SYLLABUS August 06, 2011 STAT 442/842 cross-listed as BIOC 442/842: Computational Biology Please note the NEW

OPTIONAL textbook as of July 15, 2010! Instructor: Steve (Istvan) Ladunga, Ph.D., Professor of Computational Biology, Department of Statistics, E145 Beadle Center, Phone: (402) 472-6074, [email protected] Credit hours: 3. 1 hour 15 minutes lecture, 2 hour 50 minutes computer laboratory. Term Offered: Every Fall Semester. Rooms: Lectures: Tuesdays, 2:00-3:15, Room N176, Beadle Center Computer Lab: Thursdays, 3:00-5:50 pm, Rm. 14, College Business Admin. Course Prerequisites: Any introductory course in biology or statistics: BIOS 101 General Biology OR BIOS 103 Organismic Biology OR BIOS 206 General Genetics OR BIOC 321 Elements of Biochemistry OR STAT 218 Introduction to Statistics OR BIOC 432/832 Gene Expression and Replication OR BIOS 477/877 Bioinformatics and Molecular Evolution The scope of the course: computational molecular biology helps us to do biology on computers. In ten years, this term will make no sense, since almost all biology will be both computational and experimental. Learning objectives that are measurable during tests, presentations and computer labs:

Understand the new paradigms of the new, high-throughput (and high-noise) biology Perform (semi)automatic parsing of the literature over millions of publications. Present your results in probabilistic terms using statistical significance Perform searches over enormous databases, interpret their results Perform genomic comparisons, display genes and large genomic regions in Genome Browser Identify differentially regulated genes in disease or stress conditions, as indicated by gene expression experiments. Analyze gene expression using data from microarrays or RNA sequencing.

Be able to apply Gene Ontology, pathways, gene set enrichment analysis

Analyze metabolomic, proteomic and protein-protein interaction experiments

Other objectives:

Understand and analyze sequence polymorphisms and linkage disequilibria. Understand principles of complex networks of transcriptional regulation and protein-protein interactions. Know how to integrate the results of your experiments into the vast knowledge available in biological databases Understand the trends in personalized medicine Understand and get practice in proteomics analyses

Who would benefit from taking this course? This course is designed primarily for biology, agronomy and statistics students. However, computer science, mathematics, physics and chemistry majors also may find it beneficial. This course benefits computational and experimental biologists as well as biostatisticians helping them to understand the principles of analyzing biological data, building models and testing hypotheses using computer science paradigms. This Course does not depend on any graduate course. Necessary background

Basic knowledge of molecular biology is necessary but statisticians, computer scientists and mathematicians are exempted from that. Students should be able to navigate the Internet, use Microsoft Office including Word, Powerpoint and Excel. No programming or database skills are required.

Lecture Topics/Course Outline and Assessment Plan: I believe that one of the most critical but somewhat overlooked skill is reading, understanding and presenting scientific publications that are reasonably challenging and matching to the students background (e.g., biology, statistics, or computer science). Each student will be assigned a journal article to present during the computer labs using PowerPoint. Your final grade will be based on the following scale: Minimum Percent Score 97 93 90 87 83 Grade A+ A AB+ B

80 77 73 70 0

BC+ C CF

35 percent based on the final project 25 percent based on the publication presentations 25 percent based on test assignments 15 percent based on class participation

Methods: lecture (75 minutes) and computer laboratory (170 minutes). Lectures will be delivered at N176 Beadle Center, laboratory work will be performed either at Rm. 14 of the College of Business Administration or at the Department of Statistics Computer Laboratory (Hardin Hall). Project and publication presentation will rely on the servers of the Bioinformatics Core Research Facility. References/Textbooks Most of the Course will be taught on the basis of recent scientific reviews. The new textbook is optional. Please note that this textbook covers only classic bioinformatics (sequence analysis).

Marketa Zvelebil and Jeremy O. Baum: Understanding Bioinformatics. Garland Scientific, August 2007, 800 pages: 650 fullcolor illustrations, Paperback: 978-0-8153-4024-9
We will also use selected lectures from Public Library of Science (PLoS) Computational Biology educational websites (you can reach them from: http://www.ploscollections.org) and chapters from the series: Current Protocols in Bioinformatics (Wiley Interscience). This series provides both theoretical foundations and practical instructions to the most important bioinformatics algorithms and tools. Schedule of classes

1) Aug. 23. Beyond Google, the computational revolution and high-throughput

2) Aug. 30. How to begin a research project? Computational discoveries in the ocean
of the literature. Semi-automated literature parsing.

3) Sep. 6. Sequence alignments, pairwise and multiple, and their visualization. 4) Sep. 13. Searching sequence databases, the Basic Local Alignment Search Tool,
BLAST.

5) Sep. 20. Sequence polymorphisms, variations among human genomes, medical

6) Sep. 27. The domain architecture of proteins. Hidden Markov models and the
PFAM Database. Characterizing proteins.

7) Oct. 4. Analysis of gene expression, Part I. 8) Oct. 11. Analysis of gene expression, Part II.
9) Oct. 18. Fall Break.

10) Oct. 25. RNA sequencing 11) Nov. 1. Gene Ontology, metabolic pathways, and gene set enrichment analysis. 12) Nov. 8. Gene regulation. 13) Nov. 15. Metabolomics. 14) Nov. 22). Proteomics. 15) Nov. 29. Protein-protein interactions. 16) Dec. 6. Systems biology. 17) Dec. 13. Student project presentations.
Students with disabilities are encouraged to contact the instructor for a confidential discussion of their individual needs for academic accommodation. It is the policy of the University of Nebraska--Lincoln to provide flexible and individualized accommodation to students with documented disabilities that may affect their ability to fully participate in course activities or to meet course requirements. To receive accommodation services, students must be registered with the Services for Students with Disabilities (SSD) office, 132 Canfield Administration, 472-3787 voice or TTY.