1

CURRICULUM VITAE

Yan Guo, PhD

Office Address 100A Cancer Research Facility

University of New Mexico, Comprehensive Cancer Center

Albuquerque, NM, 87131

Phone:

E-mail:

505-925-0099

yaguo@salud.unm.edu

CURRENT POSITIONS

Associate & Endowed Professor

Department of Internal Medicine, University of New Mexico

Director

Bioinformatics Shared Resources, University of New Mexico

Comprehensive Cancer Center

EDUCATION

2009 Doctor of Philosophy in Computer Science (focused on Bioinformatics)

Department of Computer Science, University of South Carolina.

2006 Master of Engineering in Computer Science

Department of Computer Science, University of South Carolina

2003 Bachelor of Science in Computer Science

Department of Computer Science, University of Minnesota

2001 Minor in Japanese

University of Minnesota

WORK EXPERIENCE

10/2017 – Present Associate and Endowed Professor, Department of Internal

Medicine, University of New Mexico

10/2017 – Present Director, Bioinformatics Shared Resources, University of New

Mexico Comprehensive Cancer Center

12/2012 – 09/2017 Technical Director of Bioinformatics, Vanderbilt Technologies for

Advanced Genomics Analysis and Research Design (VANGARD)

11/2011 – 09/2017 Assistant Professor, Department of Cancer Biology, Vanderbilt

University

06/2016 – 07/2017 Bioinformatics Consultant, Population and Precision Health Care.

Ltd

12/2009 – 10/2011 Bioinformatics System Engineer II, Vanderbilt Ingram Cancer

Center

11/2007 – 11/2009 Bioinformatics System Engineer I, Functional Genomic Shared

2

Resource, Vanderbilt University

05/2005 – 05/2007 Research Assistant, Bioinformatics Group at Department of

Computer Science and Engineering, University of South Carolina

01/2001 – 08/2001 Software Engineer (Internship), National Instrument, Austin TX

PROFESSIONAL ACTIVITIES

Intramural

Committees Hiring manager of bioinformatics search committee at Vanderbilt Center for

Quantitative Sciences (2012-2017)

Oversight Committee member of Vanderbilt Genetics Institute (2016-2017)

Hiring committee chair for computational biology faculty, University of

New Mexico, (2017-2018)

Hiring committee chair for chief informatics office, University of New

Mexico, Comprehensive Cancer Center, (2017-2018)

Mentees Jiang Li, MS, Bioinformatics System Engineer II (2011 – 2013)

Hui Wu, Ph.D., Bioinformatics System Engineer I (2013 – 2014)

Nikola Jovanovich (summer intern, 2014)

Quanhu Sheng, PostDoc (2012-2015)

Jie Ping, PostDoc, (2016-2017)

Yulin Dai, PostDoc, (2016-2017)

Pan Zhang, PostDoc, (2014-2017)

Shilin Zhao, PostDoc (2012-2017)

Jing Wang, PostDoc (2013-2017)

Bing Feng, Graduate Student, (2016-Present)

Jiandong Wang, Graduate Student, (2017-Present)

Hui Yu, PostDoc, PostDoc, (2017-Present)

Wei Yue, PostDoc, (2017-Present)

Mingsheng Guo, Bioinformatics Engineer (2011 – 2017 Research

Assistant Professor (2017 – Present)

Extramural

Professional Organization Member of TCGA Head and Neck Cancer work group (2011 – 2014)

Conferences Program committee member and session chair of International Conference

on Intelligent Biology and Medicine, 2013-2018.

Workshop/Tutorial Committee co-chair, International Conference on

Intelligent Biology and Medicine, 2016

Editorial Editor of Cancer Biology and Research (2013 - present)

Managing Editor of International Journal of Computational Biology and

Drug Design (2014-present)

Guest Editor for Special Issue on Advances in Computational Genomics,

3

BioMed Research International (2014)

Lead Editor for Special Issue on Advances in Computational Biology and

Genomic, International Journal of Computational Biology and Drug

Design, 2014

Lead Editor for Special Issue Recent Advances in High Throughput

Sequencing Analysis, International Journal of Genomics, 2016

Lead Editor for Special Issue on Non-Coding RNA, Genes, 2017

Journal (number of reviews)

Referee Advances in Genomics and Genetics 1

Applied Microbiology and Biotechnology 1

Archives of Medical Science 1

Bioinformatics 6

Biological Procedures Online 1

Biomarker Insights 1

Biomedical Research International 1

BMC Genomics 2

BMC Systems Biology 1

Briefings In Bioinformatics 7

Cancer Epidemiology 1

Cancer Management and Research 1

Clinical Epigenetics 1

Current Drug Targets 1

EBioMedicine 1

Evolutionary Bioinformatics 1

Frontiers in Genetics 1

G3, Genes, Genomes, Genetics 1

Gene 1

Genetica 1

Genetic Epidemiology 3

Genome Biology 1

Genomics 2

Human Mutation 2

IEEE Transactions on Biomedical Engineering 1

IEEE Computational Biology and Bioinformatics 1

Immunologic Research 1

International Journal of Cancer 1

International Journal of Computational Biology and Drug Design 1

International Journal of Data Mining and Bioinformatics 1

International Journal of Genomics 1

International Journal of Molecular Sciences 1

4

Journal of Genetics and Genome Research 1

Methods 1

Mitochondrion 1

Mitochondrial DNA 1

Nature Protocols 2

Nucleic Acid Research 5

Peer J 1

PLOS ONE 2

Scientific Reports 2

The Prostate 1

Transactions on Computational Biology and Bioinformatics 1

TEACHING EXPERIENCE

Courses

1. BIOM 505 (Section 9): Introduction to Genomic Data Analysis, Spring, 2018, University of New

Mexico

2. EPID 8332: Advanced Methods for Epidemiology, (8 hours) spring 2016, Vanderbilt University

3. Center for Quantitative Sciences Summer Institute 2014-2016 (three years), Bioinformatics Course

Director (6 hours per year), Vanderbilt University

4. Advanced Biostatistics Workshop (3 hours), April 8th, 2015, National Institute of Biological

Sciences, Beijing China.

5. Advanced Biostatistics (2 hours), December 2014, National Chengkung University Taiwan.

6. BMIF 310: Foundation of Bioinformatics, (1hour per year) 2014-2015, Vanderbilt University.

7. MAGEC Molecular and Genetic Epidemiology Course: 1 lecture Title: RNA and mitochondrial

DNA sequencing, April, 2014, Vanderbilt University.

8. Graduate course: CANB 347 Cancer Systems Biology Bioinformatics section (2012- present),

Vanderbilt University (5-6 hours per year).

9. Undergraduate course: CSCI1113 (C++), Taught as teaching assistant at University of Minnesota,

2001.

Patent

1. Metabolic biomarkers for early stage chronical kidney disease detection, Zhao YY, Guo Y, Patient

Number: US 62/551,192

Award and Honor

1. Center For Quantitative Sciences, High Impact Research Award, 2017

2. Genomic Workshop Travel Grant Award, Broad Institute, 2013

Invited Talks at Conferences

1. The First Annual Meeting of Functional Proteomics in Agriculture, title: “Multi-Omics Data

Analysis”, Nanjing China, July 30th, 2017

2. ICIBM 2016, title “The Discrepancy among Single Nucleotide Variants Detected by DNA and

RNA High Throughput Sequencing Data”, Huston TX, December, 2016

5

3. DNA Day 2016, title “Assessing Disease Risk Using Whole Genome Instead of Individual SNP”,

May 2016

4. Center for Quantitative Sciences, 2015 Retreat, title: “mtDNA heteroplasmy and copy number

detection”, Nashville TN, October, 2015

5. International Conference on the Frontiers of Genomic Research, title: “Finding the lost treasure of

genomic data with robust quality control”, National Cheng Kung University, Taiwan, December,

2014

6. 7th Annual World Cancer Congress, Title: High-throughput Sequencing in Mitochondrial DNA

Cancer Research, Nanjin, China, May 17, 2014

7. AACR 2014, Methods Workshops: Next Generation Sequencing: From Bench to Bedside, Title:

“Lost Treasures in Sequence Data”, April 5, 2014 San Diego, CA

8. International Conference on Intelligent Biology and Medicine, Title: “Read count RNAseq data

analysis comparison”, 2013 August 11-13, Nashville TN

9. Next Generation Sequencing Congress, Title: “The Effect of Strand Bias in Illumina Sequencing

Data”. Boston, April 26-27, 2011

Seminar/workshop

1. Title: “Using Machine Learning in Biomarker Research”, Cancer Genetics, Epigenetics and

Genomics Data Talk, UNM, Feb 15, 2017

2. Title: “Bioinformatics in Biomedical Research”, The Spatiotemporal Modeling Center, February 8,

UNM, 2017

3. Title: “An Introduction to Bioinformatics”, UNM Computer Science Department Colloquium

Series, November 29, 2017

4. Title: “Bioinformatics: Perspectives and Beyond”, Dana Farber Cancer Institute, Boston, April 14,

2017

5. Title: “How Bioinformatics Helps Solve Biological Problems”, Northwest University of China,

China, March 28th, 2017

6. Title: “Bioinformatics: Perspectives and Future”, University of New Mexico, Comprehensive

Cancer Center, March 8th, 2017

7. Title: “Bioinformatics Overview and Future”, Roche Sequencing, Belmont, CA, Feb, 2017

8. Title: “An Introduction to Bioinformatics”, Abmart, Shanghai, Dec 26th, 2016

9. Title: “High Throughput Data Analysis, DNA, RNA, Microbiome Sequencing and Genotyping”,

Huston Texas, Dec 8th 2016, ICIBM 2016

10. Title: “Genotyping Data and Innovative Analyses”, National Chengkung University Taiwan, Oct

13th 2016

11. Title: “Using a Global Heterozygosity Measure for Phenotype Association Studies”, Department

of Biostatistics, Vanderbilt University, Nashville, Nov 18th, 2015

12. Title: “The advanced data mining and quality control of high throughput sequencing data”, ICIBM

2015, University of Indiana, Nov 13th, 2015

13. Title: “High quality data mining of the human genome”, Shanghai Jiaotong University, May 25th,

2015.

14. Title: “Genomic data mining and quality control”, Center For Quantitative Sciences Bioinformatics

6

Retreat, November 2014

15. Title: “Advanced genomic data quality control and data mining”, University of Kentucky,

November, 2014.

16. Title: “Advanced genomic data analysis”, Center For Quantitative Sciences Bioinformatics Retreat,

October 2013

17. Title: “Sequencing data analysis and data mining”, Department of Cardiology, Vanderbilt

University, October 2013

18. Title: “Finding the lost treasures in NGS data”, Vanderbilt Ingram Cancer Center, April 2013

19. Title: “Bioinformatics Research”, Center For Quantitative Sciences Bioinformatics Retreat, August

2012

20. Title: “Next Generation Sequencing Data Processing and Analysis”, Shanghai Center for

Bioinformatics Technology, January 2012

CONFERENCES

Abstract/Poster Presented

1. Yu H, Wei Yue, Zhao YY, Guo Y, Deep architectures are not necessary for anomaly classification

of matrix-formed omics data, ICIBM 2018

2. Yue W, Sheng Q, Samuels D, Yu H, Zhao YY, Guo Y, eQTLs are tissue-disease specific, ICIBM

2018

3. Wiese C, Xu ZQ, Zhang Y, Guo Y, Zhong J, Ramirez M, Zhu W, Kon V, Vickers K, Chronic Kidney

Disease-Associated Atherosclerosis is Attenuated by Dual Inhibition of microRNA-92a and

microRNA-489, Arteriosclerosis, Thrombosis and Vascular Biology 2017

4. Ormseth MJ, Solus FJ, Sheng Q, Guo Y, Ye F, Allen R, Vickers KC, Stein M, Small RNA

sequencing identifies plasma microRNA panel for rheumatoid arthritis diagnosis, American

College of Rheumatology 2017

5. Ormseth MJ, Zhao S, Alle R, Solus JF, Sheng Q, Guo Y, Ye F, Ramirez MA, Vickers KC, Stein M,

Circulating microbial small RNAs are altered in patients with rheumatoid arthritis, American

College of Rheumatology 2017

6. Byram K, Solus JF, Sheng Q, Guo Y, Stein M, Ormseth MJ, Differential Plasma MicroRNA

Expression by Small RNA Sequencing in Patients with ANCA-Associated Vasculitis: A Pilot Study,

American College of Rheumatology 2017

7. Richmond BW, Guo Y, Yu C, Kendall P, Mason WR, Cogan JD, Loyd JE, A genome-wide

association study of 59 patients with fibrosing mediastinitis

8. AUA 2017, title: “The Relationship Between The Urinary Microbiome And Central Sensitization

In Women With Overactive Bladder”, May 2017

9. ARVO 2017, title: “Identification Of Hypoxia-Regulated Genes And Pathways In Mouse Retinal

Müller Cells By Rnaseq Analysis, May, 2017

10. Digestive Disease Week 2017, title “Loss Of TFF1 Activates BRD2 Through Down Regulation Of

Mir-143-3p In Gastric Cancer”

11. AACR 2017, title: “Organ-specific epigenetic reprogramming of leukemia cells: Clues to

chemoresistance.

7

12. ICIBM 2016, title: “Estimating Relative Mitochondria Copy Number Using Sequencing Data”,

December, 2016

13. AACR, 2016, title: “Robust Targeted Sequencing Strategy Identifies Highly Penetrant Mutations

in Hereditary Colorectal Cancer Cases from Colon Cancer Family Registry”

14. American College of Rheumatology Meeting 2016: title: “Small Rnaseq Reveals Different Plasma

Mirna Signature In Patients With RA And SLE: A Pilot Study”, November 2016

15. ISMB 2016, title: “Nucleotide Sequence Difference between DNA-RNA and Blood-Tissue

Samples”.

16. Clinical Congress 2016, title: “Growth Differentiation Factor 15 (GDF15) Is A Novel Regulator Of

The Stem Cell-Like Phenotype In Neuroblastoma”, October, 2016,

17. Digestive Disease Week 2016, title: “Transcriptome Sequencing Identifies Potentially Functional

Gene Fusions In Esophageal Adenocarcinomas”.

18. Digestive Disease Week 2016, title: “Integrated Expression Analysis of Mouse and Human Gastric

Neoplasm Identifies Early Molecular Changes in Gastric Carcinogenesis”.

19. Digestive Disease Week 2016, title: “Characterization of miRNA networks in mouse and human

gastric cancer”.

20. 2016 Conference on Retroviruses and Opportunistic Infection, title: “Mitochondrial DNA Copy

Number and Neurocognitive Impairment in HIV-Infected Persons”

21. Digestive Disease Week 2015, Blum A, Varadan V, Guo Y, Kieber-Emmons AM, Ravi L, Chandar

AK, Canto MI, Wang JS, Shaheen NJ, Barnholtz-Sloan J, Willis J, Markowitz S, Shyr Y, Chak A,

Guda K, Title: “Discovery of Novel Gene-Fusions in Esophageal Adenocarcinoma Using Next-Gen

RNA Sequencing”

22. Digestive Disease Week 2015, Varadan V, Blum A, Guo Y, Kieber-Emmons AM, Ravi L,

Kresak A, Chandar AK, Canto MI Wang JS, Shaheen NJ, Barnholtz-Sloan J, Willis J, Markowitz

S, Shyr Y, Chak A, Guda K, title: “Large-Scale Transcriptome Sequencing Identifies Two

Signaling Sub-Networks As Critical Mediators of Barrett's Carcinogenesis”

23. ICIBM 2015, title: “Precursor mRNA Abundance Estimation from total RNA sequencing”.

November, 2015

24. ICIBM 2015, title: “Mitochondria Single Nucleotide Variant among Six Blood Cell Types”.

November, 2015

25. 2016 Gastrointestinal cancers Syposium, title: “Frequent BRAF mutations in Colonic High-Grade

Neuroendocrine Carcinoma”, January 21-23, 2016

26. 14th Annual UT-KBRIN Bioinformatics Summit 2015, title: “Population structure analysis across

26 ancestries using dense genetic data”, March 20-22, 2015

27. 14th Annual UT-KBRIN Bioinformatics Summit 2015, title: “Practicality of Identifying

Mitochondria Variants from Exome and RNAseq data”, March 20-22, 2015

28. Digestive Disease Week 2015, title: “Large-scale Transcriptome Sequencing Identifies Two

Signaling Sub-Networks as Critical Mediators of Barrett’s Carcinogenesis”, May 17-19, 2015,

Washington DC

29. The American Society of Hemotology, title: “miRNA Predictors of Response to DNA

Methyltransferase Inhibitors”, December, 2014

8

30. ISMB 2014, title: RNA Somatic Mutation Caller (RSMC): accurately identifying somatic mutation

using RNAseq data, July, 2014

31. UT-KBRIN Bioinformatics Summit 2014, title: “Exon Deletion Detection”, April 11-13, Lake

Barkley, KY, 2014

32. Meharry Medical College/Vanderbilt Ingram Cancer Center U54 Cancer Partnership 13th annual

retreat, title: “Exon deletion detection in Notch1 of breast cancer”, Nashville, 2014

33. Recomb-Seq WorkShop, Beijing, title: “mitochondria detection using MitoSeek”, China April 11-

12, 2013

34. First Annual TCGA symposium, title: “evaluation of sequencing processing steps”, National

Harbor, Maryland, November 2012

35. Meharry Medical College/Vanderbilt Ingram Cancer Center U54 Cancer Partnership 10th annual

retreat, title: “The effect of radiation therapy on female child cancer patients and their offspring’s

mitochondria mutation”, Nashville, 2011

36. Vanderbilt Ingram Cancer Center Retreat, title: “mitochondria mutation in child cancer patients”,

May, 2012

37. 6th Workshop on Experimental Algorithms (Abstract), title: “Improving tree search in

phylogenetic reconstruction from genome rearrangement data”, June 2007 - Rome, Italy.

Conferences Attended:

1. Cancer Informatics for Cancer Centers 2017, La Jolla, CA, Oct 23-25, 2017

2. The First Annual Meeting of Functional Proteomics in Agriculture, Nanjing China, July 30th, 2017

3. 16th Annual UT-KBRIN Bioinformatics Summit 2015, April 21-23, 2017, TN

4. Vanderbilt Genetics Institute Retreat, March 17, 2017, Nashville TN,

5. International Conference on Intelligent biology and Medicine, 2016, December 2016, Huston TX

6. DNA Day 2016, Dalian China, May, 2016

7. AACR 2016, New Orleans April, 2016

8. 14th Annual UT-KBRIN Bioinformatics Summit 2015, March 20-22, 2015

9. International Conference on the Frontiers of Genomic Research, National Cheng Kung University,

Taiwan, December, 2014

10. 7th Annual World Cancer Congress, Nanjin, China, May 17, 2014

11. UT-KBRIN Bioinformatics Summit 2014, April 11-13, Lake Barkley, KY, 2014

12. AACR 2014, April 5, 2014 San Diego, CA

13. Meharry Medical College/Vanderbilt Ingram Cancer Center U54 Cancer Partnership 13th annual

retreat, Nashville, 2014

14. International Conference on Intelligent Biology and Medicine, 2013 August 11-13, Nashville

15. Recomb-Seq WorkShop, Beijing, China April 11-12, 2013

16. First Annual TCGA symposium, National Harbor, Maryland, November 2012

17. 1000 Genomes Project Community Meeting, Michigan, July 12-13, 2012

18. The 8th International R User Conference, Nashville TN, June 12th-15th, 2012

19. TCGA Head and neck Cancer Data Analysis Workshop, Chapel Hill, NC Sept, 19-20, 2012

20. International Conference on Intelligent Biology and Medicine, 2012 April 22-24, Nashville TN

21. Illumina Nashville User Group Meeting, Nashville, September 15th, 2011, Nashville

9

22. Next Generation Sequencing Congress, Boston, April 26-27, 2011,

23. Meharry Medical College/Vanderbilt Ingram Cancer Center U54 Cancer Partnership 10th annual

retreat, Nashville, 2011

24. 5th Hands-on Workshop Interrogating Cancer Resistance to Targeted Therapeutics with Systems

Biology August 22-24, 2011, Nashville

GRANTS/FUNDING

Primary Investigator

1. American Cancer Society-Institutional Research Grant: Identification of lncRNA eQTLs predictive

of drug response in breast cancer (2015). Amount: $30,000

2. Vanderbilt Institute for Clinical and Translational Research Grant: lincRNA biomarkers for Breast

cancer drug response predictability (2014). Amount: $1877

3. Center for Quantitative Sciences Pilot Project: Mitochondria Mutation in Breast Cancer (2014),

amount: $10,000

4. Vanderbilt Institute for Clinical and Translational Research Grant: Verify Notch3 regulated genes

in NSCLC cell line HCC2429 using Tagman PCR (2010), Amount: $2000

5. Vanderbilt Institute for Clinical and Translational Research Grant: Verification of heteroplasmy in

Mitochondria (2010), Amount: $2000

6. Vanderbilt Institute for Clinical and Translational Research Grant: Comparing FFPE and Frozen

Tumor RNAseq data quality (2011), Amount: $2000

7. Vanderbilt Institute for Clinical and Translational Research Grant: Mitochondria Mutation in

Breast Cancer (2013), Amount: $2000

Co-Investigator

NCI P50 CA098131 (Arteaga) 09/11/08-08/31/19

SPORE in breast cancer

The overall goal of this project is to conduct multidisciplinary, mechanism-based, translational research

of the highest possible impact that will contribute meaningfully to measurable progress in breast cancer.

Role: Bioinformatician

NCI R01 CA131225 (El-Rifai) 05/01/09-08/31/19

The Role of Aurora Kinase A in Upper Gastrointestinal Adenocarcinomas

The goal of this project is to characterize the molecular function(s) of AURKA, a frequently

overexpressed gene, in order to identify its biological, diagnostic, prognostic, and possibly therapeutic

significance.

Role: Bioinformatician

NHLBI P01 HL116263 (Linton) 06/01/14-04/30/19

HDL Function in Human Disease

The major goal of this project is to define the mechanisms for HDL dysfunction in three distinct diseases

associated with increased risk for atherosclerotic cardiovascular disease.

10

Role: Bioinformatician

NCI R01 HL127173 (Linton) 01/01/16-12/31/19

Macrophage SR-BI Regulates Autophagy, Angiogenin and tRNA-derived Small RNAs

The major goal of this project is to leverage the novel roles of SR-BI in regulating autophagy,

angiogenin and tRNA-derived small RNAs to identify potential drug targets for nucleic acid-based

therapies to treat and prevent atherosclerosis.

Role: Co-Investigator

NCI P50 CA095103 (Coffey) 05/01/0704/30/17

SPORE in GI cancer

These four projects continue to focus on transforming how we diagnose and treat individuals with

colorectal cancer and deepening our understanding of the pathobiology of colorectal neoplasia.

Role: Bioinformatician

NCI RO1 CA206563 (El-Rifai) 11/01/15-11/30/16

Molecular Functions of APE1 in Barrett’s Esophagus

This study aims to characterize the molecular functions of APE1, a frequently overexpressed gene in

esophageal adenocarcinoma (EAC), in order to identify its biological, diagnostic, prognostic, and

possibly therapeutic significance.

Role: Bioinformatician

NCI R01 CA177372 (El-Rifai) 08/01/13-07/31/16

The Role of MiRNA Network in Gastric Cancer

The goal of this project is to gain further understanding of the role of H. Pylori in shaping the miRNA

signature and promoting the multi-step gastric tumorigenesis in order to identify diagnostic, prognostic

and possibly therapeutic miRNA targets in gastric cancer.

Role: Bioinformatician

NIDDKD R24 DK103067 (Harris) 09/18/14-06/30/19

Novel Integrated Analyses of Human Diabetic Nephropathy

This study will utilize novel methods to study the biochemical changes to the kidney in response to

diabetic nephropathy and will investigate the underlying mechanisms responsible for these changes.

Role: Bioinformatician

NCI U54 CA163072 (Moses) 09/23/11-08/31/16

MMC, VICC &TSU: Partners in eliminating cancer disparities

This project aims to improve the effectiveness of the VICC by creating a collaborative relationship

between MMC, VICC & TSU in the areas of cancer research; training and development; education and

outreach.

11

Role: Bioinformatician

NCI R21 CA201856 (Oates) 12/01/15-11/30/17

Prevention of Genomic Instability by a Scavenger of Bifunctional Electrophiles

The major goal of this project is to identify the endogenous carcinogens that are responsible for the

mutations of the genome that determine the malignant nature of these cancers.

Role: Co-Investigator

NHGRI U01 HG007674 (Phillips) 07/01/14-03/31/18

Vanderbilt Center for Undiagnosed Diseases (VCUD)

The Vanderbilt Center for Undiagnosed Disease will function in the NIH funded Network of

Undiagnosed Diseases to evaluate persons afflicted with undiagnosed illnesses and to ensure an

accurate and timely diagnosis can be made, that counseling and advice be given to the patient and care

givers, and to assist in diagnosing and treating similar patients in the whole human population.

Role: Bioinformatician

Completed Research Support

American Heart Association (Vickers) 07/01/14-06/30/16

Novel small RNA intercellular communication networks mediated by HDL

The major goal of this project is to quantify inflammatory cell tDR export to HDL in

hypercholesterolemia and to quantify the impact of inflammatory cell-originating HDL-tDRs in

recipient cells.

Role: Bioinformatician

NHGRI R03 HG008055 (Multi-PI: Ye, Samuels) 04/01/14-03/31/16

Elastic Net Analysis of Phenotype Relationships in Association Studies

The major goal of this project is to increase our understanding of the complex patterns in medical

conditions as documented in electronic medical records in order to discover how rare genetic variants

in genes for mitochondrial proteins affect health.

Role: Bioinformatician

NCI R01 CA137013 (Long) 07/01/09-05/31/13

Genome-wide copy number variation and breast cancer risk

The major goal of this project is to survey the entire human genome for copy number variations

associated with breast cancer.

Role: Bioinformatician

NCI R01 CA064277 (Zheng) 08/01/10-05/31/13

Shanghai Breast Cancer Study

The major goal of this project is to provide valuable information regarding the roles of gene-gene and

12

gene-environment interaction in the etiology of breast cancer.

Role: Bioinformatician

CONTINUED EDUCATION

1. Genetic Analysis of Complex Human Diseases, University of Miami, Miller school of Medicine,

Hussman Institute for Human Genomics, May 23-26, 2011

2. 3rd NIGMS-funded Short Course on Statistical Genetics & Genomics, University of Alabama, July

8-12 2013,

3. Computational Genomics Workshop, The Center for Cell Circuits at Broad Institute, July 29-30,

2013 Boston (Travel Grant Awarded)

4. Mothur Workshop, Software for Describing and Comparing Microbial Communities, Detroit,

December 18-20, 2013

SKILLS

Omics Data Analysis: Exome sequencing, whole genome sequencing, targeted panel sequencing, RNAseq,

total RNAseq, small RNAseq, Chip-Seq, Microbiome Sequencing, gene expression microarray, genotyping

array, methylation array, pathway network analysis, cluster heatmap analysis, genome wide association

analysis, PheWAS, Mendelian Randomization, proteomic, Gene Set Enrichment Analysis.

Programming: C, C++, Java, Microsoft .net, Perl, Shell script, R.

PUBLICATIONS

Book Chapter

1. Yan Guo, Fei Ye, Margot Bjoring, AACR 2014 Education Book, chapter name: Lost Treasures in

Sequence Data, 2014 AACR.

2. Guo Y, Zhao S, Bjoring M, Han L, Big Data Analytics in Bioinformatics and Healthcare, Chapter

Name: Data Mining of High Throughput Sequencing, IGI-Global. 2014

Editorial

1. Han L, Zheng S, Lu ZX, Su, Z, Guo Y, Advances in Computational Genomics, Biomed Research

International, 2014

2. Guo Y, Sheng Q, Advances in Computational Biology and Genomics, International Journal of

Computational Biology and Drug Design, 2015

3. Guo Y, Leng H, Sheng Q, Recent Advances in High Throughput Sequencing Analysis,

International Journal of Genomics, 2017

4. Zhao Z, Liu Z, Chen K, Guo Y, Allen GI, Zhang J, Zheng W, Ruan J, The International Conference

on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics, BMC

Genomics, 2017

Peer-reviewed publications as first/co-first/last/corresponding author († equal contribution)

1. Bing F, Hoskings W, Zhang Y, Meng Z, Guo Y†, Tang J†, Down Syndrome Prediction/Screening

13

Model Based on Deep Learning and Illumina Genotyping Array, BMC Medical Genomics, 2018

2. Guo Y, Wang J, Sheng Q, Zhao S, Zhao YY, Lehmann, BD, The Landscape of small non-coding

RNAs in Triple-Negative Breast Cancer, Genes, 2018

3. Estimating Relative Mitochondria Copy Number Using High Throughput Sequencing Data, Zhang

P, Lehmann BD, Samuels DC, Zhao S, Zhao Y, Shyr Y, Guo Y, Genomics 2017

4. Wang J, Samuels DC, Shyr Y, Guo Y, StrandScript: evaluation of Illumina genotyping array

design and strand correction, Bioinformatics, 2017

5. LI CI, Zhao Y, Samuels DC, Guo Y, Power and Sample Size Calculations for High Throughput

Sequencing Based Experiments, Briefings in Bioinformatics, 2017

6. Guo Y, Zhao S, Sheng Q, Samuels DC, Shyr Y, The Discrepancy among Single Nucleotide Variants

Detected by DNA and RNA High Throughput Sequencing Data, BMC Genomics, 2017

7. Zhao S, Jing W, Samuels DC, Sheng Q, Shyr Y, Guo Y, Strategies for Processing and Quality

Control of Illumina Genotyping Arrays, Briefings in Bioinformatics, 2017

8. Guo Y, Dai Y, Yu H, Zhao S, Samuels DC, Shyr Y, Improvements and Impacts of GRCh38 Human

Reference on High Throughput Sequencing Data Analysis, Genomics, 2017

9. Guo Y, Strickland SA, Li S, Mohan S, Bosompem A, Zhao S, Sheng Q, Kim AS, MicroRNAs and

tRNA-derived fragments predict the transformation of myelodysplastic syndromes to acute

myeloid leukemia, Leukemia and Lymphoma, 2017

10. Guo Y, Vickers K, Xiong Y, Zhao S, Sheng Q, Zhang P, Zhou W, Flynn CR, Comprehensive

Evaluation of Extracellular Small RNA Isolation Methods from Serum in High Throughput

Sequencing, BMC Genomic, 2017

11. Wang J, Samuels DC, Zhao S, Xiang Y, Zhao YY, Guo Y, Current research on noncoding

Ribonucleic Acid (RNA), Genes, 2017

12. Zhao S, Samuels DC, Zhao Y, Guo Y, Tri-allelic Heteroplasmies, DNA-RNA Differences and Their

Polynucleotide Tract Associations in the Mitochondrial Genome, Genomics, 2017

13. Zhang P, Lehmann BD, Shyr Y, Guo Y, The Utilization of Formalin Fixed-Paraffin-Embedded

Specimens in High Throughput Genomic Studies, International Journal of Genomics, 2017

14. Guo Y, Zhang P, Sheng Q, Zhao S, Hackett TA, lncRNA expression in the auditory forebrain

during postnatal development, Gene, 2016, PMID 27544636

15. Guo Y, Warren Andersen S, Shu XO, Michailidou K, Bolla MK, Wang Q, Garcia-Closas M, Milne

RL, Schmidt MK, Chang-Claude J, Dunning A, Bojesen SE,Ahsan H, Aittomäki K, Andrulis

IL, Anton-Culver H, Arndt V, Beckmann MW, Beeghly-Fadiel A, Benitez J, Bogdanova

NV, Bonanni B, Børresen-Dale AL, Brand J, Brauch H, Brenner H, Brüning T, Burwinkel

B, Casey G, Chenevix-Trench G, Couch FJ, Cox A, Cross SS, Czene K, Devilee P, Dörk

T, Dumont M, Fasching PA, Figueroa J, Flesch-Janys D, Fletcher O, Flyger H, Fostira F, Gammon

M, Giles GG, Guénel P, Haiman CA, Hamann U, Hooning MJ, Hopper JL,Jakubowska A, Jasmine

F, Jenkins M, John EM, Johnson N, Jones ME, Kabisch M, Kibriya M, Knight JA, Koppert

LB, Kosma VM, Kristensen V, Le Marchand L, Lee E, Li J, Lindblom A, Luben R, Lubinski

J, Malone KE, Mannermaa A, Margolin S, Marme F, McLean C, Meijers-Heijboer H, Meindl

A, Neuhausen SL,Nevanlinna H, Neven P, Olson JE, Perez JI, Perkins B, Peterlongo P, Phillips

KA, Pylkäs K, Rudolph A, Santella R, Sawyer EJ, Schmutzler RK, Seynaeve C,Shah M, Shrubsole

14

MJ, Southey MC, Swerdlow AJ, Toland AE, Tomlinson I, Torres D, Truong T, Ursin G, Van Der

Luijt RB, Verhoef S, Whittemore AS,Winqvist R, Zhao H, Zhao S, Hall P, Simard J, Kraft

P, Pharoah P, Hunter D, Easton DF, Zheng W, Body Mass Index Genetic Scores and Breast Cancer

Risk: Mendelian Randomization Analyses of Data from 145,000 women of European Descent,

PLOS Medicine, 2016, PMID: 27551723

16. Samuels DC, Wang J, Ye F, He J, Levinson RT, Sheng Q, Zhao S, Capro JA, Shyr Y, Zheng W,

Guo Y, Heterozygosity Ratio, a Robust Global Genomic Measure of Autozygosity and Its

Association with Height and Disease Risk, Genetics, 2016

17. Guo Y, Xiong Y, Sheng Q, Zhao S, Flynn CR, A microRNA expression-signature for human

NAFLD progression, Journal of Gastroenterology, 2016, PMID: 26874844, PMCID:

PMC4983265

18. Sheng Q, Vickers K, Zhao S, Wang J, Samuels DC, Koues O, Shyr Y, Guo Y, Multi-Perspective

Quality Control of Illumina RNA Sequencing Data Analysis, Briefings in Functional Genomics,

2016

19. Zhang P, Samuels DC, Wang J, Zhao S, Shyr Y, Guo Y, Mitochondria Single Nucleotide Variation

across Six Blood Cell Types, Mitochondrion, 2016

20. Zhang P, Samuels DC, Zhao S, Wang J, Shyr Y, Guo Y, Practicability of Mitochondrial

Heteroplasmy Detection through an Illumina Genotyping Array, Mitochondrion, 2016

21. Sheng Q, Zhao S, Li C, Shyr Y, Guo Y, Practicability of Detecting Somatic Point Mutation from

RNA High Throughput Sequencing Data, Genomics, 2016

22. Guo Y, Wu J, Zhao S, Ye F, Su Y, Clark T, Sheng Q, Lehmann B, Shu X, Cai Q, RNA sequencing

of Formalin-Fixed, Paraffin-Embedded Specimens for Gene Expression Quantification and Data

Mining, International Journal of Genomics, 2016

23. Peng D†, Guo Y†, Chen H, Zhao S, El-Rifai W, Integrated Analysis Reveals Complex Associations

between Genomics and Epigenomics in Esophageal Adenocarcinoma, Scientific Reports, 2017

24. Zhang P, Samuels DC, Lehmann B, Sricker T, Pietenpol J, Shyr Y, Guo Y, Mitochondria Sequence

Mapping Strategies and Practicability of Mitochondria Variant Detection from Exome and RNA

sequencing Data, Briefings in Bioinformatics, 2015

25. Guo Y, Bosompem A, Sheng Q, Mohan S, Erdogan B, Ye F, Vickers KC, Sheng Q, Zhao S, Li CI,

Su PF, Jagasia M, Strickland SA, Griffith E, Kim A, Transfer RNA Detection by Small RNA Deep

Sequencing and Disease Association with Myelodysplastic Syndromes, BMC Genomics, 2015,

PMID:26400237, PMCID:PMC4581457

26. Vickers KC, Roteta, LA, Dilks H, Han L, Guo Y, Mining diverse small RNA species in the deep

transcriptome, Trends in Biochemical Sciences, 2015, PMID: 25435401, PMCID: PMC4362530

27. Samuels D, Han L, Li J, Sheng Q, Clark T, Yu Shyr, Guo Y, “Finding the Lost Treasures in

exome sequencing data”, Trends in Genetics, 2013 PMID: 23972387, PMCID: PMC3926691

28. Guo Y, Jing, H, Zhao S, Wu H, Sheng Q, Zhong X, Samuels DC, Shyr Y, Long J, Illumina

human exome genotyping array clustering and quality control. Nature Protocols, 2014, PMID:

25321409

29. Han L, Vickers KC, Samuels DC, Guo Y, Alternative Applications for Distinct RNA Sequencing

Strategies, Briefings in Bioinformatics, 2014, PMID:25246237

15

30. Wang J, Raskin L, Samuels DC, Shyr Y, Guo Y, Genome Measures used for Quality Control are

Dependent on Gene Function and Ancestry, Bioinformatics, 2014, PMID: 25297068, PMCID:

PMC4308666

31. Guo Y, Li J, Li CI, Shyr Y, Samuels DC, “MitoSeek: extracting mitochondria information and

performing high throughput mitochondria sequencing analysis”, Bioinformatics, 2013, PMID:

23471301, PMCID: PMC4492415

32. Guo Y, Zhao S, Sheng Q, Ye F, Li J, Lehmann, B, Pietenpol J, Samuels DC, Shyr Yu, Multi-

Perspective Quality Control of Illumina Exome Sequencing Data Using QC3, Genomics, 2014,

PMID 24703969

33. Guo Y, Li C, Ye F, Shyr Y, Evaluation of Read Count Based RNAseq Analysis Methods, BMC

Genomics. 2013, PMID: 24564449, PMCID: PMC4092879

34. Ye. F, Samuels, DC, Clark T, Guo, Y, High-Throughput Sequencing in Mitochondrial DNA

Research Mitochondrion. Mitochondrion, 2014, PMID: 24859348, PMCID: 4149223

35. Guo Y, Sheng Q, Ye F, Clark T, Samuels DC, “Three-Stage Quality Control Strategies for DNA

Sequencing Data”, Briefing in Bioinformatics, 2013 Sep 24. PMID: 24067931

36. Guo Y, Sheng Q, Li J, Ye F, Samuels DC, Shyr Y, Large scale comparison of gene expression

levels by microarrays and RNAseq using TCGA data, PloS ONE 2013, PMID: 23977046,

PMCID: 3748065

37. Guo Y, Li J, Li CI, Long J, Samuels DC, Shyr Y, The effect of strand bias in Illumina short-read

sequencing data, BMC Genomics, 2012 Nov 24;13:666. PMID: 23176052, PMCID:

PMC3532123

38. Guo Y, Long J, Cai Q, He J, Zheng W, Li C, Exome sequencing generates high quality data in non-

target regions, BMC Genomics, 2012 May 20;13:194. PMID: 22607156, PMCID: PMC3416685

39. Guo Y, Cai Q, Samuels DC, Ye F, Long J, Li CI, Winther JF, Tawn EJ, Stovall M, Lähteenmäki

P, Malila N,Levy S, Shaffer C, Shyr Y, Shu XO, Boice JD Jr., “The use of next generation

sequencing technology to study the effect of radiation therapy on mitochondrial DNA mutation”,

Mutation Research, 2012 May 15;744(2):154-60. PMID: 22387842, PMCID: PMC3354959

40. Guo Y, Miyagi M, Zeng R, Sheng, Q, O18Quant: A Semi-automatic Strategy for Quantitative

Analysis of High-Resolution 16O/18O Labeled Data, Biomed Research International, 2014, PMID

24901003, PMID: 24901003, PMCID: PMC4037588

41. Guo Y, Zhao S, Lehmann B, Pietenpol J, Shyr Yu, Detection of internal exon deletion with exon

Del, BMC Bioinformatics, 2014, PMID: 25322818, PMCID: PMC4288651

42. Guo Y, Bosompem A, Zhong, X, Clark T, Shyr Y, Kim A, “A comparison of MicroRNA

Sequencing Reproducibility and Noise Reduction Using mirVana and TRIzol Isolation Methods”,

Int J Comput Biol Drug Des. 2014. PMID 24878723

43. Guo Y, Su P, Li C, Zhao S, Ye F, Flynn CR, Shyr Yu, Statistical Strategies for microRNAseq Batch

Effect Reduction, Transl Cancer Res 2014;3(3):260-265. doi: 10.3978/ j.issn.2218-

676X.2014.06.05, PMID: 25258704, PMCID: PMC4171948

44. Guo Y, Zhao S, Sheng Q, Shyr Y. MultiRankSeq: Multiperspective Approach for RNAseq

Differential Expression Analysis and Quality Control, Biomedical Research International, 2014,

PMID: 24977143, PMCID: PMC4058234

16

45. Guo Y, Li C, Cai Q, Shyr Y, “Very Low level Heteroplasmy mtDNA Variations Are Inherited in

Humans”, Journal of Genetics and Genomics. 2014. PMID: 24377867

46. Guo Y, Zhao S, Sheng Q, Guo M, Stricker T, Lehmann B, Pietenpol J, Samuels DC, Shyr Yu,

RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA library,

Biomed Research International, 2015

47. Ye F, Samuels DC, Guo Y, Detection of Mitochondrial Mutations in Cancer by Next Generation

Sequencing, Next Generation Sequencing & Applications, 2014

48. Guo Y, Zhao S, Li C, Sheng Q, Shyr Y, RNAseqPS: A Web Tool for Estimating Sample Size

and Power for RNAseq experiment, Cancer Informatics, 2014

49. Zhao S†, Guo Y†, Sheng Q, Shyr Y, Advanced Heat Map and Clustering Analysis Using

Heatmap3, Biomed Research International, 2014, PMID: 4124803

50. Guo Y, Sheng Q, Li J, Lehmann B, Bauer J, Pietenpol J, Shyr Y, “Comparative Study of Exome

Copy Number Variation Estimation Tools Using Array Comparative Genomic Hybridization as

Control”, Biomed Res Int 2013; 2013:915636. PMID: 24303503, PMCID: PMC3835197

51. Guo Y, Cai Q, Li C, Li J, Courtney R, Li CI, Zheng W, Long J, “An evaluation of allele frequency

estimation accuracy using pooled sequencing data”, Int J Comput Biol Drug Des, 2013;6(4):279-

93. PMID: 24088264, PMCID PMC4108916

52. Guo Y, Li J, Li CI, Shyr Y, “Evaluation of allele frequency estimation using pooled sequencing

data simulation”, ScientificWorldJournal 2013, 2013:895496. PMID: 23476151, PMCID:

PMC3582166

53. Guo Y, Ye F, Tang J, "Phylogenetic reconstruction with disk-covering and Bayesian approaches,"

BioInformatics and BioEngineering, BIBE 2008.

54. Liu Q†, Guo Y†, Jiang L, Long J, Zhang B, Shyr Y, “Steps to ensure accuracy in genotype and

SNP calling from Illumina sequencing data”, BMC Genomics, 2012, PMID: 23281772, PMCID:

PMC3535703

Peer-reviewed publications as co-author

55. Wang M, Chen DD, Cao G, Zhao H, Liu D, Vaziri N, Guo Y, Zhao YY, Novel inhibitors of the

cellular RAS components, Poricoic acids, target Smad3 phosphorylation and Wnt/β-catenin

pathway against renal fibrosis, British Journal of Pharmacology, 2018

56. Chen L, Su W, Che H, Chen DD, Wang M, Guo Y, Zhao YY, Proteomics for Biomarker

Identification and Clinical Application in Kidney Disease, Advances in Clinical Chemistry, 2018

57. Ma D, Tu C, Sheng Q, Yang Y, Kan Z, Guo Y, Shyr Y, Scott IC, Lou X, Dynamics of Zebrafish

Heart Regeneration Using an HPLC-ESI-MS/MS Approach, Journal of Proteome Research, 2018

58. Wang M, Chen DD, Chen L, Zhao H, Liu D, Zhang ZH, Vaziri N, Guo Y, Cao G, Zhao YY, Novel

RAS inhibitors poricoic acid ZG and poricoic acid ZH attenuate renal fibrosis via Wnt/β-catenin

pathway and targeted phosphorylation smad3 signaling, Journal of Agricultural and Food

Chemistry, 2018

59. Idrees K, Padmanabhan C, Liu E, Guo Y, Gonzalez RS, Dahlman K, Berlin J, Shi C, Frequent

BRAF Mutations Suggest a Novel Oncogenic Driver in High-Grade Colonic Neuroendocrine

Carcinoma, Journal of Surgical Oncology, 2017

17

60. Greenplate A, Wang K, Tripathi R, Palma N, Ali S, Stephens P, Miller V, Shyr Y, Guo Y, Reddy N,

Kozhaya L, Unutmaz D, Chen X, Irish J, Dave, U, Genomic profiling of T cell neoplasms reveals

frequent JAK1 and JAK3 mutations with clonal evasion from targeted therapies, Journal of

Precision Oncology 2017

61. Richmond BW, Guo Y, Yu C, Kendall PL, Mason WR, Cogan JD, Loyd JE, GWAS of 58

individuals with fibrosing mediastinitis reveals possible underlying genetic susceptibility, Am J

Respir Crit Care Medicine, 2017

62. Spurlock CF, Shaginurova G, Tossberg JT, Hester JD, Chapman N, Guo Y, Crooke PS, Profiles of

long noncoding RNAs in human naïve and memory T cells, Journal of Immunology, 2017

63. Panaccione A, Guo Y, Yarbrough W, Ivanov S, Expression Profiling Of Clinical Specimens

Supports The Existence Of Neural Progenitor-Like Stem Cells In Basal Breast Cancers, Clinical

Breast Cancer, 2017, PMID: 28216417

64. Bing F, Lin Y, Zhao L, Guo Y, Friedman B, Xia R, Hu F, Liu C, Tang J, Reconstructing Yeasts

Phylogenies and Ancestors from Whole Genome Data, Scientific Report, 2017, PMID: 29123238

65. Durbin MD, Cadar AG, Williams CH, Guo Y, Bichell DP, Su Y, Hong, CC, Hypoplastic Left Heart

Syndrome Sequencing Reveals a Novel NOTCH1 Mutation in a Family with Single Ventricle

Defects, Pediatric Cardiology, 2017, PMID: 28608148

66. Jovanovic B, Sheng Q, Seitz RS, Lawrence KD, Morris SW, Thomas LR, Hout DR, Schweitzer

BL, Guo Y, Pietenpol JA, Lehmann BD, Comparison of triple-negative breast cancer molecular

subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue,

BMC Cancer, 2017, PMID: 28376728

67. Oelsner KT, Guo Y, To SB, Non AL, Barkin S, Maternal BMI as a predictor of methylation of

obesity-related genes in saliva samples from preschool-age Hispanic children at-risk for obesity,

BMC Genomics, 2017, PMID: 28068899

68. Ma Y, Cheng Z, Liu J, Torre-Healy L, Lathia JD, Nkano I, Guo Y, Thompson RC, Freeman ML,

Wang J, Inhibition of farnesyltransferase potentiates NOTCH-targeted therapy against

glioblastoma stem cells, Stem Cell Reports, 2017, PMID: 29198824

69. Absi TS, Galindo CL, Gumina RJ, Atkinson J, Guo Y, Thomasek K, Sawyer DB, Byrne JG,

Kaiser CA, Shah AS, Su YR, Petracek M, Altered ADAMTS5 Expression and Versican

Proteolysis: a possible molecular mechanism in Barlow’s Disease, the Annals of Thoracic

Surgery, 2017, PMID: 29248417

70. Ma Y, Wang L, Neitzel L, Loganathan S, Tang N, Emily C, Guo Y, Knapp S, Beauchamp R, Lee

E, Wang J, The MAPK Pathway Regulates Intrinsic Resistance to BET Inhibitors in Colorectal

Cancer. Clinical Cancer Research, 2017, PMID: 27678457

71. Su P, Mau YL, Guo Y, Li CI, Liu Q, Boice J, Shyr Y, Bivariate Poisson models with varying offsets:

An application to the paired mitochondrial DNA dataset, Statistical Applications in Genetics and

Molecular Biology, 2017, PMID: 28248637

72. Raskin L, Guo Y, Du L, Clendenning M, Rosty C, Colon Cancer Family Registry (CCFR), Lindor

NM, Gruber SB, Buchanan DD, Targeted sequencing of established and candidate colorectal cancer

genes in the Colon Cancer Family Registry Cohort, Oncotarget, 2017, PMID: 29212164

73. Blum A, Venkitachalam S, Guo Y, Kieber-Emmons AM, Ravi L, Chandar AK, Iyer PG, Canto MI,

18

Wang JS, Shaheen NJ, Barnholtz-Sloan JS, Markowitz SD, Willis JE, Shyr Y, Chak A, Varadan V,

Guda K, RNA Sequencing Identifies Transcriptionally Viable Gene Fusions in Esophageal

Adenocarcinomas, Cancer Research, 2016, PMID: 27503924

74. Loganathan, S, Tang N, Fleming J, Ma Y, Guo Y, Borinstein S, Chiang C, Wang J, BET

bromodomain inhibitors suppress EWS-FLI1-dependent transcription and the IGF1 autocrine

mechanism in Ewing sarcoma, Oncotarget 2016, PMID: 27259270

75. Eilertson B, Maruri F, Balckman A, Guo Y, Herrera M, van der Heijden Y, Shyr Y, Sterling T, A

Novel Resistance Mutation in eccC5 of the ESX-5 Secretion System Confers Ofloxacin Resistance

in Mycobacterium Tuberculosis, Journal of Antimicrobial Chemotherapy, 2016, PMID: 27261264

76. Rabacal W, Pabbisetty SK, Hoek K, Cendron D, Guo Y, Maseda D, Sebzda E, Transcription factor

KLF2 regulates homeostatic NK cell proliferation and survival, PNAS, 2016, PMID: 27114551

77. Panaccione A, Zhang Yi, Mi Y, Mitani Y, Guo Y, Prasad M, McDonald H, El-Naggar AK,

Yarbrough W, Ivanov S, Chromosomal Abnormalities and Molecular Landscape of Metastasizing

Mucinous Salivary Adenocarcinoma, Oral Oncology, PMID: 28249646

78. Strugill, E, Norris, S, Guo Y, Ohi R, Kinesin-5 inhibitor resistance is driven by kinesin-12, Journal

of Cell Biology, 2016, PMID: 27091450

79. NOTCH1 and SOX10 are Essential for Proliferation and Radiation Resistance of Cancer Stem-like

Cells in Adenoid Cystic Carcinoma, Panaccione A, Chang MT, Carbone BE, Guo Y, Moskaluk CA,

Virk RK, Chirboga L, Prasad ML, Judson B, Mehra S, Yarbrough WG, Ivanov SV, Clinical Cancer

Research, 2016, PMID: 27084744

80. McCann TS, Guo Y, McDonald H, Tansey W, Antagonistic roles for Asr1 and Ubp3 in subtelomeric

gene silencing PNAS, 2016

81. Herington J, Guo Y, Reese J, Paria B, Gene profiling the window of implantation: microarray

analyses from human and rodent models, Journal of Reproductive Health and Medicine, 2016

82. Flynn CR, Albaugh VL, Cai S, Cheung-Flynn J, Williams PE, Brucker RM, Bordenstein SR, Guo

Y, Wasserman DH, Abumrad NN, Bile Diversion to the Distal Small Intestine has comparable

metabolic benefits to bariatric surgery, Nature Communications, 2015, PMID:26197299, PMCID:

PMC4518285

83. Pickup M, Hover L, Guo Y, Gorska A, Chytil A, Novitskiy S, Moses H, Owens P, Deletion of

the BMP receptor BMPR1a impairs mammary tumor formation and metastasis, Oncotarget 2015

PMID: 26274893

84. Kavanaugh G, Zhao R, Guo Y, Mohni KN, Glick G, Lacy ME, Hutson MS, Ascano M, Cortez D,

Enhancer of Rudimentary Homolog affects the replication stress response through regulation of

RNA processing, Molecular Cell Biology, PMID: 26100022

85. Carroll C, Hunley T, Guo Y, Cortez D, A Novel Splice Site Mutation in SMARCAL1 Results in

Aberrant Exon Definition in a Child with Schimke Immunoosseous Dysplasia, American Journal

of Medical Genetics, 2015. PMID: 25943327

86. Spurlock CF, Tossberg, JT, Guo Y, Sriram S, Crooke SP, Aune TM, Expression and functions of

long noncoding RNAs during human T helper cell differentiation, Nature Communications, 2015

PMID: 25621826, PMCID: PMC4333215

19

87. Spurlock CF, Tossberg, JT, Guo, Y, Sriram S, Crooke PS, Aune TM, Defective structural RNA

processing in relapsing-remitting multiple sclerosis, Genome Biology, PMID: 25885816,

PMC4403723

88. TCGA HNSCC work group, Comprehensive genomic characterization of head and neck

squamous cell carcinomas, Nature, 2015, PMID: 25631445

89. Goodings C, Smith E, Mathia E, Elliott, N, Cleveland S, Tripathi R, Layer J, Chen X, Guo Y,

Shyr Yu, Hamid R, Du Y, Dave, UP, Hhex is required at multiple stages of adult hematopoietic

stem and progenitor cell differentiation, Stem Cells, 2015, PMID: 25968920

90. Hoek K, Samir P, Niu X, Howard LM, Prasad N, Galassie A, Liu Q, Allos TM, Guo Y, Shyr Y,

Levy SE, Joyce S, Edwards KM, Link AJ, A Cell-based Systems Biology Assessment of Human

Blood to Monitor Immune Responses Following Influenza Vaccination, PLOS ONE, 2015, PMID

26706537

91. Di Salvo TG, Guo Y, Su YR, Clark T, Brittain E, Absi T, Maltais S, Hemnes A, Right ventricular

long noncoding RNA expression in human heart failure, Pulmonary Circulation, 2015, PMID:

25992278

92. Hackett TA, Guo Y, Clause A, Hackett NJ, Garbett K, Zhang P, Poley Daniel, Mirnics K,

Transcriptional maturation of the mouse auditory forebrain, BMC Genomics, 2015, PMID:

26271746

93. Zhang B, Jia WH, Matsuda K, Kweon SS, Matsuo K, Xiang YB, Shin A, Jee SH, Kim DH, Cai

Q, Long J, Shi J, Wen W, Yang G, Zhang Y, Li C, Li B, Guo Y, Ren Z, Ji BT, Pan ZZ,

Takahashi A, Shin MH, Matsuda F, Gao YT, Oh JH, Kim S, Ahn YO, Chan A, Chang-Claude J,

Slattery M, Gruber S, Schumacher F, Stenzel S, Casey G, Kim HR, Jeong JY, Park JW, Li HL,

Hosono S, Cho SH, Kubo M, Shu XO, Zeng YX, Zheng W, Genome-wide association study in

East Asians identifies six novel risk loci for colorectal cancer, Nature Genetics, 2014, PMCID:

PMC3679924

94. Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow CA, Lee S,

Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J,

Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jung

J, Ojesina AI, Issaeva N, Yarbrough WG, Hayes DN, Grandis JR, El-Naggar, Meyerson M, Park

PJ, Chin Lynda, Seidman JG, Hammerman PS, Kucherlapati R, the Cancer Genome Atlas

Network, Characterization of HPV and host genome interactions in primary head and neck

cancers. Proc Natl Acad Sci U S A 2014, 111(43):15544-15549. PMID:25313082, PMCID:

PMC4217452

95. Zhuang G, Song W, Amato K, Hwang Y, Lee K, Boothby M, Ye F, Guo Y, Shyr Y, Lin L, Carbone

D, Brantley-Sieders D, Chen J, “Effects of Cancer-Associated EPHA3 Mutations on Lung Cancer”,

JNCI, 2012 Aug 8;104(15):1182-97. PMID: 22829656, PMCID: PMC3611812

96. Powell AE, Wang Y, Li Y, Poulin EJ, Means AL, Washington MK, Higginbotham JN, Juchheim

A, Prasad N,Levy SE, Guo Y, Shyr Y, Aronow BJ, Haigis KM, Franklin JL, Coffey RJ., The pan-

ErbB negative regulator Lrig1 is an intestinal stem cell marker that functions as a tumor suppressor,

Cell, 2012 Mar 30;149(1):146-58. PMID: 22464327, PMCID: PMC3563328

20

97. Saraswati S, Guo Y, Atkinson J, Young P, Prolonged hypoxia induces MCT4 expression in

MSCs resulting in a secretome that is deleterious to cardiovascular repair, Stem Cells, 2014

98. Goodings C, Tripathi R, Cleveland SM, Elliott N, Guo Y, Shyr Y, Dave, UP, Enforced

expression of E47 has differential effects on Lmo2-induced T-cell leukemias, Leukemia

Research, 2014, PMID 25499232

99. Sheng Q, Li R, Dai J, Li Q, Su Z, Guo Y, Li C, Shyr Y, Zeng R, Removing isobaric-related ions

significantly improves the peptide/protein identification sensitivity of high resolution tandem

mass spectrometry data, Molecular & Cellular Proteomics, 2014, PMID: 25435543

100. Weeke P, Mosley JD, Hanna D, Shaffer C, Delaney JT, Wells QS, Van Driest S, Karnes JH,

Ingram C, Guo Y, Shyr Y, Norris K, Kannankeril P, Ramirez AH, Smith J, Mardis ER,

Nickerson D, George AL Jr., Roden DM, Exome Sequencing Implicates an Increased Burden of

Rare Potassium Channel Variants in the Risk of Drug-Induced Long QT Interval Syndrome,

Journal of the American College of Cardiology, 2014, PMID: 24561134

101. Cleveland SM, Goodings C, Tripathi RM, Elliott N, Thompson MA, Guo Y, Shyr Y, Dave, UP,

LMO2 induces T-cell leukemia with epigenetic deregulation of CD4, Experimental Hematology,

2014, PMID: 24792354

102. Mosley JD, Van Driest SL, Larkin EK, Weeke PE, Witte JS, Wells QS, Karnes JH, Guo Y,

Bastarache L, Olson LM, McCarty CA, Pacheco JA, Jarvik GP, Larson EB, Crosslin DR, Kullo

IJ, Tromp G, Kuivaniemi H, Carey DJ, Ritchie MD, Denny JC, Roden DM, Mechanistic

Phenotypes: An Aggregative Phenotyping Strategy to Identify Disease Mechanisms Using

GWAS Data, PLOS ONE, 2013. PMID: 24349080, PMCID: PMC3861317

103. Ivanov SV, Panaccione A, Brown B, Guo Y, Moskaluk CA, Wick MJ, Brown JL, Ivanova

AV, Issaeva N, El-Naggar AK, Yarbrough WG, “TrkC signaling is activated in adenoid cystic

carcinoma and requires NT-3 to stimulate invasive behavior”, Oncogene, 2013 Aug 8;32(32):3698-

710. PMID: 23027130

104. Li CI, Su P, Guo, Y, Shyr Y, Sample size calculation for differential expression analysis of RNA-

seq data under Poisson distribution, Int J Comput Biol Drug Des, 2013 6(4), 358-375, PMID:

24088268, PMCID: PMC3874726

105. Lu X, An H, Jin R, Zou M, Guo Y, Su P-F, Liu D, Shyr Y, Yarbrough WG, “PPM1A is a RelA

phosphatase with tumor suppressor-like activity”, OncoGene, 2013 Jul 1. PMID: 23812431,

PMCID: PMC3897569

106. Yan L, Womack B, Wotton D, Guo Y, Shyr Y, Dave U, Li C, Hiebert S, Brandt S, and Hamid

R, “Tgif1 regulates the quiescence and self-renewal of hematopoietic stem cells”, Mol Cell Biol,

2013 Dec;33(24):4824-33. PMID: 24100014, PMCID: PMC3889555

107. Ivanov S, Panaccione A, Nonaka D, Prasad M, Boyd K, Brown B, Guo Y, Sewell A, Yarbrough

W, “Diagnostic SOX10 Gene Signatures in Salivary Adenoid Cystic and Breast Basal-like

Carcinomas”, Br J Cancer, 2013 Jul 23; 109(2): 444–451. PMID: 23799842, PMCID:

PMC3721393

108. Savani M, Guo Y, Carbone DP, Csiki I, “Sonic hedgehog pathway expression in non-small cell

lung cancer”, Ther Adv Med Oncol, 2012 Sep; 4(5): 225-33. PMID: 22942905, PMCID:

PMC3424496

21

109. Yu DS, Zhao R, Hsu EL, Cayer J, Ye F, Guo Y, Shyr Y, Cortez D, “Cyclin-dependent kinase 9-

cyclin K functions in the replication stress response”, EMBO Rep, 2010 Nov;11(11):876-82. PMID:

20930849, PMCID: PMC2966956

110. Hatakeyama H, Cheng H, Wirth P, Counsell A, Marcrom S, Wood C, Pohlmann P, Gilbert J,

Murphy B, Yarbrough W, Wheeler D, Harari P, Guo Y, Shyr Y, Slebos R, Chung CH, “Regulation

of heparin-binding EGF-like growth factor by miR-212 and acquired cetuximab-resistance in head

and neck squamous cell carcinoma. PLoS ONE, 2010 Sep 13;5(9):e12702. PMID: 20856931,

PMCID: PMC2938338

111. Ye F, Guo Y, Lawson A, and Tang J, "Improving tree search in phylogenetic reconstruction from

genome rearrangement data". JEA 4525/2007:352-364, 2007