Bioinformatics Reading Group

Our goal is to read and discuss about computational methods for analyzing biological systems. Our interests include but not limited to genomics and proteomics based approaches for studying RNAi, regulatory genomics and systems biology. This is an interdiscplinary group and we encourage people from diverse backgrounds (Biology, Computer Science, Math, Physics, Chemistry) to attend. If you are interested in knowing about the activities of the group please subscribe to our mailing list.

Meeting time and place

The meeting time for the Fall 2008 semester is 3:30-4:30 pm every other Tuesday. We meet in the Farris Engineering center in conference room near Rooms 323-326.


Sep 16
D. S. Lee, J. Park, K. A. Kay, N. A. Christakis, Z. N. Oltvai, and A. L. Barabási. The implications of human metabolic network topology for disease comorbidity PNAS. 2008.

Papers read in Summer 2008

Aug 5
Karthik Devarajan. Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology PLOS Computational Biology. 2008.
July 22
Ivan G. Costa, Stefan Roepcke, Christoph Hafemeister, and Alexander Schliep. Inferring differentiation pathways from gene expression ISMB. 2008.
June 10
Lukas Burger and Erik van Nimwegen. Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method Molecular systems biology. 2008.
May 27
Domitilla Del Vecchio, Alexander J Ninfa and Eduardo D Sontag Modular cell biology: retroactivity and insulation. Molecular systems biology. 2008.

Papers read in Spring 2008

May 6
Grigory Kolesov, Zeba Wunderlich, Olga N. Laikova, Mikhail S. Gelfand, and Leonid A. Mirny. How gene order is influenced by the biophysics of transcription regulation. PNAS. 2007.
Apr 22
I. Nachman, A. Regev and N. Friedman. Inferring quantitative models of regulatory networks from expression data Bioinformatics. 2004.
Mar 25
Xiaoyu Chen and Mathieu Blanchette Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees NIPS workshop on New Problems and Methods in Computational Biology. 2006.
Mar 11
Eran Segal and Tali Raveh-Sadka and Mark Schroeder and Ulrich Unnerstall and Ulrike Gaul Predicting expression patterns from regulatory sequence in Drosophila segmentation Nature. 2008.
Feb 26
Gangman Yi, Sing-Hoi Sze and Michael R. Thon Identifying clusters of functionally related genes in genomes Bioinformatics. 2007.
Feb 12
Eran Segal, Michael Shapira, Aviv Regev, Dana Pe'er, David Botstein, Daphne Koller and Nir Friedman. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data Nature Genetics. 2003.
Jan 29
Robert Clarke, Habtom W. Ressom, Antai Wang, Jianhua Xuan, Minetta C. Liu, Edmund A. Gehan and Yue Wang. The properties of high-dimensional data spaces: implications for exploring gene and protein expression data. Nature Reviews Cancer. 2008.

Papers read in Fall 2007

Dec 7
Yuan Yuan, Lei Guo, Lei Shen, Jun S. Liu Predicting Gene Expression from Sequence: A Reexamination. PLOS Computational Biology. 2007.
Nov 9
A. D Aragon, G. A Quinones, E. V. Thomas, S. Roy and M. Werner-Washburne Release of extraction-resistant mRNA in stationary phase Saccharomyces cerevisiae produces a massive increase in transcript abundance in response to stress. Genome Biology. 2006.
Oct 26
Regina Brockmann, Andreas Beyer, Juergen J. Heinisch, Thomas Wilhelm Posttranscriptional Expression Regulation: What Determines Translation Rates? PLOS Computational Biology. 2007;3(3).
Sep 28
Lawrence S Hon and Zemin Zhang The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression Genome Biology. 2007;8(8).
Sep 14
Roded Sharan, Igor Ulitsky and Ron Shamir Network-based prediction of protein function Molecular Systems Biology. 2007.
Aug 31
Cecile Caretta-Cartozo, Paolo De Los Rios, Francesco Piazza, Pietro Lio Bottleneck Genes and Community Structure in the Cell Cycle Network of S. pombe PLOS CompBio. 2007.

Papers read in Spring 2007

Apr 19
Joshua A. Grochow and Manolis Kellis Network Motif Discovery Using Subgraph Enumeration and Symmetry-Breaking RECOMB. 2007.
Mar 6
Stefano Ciliberti, Olivier C. Martin and Andreas Wagner. Robustness can gradually evolve in complex regulatory gene networks with varying topology PLOS Computational Biology. 2007;3(2)
Feb 22
Chen-Hsiang Yeang and Martin Vingron. A joint model of regulatory and metabolic networks BMC Bioinformatics. 2006;7(332)
Feb 8
Chen-Hsiang Yeang and Martin Vingron. A joint model of regulatory and metabolic networks BMC Bioinformatics. 2006;7(332)
Jan 25
Philip M. Kim, Long J. Lu, Yu Xia and Mark B. Gerstein. Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights Science. 2006;314(5807)

Papers read in Fall 2006

Aug 28
Yuan Qi, Alex Rolfe, Kenzie D MacIsaac, Georg K Gerber, Dmitry Pokholok, Julia Zeitlinger, Timothy Danford, Robin D Dowell, Ernest Fraenkel, Tommi S Jaakkola, Richard A Young, and David K Gifford. High-resolution computational models of genome binding events. Nature Biotech. 2006;24(8), 1938-1941
Sep 11
Jose C. Nacher, Jean-Marc Schwartz, Minoru Kanehisa and Tatsuya Akutsu. Identification of metabolic units induced by environmental signals. In proceedings of Fourteeth Annual International Conference on Intelligents Systems for Molecular Biology (2006).
Sep 25
Chang S. Chan, Olivier Elemento, Saeed Tavazoie. Revealing Posttranscriptional Regulatory Elements Through Network-Level Conservation. PLOS Computational Biology. 2006;1(7).
Oct 9
Jana Hertel and Peter F. Stadler. Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. In proceedings of Fourteeth Annual International Conference on Intelligents Systems for Molecular Biology (2006).
Oct 23
Zhidong Tu , Li Wang , Michelle N. Arbeitman , Ting Chen and Fengzhu Sun. An integrative approach for causal gene identification and gene regulatory pathway inference. In proceedings of Fourteeth Annual International Conference on Intelligents Systems for Molecular Biology (2006).
Nov 6
Karsten M. Borgwardt, Arthur Gretton, Malte J. Rasch, Hans-Peter Kriegel, Bernhard Scholkopf and Alex J. Smola. Integrating structured biological data by Kernel Maximum Mean Discrepancy. In proceedings of Fourteeth Annual International Conference on Intelligents Systems for Molecular Biology (2006).
Nov 20
Amos Tanay and Ron Shamir. Modeling transcription programs: inferring binding site activity and dose-response model optimization. In proceedings of Seventh Annual International Conference on Research in computational molecular biology (2003).
Dec 4
Michael A. Beer and Saeed Tavazoie. Predicting Gene Expression from Sequence. Cell. 2004. 16;117(2): 185-98.

Papers read in Summer 2006

May 22
Dennis Vitkup, Peter Kharchenko, and Andreas Wagner. Influence of metabolic network structure and function on enzyme evolution. Genome Biology. 2006;7(5)
Jun 5
Theodore J. Perkins, Johannes Jaeger, John Reinitz and Leon Glass. Reverse Engineering the Gap Gene Network of Drosophila melanogaster. PLOS Computational Biology. 2006; 2(5) e51.
Jun 12
Chen-Hsiang Yeang and Tommi Jaakkola. Modeling the combinatorial functions of multiple transcription factors. RECOMB (2005).
Jun 19
Reinhard Hoffmann, Ludovica Bruno, Thomas Seidl, Antonius Rolink, and Fritz Melchers. Rules for Gene Usage Inferred from a Comparison of Large-Scale Gene Expression Profiles of T and B Lymphocyte Development. The Journal of Immunology. 2003; 170: 1339-1353.
July 17
Diana Ekman, Sara Light, Asa K Bjorklund and Arne Elofsson. What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?. Genome Biology. 2006; 7:R45

Papers read in Spring 06

Jan 30
Hidde de Jong. Modeling and Simulation of Genetic Regulatory Systems: A Literature Review. J Comput Biol. 2002;9(1):67-103
Feb 20
Adam M Feist, Johannes CM Scholten, Bernhard Palsson, Fred J Brockman and Trey Ideker. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri . Molecular Systems Biology. 2006;2(1): msb4100046-E1-E14
Feb 27
Natalie C. Duarte, Markus J. Herrgard and Bernhard Palsson. Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model . Genome Research. 2004;14: 1298-1309
Mar 6
Christopher H. Schilling, Stefan Schuster, Bernhard O. Palsson, and Reinhart Heinrich. Metabolic Pathway Analysis: Basic Concepts and Scientific Applications in the Post-genomic Era. Biotechnol. Prog. 1999;15: 296-303
Mar 20
Jan Ihmels, Ronen Levy and Naama Barkai. Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nature Biotechnology 22,86-92 (2003)
Sven Bergmann, Jan Ihmels and Naama Barkai. The Iterative Signature Algorithm for the analysis of large scale gene expression data. Physical Review E 67 (2003)
Apr 10
Roded Sharan and Trey Ideker. Modeling cellular machinery through biological network comparison. Nature Biotechnology 24,427-433 (2006)
Apr 17
Balaji S Srinivasan, Nora B Caberoy, Garret Suen, Rion G Taylor, Radhika Shah, Farah Tengra, Barry S Goldman, Anthony G Garza and Roy D Welch. Functional genome annotation through phylogenomic mapping. Nature Biotechnology 23,691-698 (2005)
Apr 24
Balaji S. Srinivasan, Antal F. Novak, Jason A. Flannick, Serafim Batzoglou and Harley H. McAdams Integrated Protein Interaction Networks for 11 Microbes. RECOMB (2006)
May 1
Kai Wang, Ilya Nemenman, Nilanjana Banerjee, Adam A. Margolin and Andrea Califano Genome-wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocyte. RECOMB (2006)

Send questions or comments to Sushmita Roy