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• Previous presentations and presentation files (Fall 2001, Spring 2002)

• Future presentations (schedule your presentation)

Time and Place

This course is cross-listed as CS 726 (Computer Science),  PB 726 (Plant Breeding) and BSCB 726 (Biometrics)
1 credit, S/U only.
Prerequisites:� Permission of instructor.
The seminar is required from students of the Computational Molecular Biology Program.

Instructors

Links

• Introduction
• Books on Bioinformatics and Computational Biology
• Journal webpages
• Recommended background reading
• Suggested papers
  • Gene networks
  • Whole-cell simulations
  • Phylogenetics, Comparative genomics

• Friedman N, Linial M, Nachman I, Pe'er D. (2000). Using Bayesian networks to analyze expression data. J Comput Biol. 7, 601-20. abstract
• Pe'er D, Regev A, Elidan G, Friedman N. (2001). Inferring subnetworks from perturbed expression profiles. Bioinformatics 17 abstract

session 3+4 - Modeling gene networks using a system of differential equations

• Erina Sakamoto (2001). Inferring a System of Differential Equations for a Gene Regulatory Network by using Genetic Programming. paper
• Chen T, He HL, Church GM. (1999). Modeling Gene Expression With Differential Equations. Pac Symp Biocomput, 29-40 paper
• D'haeseleer, P., Liang, S. , and Somogyi, R. (2000). Genetic Network Inference: From Co-Expression Clustering to Reverse Engineering. Bioinformatics 16, 707-26 paper
• Yeung, M.K.S., Tegn�r, J. and Collins, J.J. (2002). Reverse engineering gene networks using singular value decomposition and robust regression Proc. Natl. Acad. Sci. 99, 6163-6168
• Getz, G., Levine, E. and Domany, E. (2000). Coupled two-way clustering analysis of gene microarray data Proc. Natl. Acad. Sci. 97, 12079-12084
• Wessels LF, van Someren EP, Reinders MJ. (2001). A comparison of genetic network models. Pac Symp Biocomput. 508-19. abstract
• Eugene P. van Someren, L.F.A. Wessels, M.J.T. Reinders. (2001). Genetic Network Models: A Comparative Study paper
• Maki Y, Tominaga D, Okamoto M, Watanabe S, Eguchi Y. (2001). Development of a system for the inference of large scale genetic networks. Pac Symp Biocomput. 446-58. abstract

Pathways and cell simulation

session 6 - Pathways

• Goto S, Bono H, Ogata H, Fujibuchi W, Nishioka T, Sato K, Kanehisa M. (1997) Organizing and computing metabolic pathway data in terms of binary relations. Pac Symp Biocomput, 175-86 abstract
• Bono H, Ogata H, Goto S, Kanehisa M. (1998). Reconstruction of amino acid biosynthesis pathways from the complete genome sequence. Genome Res 8, 203-10 abstract
• Karp PD. (2001). Pathway databases: a case study in computational symbolic theories. Science. 293, 2040-4. abstract
• P.R. Romero and P. Karp Nutrition-Related Analysis of Pathway/Genome Databases Pacific Symposium on Biocomputing 6:470-482 (2001). abstract

session 7 - Cell simulation/networks

• Goryanin I, Hodgman TC, Selkov E. (1999) Mathematical simulation and analysis of cellular metabolism and regulation. Bioinformatics 1999, 749-58. abstract
• Tomita et al. (1999). E-CELL: software environment for whole-cell simulation. Bioinformatics 15, 72-84. abstract
• Saqi MA, Sternberg MJ. (2001). A structural census of metabolic networks for E. coli. J Mol Biol. 313, 1195-206. abstract
• Ideker T, Galitski T, Hood L. (2001). A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet. 2, 343-72. abstract

Phylogenetics, Comparative genomics

session 10 - Phylogenetics

• Pearson WR, Robins G, Zhang T. (1999) Generalized neighbor-joining: more reliable phylogenetic tree reconstruction. Mol Biol Evol 1999, 806-16 abstract
• J. Kim and B.A. Salisbury A Tree Obscured By Vines: Horizontal Gene Transfer and the Median Tree Method of Estimating Species Phylogeny Pacific Symposium on Biocomputing 6:571-582 (2001). abstract
• Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ. (2001) Universal trees based on large combined protein sequence data sets. Nat Genet 2001 28, 281-5. abstract

session 12 - Phylogenetics/comparative genomics

• R.D.M. Page and J.A. Cotton Vertebrate Phylogenomics: Reconciled Trees and Gene Duplications Pacific Symposium on Biocomputing 7:536-547 (2002). abstract
• L.-S. Wang, R.K. Jansen, B.M.E. Moret, L.A. Raubeson, and T. Warnow; Fast Phylogenetic Methods for the Analysis of Genome Rearrangement Data: An Empirical Study Pacific Symposium on Biocomputing 7:524-535 (2002). abstract