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
Joseph Michael Czop Viktoriya Golubenko Marco Antonio Lopez Elizabeth Rasmussen

Biology
Swapan Bhuiyan Mehul Jani Khem Lal Kadel Huaiying Lin Charles Immanual Rinerson Deena Lynn Rinerson Garima Girish Saxena Danyang Shao Lei Wang Abdelrahman Obaid

CSE
Prudhvi Venkata Sai Velupucharla

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% 10% 35% 30% class participation (15% attendance, 10% discussions) in-class presentation homework assignments 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

protein

phenotype

www.bioinfbook.org

DNA molecule

Central dogma of molecular biology

DNA

RNA

protein

genome

transcriptome

proteome
www.bioinfbook.org

Central dogma of bioinformatics and genomics

DNA

RNA

protein

phenotype

genomic DNA databases

cDNA ESTs UniGene

protein sequence databases

www.bioinfbook.org

Omes and Omics

Genomics
Primarily sequences (DNAs) Databanks and search algorithms Supports studies of molecular evolution (Tree wars) Microarray data Databanks, analysis tools, controlled terminologies

Functional Genomics (Transcriptomics)

Proteomics

Sequences (Protein) and structures Mass spectrometry, X-ray crystallography Databanks, knowledge bases, visualization Metabolites and interacting systems (interactomics) Graphs, visualization, modeling, networks of entities
Joyce Mitchell, http://uuhsc.utah.edu/medinfo

Systems Biology (metabolomics)

http://genomesonline.org/

The Human Genome Project

3 billion bases
Brian Rybarczyk, UNC

30,000 genes

http://www.genome.gov/

Rui Kuang, UNM

Rui Kuang, UNM

From genes to proteins

Vaisman, I., Bioinformatics tutorials

Proteins are amino acid polymers

Intro to Bioinformatics Sequence Alignment

birg.cs.wright.edu/text/Ch2.ppt

The genetic code

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

Second perspective: the organism

Time of development

Body region, physiology, pharmacology, pathology

www.bioinfbook.org

Third perspective: the tree of life

After Pace NR (1997) Science 276:734 www.bioinfbook.org