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Daphne Koller Publications
Research Areas (all)Publication TypeYears (all)
BMBiology and Medicine   LGMLearning Graphical Models
RPMRicher Probabilistic Models   SLSupervised Learning
JJournal Article
CConference Paper
ChBook Chapter
TTechnical Report
PhDPhD Disseration
1985 - 1989
1990 - 1994
1995 - 1999
2000 - 2004
2005 - 2009
2010 - 2014


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 pdf html
topics: BM         

J   D. Fiedler, H. Braberg, M. Mehta, G. Chechik, G. Cagney, P. Mukherjee, 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 pdf html
topics: BM         

J   G. Chechik and D. Koller (2009). "Timing of gene expression responses to environmental changes." Journal of Computational Biology, 16(2), 279-290. bib pdf
topics: BM         

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 pdf ppt
topics: BM         

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 pdf html
topics: BM         

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 pdf html
topics: BM         

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 html
topics: BM         

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 html
topics: BM         

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 pdf
topics: BM         

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 pdf
topics: BM         

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 pdf
topics: BM         

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 pdf
topics: BM         

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 pdf
topics: BM 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 pdf ps.gz
topics: BM 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 pdf
topics: BM    RPM   

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