Quantitative & Computational Biology

BIOL 5005.007 MATH 6710.001 CSCE 5933.002

A course on biological sequences & their analysis

Instructor: Rajeev Azad (Rajeev.Azad@unt.edu)

Tuesday & Thursday 11:00 AM – 12:20 PM at GAB 461

Office hours: 12:30 – 2:00 PM Tuesday & Thursday (GAB 434) or by appointment

Students taking this course

Math Biology Joseph Michael Czop Swapan Bhuiyan Viktoriya Golubenko Mehul Jani Marco Antonio Lopez Khem Lal Kadel Elizabeth Rasmussen Huaiying Lin Charles Immanual Rinerson Deena Lynn Rinerson Garima Girish Saxena

CSE Danyang Shao Prudhvi Venkata Lei Wang Sai Velupucharla Abdelrahman Obaid

Course objectives

• To help you understand interdisciplinary approaches to solving problems in biology

• To help you understand the essence of computational and mathematical methods in biology and medicine

• To familiarize you with principles and models underlying standard bioinformatics methods/algorithms

• To help you get practical experience of using bioinformatics tools for sequence analysis

Recommended Textbooks

• Bioinformatics and Functional Genomics Author: Jonathan Pevsner Publisher: Wiley-Blackwell • Biological Sequence Analysis: Probabilistic Models of Proteins and

Nucleic Acids Authors: Richard Durbin, Sean Eddy, Anders Krogh, Graeme Mitchison Publisher: Cambridge University Press • Statistical Methods in Bioinformatics Authors: Warren Ewens, Gregory Grant Publisher: Springer

Grading

25% class participation (15% attendance, 10% discussions) 10% in-class presentation 35% homework assignments 30% final project (25% work + written report +peer review, 5% presentation)

Bioinformatics: An interdisciplinary field for biological sequence analysis

• Bioinformatics is the interdisciplinary field of science which combines Biology, Computer Science, Mathematics, and other quantitative sciences to study biological sequences or data.

• The ultimate goal of the field is to enable the discovery of new biological insights as well as to create a global perspective from which unifying principles in biology can be discerned. (Source: NCBI)

Rui Kuang, UNM

Rui Kuang, UNM

Rui Kuang, UNM

Three perspectives on Bioinformatics

The Cell The Organism

The Tree of Life

J. Pevesner, www.bioinfbook.org

First perspective: the cell

www.bioinfbook.org

DNA RNA phenotype protein

www.bioinfbook.org

DNA molecule

DNA RNA protein

Central dogma of molecular biology

genome transcriptome proteome

Central dogma of bioinformatics and genomics www.bioinfbook.org

DNA RNA

cDNA ESTs UniGene

phenotype

genomic DNA databases

protein sequence databases

protein

www.bioinfbook.org

Omes and Omics • Genomics

– Primarily sequences (DNAs) – Databanks and search algorithms – Supports studies of molecular evolution (“Tree wars”)

• Functional Genomics (Transcriptomics) – Microarray data – Databanks, analysis tools, controlled terminologies

• Proteomics – Sequences (Protein) and structures – Mass spectrometry, X-ray crystallography – Databanks, knowledge bases, visualization

• Systems Biology (metabolomics) – Metabolites and interacting systems (interactomics) – Graphs, visualization, modeling, networks of entities

Joyce Mitchell, http://uuhsc.utah.edu/medinfo

http://genomesonline.org/

The Human Genome Project

3 billion bases 30,000 genes http://www.genome.gov/

Brian Rybarczyk, UNC

Rui Kuang, UNM

Rui Kuang, UNM

From genes to proteins

Vaisman, I., Bioinformatics tutorials

Intro to Bioinformatics – Sequence Alignment birg.cs.wright.edu/text/Ch2.ppt

Proteins are amino acid polymers

The genetic code

©Copyright 2009, Nature Education http://www.nature.com/scitable/content/the-genetic-code-6903567

Time of development

Body region, physiology, pharmacology, pathology

Second perspective: the organism

www.bioinfbook.org

After Pace NR (1997) Science 276:734

Third perspective: the tree of life

www.bioinfbook.org