UT BioDM (Biological Data Mining) Group Meeting

[ Meeting Schedule | Participants | Links | Proposed Papers | Previous Discussions ]

We review local research progress and read and discuss papers in the area of biological data mining in connection with the UT Austin NSF ITR project on biological data mining.

Regular Meeting Time

The BioDM group meets every other Friday at 2:30pm

Next Scheduled Meeting

Friday, May 11 2007 @ 2:30pm, ACES 3.408.

Please send in suggestions for new papers to discuss, or vote for a paper from the currently proposed papers.

Current Participants (Local and Nonlocal)

If I have missed your name please let me know

Raymond Mooney	Edward Marcotte	Inderjit Dhillon	Joydeep Ghosh
Daniel Miranker	Vishy Iyer	Orly Alter	Arun
Gunjan Gupta	Hyuk Cho	Kris McGary	Chase Krumpelman
Patrick Killion	Razvan Bunescu	Shulin Ni	Sugato Basu
Suvrit Sra	Cara Stockham	Glen Nuckolls
Dongmin Kim	Chendi Zhang
Mikhail Bilenko	Prem Melville	Smriti Ramakrishnan
Akshay	Razvan Surdulescu	Larsson Omberg	Insuk Lee
Christine Vogel

Currently Proposed Papers

De novo analysis of peptide tandem mass spectra by spectral graph partitioning, Bern, M. W.; Goldberg, D., Journal of Computational Biology. 2006 Mar; 13(2): 364-78.
OLAV: towards high-throughput tandem mass spectrometry data identification Colinge J, Masselot A, Giron M, Dessingy T, Magnin J.. Proteomics. 2003 Aug;3(8):1454-60.

Supervised Enzyme Network Inference from the Integration of Genomic Data and Chemical Information. Yamanishi, Vert, Kanehisa.
Data Integration and Visualization System for Enabling Conceptual Biology." Gopalacharyulu, Lindfors, Bounsaythip, Kivioja, Yetukuri, Hollmen, Oresic.
Wnt Pathway Analysis with Automated Natural Language Processing. C. Santos, D. Eggle, and D. States. ISMB-05.
Combining Phylogenetic Data and Network Topology to Identify Regulatory Motifs. T. Wang and G. Stormo ISMB-05
Conditional network analysis: exploring network dynamics and identifying key modulator genes from gene expression data. K. Wang, N. Banerjee, A. Margolin, et al. ISMB-05
Systems Approach to High Throughput Data Analysis. A. Vailaya, A. Kuchinsky, R. Kincaid, et al. ISMB-05.
Combinatorial Synthesis of Genetic NetworksCălin C. Guet, Michael B. Elowitz, Weihong Hsing, Stanislas Leibler. Science, Vol 296, Issue 5572, 1466-1470 , 24 May 2002
Inclusion of Textual Documentation in the Analysis of Multidimensional Data Sets: Application to Gene Expression Data. Soumya Raychaudhuri, Hinrich Schütze, Russ B. Altman. Machine Learning Journal. 52, 2003.
Predicting Genetic Regulatory Response Using Classification Manuel Middendorf, Anshul Kundaje, Chris Wiggins, Yoav Freund, Christina Leslie, ISMB 2004.

Previous Discussions

2007.05.11	Presentation by Shu Wang from Dr. Miranker's group on her research: "A Biclustering Approach to Multiple Sequence Alignment", joint work with Robin Gutell and Daniel Miranker
2007.04.27	Presentation by XioChitl Morgan from Dr. Iyer's group, on her research: "Predicting Combinatorial Binding of Transcription Factors to Regulatory Elements in the Human Genome by Association Rule Mining", joint work with Shulin Ni, Vishy Iyer and Daniel Miranker
2007.04.13	Paper Discussion: An Ensemble Framework for Clustering Protein-Protein Interaction Networks, Sitaram Asur, Srinivasan Parthasarathy and Duygu Ucar, to appear in ISMB 2007. Related paper: Cluster ensembles - a knowledge reuse framework for combining partitionings, In Proc. Conference on Artificial Intelligence (AAAI 2002), pages 93-98, July 2002.
2007.03.30	Paper Discussion: Dynamic Spectrum Quality Assessment and Iterative Computational Analysis of Shotgun Proteomic Data Nesvizhskii AI, Roos FF, Grossmann J, Vogelzang M, Eddes JS, Gruissem W, Baginsky S, Aebersold R. Mol Cell Proteomics. 2006 Apr;5(4):652-70.
2007.03.02	Paper Discussion:Clustering by Passing Messages Between Data Points, Brendan J. Frey and Delbert Dueck, Science,2007 Feb 16;315(5814):972-6
2007.02.09	Presentation by Smriti Ramakrishnan: 'Mass spectrometry (MS/MS) database search for protein identification: computational challenges & machine learning approaches'
2006.12.01	Presentation of mass spectrography technology by John Prince of the Marcotte Lab. Slides available here.
2006.11.17	Discussion of Protein names peeled off free text by Sven Mika and Burkard Rost (ISMB 04)
2006.11.03	Presentation by Dr. Gunjan Gupta on his dissertation research on density based cluster mining and bioinformatics applications. There will be a special demo of a product developed called Gene DIVER. Related Papers: ICDM 2006 HDS Tech Report
2006.10.20	Reconstructing the pathways of a cellular system from genome-scale signals by using matrix and tensor computations Orly Alter, and Gene H. Golub PNAS 12/6/2005 102:49 17559-17564 Supplementary Materials: http://www.stanford.edu/group/mmds/slides/alter-mmds.pdf http://www.bme.utexas.edu/research/ orly/network_decomposition Discussion led by Dr. Alter.
2006.10.06	Functional clustering of yeast proteins from the protein-protein interaction networkTaner Z Sen, Andrzej Kloczkowski and Robert L Jernigan BMC Bioinformatics 2006, 7:355
2006.09.22	A discussion by Chase Krumpelman, Wan Kyu Kim, and Edward Marcotte on approaches to gene function prediction in the context of the Mousefunc I competition
2006.05.01	Categorization Approach to Automated Ontological Protein Function AnnotationKM Verspoor, JD Cohn, SM Mniszewski, and CA Joslyn Protein Science, 2006, in press. A Related paper: Improving Protein Function Prediction using the Hierarchical Structure of the Gene Ontology R. Eisner, B,.Poulin, D. Szafron, P. Lu and R. Greiner 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, November 2005.
2006.04.17	Inferring protein domain interactions from databases of interacting proteins. Genome Biol. 2005; 6(10): R89. Discussion to be let by Akshay Bhinge of the Iyer Lab
2006.04.03	A review of recent results in graph clustering by Brian Kulis of Inderjit Dhillon's group, entitled Spectral Clustering without Eigenvectors. (Note: Relevant to protein interaction networks.) Papers: Kernel k-means, Spectral Clustering and Normalized Cuts A Fast Kernel-Based Multilevel Algorithm for Graph Clustering
2006.03.20	Metagenes and molecular pattern discovery using matrix factorization. Jean-Philippe Brunet, Pablo Tamayo, Todd R. Golub, and Jill P. Mesirov Proc Natl Acad Sci USA March 23, 2004. v. 101 # 12, 4164-4169.
2006.03.06	Integrating Co-occurence Statistics with Information Extraction for Robust Retrieval of Protein Interactions from Medline Bunescu, Mooney, Ramani, Marcotte
2006.02.20	Discovery of biological networks from diverse functional genomic data C. Myers, D. Robson, A. Wible, C. Theesfeld, K. Dolinski and O. Troyanskaya
2006.02.06	Discussion of Lise Getoor's work on link-based analysis: Link Mining: A New Data Challenge Lise Getoor From Instances to Classes in Probabilistic Models Getoor, Koller, Friedman Learning Probabilistic Models of Link Structure Getoor, Friedman, Koller, Taskar
2005.12.16	A data integration methodology for systems biology Hwang, et al. and A data integration methodology for systems biology: Experimental verification Hwang, et al.
2005.12.2	Clustering Short Time Series Gene Expression Data. Ernst, Nau, Bar-Joseph
2005.11.18	Phenotypic diversity, population growth, and information in fluctuating environments. Kussell E, Leibler S. Science. 2005 Sep 23;309(5743):2005-7.
2005.11.4	Discussion led by Chase: Mining Coherent Dense Subgraphs Across Massive Biological Networks for Functional Discovery. Hu, Yan, Huang, Han, Zhou
2005.10.21	Discussion led by David Reynolds and Larsson Omberg 1. Robustness of cellular functions J. Stelling, U. Sauer, Z. Szallasi, F. J. Doyle III, and J. Doyle. Cell, October, 2004. 2. The Robust Yet Fragile Nature of the Internet Doyle et al, (2005) P Natl Acad Sci USA. vol. 102 no. 41, October 11, 2005
2005.10.07	Whole-proteome Prediction of Protein Function via Graph-theoretic Analysis of Interaction Maps. Nabieva, Jim, Agarwal, Chazelle, and Singh
2005.09.23	Causal protein-signaling networks derived from multiparameter single-cell data. Sachs K, Perez O, Pe'er D, Lauffenburger DA, Nolan GP. Science. 2005 Apr 22;308(5721):523-9.
2005.04.22	Paper discussion (and presentation) led by Christine Vogel: Functional annotation and network reconstruction through cross-platform integration of microarray data. Zhou XJ, Kao MC, Huang H, Wong A, Nunez-Iglesias J, Primig M, Aparicio OM, Finch CE, Morgan TE, Wong WH. Nat. Biotechnology 2005 Feb;23(2):238-43. Epub 2005 Jan 16
2005.03.25	Paper Discussion: LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Brudno M, Do C, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S. Genome Research 13: 721-731, 2003.
2005.03.11	Paper Discussion: GEST: a gene expression search tool based on a novel Bayesian similarity metric. Lawrence Hunter, Ronald C. Taylor, Sonia M. Leach and Richard Simon Bioinformatics. Vo. 17, No. 90001. 2001. ppS115--S122.
2005.02.25	Paper presentation (led by Arun and Razvan) Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome Arun K Ramani, Razvan C Bunescu, Raymond J Mooney and Edward M Marcotte. Genome Biology (conditionally accepted)
2005.02.11	Paper discussion (led by Dr. Orly Alter): Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription, Orly Alter and Gene H. Golub. PNAS November 23, 2004 vol. 101(47)
2005.01.28	Paper discussion: "Multi-Relational Learning, Text-Mining, and Semi-Supervised Learning for Functional Genomics" Krogel & Scheffer, Machine Learning, 57, 2004
2004.12.3	Paper discussion: A Probabilistic Functional Network of Yeast Genes: I. Lee, S. V. Date, A. T. Adai and E. M. Marcotte. Science. 2004 (306): 1555--1558
2004.11.15	Talk: SPEAKER: Jack Y. Yang/Indiana School of Medicine TITLE: Sequential Bifurcation Approaches in Genomic Data
2004.10.29	Paper discussion: Into the Heart of Darkness: Large Scale Clustering of Human Non-Coding DNA Gill Bejerano, David Haussler, Mathieu Blanchette, ISMB 2004.
2004.10.15	Paper discussion: Protein Network Inference from Multiple Genomic Data: A Supervised Approach Yoshihiro Yamanishi, Minoru Kanehisa
2004.10.01	Paper discussion: Combining inductive logic programming, active learning and robotics to discover the function of genes C.H. Bryant, S.H. Muggleton, S.G. Oliver, D.B. Kell, P. Reiser, and R.D. King. Electronic Transactions in Artificial Intelligence, 5-B1(012):1-36, November 2001.
2004.07.16	Paper discussion: Imputing Missing Data for Gene Expression Arrays Olga Troyanskaya, Michael Cantor, Gavin Sherlock, Pat Brown, Trevor Hastie, Robert Tibshirani, Davit Botstein, Russ Altman.
2004.06.25	Paper discussion: Confirmation of data mining based predictions of protein function. King RD, Wise PH, Clare A. Functional genomic hypothesis generation and experimentation by a robot scientist. King RD, Whelan KE, Jones FM, Reiser PG, Bryant CH, Muggleton SH, Kell DB, Oliver SG.
2004.06.11	Paper discussion: Machine learning of functional class from phenotype data Amanda Clare and Ross D. King Predicting gene function in Saccharomyces cerevisiae A. Clare and R. D. King
2004.05.28	Paper discussion: A Bayesian framework for combining heterogeneous data sources for gene function prediction Troyanskaya OG, et al.
2004.04.30	Paper discussion: Decomposing Gene Expression into Cellular Processes E. Segal, A. Battle, D. Koller. In Proc. 8th Pacific Symposium on Biocomputing (PSB), Kaua'i, January 2003 Probabilistic Discovery of Overlapping Cellular Processes and their Regulation Using Gene Expression Data A. Battle, E. Segal, D. Koller. In Proc. 8th Inter. Conf. on Research in Computational Molecular Biology (RECOMB), San-Diego, CA, April 2004 Both papers available from: http://robotics.stanford.edu/~erans/
2004.04.30	Presentation by visiting faculty: Prof. Dan Boley, University of Minnesota Automated Data Cleaning
2004.04.16	Overview of Inderjit Dhillon's research Diametrical Clustering for identifying Anti-Correlated Gene Clusters Minimum Sum-Squared Residue Co-clustering of Gene Expression Data
2004.03.12	Overview of Joydeep Ghosh's research On the Theory and Practice of Co-clustering Reference:Arindam Banerjee, Inderjit Dhillon, Joydeep Ghosh, Srujana Merugu and Dharmendra Modha, "A Generalized Maximum Entropy Approach to Bregman Co-clustering and Matrix Approximation", Feb 2004.
2004.02.27	Overview of Orly Alter's research Genomic Signal Processing: Large-Scale Data, Matrix Algebra Models and Basic Biological Principles
2004.02.13	Overview of research in the Marcotte lab.
2004.01.30	Overview of Dr. Miranker's biological databases research. Papers: Architectural overview paper Application, CS-facing description Application, biology-facing description
2003.12.05	Overview of research in the Iyer lab. Suggested Reading: Transcriptional Regulatory Networks in Saccharomyces cerevisiae Lee, Tonh Ihn et al.
2003.11.14	Research in Dr. Mooney's group. Learning to Extract Proteins and their Interactions from Medline Abstracts Razvan Bunescu, Ruifang Ge, Rohit J. Kate, Raymond J. Mooney, Yuk Wah Wong, Edward M. Marcotte, and Arun Kumar Ramani Proceedings of the ICML-2003 Workshop on Machine Learning in Bioinformatics, pp.46-53, Washington DC, August 2003.

For more information, please contact Ray Mooney

Last modified: Sun Dec 11 12:37:44 CST 2005