAM) (2011-present) Teaching Activities: Classroom teaching: Spring 2014: CHEM  5781:  Advanced  General  Biochemistry  2  Spring 2013: CHEM 4921/5921 (cross-listed as APPM 4720/5720; CSCI 4830/7000;

MCDB 6440): Statistics and Computations for Genomes and Meta-Genomes. IQ Biology Program.

Fall 2012: CHEM 5561: Methods of Molecular Biophysics. Contributed 2 guest lectures on Nov 6 and Nov 8.

Fall 2012: CSCI/MCDB 4314: Algorithms for Molecular Biology. Contributed a guest lecture on Dec 7 and a career panel for that class on Dec 19.

Fall 2011: MCDB 1150: Phage lab. Contributed a guest lecture and Q&A on bioinformatics, assisting freshmen in their analysis of phage sequences in this innovative HHMI-supported course providing early research experiences.

Fall 2010: MCDB 1150: Phage lab. Contributed a guest lecture and Q&A on bioinformatics, assisting freshmen in their analysis of phage sequences in this innovative HHMI-supported course providing early research experiences.

Spring 2010: *CHEM 4621/5621 (cross-listed as MCDB 4621/5621 and CSCI 4317/5317): Genome Databases, Mining and Management. Cross-listed course, enrollment 20 students, 3 credits, teaching 45 hours, organized class and graded assignments. Cross-disciplinary course providing hands-on training with advanced bioinformatics techniques: revised substantially from previous year for tighter integration of genomics and database work (due to student demand).

Spring 2009: *CHEM 4621/5621 (cross-listed as MCDB 4621/5621 and CSCI 4317/5317): Genome Databases, Mining and Management. Cross-listed course, enrollment 22 students, 3 credits, teaching 45 hours, organized class and graded assignments. Cross-disciplinary course providing hands-on training with advanced bioinformatics techniques: revised substantially for greater focus on metagenomics (due to student demand).

Fall 2008: CHEM 5561: Methods in Molecular Biophysics. Graduate course. Taught 3 hours. Introduction to statistical concepts and data analysis.

Spring 2008: *CHEM 4621/5621 (cross-listed as MCDB 4621/5621 and CSCI 4317/5317): Genome Databases, Mining and Management. Cross-listed course, enrollment 23 students, 3 credits, teaching 45 hours, organized class and graded assignments. New, cross-disciplinary course providing hands-on training with advanced bioinformatics techniques.

Spring 2007: *CHEM 4711: Introduction to Biochemistry (CHEM 5711 for graduate students). Undergraduate course, 82 students. 3 credits, teaching 45 hours, organized class and graded exams and homework.

Spring 2007: CSCI 4830: Special Topics in Computer Science: Algorithms for Molecular Biology. Taught 1.5 hours on RNA structure prediction.

Spring 2006: *CHEM 5781: Advanced General Biochemistry 2. 11 students. 5 credits, taught 45 hours, organized class and graded exams and homework.

Fall 2006: CHEM 5561: Methods in Molecular Biophysics. Graduate course. Taught 3 hours on RNA structure prediction.

Fall 2006: BIOI 7711: Introduction to Bioinformatics (at University of Colorado Health Sciences Center). Graduate course. Taught 1.5 hours.

Spring 2005 *CHEM 5781: Advanced General Biochemistry 2. Graduate course focused on biochemical networks and high-throughput techniques. 12 students. 5 credits, taught 45 hours, organized class and graded exams and homework.

Fall 2005: CHEM 5561: Methods in Molecular Biophysics. Graduate course. Taught 3 hours on RNA structure prediction.

Fall 2005: BIOI 7711: Introduction to Bioinformatics (at University of Colorado Health Sciences Center). Graduate course. Taught 1.5 hours.

Fall 2005: MCDB 4520: Bioinformatics and Genomics. Taught 1.5 hours. *Primary instructor for these courses. Student and faculty evaluations solicited by the Department following each course are available in my permanent file. Copies of the individual FCQs (Faculty Course Questionnaire) from courses in which I was the principal instructor are also included in my file. Non-classroom teaching: Principal Dissertation/Thesis Advisor for Graduate Students: Catherine Lozupone (MCDB, 2004-2007): graduated summer 2007 Micah Hamady (Computer Science, 2004-2009): graduated summer 2009 Jesse Zaneveld (MCDB, 2006-2011): graduated summer 2011 Justin Kuczynski (MCDB, 2008-2011): graduated summer 2011 Meg Pirrung (Chemistry & Biochemistry/Computational Biosciences Program, 2009-present) Tony Walters (MCDB, 2009-present) Dan Knights (Computer Science, 2008-2012; graduated summer 2012) Antonio Gonzalez (Computer Science, 2010-2012; graduated fall 2012) Luke Ursell (Chemistry & Biochemistry, 2011-present) Daniel McDonald (IQBio, 2011-present) Adam Robbins-Pianka (IQBio, 2012-present) Andre Hersan (Chemistry & Biochemistry, 2012-present, on leave) Josh Shorenstein (Chemistry & Biochemistry, 2012-present) Jose Navas (Computer Science, 2012-present) Justine Debelius (Chemistry & Biochemistry, 2013-present)

Sam Way (IQBio, 2013-present) Yoshiki Baeze (Computer Science, 2013-present) Jorge Alastuey (Compuer Science, 2014-present) Co-supervisor for Graduate Student Dissertations Sandra Smit (Amsterdam Free University 2006-2008, degree granted based on work at CU 2004-2006), graduated summer 2008 (Jaap Heringa principal supervisor in Amsterdam) Thesis Committee Member for Graduate Students: Jerrad Hampton (Applied Mathematics, 2011-2012) Michelle Turco (Chemistry & Biochemistry, 2011-present) Chelsea Walters (Chemistry & Biochemistry, 2011-present) Philip Calabrese (Chemistry & Biochemistry, 2011-present) Robert Brown (Chemistry & Biochemistry, 2011-present) Simone Stahringer (Molecular, Cellular & Developmental Biology, 2008-2012) Colby Stoddard (Chemistry & Biochemistry, 2009-present) Nicholas Sandoval (Chemical and Biological Engineering, 2009-2012) Tom Cheung (Chemistry & Biochemistry, 2005-2006) Karen Meyer-Arendt (Chemistry & Biochemistry, 2005-present) Rotation Advisor for Graduate Students: Eric Kightley (IQBio, spring 2014) Kevin Hemphill (MCDB, spring 2014) Daniel Malmer (IQBio, spring 2014) Michael Minson (Chemistry & Biochemistry, fall 2013) Justine Debelius (Chemistry & Biochemistry, spring 2013) Anna Broido (IQBio, fall 2012) Neil Lloyd (Chemistry & Biochemistry, fall 2012) Briana Van Treeck (Chemistry & Biochemistry, fall 2012) Samuel Way (IQBio, fall 2012) Nora Connor( IQBio, spring 2012) Joshua Shorenstein (Chemistry & Biochemistry, spring 2012) David Smith (Chemistry & Biochemistry, spring 2012) Adam Robbins-Pianka (IQBio, spring 2012) Topher Weiss-Lehman (IQBio, fall 2011) Dan Knights (Computer Science, summer/fall 2009) Tony Walters (MCDB, spring 2009) Meg Pirrung (Chemistry & Biochemistry, summer 2008) Patrick Yannul (MCDB, 2008) Anne Schwabe (Chemistry & Biochemistry, 2007) Jamie Phelps (Chemistry & Biochemistry, 2007) Jesse Zaneveld (MCDB, 2006) Michael Robeson (EEB, 2006) Karen Meyer-Arendt (Chemistry & Biochemistry, 2005) Supervised Undergraduate Independent Study: Julia Goodrich (2008, Computer Science) Nick Zhou (2007, undeclared major)

Anh Vu (2007, Chemistry and Biochemistry) Jason Forbes (2007, Computer Science) Preston Galais (2006, Chemistry & Biochemistry) Ian Sharp (2006, Computer Science) Vikas Malaiya (2005, MCDB) Stephanie Wilson (2005, Computer Science) Ravi Kumar (2005, MCDB) Michael Eaton (2004, Chemistry & Biochemistry) Supervised Human-Computer Interaction Class Projects: 2009: TopiaryExplorer: large tree visualization Ryan Kennedy, Moss Prescott, Hampton Brown, Anwen Fredriksen 2006: BayesFold user interface improvements Jason Forbes, Andrew Hill, Andrew Magill, Marc Hesse 2005: CodonExplorer user interface improvements Brice Pelle, James Michaelis (acknowledged on CodonExplorer paper in 2009) 2004: TAFT: Temporal Analysis of Transcription Factors Micah Hamady, Gary Yee, Mandana Hakimi, Ziesche Newman, Le Phong Honors thesis advisor: Robert McFaedzen (2014, Integrative Physiology), B.S. cum laude Kumar Thurimella (2013, Applied Math) B.S. magna cum laude Will van Treuen (2011, MCDB/Applied Math) B.S. summa cum laude Julia Goodrich (2010, Computer Science) B.S.* Anh Vu (2009, Chemistry & Biochemistry) B.S. cum laude Ryan Kennedy (2009, Computer Science) B.S.* Stephanie Wilson (2007, Computer Science) B.S.* Vikas Malaiya (2007, MCDB) B.S. cum laude *The Department of Computer Science is in the College of Engineering and uses a different honors system from the College of Arts and Sciences: both these students graduated with Engineering Honors. Member of Honors Thesis Committee (other than principal advisor): Eric Greene, 2014, B.S. summa cum laude Arielle Baker, 2014, B.S. magna cum laude Clarinda Hougen, 2013, B.S. cum laude Phillip Ross, 2013, B.S. cum laude Ethan Evans, 2013, B.S. summa cum laude Caleb Ulliman, 2013, B.S. summa cum laude Sara Coulop, 2013, B.S. summa cum laude Nick Parsonnet, 2011, B.S. magna cum laude Chelsea Water, 2011, B.S. summa cum laude Linda Nguyen, 2011, B.S. magna cum laude Caitlin Stoddard, 2010, B.S. summa cum laude Craig Manahan, 2010, B.S. cum laude Carly Loner, 2010, B.S. cum laude Tristan Lipke, 2010, B.S. summa cum laude

Jacob Lebin, 2010, B.S. summa cum laude Jennifer Binder, 2010, B.S. magna cum laude Alexander Rowan, 2010, B.S. magna cum laude Anna Chase, 2010, B.S. summa cum laude Shannon Mackay, 2009, B.S. summa cum laude Jesse Goossens, 2009, B.S. cum laude Adam Berlinberg, 2009, B.S. summa cum laude Nathan Hawkey, 2009, B.S. summa cum laude Shervin Rahimpour, 2009, B.S. summa cum laude Justin Rolando, 2009, B.S. magna cum laude Igor Shumskiy, 2009, B.S. magna cum laude Nicolette Wolters, 2008, B.S. summa cum laude Mark McClintock, 2008. B.S. summa cum laude Autumn York, 2008, B.S. magna cum laude Michael Trostler, 2008. B.S. cum laude Estefania Mondragon, 2007, B.S. cum laude Akiko Komura, 2007, B.S. magna cum laude Doug Bevan, 2007, B.S. summa cum laude Jue Cao, 2007, B.S. magna cum laude Tam Nguyen, 2007, B.S. magna cum laude Maja Janas, 2007, B.S. summa cum laude Shelby Padway, 2006, B.S. magna cum laude Crystal Love, 2005, B.S. magna cum laude Participant in FTEP (Faculty Teaching Excellence Program) activities: 2009 “Teaching in a Nutshell” 2007 “Preparing a Teaching Portfolio for Tenure and Review” 2005 “Peer Perspectives in the Natural Sciences” 2004 “Teaching in a Nutshell” Service Activities: Service to the University of Colorado at Boulder Advising: 2004-2011, 2012-present

Advisor for Chemistry & Biochemistry undergraduate honors students (one of two faculty 2004-2006, one of three 2008-2011, 2012-present).

Seminars: 2002-present Initiated and organized the Bioinformatics Supergroup seminar series, an

interdisciplinary research seminar that draws participants from seven departments on the Boulder campus, as well as from industry and the Health Sciences Center. Schedule at http://bayes.colorado.edu/bioinfo/

Training grants: 2004-present Participant in the Signal Transduction and Cell Cycle Regulation, Biophysics, and

Creative Training in Molecular Biology training grants, and the IQBio IGERT.

Other: 2011-present Member, Boulder Campus Cyberinfrastructure Board 2011-present Member, Allocations Committee for the Janus Supercomputer 2009-2010 Grant reviews for CO-PILOT program at the University of Colorado 2008-2009 Participated in design meetings for computational space in Colorado Initiative in

Molecular Biotechnology (CIMB) building 2008 Participated in LEAP Introductory Leadership Workshop 2007 Helped define the Bioinformatics Track in the Department of Computer Science 2004-present Member, Colorado Initiative in Molecular Biotechnology (now BioFrontiers) Task

Force Service Outside the University of Colorado at Boulder Reviewer for Journals 2004-present Refereed papers submitted to the journals Science, Nature, Cell, PNAS, PLoS

Biology, Genome Research, Ecology Letters, Science Translational Medicine, Cell Host & Microbe, GenomeBiology, Microbial Ecology, Evolution, Applied and Environmental Microbiology, PLoS Computational Biology, Journal of Molecular Evolution, Journal of Theoretical Biology, BMC Evolutionary Biology, Molecular Biology and Evolution, BMC Bioinformatics, RNA, Nucleic Acids Research, Astrobiology, Gene, Extremophiles, BiologyDirect, Origins of Life and Evolution of the Biosphere, Trends in Genetics, BMC Microbiology, BMC Genomics, Nature Methods, Nature Protocols, Gastroenterology, Gut, Gut Microbes, etc.

Editorial Board Membership 2006-present Member, editorial board, BiologyDirect. 2011-present Member, editorial boards, Gut Microbes, AEM, Env Micro, Genome

Biology 2012-present Member, editorial board, Microbiome 2011-present Senior Editor, ISME J Grant Review 2012 NIH, Israel Science Foundation, HHMI predoc, NSF, DOE 2011 NAKFI Genomics and Smart Prosthetics Review 2011 NIH, European Research Council, INRA (French National Institute for Agricultural

Research), NASA Postdoctoral fellowships, Canada Research Chairs, DOE ENIGMA review, Austrian Science Fund, NSF

2010 NIH, Italian Ministry of Health, Agence Nationale Recherche (France), 2009 NSF, Agence Nationale Recherche (France), Canada Research Chairs, NIH, DOE

Community Sequencing Panel, NASA postdoctoral fellowships, Dutch Cancer Society, Rutherford Discovery Fellowships (New Zealand)

2008 NSF, Science Foundation Ireland, Israel Science Foundation, Agence Nationale Recherche (France), Canada Research Chairs, NASA postdoctoral fellowships

2006 NSF Thesis committee member for non-Boulder students 2005-2009 J. Greg Caporaso, Ph.D. student, UCDHSC 2004 Steve Russell, Ph.D. student, UCDHSC 2006-2010 Todd Gibson, Ph.D. student, UCDHSC

Other service activities: 2011- Expert Adviser for Nature Index 2011- Member, Earth Microbiome Project Steering Committee 2009- Member, NHLBI Lung Microbiome Steering Committee 2009- Member, Genomic Standards Consortium, working group on MIENS (Minimal

Information about Environmental Surveys; Board member 2011-) 2006- Member, RNA Ontology Consortium 2005 Session co-organizer, “The Modern RNA World”, Society for Molecular Biology and Evolution 2005 meeting, Auckland, New Zealand June 19-23. 2004-7 Associate Director, University of Colorado Center for Computational Biology

(organization is currently inactive) 2004- Graduate faculty member, University of Colorado Health Sciences Center

Computational Biology Program