Publications

• 2012
• 2011
• 2009
• 2008
• 2007
• 2006
• 2005
• 2004
• 2003
• 2002
• 1998-2001

• 2013

• A. Gitter, M. Carmi, N. Barkai, Z. Bar-Joseph.
  Linking the signaling cascades and dynamic regulatory networks controlling stress responses
  Genome Research, 23: 365-376, 2013
  Supporting website
  
• H.S. Le*, M. H. Schulz*, B.M. McCauley, V.F. Hinman, Bar-Joseph
  Probabilistic error correction for RNA sequencing
  Nucleic Acids Research, nar/gkt215, 2013
  Supporting website
  
• S. Navlakha , J. Suhan, A. Barth, Z. Bar-Joseph
  A High-Throughput Framework to Detect Synapses in Electron Microscopy Images
  Bioinformatics (Proceedings of The 21th Annual International Conference Intelligent Systems for Molecular Biology, ISMB), to appear, 2013
  
• A. Gitter, Z. Bar-Joseph
  Identifying proteins controlling key disease signaling pathways
  Bioinformatics (Proceedings of The 21th Annual International Conference Intelligent Systems for Molecular Biology, ISMB), to appear, 2013
  
• H.S. Le, Z. Bar-Joseph
  Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation
  Bioinformatics (Proceedings of The 21th Annual International Conference Intelligent Systems for Molecular Biology, ISMB), to appear, 2013
  
• K.N. Chang, S. Zhong, M.T. Weirauch,G. Hon, M. Pelizzola, H. Li, S.C. Huang, R.J. Schmitz, M.A. Urich, D. Kuo, J. Nery, H. Qiao, A. Yang, A. Jamali, T. Ideker, B. Ren, Z. Bar-Joseph, T.R. Hughes, J.R. Ecker
  Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis
  eLife, to appear, 2013
  
• K. Duskova, P. Nagilla, H.S. Le, P. Iyer, A. Thalamuthu, J. Martinson, Z. Bar-Joseph, W. Buchanan, C. Rinaldo and V. Ayyavoo
  MicroRNA regulation and its effects on cellular transcriptome in Human Immunodeficiency Virus-1 (HIV-1) infected individuals with distinct viral load and CD4 cell counts
  BMC Infectious Diseases, to appear, 2013
  

• 2012

• S. Navlakha, A. Gitter, Z. Bar-Joseph
  A network-based approach for predicting missing pathway interactions
  PLoS Computational Biology, 8:8, 2012
• Z. Bar-Joseph, A. Gitter, I. Simon
  Studying and modelling dynamic biological processes using time-series gene expression data
  Nature Reviews Genetics, 13, 552-564, 2012
• M.H. Schulz, W.E. Devanny, A. Gitter, S. Zhong, J. Ernst, Z. Bar-Joseph
  DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data
  BMC Systems Biology, 6:1, 2012
  Supporting website
  
• Y. Afek, N. Alon, Z. Bar-Joseph, A. Cornejo, B. Haeupler, F. Kuhn
  Beeping a maximal independent set
  Ditributed Computing , in press, 2012
  
• A. Wise, Z. Oltvai, Z. Bar-Joseph
  Matching experiments across species using expression values and textual information
  Bioinformatics (Proceedings of The 20th Annual International Conference Intelligent Systems for Molecular Biology, ISMB), 28: i258-264i, 2012
  Supporting website
  
• 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, 22;483(7388):218-21, 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