Syllabus in pdf
Calendar
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Introduction to Molecular Biology
Life, cell, genes, DNA, RNA, proteins, structure, function, evolution, central dogma, domains of life.
- L. Hunter, Life and its molecules: A brief introduction", AI Magazine, 2004.
- A. Brazma, H. Parkinson, T. Schlitt, M. Shojatalab, A quick introduction to elements of biology - cells, molecules, genes, functional genomics, microarrays.
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Introduction to Systems Biology
Concepts relating to systems biology, properties of biological systems, level of detail in modeling and studying systems, organization vs dynamics, modularity, promises, challenges.
- H. Kitano, Systems biology: A brief overview, Science, 2002.
- O. Wolkenhauer, Systems biology: Data analysis, mathematical modelling and simulation in the post-genome era.
- L. Hartwell, J. J. Hopfield, S. Leibler, and A. W. Murray, From molecular to modular cell biology, Nature, 1999.
- Z. Oltvai & A. Barabasi, Life's complexity pyramid Science, 2002.
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DNA Microarrays
DNA microarray technology, oligonucleotide arrays, cDNA arrays, normalization and transformation of micorarray data.
- A. Schulze & J. Downward, Navigating gene expression using microarrays: A technology review, Nature Cell Biology, 2001.
- J. Quackenbush, Microarray data normalization and transformation, Nature Genetics, 2002.
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Knowledge Discovery on Gene Expression Data
Pattern discovery, clustering, biclustering, SVD.
- G. Sherlock, Analysis of large-scale gene expression data, Briefings in Bioinformatics, 2001.
- D. Jiang, C. Tang, and A. Zhang, Cluster analysis for gene expression data: A survey, IEEE Transactions on Knowledge & Data Engineering, 2004.
- S. C. Madeira and A. L. Oliveira, Biclustering algorithms for biological data analysis: A survey, IEEE Transactions on Computational Biology & Bioinformatics, 2004.
- O. Alter, P. O. Brown, and D. Botstein, Singular value decomposition for denome-wide expression data processing and modeling, PNAS, 2000.
- O. Alter, P. O. Brown, and D. Botstein, Generalized singular value decomposition for comparative analysis of genome-scale expression datasets of two different organisms, PNAS, 2003.
- Supervised Analysis of Gene Expression Data
Differential gene expression, classification, functional annotation, gene selection.- D. K. Slonim, From patterns to pathways: Gene expression data analysis comes of age, Nature Genetics, 2002.
- A. Ben-Dor, L. Bruhn, N. Friedman, I. Nachman, M. Schummer, and Z. Yakhini, Tissue classification with gene expression profiles, Journal of Computational Biology, 2000.
- Gene Regulatory Networks
Graph models for genetic regulation, Boolean network model, Bayesian network model, network dynamics, inference of genetic networks.- J. Hasty, D. McMillen, F. Isaacs, and J. J. Collins,Computational studies of gene regulatory networks: in numero molecular biology, Nature Reviews Genetics, 2001.
- N. Friedman, Inferring genetic networks using probabilistic graph models, Science, 2003.
- R. Xu, X. Hu, and D. C. Wunch, Inference of genetic regulatory networks from time series gene expression data, IEEE International Joint Conference on Neural Networks, 2004.
- Protein Interaction Networks
Protein-protein interactions, high-throughput screening of protein interactions (Y2H, TAP), prediction of protein interactions (co-expression, co-evolution, gene fusion, in silico two-hybrid, structural prediction).- P. Legrain, J. Wojcik, and J. M. Gauthier, Protein-protein interaction maps: A lead towards cellular functions, TRENDS in Genetics, 2001.
- B. Titz, M. Schlesner, and P. Uetz, What do we learn from high-throughput protein interaction data?, Expert Rev. Proteomics, 2004.
- A. Valencia and F. Pazos, Computational methods for the prediction of protein interactions, Current Opinion in Structural Biology, 2002.
- I. Lee, S. V. Date, A. T. Adai, and E. M. Marcotte, A probabilistic functional network of yeast genes, Science, 2004.
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Topology of Biological Networks
Degree distribution, clustering coefficient, scale-free networks, hierarchy, modularity, topological motifs, robustness.- A. L. Barabasi and Z. N. Oltvai, Network biology: Understanding the cell's functional organization, Nature Reviews Genetics, 2004.
- R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, and U. Alon, Network motifs: Simple building blocks of complex networks, Science, 2002.
- N. Przulj, D. A. Wigle, and I. Jurisica, Functional topology in a network of protein interactions, Bioinformatics, 2004.
- S. Wuchty, Z. N. Oltvai, and A. L. Barabasi, Evolutionary conservation of motif constituents in the yeast protein interaction network, Nature Genetics, 2003.
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Pattern Discovery in Molecular Interaction Networks
Reconstructing signaling networks, identification of functional modules, network clustering, modular decomposition of networks, identification of signaling pathways.- J. A. Papin, T. Hunter, B. O. Palsson, and S. Subramaniam, Reconstruction of cellular signalling networks and analysis of their properties, Nature Reviews Molecular Cell Biology, 2005.
- T. Aittokallio and B. Schwikowski, Graph-based methods for analysing networks in cell biology, Briefings in Bioinformatics, 2006.
- J. Gagneur, R. Krause, T. Bouwmeester, and G. Casari, Modular decomposition of protein-protein interaction networks, Genome Biology, 2004.
- J. Scott, T. Ideker, R. M. Karp, and R. Sharan, Efficient algorithms for detecting signaling pathways in protein interaction networks, RECOMB, 2005.
- Comparative Interactomics
Alignment of molecular interaction networks, multiple network alignment, global network alignment, graph mining.- R. Sharan and T. Ideker, Modeling cellular machinery through biological network comparison, Nature Biotechnology, 2006.
- R. Sharan, S. Suthram, R. M. Kelley, T. Kuhn, S. McCuine, P. Uetz, T. Sitter, R. M. Karp, and T. Ideker, Conserved patterns of protein interaction in multiple species, PNAS, 2005.
- M. Koyuturk, Y. Kim, S. Subramaniam, W. Szpankowski, and A. Grama, Detecting conserved interaction patterns in biological networks, Journal of Computational Biology, 2006.
- Network Based Functional Annotation
Projection of function based on network neighborhood, modularity based annotation, network based ortholog identification.- R. Sharan, I. Ulitsky, and R. Shamir. Network based prediction of protein function, Molecular Systems Biology, 2007.
- A. Vazquez, A. Flammini, A. Maritan, and A. Vespignani, Global protein function prediction from protein-protein interaction networks, Nature Biotechnology, 2003.
- Integration of Interaction Data
12.a. Discussion paper: R. Kelley and T. Ideker, Systematic interpretation of genetic interactions using protein networks, Nature Biotechnology, 2005. - Domain Interaction Networks
Inferring domain-domain interactions from protein-protein interactions, domain interaction databases.- H. Lee, M. Deng, F. Sun, and T. Chen, An integrated approach to the prediction of domain-domain interactions, BMC Bioinformatics, 2006.
- K. S. Guimaraes, R. Jothi, E. Zotenko, and T. M. Przytycka, Predicting domain-domain interactions using a parsimony approach, Genome Biology, 2006.
Guest Lectures
- Gurkan Bebek, Center for Proteomics and Mass Spectrometry, November 21, 2007.
- Sree Sreenath, Department of Electrical Enginering & Computer Science,Complex Systems Biology Center, December 3, 2007.
Class Presentations
- Vishal Patel, Identification of active pathways based on genomic and
proteomic data, November 5, 2007.
- J. Ihmels, R. Levy, and N. Barkai, Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae, Nature, 2003.
- M. R. Said, T. J. Begley, A. V. Oppenheim, D. A. Lauffenburger, L. D. Samson, Global network analysis of phenotypic effects: Protein networks and toxicity modulation in Saccharomyces cerevisiae, PNAS, 2004.
- Nathan Johnson, Use of ontologies in understanding biological networks,
November 7, 2007.
- M. Suderman and M. Hallett, Tools for visually exploring biological networks Bioinformatics, 2007.
- M. S. Celine et al., Integration of biological networks and gene expression data using Cytoscape, Nature Protocols, 2007.
- Van Anh Tran, PPI network alignment, November 12, 2007.
- R. Sharan and T. Ideker, Modeling cellular machinery through biological network comparison, Nature Biotechnology, 2006.
- J. Flannick, A. Novak, C. B. Do, B. S. Srinivasan, S. Batzoglou, Automatic parameter learning for multiple network alignment, Genome Informatics, 2007.
- Sinan Erten, Evolution of PPI networks, November 19, 2007.
- G. Bebek, P. Berenbrink, C. Copper, T. Friedetzky, J. H. Nadeau, and S. C. Sahinalp, Improved duplication models for proteome network evolution, RECOMB Workshop on Regulatory Genomics, 2005.
- E. Eisenberg and E. L. Levanon, Preferential attachment in the protein network evolution, Physical Review Letters, 2003.
- K.-I. Goh, B. Kahngand, and D. Kim, Evolution of the protein interaction network of budding yeast: Role of the protein family compatibility constraint, Journal of the Korean Physical Society, 2005.
- Michael Weis, Using protein-level data to predict cell-level response, November 26, 2007.
- S. Kharait, S. Hautaniemi, S. Wu, A. Iwabu, D.A. Lauffenburger, A. Wells, Decision tree modeling predicts effects of inhibitin contractility signaling on cell motility, BMC Systems Biology, 2007.
- K.A. Janes, J.G. Albeck, S. Gaudet, P.K. Sorger, D.A. Lauffenburger, M.B. Yaffe, A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis", Science, 2005.
- Xin Li, Clustering methods in biological networks, November 28, 2007.
- D. S. Goldberg and F. P. Roth, Assessing experimentally derived interactions in a small world, PNAS, 2003.
- J. Berg and M. Lassig, Cross-species analysis of biological networks by Bayesian alignment, PNAS, 2006.
Assignments
- Clustering gene expression data, Due:October 3, 2007
- Network based functional annotation, Due:December 5, 2007