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

TypeReferenceDownload
topics: BMLTWLGMRPMRPSL

2011
J   A.H. Beck, A.R. Sangoi, S. Leung, R.J. Marinelli, T.O. Nielsen, M.J. van de Vijver, R.B. West, M. van de Rijn, and D. Koller (2011). "Systematic Analysis of Breast Cancer Morphology Uncovers Stromal Features Associated with Survival." Science Translational Medicine, 3(108). bib html
topics: BM               

J   J. Laserson, V. Jojic, and D. Koller (2011). "Genovo: De Novo Assembly For Metagenomes." Journal of Computational Biology, 18(3), 429-43. bib pdf
topics: BM               

2010
J   S. Saria, A.K. Rajani, J. Gould, D. Koller, and A.A. Penn (2010). "Integration of early physiological responses predicts later illness severity in preterm infants." Science Translational Medicine, 2(48). bib html
topics: BM               

J   A.J. Battle, M. Jonikas, P. Walter, J. Weissman, and D. Koller (2010). "Automated identification of pathways from quantitative genetic interaction data." Molecular Systems Biology, 6, 379. bib pdf
topics: BM               

J   F. Moussavi, G. Heitz, F. Amat, L.R. Comolli, D. Koller, and M.A. Horowitz (2010). "3D Segmentation of Cell Boundaries from Whole Cell Cryogenic Electron Tomography Volumes." Journal of Structural Biology, 170(1), 134-145. bib html
topics: BM          RP   

J   M.E. Hillenmeyer, E. Ericson, R.W. Davis, C. Nislow, D. Koller, and G. Giaever (2010). "Systematic analysis of genome-wide fitness data reveals novel gene function and drug action." Genome Biology, 11(R30). bib pdf
topics: BM               

C   S. Saria, G. McElvain, A. Rajani, A. Penn, and D. Koller (2010). "Combining Structured and Free-text Data for Automatic Coding of Patient Outcomes." Proceedings of the Americal Medical Informatics Association (AMIA) Annual Symposium. bib
topics: BM LTW          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 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               

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 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               

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 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               

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 pdf
topics: BM               

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 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      

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 pdf
topics: BM               

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 pdf ps.gz
topics: BM    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 pdf
topics: BM               

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: BM       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 pdf ps.gz
topics: BM               

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 pdf
topics: BM               

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 pdf
topics: BM               

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

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