STAT598N •  Statistics in Systems Biology
Overview | Course Requirements | Schedule of Readings

January 13: Administrative details and Molecular biology primer for CS and engineering students ------Presentation: Alan Qi

January 15: Statistical learing primer for biologists-----Presentation: Alan Qi

Reading list:

1.    Jan. 20  Thomas P. Minka (1998), Expectation-Maximization as lower bound maximization, MSR Tech Report.
    Pattern Recognition and Machine Learning, Chris Bishop, EM Part of Chapter 9.

2.    Jan. 22 Timothy L. Bailey and Charles Elkan (1994), Fitting a mixture model by expectation maximization to discover motifs in biopolymers, Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California.
http://www.sdsc.edu/~tbailey/papers/ismb94.pdf

3.    Jan. 27 Albert-László Barabási and Zoltán N. Oltvai (2004), Network Biology: Understanding the Cells's Functional Organization. Nature Reviews Genetics 5, 101-113.
http://www.nature.com/nrg/journal/v5/n2/full/nrg1272.html

4.    Jan. 29 Duncan J. Watts, "The 'New' Science of Networks (2004),  Annual Review of Sociology 30: 243-270.
http://www.sociology.columbia.edu/pdf-files/watts02.pdf

5.    Feb. 3 V.Colizza, R. Pastor-Satorras and A. Vespignani (2007), Reaction-diffusion processes and metapopulation models in heterogeneous networks, Nature Physics 3, 276-282.
http://www.nature.com/nphys/journal/v3/n4/full/nphys560.html

6.    Feb. 5  Robins, G., T. Snijders, P. Wang, M. Handcock, and P. Pattison (2007). Recent developments in exponential random graph (p*) models for social networks. Social Networks 29:192-215.
http://www.stats.ox.ac.uk/~snijders/siena/RobinsSnijdersWangHandcockPattison2007.pdf

7.    Feb. 10 Zachary M. Saul and Vladimir Filkov (2007). Exploring biological network structure using exponential random graph models,
http://bioinformatics.oxfordjournals.org/cgi/content/full/23/19/2604

8.    Feb. 12 Ariel Jaimovich , Gal Elidan , Hanah Margalit , Nir Friedman (2006). Towards an integrated protein-protein interaction network: a relational markov network approach. J. Comput Biol. 2006 Mar ;13 (2):145-64 16597232
http://www.robotics.stanford.edu/~galel/papers/ElidanProtProtJCB.pdf

9.    Feb. 17 Yanjun Qi, Fernanda Balem, Christos Faloutsos, Judith Klein-Seetharaman, and Ziv Bar-Joseph (2008). Protein complex identification by supervised graph local clustering, Bioinformatics 24: i250-i268; doi:10.1093/bioinformatics/btn164
http://bioinformatics.oxfordjournals.org/cgi/reprint/24/13/i250

10.    Feb. 19  Allister Bernard, David Vaughn, Alexander J. Hartemink (2007). Reconstructing the topology of protein complexes
http://www.cs.duke.edu/~dsv/professional/proctor.pdf

11.    Feb. 24  Airoldi, E., D. Blei, S. Fienberg, E. Xing (2007). Mixed Membership Stochastic Blockmodels. Statistics ArXiv.
http://arxiv.org/PS_cache/arxiv/pdf/0705/0705.4485v1.pdf

12.    Feb. 26. Eran Segal, Dana Pe'er, Aviv Regev, Daphne Koller, Nir Friedman (2005), Learning Module Networks, JMLR, 6(Apr):557--588.
http://jmlr.csail.mit.edu/papers/v6/segal05a.html

13.    March 3   Modularity and Dynamics of Cellular Networks (2006), Y. Qi and H. Ge, PLoS Computational Biology, vol. 2, no. 12, 1502-1510, December.
http://compbiol.plosjournals.org/archive/1553-7358/2/12/pdf/10.1371_journal.pcbi.0020174-L.pdf

14.    March 5  Sachs K, Perez O, Pe'er D, Lauffenburger DA, Nolan GP (2005) Causal protein-signaling networks derived from multiparameter single-cell data. Science 308: 523-529.
http://www.sciencemag.org/cgi/content/full/308/5721/523

15.    March 10  Srinivasan BS, Shah NH, Flannick JA, Abeliuk E, Novak AF, Batzoglou S (2007).  Current progress in network research: toward reference networks for key model organisms.  Briefings in Bioinformatics 8(5): 318-32.
http://ai.stanford.edu/~serafim/Publications/2007_NetworksReview.pdf

16.    March 12 G. K. Gerber, R. D. Dowell, T. S. Jaakkola, D. K. Gifford (2007). Hierarchical Dirichlet Process-Based Models For Discovery of Cross-species Mammalian Gene Expression Programs. MIT-CSAIL Technical Report, MIT-CSAIL-TR-2007-037.
http://dspace.mit.edu/bitstream/1721.1/37817/2/MIT-CSAIL-TR-2007-037.pdf

17.    March 24 Beal, M.J. and Krishnamurthy, P. (2006), Clustering Gene Expression Time Course Data with Countably Infinite Hidden Markov Models, in Proceedings of 22nd Conference on Uncertainty in Artificial Intelligence UAI 2006, 13-16 July, MIT.
http://www.cse.buffalo.edu/faculty/mbeal/papers/ihmmgen.pdf

18.    March 26   Adam Siepel, David Haussler (2004). Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis, Journal of Computational Biology. 2004, 11(2-3): 413-428. doi:10.1089/1066527041410472.
http://compgen.bscb.cornell.edu/~acs/JCB04.pdf

19.    March 31 Y. Qi, A. Rolfe, K. D. MacIsaac, G. K. Gerber, D. Pokholok, J. Zeitlinger, T. Danford, R. D. Dowell, E. Fraenkel, T. S. Jaakkola, R. A. Young and D. K. Gifford (2006., High-resolution Computational Models of Genome Binding Events, , Nature Biotechnology, vol. 24, 963-970.
http://www.nature.com/nbt/journal/v24/n8/abs/nbt1233.html

20.    April 2 Yunpen Xu, Xuefeng Zhou, and Weixiong Zhang (2008), MicroRNA prediction with a novel ranking algorithm based on random walks, Bioinformatics 24: i50-i58; doi:10.1093/bioinformatics/btn175
http://bioinformatics.oxfordjournals.org/cgi/reprint/24/13/i50

21.    April 4  Hetunandan Kamisetty Eric P. Xing Christopher J. Langmead (2008), Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation
http://www.cs.cmu.edu/~epxing/papers/recomb-hetu.pdf

22.    April 9 Chen Yanover, Ora Schueler-Furman, Yair (2007). Minimizing and Learning Energy Functions for Side-Chain Prediction
 http://www.liebertonline.com/doi/abs/10.1089/cmb.2007.0158

23.    April 14  Peter Kharchenko, Lifeng Chen, Yoav Freund, Dennis Vitkup, and George M Church (2006), Identifying metabolic enzymes with multiple types of association evidence, BMC Bioinformatics. 2006; 7: 177.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1450304

24.    April 16 Yeang CH, Vingron M. (2006), A joint model of regulatory and metabolic networks, BMC Bioinformatics. 2006 July http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16820044

25.    April 21 Esa Pitkanen, Ari Rantanen, Juho Rousu, and Esko Ukkonen (2008). A computational method for reconstructing gapless metabolic networks, Bioinformatics Research and Development.
http://www.cs.helsinki.fi/u/epitkane/pub/gapless_reconstructions.pdf

26.    April 23  Markus J. Herrgård, Baek-Seok Lee1, Vasiliy Portnoy, and Bernhard Ø. Palsson (2006). Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. Genome Research.
http://genome.cshlp.org/content/16/5/627.full.pdf+html