Papers Daphne Koller Publications Research Areas (all) Publication Type Years CB Computational Biology    LGM Learning Graphical Models RPM Richer Probabilistic Models    SL Supervised Learning J Journal Article C Conference Paper B Book Ch Book Chapter T Technical Report PhD PhD Disseration 1985 - 1989 1990 - 1994 1995 - 1999 2000 - 2004 2005 - 2009 Type Reference Download topics: CB LGM RPM SL 2009 J   H. Wang, B. Kakaradov, S.R. Collins, L. Karotki, D. Fiedler, M. Shales, K.M. Shokat, T. Walther, N.J. Krogan, and D. Koller (2009). "A complex-based reconstruction of the S. cerevisiae interactome." Molecular Cell Proteomics, 8(6), 1361-81. bib topics: CB          J   D. Fiedler, H. Braberg, M. Mehta, G. Chechik, G. Cagney, P. Mukherjee, and A.C. Silva, M. Shales, S.R. Collins, S. van Wageningen, P. Kemmeren, F.C.P. Holstege, J.S. Weissman, M. Christopher-Keogh, D. Koller, K.M. Shokat, and N.J. Krogan (2009). "Functional Organization of the S. cerevisiae Phosphorylation Network." Cell, 136(5), 952-63. bib topics: CB          J   G. Chechik and D. Koller (2009). "Timing of gene expression responses to environmental changes." Journal of Computational Biology, 16(2), 279-290. bib topics: CB          J   S.-I. Lee, A.M. Dudley, D. Drubin, P.A. Silver, N.J. Krogan, D. Pe’er, and D. Koller (2009). "Learning a Prior on Regulatory Potential from eQTL Data." PLOS Genetics, 5(1), e1000358. bib topics: CB          J   A.J. Gentles, A.A. Alizadeh, S.-I. Lee andJ.H. Myklebust, C.M. Shachaf, B. Shahbaba, R. Levy, D. Koller, and S.K. Plevritis (2009). "A pluripotency signature predicts histologic transformationand influences survival in follicular lymphoma patients." Blood, 114, 3158-66. bib topics: CB          2008 J   G. Chechik, E. Oh, O. Rando, J. Weissman, A. Regev, and D. Koller (2008). "Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network." Nature Biotechnology, 26(11), 1251-1259. bib topics: CB          J   M. Boxem, Z. Maliga, N. Klitgord, N. Li, I. Lemmens, M. Mana, L. de Lichtervelde, J.D. Mul, D. van de Peut, M. Devos, N. Simonis, M.A. Yildirim, M. Cokol, H.-L. Kao, A.-S. de Smet, H. Wang, A.-L. Schlaitz, T. Hao, S. Milstein, C. Fan andd M. Tipsword, K. Drew, M. Galli, K. Rhrissorrakrai, D. Drechsel, D. Koller, F.P. Roth, L.M. Iakoucheva, A.K. Dunker, R. Bonneau, K.C. Gunsalus, D.E. Hill, F. Piano andd J. Tavernier, S. van den Heuvel, A.A. Hyman, and M. Vidal (2008). "A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis." Cell, 134(3), 534-545. bib topics: CB          J   M.E. Hillenmeyer, E. Fung, J. Wildenhain, S.E. Pierce, S. Hoon, W. Lee, M. Proctor, R.P. St.Onge, M. Tyers, D. Koller, R.B. Altman, R.W. Davis, C. Nislow, and G. Giaever (2008). "The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes." Science, 18, 362-365. bib topics: CB          2007 J   B.E. Stranger, A.C. Nica, M.S. Forrest, A. Dimas, C.P. Bird C. Beazley, C.E. Ingle, M. Dunning, P. Flicek, D. Koller, S. Montgomery, S. Tavaré, P. Deloukas, and E.T. Dermitzakis (2007). "Population genomics of human gene expression." Nature Genetics, 39(10), 1217-24. bib topics: CB          J   H. Wang, E. Segal, A. Ben-Hur, Q. Li, M. Vidal, and D. Koller (2007). "InSite: A computational method for identifying protein-protein interaction binding sites on a proteome-wide scale." Genome Biology, 8(9), R192.1-R192.18. bib topics: CB          2006 J   S.-I. Lee, D. Pe'er, A. Dudley, G. Church, and D. Koller (2006). "Identifying Regulatory Mechanisms using Individual Variation Reveals Key Role for Chromatin Modification." Proc. National Academy of Sciences, 103(38), 14062-14067. bib topics: CB          2005 J   E. Segal, N. Friedman, N. Kaminski, A. Regev, and D. Koller (2005). "From signatures to models: Understanding cancer using microarrays." Nature Genetics, 37, S38-S45. By invitation. bib/abs topics: CB          J   E. Segal, D. Pe'er, A. Regev, D. Koller, and N. Friedman (2005). "Learning Module Networks." Journal of Machine Learning Research, 6, 557-588. [older version, 2003] bib/abs topics: CB LGM RPM    C   B. Taskar, V. Chatalbashev, D. Koller, and C. Guestrin (2005). "Learning Structured Prediction Models: A Large Margin Approach." Twenty-Second International Conference on Machine Learning (ICML). bib/abs topics: CB LGM RPM SL C   H. Wang, E. Segal, A. Ben-Hur, D. Koller, and D. Brutlag (2005). "Identifying protein-protein interaction sites on a genome-wide scale." Advances in Neural Information Processing Systems (NIPS 2004). bib/abs topics: CB    RPM    2004 J   E. Segal, N. Friedman, D. Koller, and A. Regev (2004). "A Module Map Showing Conditional Activity of Expression Modules in Cancer." Nature Genetics, 36(3), 1090-1098. bib/abs topics: CB          C   A.J. Battle, E. Segal, and D. Koller (2004). "Probabilistic Discovery of Overlapping Cell Processes and Their Regulation." Eight Annual International Conference on Research in Computational Molecular Biology (RECOMB). bib/abs topics: CB LGM       J   R.M. Marion, A. Regev, E. Segal, Y. Barash, D. Koller, N. Friedman, and E. O'Shea (2004). "Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression." Proc. National Academcy of Sciences USA, 101, 14315-22. bib/abs topics: CB          J   L. Getoor, J. Rhee, D. Koller, and P. Small (2004). "Understanding Tuberculosis Epidemiology using Probabilistic Relational Models." Journal of Artificial Intelligence in Medicine, 30, 233-256. bib topics: CB    RPM    C   E. Segal, R. Yelensky, A. Kaushal, T. Pham, A. Regev, D. Koller, and N. Friedman (2004). "GeneXPress: A Visualization and Statistical Analysis Tool for Gene Expression and Sequence Data." Proceedings of the 11th International Conference on Intelligent Systems for Molecular Biology (ISMB). bib/abs topics: CB          2003 J   J. Stuart, E. Segal, D. Koller, and S. Kim (2003). "A Gene Co-Expression Network for Global Discovery of Conserved Genetic Modules." Science, 302(5643), 249-55. bib/abs topics: CB          J   E. Segal, M. Shapira, A. Regev, D. Pe'er, D. Botstein, D. Koller, and N. Friedman (2003). "Module Networks: Identifying Regulatory Modules and Their Condition-Specific Regulators from Gene Expression Data." Nature Genetics, 34(2), 166-176. bib/abs topics: CB          C   E. Segal, A.J. Battle, and D. Koller (2003). "Decomposing gene expression into cellular processes." Proc. Pacific Symposium on Biocomputing (PSB) (pp. 89-100). bib/abs topics: CB    RPM    C   E. Segal, D. Pe'er, A. Regev, D. Koller, and N. Friedman (2003). "Learning Module Networks." Proc. Nineteenth Conference on Uncertainty in Artificial Intelligence (UAI) (pp. 525-534). [newer version, 2005] bib/abs topics: CB LGM RPM    J   E. Segal, R. Yelensky, and D. Koller (2003). "Genome-wide Discovery of Transcriptional Modules from DNA Sequence and Gene Expression." Bioinformatics, 19(S1 (Proc. ISMB)), 1273-82. Winner of the ISMB Best Paper Award. bib/abs topics: CB    RPM    J   E. Segal, H. Wang, and D. Koller (2003). "Discovering Molecular Pathways from Protein Interaction and Gene Expression data." Bioinformatics, 19(S1 (Proc ISMB)). Winner of the ISMB Best Student Paper Award. bib/abs topics: CB    RPM    2002 C   E. Segal, Y. Barash, I. Simon, N. Friedman, and D. Koller (2002). "From Promoter Sequence to Expression: A Probabilistic Framework." Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB) (pp. 263-272). bib topics: CB    RPM    2001 J   E. Segal, B. Taskar, A. Gasch, N. Friedman, and D. Koller (2001). "Rich probabilistic models for gene expression." Bioinformatics, 17(Suppl 1), S243-52. Proc. ISMB 2001. bib/abs topics: CB    RPM
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