Computational Biology Journal Club


Computational and systems biology research explores biology from an analytical and theoretical perspective, applying many computational and engineering tools to understand, predict, solve, and interpret biological systems at the molecular, cellular, and systems levels.

This journal club meets regularly to read and discuss current research in computational and systems biology. Topics may include, but are not limited to, automation of protein structure determination, computational docking of protein-protein complexes, analysis of functional genomics data (e.g. from micro-arrays and mass spectrometry), modeling of gene regulatory networks, cellular signaling pathways, cell adhesion and receptor models.

Anyone with an interest in these areas is encouraged to join; there is no particular background required. The meetings are intended to be informal, participatory, and broadly accessible.

For more information or to subscribe to the mailing list, contact Ann Rundell or Chris Bailey-Kellogg.

Time & Place Spring 2004 meetings will be in CS 111. We will meet every other Thursday at 9:30 for an hour.
Schedule & Readings Spring 2004:
Jan. 22ChrisA. Califano, "SPLASH: structural pattern localization analysis by sequential histograms", Bioinformatics, 16(4):341-57, 2000 (paper)
Feb. 5AnnB.N. Kholodeno, A. Kiyatkin, F.J. Bruggeman, E. Sontag, H.V. Westerhoff, and J.B. Hoek, "Untangling the wires: A strategy to trace functional interactions in signaling and gene networks", PNAS 99(20);12841-6, 2002 (paper)
Feb. 19XiaoduanI.N. Berezovsky and E.N. Trifonov, "Van der Waals locks: loop-n-lock structure of globular proteins", J Mol Biol, 307:1419-26, 2001 (paper)
Mar. 4JunJ.W. Pitera and W. Swope, "Understanding folding and design: Replica-exchange simulations of Trp-cage miniproteins", PNAS, 100(13):7587-7592, 2004 (paper)
Details of algorithm: U.H.E. Hansmann, "Parallel tempering algorithm for conformational studies of biological molecules" (paper)
Mar. 25CurtE. Segal, M. Shapira, A. Regev, D. Pe'er, D. Botstein, D. Koller, and N. Friedman, "Module Networks: Identifying Regulatory Modules and their Condition Specific Regulators from Gene Expression Data", Nature Genetics, 34(2):166-76, 2003 (paper)
Apr. 8Greg J. Fox, M. Riccio, F. Hua, E. Bodenschatz, R. Gilmour, "Spatiotemporal Transition to Conduction Block in Canine Ventricle," Circ Res, 90:289-296, 2002 (paper)
Apr. 22Daisuke M.E. Ochagavia and S. Wodak, "Progressive combinatorial algorithm for multiple structural alignments: application to distantly related proteins", Proteins, 55(2):436-54, 2004 (paper)
Fall 2003:
Sept. 4J. Club canceled so we can attend the seminar by Manoj Samanta, NASA Ames, on "Networking in a Biological Cell", at 10:30 in the Fu Room (POTR 234).
Sept. 18Ann W.S. Hlavacek, A. Redondo, C. Wofsy and B. Goldstein, "Kinetic Proofreading in Receptor-Mediated Transduction of Cellular Signals: Receptor Aggregation, Partially Activated Receptors, and Cytosolic Messengers", Bulletin of Mathematical Biology, 64(5):829-1031, 2002.
Oct. 2Xiaoduan C.A. Voigt, C. Martinez, Z.G. Wang, S.L. Mayo, and F.H. Arnold, "Protein building blocks preserved by recombination", Nat Struct Biol, 9(7):553-8, 2002. (paper)
M.M. Meyer, J.J. Silberg, C.A. Voigt, J.B. Endelman, S.L. Mayo, Z.G. Wang, and F.H. Arnold, "Library analysis of SCHEMA-guided protein recombination", Prot Sci, 12(8):1686-93, 2003. (paper)
Oct. 16Shobha S.W. Lockless and R. Ranganathan, "Evolutionarily conserved pathways of energetic connectivity in protein families", Science, 286(5438):295-9, 1999 (paper)
G.M. Suel, S.W. Lockless, M.A. Wall, R. Ranganathan, "Evolutionarily conserved networks of residues mediate allosteric communication in proteins", Nat Struct Biol, 10(1):59-69, 2003 (paper)
Oct. 30Curt R. Elkon, C. Linhart, R. Sharan, R. Shamir, and Y. Shiloh, "Genome-wide In-silico Determination of Transcriptional Regulation Modules Controlling Cell Cycle in Human Cells", Genome Research, 13:773-780, 2003 (paper)
R. Sharan, I. Ovcharenko, A. Ben-Hur, and R.M. Karp, "CREME: A Framework for Identifying Cis-Regulatory Modules in Human-Mouse", Proc. ISMB, pp. 283-291, 2003 (paper)
E. Segal and R. Sharan, "A Discriminative Model for Identifying Spatial Cis-Regulatory Modules" TR-03-004, International Computer Science Institute, Berkeley, 2003 (paper)
Nov. 13Jiangtian E. Segal, R. Yelensky, and D. Koller, "Genome-wide Discovery of Transcriptional Modules from DNA Sequence and Gene Expression", Bioinformatics, 19(Suppl 1):i273-i282, 2003 (paper)
E. Segal, H. Wang, and D. Koller, "Discovering Molecular Pathways from Protein Interaction and Gene Expression Data", Bioinformatics, 19(Suppl 1):i264-i272, 2003 (paper)
Dec. 11Tim W. Zheng and S. Doniach, "Protein structure prediction constrained by solution X-ray scattering data and structural homology identification", J. Mol. Biol., 316:173-187, 2002 (paper)
Summer 2003:
June 5AnnJ. Faeder et al, "Investigation of Early Events in FceRI-Mediated Signaling Using a Detailed Mathematical Model", Journal of Immunology, 170:3769-3781, 2003.
Abstract. Preprint available at Faeder's home page.
June 19ChrisR. Chen and Z. Weng, "A novel shape complementarity scoring function for protein-protein docking", Proteins, 51(3):397-408, 2003.
Abstract. Paper.
July 3OlgaS. Schmidler, J. Liu, and D. Brutlag, "Bayesian protein structure prediction", Case Studies in Bayesian Statistics, Vol. 5, pp.363-378, 2001.
July 17JunS. Jones and J. M. Thornton, "Analysis of Protein-Protein Interaction Sites using Surface Patches", J. Mol. Biol., 272:121-132, 1997.
July 31TimD. I. Svergun, M. V. Petoukhov, and M. H. J. Koch, "Determination of Domain Structure of Proteins from X-ray Solution Scattering", Biophys. J., 80:2946-2953, 2001.
Aug. 14CurtM. L. Bulyk, P. L. F. Johnson, and G. M. Church, "Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors", Nucleic Acids Res., 30:1255-61, 2002 (paper).
E. Roulet, P. Bucher, R. Schneider, E. Wingender, Y. Dusserre, T. Werner, and N. Mermod, "Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites", J Mol Biol, 297:833-48, 2000 (paper).
Spring 2003:
Jan. 23ChrisL. Lu, H. Lu, and J. Skolnick, "MULTIPROSPECTOR: An Algorithm for the Prediction of Protein-Protein Interactions by Multimeric Threading", Proteins, 49:350-364, 2002.
Feb. 6OlgaK. Yeung, C. Fraley, A. Murua, A. Raftery, W. Ruzzo, "Model-Based Clustering and Data Transformations for Gene Expression Data", Bioinformatics, 17:977-987, 2001.
Feb. 20AnnY. Hori, S. Raychaudhuri, and A. Charkraborty, "Analysis of pattern formation and phase separation in the immunological synapse", Journal of Chemical Physics, 117(20):9491-9501, 2002.
Mar. 6ShobhaC.W. Carter, B.C. LeFebvre, S.A. Cammer, A. Tropsha, and M.H. Edgell, "Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations", J. Mol. Biol., 311(4):625-638, 2001.
Mar. 27YananFriedman et al., "Using Bayesian Networks to Analyze Expression Data", J. Comp. Biol. 7:601-620, 2000.
Apr. 10ChongStorch et al., "Extensive and divergent circadian gene expression in liver and heart", Nature, 417:78-83, 2002.
Apr. 24Curt L. Elnitski, et al., "Distinguishing Regulatory DNA From Neutral Sites", Genome Res., 12:64-72, 2003 (paper).
W. Wasserman, et al., "Human-mouse genome comparisons to locate regulatory sites", Nature Genetics, 26: 225-228, 2000 (paper).
E. Cheremushkin and A. Kel, "Whole genome human/mouse phylogenetic footprinting of potential transcription regulatory signals", PSB, 8: 291-307, 2003 (paper).
Fall 2002:
Aug. 29AnnR. Heinrich, B. Neel, and T. Rapoport, "Mathematical Models of Protein Kinase Signal Transduction", Molecular Cell, Vol 9, 957-970, May 2002.
Sep. 12ChrisJ. Liang, H. Edelsbrunner, P. Fu, V. Sudhakar, and S. Subramanian, "Analytical shape computation of macromolecules", Proteins, 33(1):1-17, 18-29, Oct. 1998.
PubMed abstracts and pointers to papers: Part I; Part II
Sep. 26Shobha W. Wriggers and P. Chacon, "Modeling Tricks and Fitting Techniques for Multi-Resolution Structures", Structure, 9:779-788, 2001.
Oct. 10Santhoji J. Shrager, P. Langley, and A. Pohorille, "Guiding revision of regulatory models with expression data", Proceedings of the Pacific Symposium on Biocomputing, pp. 486-497, 2002.
Oct. 24RaguA. Becskel and L. Serrano, "Engineering stability in gene networks by autoregulation", Nature, 405:590-593, 2000.
Abstract, html, pdf at Nature.
Nov. 7YananH. Cateau and S. Tanaka, "Kinetic analysis of multisite phosphorylation using analytic solutions to michaelis-menten equations", J. Theoretical Biology, 217:1-14, 2002.
Nov. 21OlgaB. Simon, M. Sattler, "De novo structure determination from residual dipolar coupling by NMR spectrocopy", Angewandte Chemie, Int. Ed., 2002.
Dec. 5CurtM. C. Frith, U. Hansen, and Z. Weng, "Detection of cis-element clusters in higher eukaryotic DNA", Bioinformatics 17:878-889, 2001.
Summer 2002:
May 29ChrisA.H. Tong et al., "A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules", Science, 295:321-324, 2002.
June 5YananSimulation of T-cell MAPK Signaling Pathway
June 19AnnGordon Conference highlights
July 10RachelCanceled
July 24Santhoji &
T. Ideker et al., "Integrated genomic and proteomic analyses of a systematically perturbed metabolic network," Science, 292:929-934, 2001.
Spring 2002:
Jan. 10AnnJohn Tyson and Bela Novak, "Regulation of the Eukaryotic Cell Cycle: Molecular Antagonism, Hysteresis, and Irreversible Transitions", Journal of Theoretical Biology, 210, 249-263, 2001.
Jan. 24ChrisC.J. Langmead, A.K. Yan, C.R. McClung, and B.R. Donald, "Phase-Independent Rhythmic Analysis of Genome-Wide Expression Patterns", The Sixth Annual International Conference on Computational Molecular Biology (RECOMB), to appear, 2002.
Abstract; PDF.
Feb. 7PeterJohn Board and Klaus Schulten, "The fast multipole algorithm", Computing in Science and Engineering, 4(1):76-79, Jan/Feb 2000.
L. Greengard and V. Rokhlin, "A fast algorithm for particle simulations", J. Computational Physics, 73:325-348, 1987.
Feb. 21PrasanaS. Eddy, "Profile hidden Markov models", Bioinformatics, 14(9):755-763, 1998.
Mar. 7YananKim et al., "Modeling of Early Events in T cell signal transduction after controlled T cell activation by peptide major histocompatibility complex", Annals of Biomedical Engineering vol 29, 373-383, 2001.
Mar. 21RachelJ. Sousa, J. Carneiro, "A mathematical analysis of TCR serial triggering and down-regulation", European Journal of Immunology, 30:3219-3227 (2000).
Apr. 4RaguC. Reder, "Metabolic control theory: a structural approach", J. Theoretical Biology, 133:175201, 1988.

Last modified: Thu Apr 22 08:52:11 EST 2004