The format of the course will be different from previous semesters. We will mimic the review system used to evaluate grant applications at NIH. I think this will be useful when some of you will be applying for grants in the future.

Briefly, the audience (You) will be the equivalent of a Review Panel. There will be the Primary Reviewer who will pick, present the paper, and evaluate the paper for its significance to biomedical research, the quality of the approach, and innovation. There will be a secondary reviewer who will write a short report on the same aspects. There will also be a Reader who will read the paper to specifically evaluate any major flaw in the paper but will not write any report.

At the end of the presentation by Reviewer 1 (25-35 min), Reviewer 2 will verbally summarize in 10-15 minutes (no power point) his evaluation about the paper. The reader will also summarize any concern (if any) regarding the paper (5 mins). The Panel members will discuss the paper further as needed and evaluate the paper on a scoring system of 100 to 300 (100 being the best score and 300 being the worst). The evaluations of each paper will be kept on a record for fun. Note that the final evaluation score of a paper has no impact on your grade.

The following are the topics that we will cover during your presentations. To get things off the ground, I will assign Ahmet Bakan to present the first paper on Multidimensional Drug Profiling By Automated Microscopy. Science. 2004 on 1/29/07. The secondary reviewer for this round will be Luis Pedro Coelho and the reader will be Chuang Wu. More details to follow regarding how papers will be picked. But feel free to discuss with me about papers related to computational biology in any of the topics below.

Topic Candidate Paper
Chemical Genomics Multidimensional Drug Profiling By Automated Microscopy. Science. 2004

Embryonic stem cells One possibility is a review on embryonic stem cells and your thoughts on how computational biology may be used to advance the field. Can be done as a team of two or three students. The advantage is that each person will only have to prepare for 15 or 25 minutes of presentation depending on the number of presenters!

Genomics for drug-discovery The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease, Science. 2006
Nano biotechnology Folding DNA to create nanoscale shapes and patterns, Nature. 2006
Non-protein-coding RNAs Control of gene expression by a natural metabolite-responsive ribozyme. Nature. 2004
Posttranscriptional regulation Natural selection on human microRNA binding sites inferred from SNP data. Nat Genet. Epub 2006
Primate evolution An RNA gene expressed during cortical development evolved rapidly in humans., Nature. 2006
Systems biology A Systems Approach to Mapping DNA Damage Response Pathways. Science. 2006
Transcriptional regulation Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nature Biotechnology. 2006

Date Primary Reviewer (Speaker) Secondary Reviewer Reader
1/29/07 Ahmet Bakan Luis Pedro Coelho Chuang Wu

2/5/07 Rachel Brower Suvrajit Maji Kui Shen

2/12/07 Taraz Buck Kui Shen Aabid Shariff

2/19/07 Luis Pedro Coelho Justin Hogg Arvind Ramanathan

2/26/07 Justin Hogg Jacob Joseph Lidio Meireles

3/5/07 Judie Howrylak Jacob Joseph Suvrajit Maji

A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules, Science 2003

3/12/07 Jacob Joseph Chuang Wu Ying Liu

An RNA Gene Expressed During Cortical Development Evolved Rapidly in Humans, Nature 2006

3/19/07 Byoungkoo Lee Ying Liu Jacob Joseph

A Systems Approach to Mapping DNA Damage Response Pathways

3/26/07 Ying Liu Judie Howrylak Luis Pedro Coelho

4/2/07 Suvrajit Maji Rachel Brower Byoungkoo Lee

4/9/07 Lidio Meireles Aabid Shariff Justin Hogg

Natural Selection on Human microRNA Binding Sites Inferred From SNP Data. Nat Genet. Epub 2006

4/16/07 Arvind Ramanathan Ahmet Bakan Judie Howrylak

4/23/07 Aabid Shariff Taraz Buck Ahmet Bakan

4/30/07 Kui Shen Arvind Ramanathan Rachel Brower

5/7/07 Chuang Wu Lidio Meireles Taraz Buck

Note: The weeks in italics, 4/23 - 5/7, are hypothetical. I expect that some of you will form teams to present your views on embryonic stem cell research and computational problems not addressed in this field.

Fall 2006 organized by William Cohen

Announcements

oGNM: Online Computation of Structural Dynamics Using the Gaussian Network Model - Lidio Meireles

Multiple Knockout Analysis of Genetic Robustness in the Yeast Metabolic Network - Byoungkoo Lee

Computational Redesign of Endonuclease DNA Binding and Cleavage Specificity - Ahmet Bakan

Bayesian Segmentation of Protein Secondary Structure - Ying Liu

Protein Flexibility Using Constraints from Molecular Dynamics Simulations - Arvind Ramanathan

Modeling Inflammation and Wound Healing: Translational Insights into Diabetic Foot Ulcer Pathology - Yoram Vodovotz

Convergence of the Proteomic Pattern in Cancer - Taraz Buck

A Mathematical Analysis of the Dynamics of Prion Proliferation - Justin Hogg

A Genomic Strategy to Refine Prognosis in Early-Stage Non-Small-Cell Lung Cancer - Judie Howrylak

Using RNA Secondary Structure to Guide Sequence Motif Finding Toward Single-Stranded Regions - Rachel Brower-Sinning

Long-Range Periodic Patterns in Microbial Genomes Indicate Significant Multi-Scale Chromosomal Organization - Suvrajit Maji

Stochastic Effects of Multiple Regulators on Expression Profiles in Eukaryotes - Kui Shen

Cooperativity Between Cell Contractility and Adhesion - Aabid Shariff

The Yeast Gene Order Browser: Combining Curated Homology and Syntenic Context Reveals Gene Fate in Polyploid Species - Jacob Joseph

Genomic Analysis of the Hierarchical Structure of Regulatory Networks - Chuang Wu

Dynamic Proteomics: Cell Cycle Dependence of Nuclear Proteins - Luis Pedro Coelho

Joint CMU-Pitt Ph.D. Program in Computational Biology

Robert F. Murphy and Ivet Bahar, Directors

Current Topics in Computational Biology (Journal Club)

Mondays from 12:30 pm to 1:30 pm at BST3

CMU course number 02-701 Pitt course number MSCBIO/CMPBIO 2060

Organizers: William Cohen and Bino John Spring 2007 organized by Bino John

Fall 2006 organized by William Cohen

Current Topics in Computational Biology
(Journal Club)

CMU course number 02-701
Pitt course number MSCBIO/CMPBIO 2060

Organizers: William Cohen and Bino John
Spring 2007 organized by Bino John