Systems Biology Group, Carnegie Mellon University - Publications

Systems Biology Group
School of Computer Science
Carnegie Mellon University

     HOME

     PEOPLE

     RESEARCH

     SOFTWARE

     PUBLICATIONS

     POSITIONS

     LINKS

     NEWS

     CONTACT

Publications
2012
Y. Kanfi, S. Naiman, G. Amir, V. Peshti, G. Zinman, L. Nahum, Z. Bar-Joseph, H.Y. Cohen The sirtuin SIRT6 regulates lifespan in male mice Nature, doi: 10.1038, 2012
2011
S. Navlakha, Z. Bar-Joseph Algorithms in nature: the convergence of systems biology and computational thinking Nature-EMBO Molecular Systems Biology, 7:546, 2011 Y. Afek, N. Alon, O. Barad, E. Hornstein, N. Barkai, Z. Bar-Joseph A biological solution to a fundamental distributed computing problem Science, 331(6014):183-5, 2011 Supporting information Selected as a highlight paper by the editors at Science Signaling and Cell H.S. Le, Z. Bar-Joseph Inferring Interaction Networks using the IBP applied to microRNA Target Prediction Twenty-Fifth Annual Conference on Neural Information Processing Systems (NIPS), to appear, 2011 H.T. Lin, Z. Bar-Joseph, B.F. Murphy Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs Journal of Computational Biology 18(11):1709-22, 2011 Supporting website G.E. Zinman, S. Zhong, Z. Bar-Joseph Biological interaction networks are conserved at the module level BMC Systems Biology, 5:134, 2011 Supporting website * co-first authors G. Zinman, R. Brower-Sinning, C.H. Emeche, J. Ernst, G.T. Huang, S. Mahony, A.J. Myers, D.M. O’Dee, J.L. Flynn, G.J. Nau, T.M. Ross, R.D. Salter, P.V. Benos, Z. Bar-Joseph, P.A. Morel Large Scale Comparison of Innate Responses to Viral and Bacterial Pathogens in Mouse and Macaque PLoS ONE, 6(7):e22401, 2011 corresponding authors P. Huggins, S. Zhong, I. Shiff, R. Beckerman, O. Laptenko, C. Prives, M.H. Schulz, I. Simon, Z. Bar-Joseph DECOD: Fast and Accurate Discriminative DNA Motif Finding Bioinformatics, 27(17):2361-7, 2011 Supporting website * co-first authors Y. Afek, N. Alon, Z. Bar-Joseph, A. Cornejo, B. Haeupler, F. Kuhn Beeping a maximal independent set Proceedings of the 25th International Symposium on DIStributed Computing (DISC), pp 32-50, 2011 A. Gitter, J. Klein-Seetharaman, A. Gupta, Z. Bar-Joseph Discovering pathways by orienting edges in protein interaction networks Nucleic Acids Research, 39(4):e22, 2011 Supporting website Selcted as a Featured Article (top 5% of NAR papers) H.T. Lin, Z. Bar-Joseph, B.F. Murphy Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pp 204-221, 2011 Supporting website H.T. Lin, B.F. Murphy, Z. Bar-Joseph Discriminative Motif Finding for Predicting Protein Subcellular Localization IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(2):441-51, 2011 Supporting website
2010
H.S. Le, Z. Bar-Joseph Cross Species Expression Analysis using a Dirichlet Process Mixture Model with Latent Matchings Twenty-Fourth Annual Conference on Neural Information Processing Systems (NIPS), pages 1270-1278, 2010 H.S. Le, Z.N. Oltvai, Z. Bar-Joseph Cross Species Queries of Large Gene Expression Databases Bioinformatics, 26(19):2416-23, 2010 Supporting website M. Klutstein, Z. Siegfried, A. Gispan, S. Farkash-Amar, G. Zinman, Z. Bar-Joseph, G. Simchen, I. Simon Evolutionary Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle-phase meiosis genes BMC Genomics, 11(1):478, 2010 D. Kuo^, K. Tan^, G. Zinman^, T. Ravasi, Z. Bar-Joseph, T. Ideker Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering Genome Biol., 11(7):R77, 2010 ^ equal contribution * corresponding authors Supporting information J. Ernst, H.L. Plasterer, I. Simon, Z. Bar-Joseph Integrating Multiple Evidence Sources to Predict Transcription Factor Binding in the Human Genome Genome Research, 20(4):526-36, 2010 Supporting website Y. Lu, R. Rosenfeld, G.J. Nau, Z. Bar-Joseph Cross species expression analysis of innate immune response Journal of Computational Biology, 17(3):253-68, 2010 A. Gitter, Y. Lu, Z. Bar-Joseph Computational methods for analyzing dynamic regulatory networks Computational Biology of Transcription Factor Binding, Book chapter, Methods in Molecular Biology, Humana Press, 674:419-41., 2010
2009
Y. Qi, H.K. Dhiman, N. Bhola, I. Budyak, S. Kar, D. Man, A. Dutta, K. Tirupula, B.I. Carr, J. Grandis, Z. Bar-Joseph, J. Klein-Seetharaman * corresponding authors Systematic prediction of human membrane receptor interactions Proteomics, 9(23):5243-55, 2009 Supporting website M. Lau, Z. Bar-Joseph and J. Kuffner Modeling Spatial and Temporal Variation in Motion Data ACM Transactions on Graphics (SIGGRAPH ASIA 2009) , 28(5), 2009 Supporting website A. Gitter, Z. Siegfried, M. Klutstein, O. Fornes, B. Oliva, I. Simon, Z. Bar- Joseph Backup in gene regulatory networks explains differences between binding and knockout results Nature-EMBO Molecular Systems Biology, 5:276, 2009 Supplementary information Z. Bar-Joseph Schools Anxiously Await NRC Program Rankings Science, 324(5931):1140-1, 2009 Y. Lu, P. Huggins, Z. Bar-Joseph Cross species analysis of microarray expression data Bioinformatics, 25(12), pp. 1476-1483, 2009 L. Li, Y. Lu, L.X. Qin, Z. Bar-Joseph, M. Werner-Washburne, L.L. Breeden Budding Yeast SSD1-V Regulates Transcript Levels of Many Longevity Genes and Extends Chronological Life Span in Purified Quiescent Cells Mol Biol Cell. , 20(17):3851-64, 2009 J. Ernst, L. Ghanem, Z. Bar-Joseph, M. McNamara, J. Brown, R.A. Steinman IL-3 and oncogenic Abl regulate the myeloblast transcriptome by altering mRNA stability PLoS ONE, 4(10):e7469, 2009 Y. Lu, R. Rosenfeld, G.J. Nau, Z. Bar-Joseph Cross Species Expression Analysis of Innate Immune Response Proceedings of The 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pp. 90-107, 2009 Supporting website Y. Shi, M. Klutstein, I. Simon, T. Mitchell1 and Z. Bar-Joseph A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors Journal of Computational Biology, 16(8):1035-49, 2009
2008
Y. Lu, R. Rosenfeld, I. Simon, G.J. Nau and Z. Bar-Joseph A Probabilistic Generative Model for GO Enrichment Analysis Nucleic Acids Research, 2008 Supporting website T.H. Lin, N. Kaminski and Z. Bar-Joseph Alignment and Classification of Time Series Gene Expression in Clinical Studies Bioinformatics (Proceedings of The 16th Annual International Conference Intelligent Systems for Molecular Biology, ISMB), 24(13) pp. i147-i155, 2008 Supporting website Y. Qi, F. Balem, C. Faloutsos, J. Klein-Seetharaman and Z. Bar-Joseph Protein Complex Identification by Supervised Graph Clustering Bioinformatics (Proceedings of The 16th Annual International Conference Intelligent Systems for Molecular Biology, ISMB), 24(13) pp i250-i258, 2008 Supporting website L. Peña-Castillo, M. Tasan, ... , Y. Qi, J. Klein-Seetharaman, Z. Bar-Joseph, ... , T.R. Hughes and F.P. Roth *A critical assessment of Mus musculus* gene function prediction using integrated genomic evidence** Genome Biology, 9(Suppl 1):S2, 2008 Y. Lu, S. Mahony, P.V. Benos, R. Rosenfeld, I. Simon, L.L. Breeden, and Z. Bar-Joseph Selecting a threshold for identifying cell cycle genes Genome Biology, 9:403, 2008 J. Ernst, Q.K. Beg, K.A. Kay, G. Balázsi, Z.N. Oltvai, Z. Bar-Joseph. A Semi-Supervised Method for Predicting Transcription Factor-Gene Interactions in Escherichia coli. PLoS Computational Biology, 4(3): e1000044, 2008 Supporting website Z. Bar-Joseph, Z. Siegfried, M. Brandeis, B. Brors, Y. Lu, R. Eils, B.D. Dynlacht and I. Simon Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells Proceedings of the National Academy of Science (PNAS), 105(3), pp 956-961, 2008 Supporting website Y. Shi, I. Simon, T. Mitchell1 and Z. Bar-Joseph A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors Proceedings of The 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB),pp. 82-97, 2008 Supporting website A. Vazquez, Q.K. Beg, M.A. de Menezes, J. Ernst, Z. Bar-Joseph, A.-L. Barabási, L.G. Boros, Z.N. Oltvai Impact of the solvent capacity constraint on E. coli metabolism BMC Systems Biology, 2:7, 2008. A. Gupta and Z. Bar-Joseph Extracting dynamics from static cancer expression data IEEE/ACM Transactions on Computational Biology and Bioinformatics, 5(2) pp 172-82, 2008 Supporting website
2007
Y. Lu, S. Mahony, P.V. Benos, R. Rosenfeld, I. Simon, L.L. Breeden, and Z. Bar-Joseph Combined analysis reveals a core set of cycling genes Genome Biology, 8(7):R146, 2007 Supporting website Q.K. Beg, A. Vazquez, J. Ernst, M.A. de Menezes, Z. Bar-Joseph, A.-L. Barabási, and Z.N. Oltvai Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity Proceedings of the National Academy of Science (PNAS), 104(31), pp 12663-12668, 2007 Supporting Information Y. Shi, M. Klustein, I. Simon, T. Mitchell, and Z. Bar-Joseph Continuous hidden process model for time series expression experiments Bioinformatics (Proceedings of ISMB 2007), 23(13), pp i459-i467, 2007 Supporting website Y. Qi, J. Klein-Seetharaman and Z. Bar-Joseph mixture of feature experts approach for protein-protein interaction prediction BMC Bioinformatics, 8(Suppl 10):S6, 2007 Supporting website J. Ernst, O. Vainas, C.T. Harbison, I. Simon and Z. Bar-Josep Reconstructing dynamic regulatory maps Nature-EMBO Molecular Systems Biology, 3:74, 2007 Supporting website N. Kaminski and Z. Bar-Joseph A patient-gene model for temporal expression profiles in clinical studies Journal of Computational Biology, 14(3), pp 324-338, 2007 Supporting website Y. Shi, T. Mitchell and Z. Bar-Joseph Inferring Gene Regulatory Relationships from Multiple Time Series Datasets Bioinformatics, 23(6), pp. 755-63, 2007 Supporting website
2006
Y. Lu, R. Rosenfeld and Z. Bar-Joseph Identifying cycling genes by combining sequence homology and expression data Bioinformatics (Proceedings of ISMB 2006), 22(14):e314-22, 2006 J. Ernst, Z. Bar-Joseph STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics, 7:191, 2006 Supporting website Y. Qi, Z. Bar-Joseph and J. Klein-Seetharaman. Comprehensive comparison of approaches for predicting protein-protein interactions from multiple data sources Proteins: Structure, Function, and Bioinformatics,, 63(3), pp. 490-500, 2006 N. Kaminski and Z. Bar-Joseph A patient-gene model for temporal expression profiles in clinical studies Proceedings of The Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB), pp 69-82, 2006

2005
I. Simon, Z. Siegfried, J. Ernst and Z. Bar-Joseph. Combined Static and Dynamic Analysis for Determining the Quality of Time-Series Expression Profiles Nature Biotechnology, 23(12), pp 1503-1508, 2005. Supporting website Supporting Methods Supporting Results J. Ernst, G. Nau, Z. Bar-Joseph Clustering Short Time Series Gene Expression Data. Bioinformatics (Proceedings of ISMB 2005), 21 Suppl 1, pp. I159-I168, 2005 Supporting website Y. Qi, J. Klein-Seetharaman and Z. Bar-Joseph A mixture of experts approach for protein-protein interaction prediction. Proceedings of NIPS workshop on Computational Biology and the Analysis of Heterogeneous Data 2005 R Singh, N. Palmer, D. Gifford, B. Berger and Z. Bar-Joseph Active Learning for Sampling in Time-Series Experiments With Application to Gene Expression Analysis. In Proceedings of the 22nd International Conference on Machine Learning (ICML), pp 833-840, 2005 Supporting website Y. Qi, J. Klein-Seetharaman and Z. Bar-Joseph Random Forest Similarity for Protein-Protein Interaction Prediction from Multiple Sources Proceedings of the Pacific Symposium on Biocomputing (PSB), 10, 2005.
2004
Z. Bar-Joseph, S. Farkash, D.K.Gifford, I Simon, R. Rosenfeld Deconvolving cell cycle expression data with complementary information Bioinformatics (Proceedings of ISMB 2004), 20 Suppl 1, pp. I23-I30, 2004 Supporting website Z. Bar-Joseph Analyzing time series gene expression data Bioinformatics, 20(16), pp 2493-2503, 2004
2003
Z. Bar-Joseph, G. Gerber, T. Lee, N. Rinaldi, J. Yoo, F. Robert, B. Gordon, E. Fraenkel, T. Jaakkola, R. Young, and D. Gifford Computational discovery of gene modules and regulatory networks.* Nature Biotechnology, 21(11) pp. 1337-42, 2003 * Equal contributing author Supporting website Z. Bar-Joseph, G. Gerber, I. Simon, D. Gifford and T. Jaakkola Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes. Proceedings of the National Academy of Science (PNAS), 100(18), pp 10146-51, 2003 Supporting website Appendix Z. Bar-Joseph, G. Gerber, D. Gifford, T. Jaakkola and I. Simon Continuous Representations of Time Series Gene Expression Data. Journal of Computational Biology, 10(3-4), pp 241-256, 2003 Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Angèle M. Hamel, Tommy S. Jaakkola and Nathan Srebro K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data. Bioinformatics, 19(9), pp 1070-8, 2003 Z. Bar-Joseph and D. Cohen-Or. Hierarchical Context-based Pixel Ordering. Computer Graphics Forum (Proceedings of Eurographics) 22(3), pp. 349-358, 2003 M. Cardle, S. Brooks, Z. Bar-Joseph and P. Robinson Sound-by-Numbers: Motion-Driven Sound Synthesis. SIGGRAPH Symposium on Computer Animation (SCA), 2003
2002
T.I. Lee, N. J. Rinaldi, F. Robert, D. T. Odom, Z. Bar-Joseph, G. K. Gerber, ... D. K. Gifford and R. A. Young Transcriptional Regulatory Networks in Saccharomyces cerevisiae Science, 798, pp 799-804, 2002 Supporting website S. Dubnov, Z. Bar-Joseph, R. El-Yaniv, D. Lischinski, and M. Werman Synthesizing sound textures through wavelet tree learning. IEEE Computer Graphics and Applications, 22(4) pp. 38-48, 2002 Z. Bar-Joseph, I. Keidar, and N. Lynch Early-Delivery Dynamic Atomic Broadcast. 16th International Symposium on DIStributed Computing (DISC), pp 1-16, 2002. Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Angèle M. Hamel, Tommi S. Jaakkola and Nathan Srebro K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data. Proceedings of the 2nd Workshop on Algorithms in Bioinformatics (WABI 2002), LNCS 2452, pp 506-520, 2002 Z. Bar-Joseph, G. Gerber, D. Gifford, T. Jaakkola and I. Simon. A new approach to analyzing gene expression time series data. In Proceedings of The Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB), pp 39-48, 2002
1998-2001
Z. Bar-Joseph, R. El-Yaniv, D. Lischinski, and M. Werman Texture mixing and texture movie synthesis using statistical learning. IEEE Transactions on Visualization and Computer Graphics, 7(2), pp. 120-135, 2001 Z. Bar-Joseph, D. Gifford, and T. Jaakkola Fast optimal leaf ordering for hierarchical clustering. Bioinformatics (Proceedings of ISMB 2001),, 17(S1), pp 22-29, 2001 Supporting website Software Z. Bar-Joseph, I. Keidar, T. Anker, and N. Lynch QoS Preserving Totally Ordered Multicast. In the 5th International Conference On Principles Of DIstributed Systems (OPODIS), pages 143-162, 2000 Z. Bar-Joseph, D. Lischinski, M. Werman, S. Dubnov and R. El-Yaniv Granular Synthesis of Sound Textures using Statistical Learning. Proceedings of the International Computer Music Conference (ICMC) pp. 178-181, 1999 Z. Bar-Joseph and M. Ben-Or A Tight Lower Bound for Randomized Synchronous Consensus in proceedings of the Seventeenth Annual ACM Symposium on Principles of Distributed Computing (PODC), pp. 193-199, Puerto Vallarta, Mexico, 1998 Best student paper award