| Schedule & Readings |
Spring 2004:
| Date | Leader | Topic |
|---|
| Jan. 22 | Chris | A. Califano, "SPLASH: structural pattern localization analysis by sequential histograms", Bioinformatics, 16(4):341-57, 2000 (paper) |
| Feb. 5 | Ann | B.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. 19 | Xiaoduan | I.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. 4 | Jun | J.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. 25 | Curt | E. 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. 8 | Greg |
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. 22 | Daisuke |
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:
| Date | Leader | Topic |
|---|
| Sept. 4 | | J. 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. 18 | Ann |
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.
paper. |
| Oct. 2 | Xiaoduan |
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. 16 | Shobha |
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. 30 | Curt |
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. 13 | Jiangtian |
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. 11 | Tim |
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:
| Date | Leader | Topic |
|---|
| June 5 | Ann | J. 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 19 | Chris | R. Chen and Z. Weng, "A novel shape complementarity scoring function for protein-protein docking", Proteins, 51(3):397-408, 2003.
Abstract. Paper. |
| July 3 | Olga | S. Schmidler, J. Liu, and D. Brutlag, "Bayesian protein structure prediction", Case Studies in Bayesian Statistics, Vol. 5, pp.363-378, 2001.
Paper. |
| July 17 | Jun | S. Jones and J. M. Thornton, "Analysis of Protein-Protein Interaction Sites using Surface Patches", J. Mol. Biol., 272:121-132, 1997.
Paper |
| July 31 | Tim | D. 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.
Paper |
| Aug. 14 | Curt | M. 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:
| Date | Leader | Topic |
|---|
| Jan. 23 | Chris | L. Lu, H. Lu, and J. Skolnick, "MULTIPROSPECTOR: An Algorithm for the Prediction of Protein-Protein Interactions by Multimeric Threading", Proteins, 49:350-364, 2002.
Paper. |
| Feb. 6 | Olga | K. Yeung, C. Fraley, A. Murua, A. Raftery, W. Ruzzo, "Model-Based Clustering and Data Transformations for Gene Expression Data", Bioinformatics, 17:977-987, 2001.
Paper |
| Feb. 20 | Ann | Y. 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.
Paper |
| Mar. 6 | Shobha | C.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.
Paper |
| Mar. 27 | Yanan | Friedman et al., "Using Bayesian Networks to Analyze Expression Data", J. Comp. Biol. 7:601-620, 2000.
Paper |
| Apr. 10 | Chong | Storch et al., "Extensive and divergent circadian gene expression in liver and heart", Nature, 417:78-83, 2002.
Paper |
| Apr. 24 | Curt |
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:
| Date | Leader | Topic |
|---|
| Aug. 29 | Ann | R. Heinrich, B. Neel, and
T. Rapoport, "Mathematical Models of Protein Kinase Signal
Transduction", Molecular Cell, Vol 9, 957-970, May 2002.
Abstract. |
| Sep. 12 | Chris | J. 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. 26 | Shobha |
W. Wriggers and P. Chacon, "Modeling Tricks and Fitting Techniques for
Multi-Resolution Structures", Structure, 9:779-788, 2001.
Paper
|
| Oct. 10 | Santhoji |
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.
Paper
|
| Oct. 24 | Ragu | A. Becskel and L. Serrano, "Engineering stability in gene networks by autoregulation", Nature, 405:590-593, 2000.
Abstract, html, pdf at Nature. |
| Nov. 7 | Yanan | H. Cateau and S. Tanaka, "Kinetic analysis of multisite phosphorylation using analytic solutions to michaelis-menten equations", J. Theoretical Biology, 217:1-14, 2002.
Paper
|
| Nov. 21 | Olga | B. Simon, M. Sattler, "De novo structure determination from residual dipolar coupling by NMR spectrocopy", Angewandte Chemie, Int. Ed., 2002.
Paper
|
| Dec. 5 | Curt | M. C. Frith, U. Hansen, and
Z. Weng, "Detection of cis-element clusters in higher eukaryotic DNA",
Bioinformatics 17:878-889, 2001.
paper |
Summer 2002:
| Date | Leader | Topic |
|---|
| May 29 | Chris | A.H. Tong et al., "A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules", Science, 295:321-324, 2002.
PubMed |
| June 5 | Yanan | Simulation of T-cell MAPK Signaling Pathway |
| June 19 | Ann | Gordon Conference highlights |
| July 10 | Rachel | Canceled |
| July 24 | Santhoji &
Priyan | T. Ideker et al., "Integrated genomic and proteomic analyses of a systematically perturbed metabolic network," Science, 292:929-934, 2001.
PubMed. |
Spring 2002:
| Date | Leader | Topic |
|---|
| Jan. 10 | Ann | John 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. 24 | Chris | C.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. 7 | Peter | John 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. 21 | Prasana | S. Eddy, "Profile hidden
Markov models", Bioinformatics, 14(9):755-763, 1998.
PDF. |
| Mar. 7 | Yanan | Kim 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.
PDF. |
| Mar. 21 | Rachel | J. Sousa, J. Carneiro, "A
mathematical analysis of TCR serial triggering and down-regulation",
European Journal of Immunology, 30:3219-3227 (2000).
PDF. |
| Apr. 4 | Ragu | C. Reder, "Metabolic control
theory: a structural approach", J. Theoretical Biology, 133:175201,
1988. |
|