Publications

Journal papers

  • Y. Lu, R. Rosenfeld and Z. Bar-Joseph
    Identifying cycling genes by combining sequence homology and expression data
    Bioinformatics (Proceedings of ISMB 2006), in press, 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
    • Supporting website

  • 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

  • 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

  • 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

  • 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, 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

    Papers in refereed conferences (not listed above)

  • 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

  • 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.

  • M. Cardle, S. Brooks, Z. Bar-Joseph and P. Robinson
    Sound-by-Numbers: Motion-Driven Sound Synthesis.
    SIGGRAPH Symposium on Computer Animation (SCA), 2003

  • 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

  • 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

    • Thesis, reports etc.

  • Z. Bar-Joseph, I. Keidar, and N. Lynch
    Early-Delivery Dynamic Atomic Broadcast.
    MIT Technical Report MIT-LCS-TR-840, April 2002.

  • Z. Bar-Joseph, I. Keidar, T. Anker, and N. Lynch:
    QoS Preserving Totally Ordered Multicast.
    MIT Technical Report MIT-LCS-TR-796, January 2000.

  • Z. Bar-Joseph.
    Statistical Learning of Multi-Dimensional Textures.
    Masters thesis, Department of Computer Science, Hebrew University, 1999.