Publications

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

• 2023

• J. Hislop, Q. Song, K. Keshavarz., A. Alavi,. . ., Z. Bar-Joseph and M.R. Ebrahimkhani.
  Modeling post-implantation human development to yolk sac blood emergence.
  Nature , online ahead of print, 2023
  
• M. Bailey, S. Moayedpour, . Li, A. Corrochano-Navarro, A. Kotter, L. Kogler-Anele, S. Riahi, C. Grebner, G. Hessler, H. Matter, M. Bianciotto, P. Mas, Z. Bar-Joseph*, and S. Jager*.
  Deep Batch Active Learning for Drug Discovery.
  eLife , 2023
  
• S. Li, S. Moayedpour, R. Li, M. Bailey,. . ., Z. Bar-Joseph* and S. Jager*.
  CodonBERT: Large Language Models for mRNA design and optimization.
  Nuerips Workshop on Generative AI and Biology (GenBio@NeurIPS2023). , 2023
  
• H. Chen, D. Li and Z. Bar-Joseph
  SCS: Cell Segmentation for High-Resolution Spatial Transcriptomics
  Nature Methods , 20(8):1237-1243, 2023
  
• A. Gurkar , A. Gerencser , A. Mora , A. ,. . ., Z. Bar-Joseph , Z Ji and J.F. Passos
  Spatial mapping of cellular senescence: emerging challenges and opportunities
  Nature Aging , 3, 776-790, 2023
  
• M. Dayao, A. Trevino, H. Kim, M. Ruffalo, H.B. D'Angio, R. Preska, U. Duvvuri, A. Mayer and Z. Bar-Joseph
  Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis
  Bioinformatics (Proceedings of the 31st Annual International Conference Intelligent Systems for Molecular Biology, ISMB) , 9(39 Suppl 1, i140-i148, 2023
  
• H. Chen, D. Li and Z. Bar-Joseph
  Cell Segmentation for High-Resolution Spatial Transcriptomics
  Proceedings of the 27th Annual International Conference on Research in Computational Molecular Biology (RECOMB) , 51 (7), 251-253, 2023
  
• Q. Song, M. Ruffalo and Z Bar-Joseph
  Using single cell atlas data to reconstruct regulatory networks
  Nucleic Acids Research , 51 (7), e38-e38, 2023
  

• 2022

• Q. Song, J. Wang and Z. Bar-Joseph
  scSTEM: clustering pseudotime ordered single-cell data
  Genome Biology. , 23, 150 2022
  
• E. Hasanaj, A. Alavi, A. Gupta, B. Poczos and Z Bar-Joseph
  Multiset multicover methods for discriminative marker selection
  Cell Reports Methods. , 100332, 2022
  
• B. Berger, D. Tian, W. Vivian Li, M. El-Kebir, A.I. Tomescu, R. Singh, N. Beerenwinkel, Y. Li, C. Boucher and Z. Bar-Joseph h
  What are the keys to succeeding as a computational biologist in todays research climate?
  Cell Systems. , 13(10), 781-785, 2022
  
• E. Hasanaj, J. Wang, A. Sarathi, J. Ding and Z. Bar-Joseph
  Interactive single-cell data analysis using Cellar
  Nature Communications. , 13 (1), 1-6, 2022
  
• Y. Yuan, C. Cosme, T. Adams, J. Schupp, K. Sakamoto, N. Xylourgidis, M. Ruffalo, J. Li, N. Kaminski and Z. Bar-Joseph
  CINS: Cell Interaction Network inference from Single cell expression data
  PLoS Comput Biol. , 18 (9), e1010468, 2022
  
• A. Zeleniak, C. Wiegand, W. Liu, R. McCormick, A. Alavi, H. Guan, S. Bertera, R. Lakomy, A. Tajima, H. Cohen, S. Wong, L. Balikani, B. Mizerak, Z. Bar-Joseph, M. Trucco, I. Banerjee, Y. Fan
  De novo construction of T cell compartment in humanized mice engrafted with iPSC-derived thymus organoids
  Nature Methods. , 19, 1306-1319, 2022
  
• J. Lugo-Martinez, S. Xu, J. Levesque, D. Gallagher, L.A. Parker, J. Neu, C.J. Stewart, J. E. Berrington, N.D. Embleton, G. Young, K.E. Gregory, M. Good, A. Tandon, D. Genetti, T. Warren, Z. Bar-Joseph.
  Integrating longitudinal clinical and microbiome data to predict growth faltering in preterm infants
  Journal of Biomedical Informatics , in press, 2022
  
• D. Li, J. Ding, Z, Bar-Joseph
  UNIFAN: A Tool for Unsupervised Single-Cell Clustering and Annotation
  Journal of Computational Biology , in press, 2022
• D. Li, J. Ding, Z, Bar-Joseph
  Unsupervised cell functional annotation for single-cell RNA-seq
  Genome Research, 32: 1765-1775, 2022
  Previous version in Proceedings of the 26th Annual International Conference on Research in Computational Molecular Biology (RECOMB) , pages 349-352, 2022
  
• P. Lee, P. Blood, K. Borner,. . ., Laura Niedernhofer
  NIH SenNet Consortium: Mapping Senescent Cells in the Human Body to Understand Health and Disease
  Nature Aging, 2, 1090--1100, 2022
  
• D. Li, J.J. Velazquez, J. Ding, J. Hislop, M.R. Ebrahimkhani, Z, Bar-Joseph
  TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data
  Genome Biology. , 23, 73, 2022
  
• M.T. Dayao, M. Brusko, C. Wasserfall, and Z. Bar-Joseph
  Membrane marker selection for segmenting single cell spatial proteomics data.
  Nature Communications. , 13 (1), 1-10, 2022
  
• J. Ding, N. Sharon, Z. Bar-Joseph
  Temporal modelling using single-cell transcriptomics.
  Nat Rev Gene. , 23 (6), 355-368, 2022
  

• 2021

• S. Rashid, G. Taubenfeld, Z. Bar-Joseph
  The Epigenetic Consensus Problem.
  International Colloquium on Structural Information and Communication Complexity (SIROCCO). , pp 146-163, 2021
  
• H. Teng, Y. Yuan, Z. Bar-Joseph
  Clustering Spatial Transcriptomics Data.
  Bioinformatics. , 38(4):997-1004, 2021
  
• J. Ding, A. Alavi, M. R.Ebrahimkhani, Z. Bar-Joseph.
  Computational tools for analyzing single-cell data in pluripotent cell differentiation studies.
  Cell Reports Methods. , 1(6), 2021
  
• Y Yuan, Z Bar-Joseph.
  Deep learning of gene relationships from single cell time-course expression data.
  Briefings in Bioinformatics. , 22(5), 2021
  
• S. Rashid, S. Shah, Z. Bar-Joseph, R. Pandya
  Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data
  Bioinformatics, 37 (11), 1535-1543, 2021
  Previous version in Proceedings of the RECOMB-Computational Cancer Biology (CCB) meeting, 2018
  
• D. Ruiz-Perez^, J. Lugo-Martinez^, N. Bourguignon, K. Mathee, B. Lerner, Z. Bar-Joseph*, G. Narasimhan*
  Dynamic Bayesian networks for integrating multi-omics time-series microbiome data.
  mSystems , 6(2):e01105-20, 2021
  ^ co-first authors
  *corresponding authors
  
• D. Li, J. Ding, Z. Bar-Joseph
  Identifying signaling genes in spatial single cell expression data.
  Bioinformatics , 37(7), Pages 968-975, 2021
  
• G. Songwei, H. Wang, A. Alavi, E. Xing and Z. Bar-Joseph
  Supervised Adversarial Alignment of Single-Cell RNA-seq Data
  Journal of Computational Biology , 28(5):501-513, 2021
  Original version appeared in Proceedings of the 24th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pp 72-87, 2020
  

• 2020

• Y. Yuan, Z. Bar-Joseph
  GCNG: Graph convolutional networks for inferring cell-cell interactions
  Genome Biology , 21(1):300, 2020
  
• A. Alavi, Z. Bar-Joseph.
  Iterative point set registration for aligning scRNA-seq data.
  PLoS Comput Biol. , 16(10):e1007939, 2020
  
• J Ding, Z Bar-Joseph.
  Analysis of time series regulatory networks .
  Current Opinion in Systems Biology. , 21, Pages 16-24, 2020
  
• H. Zafar, C. Lin, Z. Bar-Joseph.
  Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data
  Nature Communications , 11:3055, 2020
  
• C. Lin, J. Ding, Z. Bar-Joseph.
  Inferring TF activation order in time series scRNA-Seq studies
  PLoS Comput Biol. , 16(2):e1007644, 2020
  
• Z. Bar-Joseph, I. Simon.
  Introduction to Special Issue Focused on Regulatory Genomics
  Current Opinion in Systems Biology. , to appear, 2020
  
• K. Hurley, J. Ding, C. Villacorta-Martin, M.J. Herriges, A. Jacob, M. Vedaie, K.D. Alysandratos, Y.L. Sun, C. Lin, R.B. Werder, J. Huang, A.A. Wilson, A. Mithal, G. Mostoslavsky, I. Oglesby, I.S. Caballero, S.H. Guttentag, F. Ahangari, N. Kaminski, A. Rodriguez-Fraticelli, F. Camargo, Z. Bar-Joseph*, D.N. Kotton*.
  Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors.
  *corresponding authors
  Cell Stem Cell , S1934-5909(19)30527-2, 2020
  
• M. Zander, M.G. Lewsey, N.M. Clark, L. Yin, A. Bartlett, J.P. Saldierna Guzman, E. Hann, A.E. Langford, B. Jow, A. Wise, J.R. Nery, H. Chen, Z. Bar-Joseph, J.W. Walley, R. Solano, J.R. Ecker
  Integrated multi-omics framework of the plant response to jasmonic acid
  Nature Plants, 6(3):290-302, 2020
  

• 2019

• Y. Yuan, and Z. Bar-Joseph
  Deep learning for inferring gene relationships from single-cell expression data
  Proceedings of the National Academy of Science (PNAS) , epub ahead of print, 2019
  Software available in GitHub
  
• J. Ding, F. Ahangari, C.R. Espinoza, D. Chhabra, T. Nicola, X. Yan, C.V. Lal, J.S Hagood, N. Kaminski, Z. Bar-Joseph*, N. Ambalavanan*.
  Integrating multi-omics longitudinal data to reconstruct networks underlying lung development.
  *corresponding authors
  Am J Physiol Lung , 2019
  Supporting website
  
• M.P. Snyder, S. Lin, A. Posgai, M. Atkinson, R. Satija, N. Gehlenborg, J. Laskin, P. Harbury, N.A. Nystrom, J.C. Silverstein, Z. Bar-Joseph*, K. Zhang, K. Borner, L. Cai, S.A. Teichmann, B. Paten, P. Mabee R. Conroy.
  The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.
  Nature, 574(7777):187-192. 2019.
  *corresponding author
  
• J. Lugo-Martinez, J. Dengjel, Z. Bar-Joseph, R.F. Murphy
  Integration of Heterogeneous Experimental Data Improves Global Map of Human Protein Complexes
  Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB), pp144-53, 2019
  
• S. Rashid, Z. Long, S. Singh, M. Kohram, H. Vashistha, S. Navlakh, H. Salman, Z.N. Oltvai and Z. Bar-Joseph
  Adjustment in tumbling rates improves bacterial chemotaxis on obstacle-laden terrains.
  Proceedings of the National Academy of Science (PNAS) , 116(24):11770-11775, 2019
  Nature Reviews Microbiology News and Views: E. coli takes every hurdle in stride
  
• M. Ruffalo and Z. Bar-Joseph Z.
  Protein interaction disruption in cancer.
  BMC Cancer, 19(1):370, 2019
  
• J.E. McDonough, F. Ahangari, Q. Li, S. Jain, W.E. Verleden, J. Herazo-Maya, M. Vukmirovic, G. DeIuliis, A. Tzouvelekis, N. Tanabe, F. Chu, X. Yan, J. Verschakelen, R.J. Homer, D.V. Manatakis, J. Zhang, J. Ding, K. Maes, L. De Sadeleer, R. Vos, A. Neyrinck, P.V. Benos, Z. Bar-Joseph, D. Tantin, J.C. Hogg, B.M. Vanaudenaerde, W.A. Wuyts, N. Kaminski
  Transcriptional regulatory model of fibrosis progression in the human lung
  JCI Insight, [Epub ahead of print], 2019
  
• H. Liu, C.H. Zhang, N. Ammanamanchi, S. Suresh, C. Lewarchik, ..., J. Ding, Z. Bar-Joseph, Y. Wu, V. Yechoor, M. Moulik, J. Johnson, J. Weinberg, M. Reyes-Mugica, M.L. Steinhauser, B. Kuhn.
  Control of cytokinesis by ?-adrenergic receptors indicates an approach for regulating cardiomyocyte endowment.
  Sci Transl Med., 11(513), 2019
  
• C. Lin and Z. Bar-Joseph
  Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data.
  Bioinformatics, epub ahead of print, 2019
  
• J. Ding C. Lin and Z. Bar-Joseph
  Cell lineage inference from SNP and scRNA-Seq data
  Nucleic Acids Res., 47(10):e56 of print, 2019
  
• J. Lugo-Martinez, D. Ruiz-Perez, G. Narasimhan and Ziv Bar-Joseph
  Dynamic interaction network inference from longitudinal microbiome data
  Microbiome , 7(1):54, 2019
  
• S. Rashid, S. Singh, S. Navlakha, and Ziv Bar-Joseph
  A bacterial based distributed gradient descent model for mass scale evacuations
  Swarm and Evolutionary Computation , 46:97-103, 2019
  
• M. Ruffalo, R. Thomas, J. Chen, A.V. Lee, S. Oesterreich, and Z. Bar-Joseph
  Network-guided prediction of aromatase inhibitor response in breast cancer
  PLoS Comput Biol., 15(2):e1006730, 2019
  
• M. Ray, M.M. Ruffalo and Ziv Bar-Joseph
  Construction of integrated microRNA and mRNA immune cell signatures to predict survival of patients with breast and ovarian cancer.
  Genes, Chromosomes and Cancer, 58(1):34-42, 2019
  

• 2018

• J. Ding, J.S. Hagood, N. Ambalavanan, N. Kaminski, Z. Bar-Joseph
  iDREM: Interactive visualization of dynamic regulatory networks.
  PLoS Computational Biology, 14(3):e1006019 2018
  Supporting website
  
• C. Firtina, Z. Bar-Joseph, C. Alkan and A.E. Cicek
  Hercules: a profile HMM-based hybrid error correction algorithm for long reads.
  Nucleic Acids Res., Epub ahead of print, 2018
  Supporting website
  
• C.E. Friedman, Q. Nguyen, S.W. Lukowski, ..., J. Ding, Y. Wang, J. Hudson, H. Ruohola-Baker, Z. Bar-Joseph, P.P. Tam, J.E. Powell, N.J. Palpant
  Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation.
  Cell Stem Cell. , 23(4):586-598, 2018
  
• A. Alavi, M. Ruffalo, A. Parvangada, Z. Huang, Z. Bar-Joseph
  A web server for comparative analysis of single-cell RNA-seq data .
  Nature Communications , 9 (1), 4768, 2018
  Supporting website
  
• J. Ding, B.J. Aronow, N. Kaminski, J. Kitzmiller, J.A. Whitsett, Z. Bar-Joseph
  Reconstructing differentiation networks and their regulation from time series single-cell expression data.
  Genome Research, 28: 383-395, 2018
  Supporting website
  
• S. Rashid, S. Shah, Z. Bar-Joseph, R. Pandya
  Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data .
  Proceedings of the RECOMB-Computational Cancer Biology (CCB) meeting, 2018
  
• S. Navlakha, Z. Bar-Joseph, A.L. Barth.
  Network Design and the Brain.
  Trends Cogn Sci., 22(1):64-78, 2018
  
• S. Rashid, G. Taubenfeld, and Z. Bar-Joseph
  Genome Wide Epigenetic Modifications as a Shared Memory Consensus Problem
  6th Workshop on Biological Distributed Algorithms , 2018
  

• 2017

• J. Ding, Z. Bar-Joseph.
  MethRaFo: MeDIP-seq methylation estimate using a Random Forest Regressor
  Bioinformatics , 33(21):3477-3479, 2017
  Supporting website
  
• M. Ruffalo, P. Stojanov P, V.K. Pillutla, R. Varma, Z. Bar-Joseph.
  Reconstructing cancer drug response networks using multitask learning.
  BMC Syst Biol. , 11(1):96, 2017
  Supporting website
  
• J.D. Herazo-Maya, J. Sun, P.L. Molyneaux, Q. Li, J.A. Villalba, ..., Z. Bar-Joseph, K.F. Gibson, H. Zhao, E.L. Herzog, I.O. Rosas, T.M. Maher, N. Kaminski.
  Validation of a 52-gene risk profile for outcome prediction in patients with idiopathic pulmonary fibrosis: an international, multicentre, cohort study.
  Lancet Respir Med. , 2600(17)30349-1, 2017
  
• C. Lin, S. Jain, H. Kim, Z. Bar-Joseph.
  Using neural networks for reducing the dimensions of single-cell RNA-Seq data
  Nucleic Acids Research , 45(17):e156, 2017
  Supporting website
  
• S. Rashid, D.N. Kotton, Z. Bar-Joseph.
  TASIC: Determining branching models from time series single cell data.
  Bioinformatics , 33(16):2504-2512, 2017
  Supporting website
  
• M. Kleyman*, E. Sefer*, T. Nicola, C. Espinoza, D. Chhabra, J.S. Hagood, N. Kaminski, N. Ambalavanan, and Z. Bar-Joseph
  Selecting the most appropriate time points to profile in high-throughput studies
  eLife pii: e18541, 2017
  Supporting website
  
• N.J. Venkatachari, S. Jain, L. Walker, S. Bivalkar-Mehla, A. Chattopadhyay, Z. Bar-Joseph, C. Rinaldo, A. Ragin, E. Seaberg, A. Levine, J. Becker, E. Martin, N. Sacktor, V. Ayyavoo.
  Transcriptome analyses identify key cellular factors associated with HIV-1 associated neuropathogenesis in infected men.
  AIDS, 31(5):623-633, 2017
  
• M.H. Schulz and Ziv Bar-Joseph.
  Probabilistic models for error correction of non-uniform sequencing data.
  Chapter in Algorithms for Next-Generations Sequencing Data: Techniques, Approaches and Applications, Springer Press, to appear, 2017
  

• 2016

• L. Song, S.C. Huang, A. Wise, R. Castanon, J.R. Nery, H. Chen, M. Watanabe, J. Thomas, Z. Bar-Joseph and J.R. Ecker
  A transcription factor hierarchy defines an environmental stress response network
  Science, 354(6312), pii: aag1550, 2016
  
• E. Sefer, M. Kleyman and Z. Bar-Joseph
  Tradeoffs between Dense and Replicate Sampling Strategies for High-Throughput Time Series Experiments.
  Cell Systems, 3(1):35-42, 2016
  Supporting website
  
• M. Ruffalo and Z. Bar-Joseph.
  Genome-wide predictions of miRNA regulation by transcription factors.
  Bioinformatics (Proceedings of the 15th European Conference on Computational Biology, ECCB), 32(17):i746-i754, 2016
  Supporting website
  
• S. Jain, J. Arrais, N.J. Venkatachari, V. Ayyavoo, and Z. Bar-Joseph.
  Reconstructing the temporal progression of HIV-1 immune response pathways.
  Bioinformatics (Proceedings of the 24th Annual International Conference Intelligent Systems for Molecular Biology, ISMB) 32(12):i253-i261, 2016
  Supporting website
  
• E. Sefer and Z. Bar-Joseph.
  Shall we dense? Comparing design strategies for time series expression experiments*
  Proceedings of the 20th Annual International Conference on Research in Computational Molecular Biology (RECOMB) to appear, 2016
  *Winner of the 'Best Papepr Award'
  Supporting website
  
• S. Singh*, S. Rashid*, S. Navlakha and Z. Bar-Joseph.
  Distributed Gradient Descent in Bacterial Food Search
  Proceedings of the 20th Annual International Conference on Research in Computational Molecular Biology (RECOMB) to appear, 2016
  Supporting website
  

• 2015

• X. He, A.E. Cicek, Y. Wang, M.H. Schulz, H. Le, and Z. Bar-Joseph
  De novo ChIP-seq analysis
  Genome Biology 16(1):205, 2015
  Supporting website
  
• S. Chandrasekaran, S. Navlakha, N.J. Audette, D.D. McCreary, J. Suhan, Z. Bar-Joseph and A.L. Barth
  Unbiased, High-Throughput Electron Microscopy Analysis of Experience-Dependent Synaptic Changes in the Neocortex
  The Journal of Neuroscience 35(50):16450-62, 2015
  Cover story for the issue
  
• N.J. Venkatachari, J.M. Zerbato, S. Jain, A.E. Mancini, A. Chattopadhyay, N. Sluis-Cremer, Z. Bar-Joseph, and V. Ayyavoo
  Temporal transcriptional response to latency reversing agents identifies specific factors regulating HIV-1 viral transcriptional switch
  Retrovirology 12(1):85, 2015
• S. Navlakha A. Barth and Z. Bar-Joseph
  Decreasing-Rate Pruning Optimizes the Construction of Efficient and Robust Distributed Networks
  PLoS Comput Biol. , , 11(7):e1004347, 2015
  
• S. Navlakha and Z. Bar-Joseph
  Distributed Information Processing in Biological and Computational Systems
  COMMUNICATIONS OF THE ACM (CACM), 58 (1), Pages 94-102, 2015
  Video interview with Saket for this paper
  * Cover page story of the CACM January 2015 issue
  
• S. Navlakha, C. Faloutsos and Z. Bar-Joseph.
  MASSEXODUS: Modeling evolving networks in adversarial environments
  Data Mining and Knowledge Discovery (DAMI), 29(5): 1211-1232, 2015
  
• A. Gitter and Z. Bar-Joseph
  The SDREM method for reconstructing signaling and regulatory response networks: Applications applications for studying disease progression
  Methods Mol. Biol. , 1303:493-506, 2015
  
• A. Wise and Z. Bar-Joseph
  cDREM: Inferring dynamic combinatorial gene regulation
  Journal of Computational Biology, 22(4):324-33, 2014
  Supporting website
  Also appeared in:
  Proceedings of the 7th RECOMB/ISCB Conference on Regulatory and Systems Genomics

• 2014

• S. Jain, A. Gitter and Z. Bar-Joseph
  Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu
  PLoS Computational Biology, 10(12):e1003943, 2014
  Supporting website
  
• S. Singh, S. Navlakha, and Z. Bar-Joseph
  Distributed and computationally efficient belief propagation based on swarms of foraging bacteria
  2nd workshop on Biological Distributed Algorithms (BDA), 2014
  
• A. Wise and Z. Bar-Joseph
  SMARTS: Reconstructing disease response networks from multiple individuals using time series gene expression data
  Bioinformatics, in press, 2014
  Supporting website
  A prelimanry version appeared as:
  Reconstructing dynamic regulatory developmental networks in multiple brain regions
  Proceedings of the NIPS 2014 workshop on Analyzing the omics of the brain
• G.E. Zinman, S. Naiman, D.M. O'Dee, N. Kumar, G.J. Nau, H.Y. Cohen and Z. Bar-Joseph
  ModuleBlast: identifying activated sub-networks within and across species
  Nucleic Acids Research, advanced online publication, 2014
  Supporting website
  
• B.D. Modena, J.R. Tedrow, J. Milosevic, E.R. Bleecker, D.A. Meyers, W. Wu, Z. Bar-Joseph, S.C. Erzurum, B.M. Gaston, W.W. Busse, N.N. Jarjour, N. Kaminski and S.E. Wenzel.
  Gene Expression in Relation to Exhaled NO Identifies Novel Asthma Phenotypes with Unique Biomolecular Pathways.
  Am J Respir Crit Care Med, Epub ahead of print, 2014
  
• S. Navlakha, X. He, C. Faloutsos, and Z. Bar-Joseph.
  Topological Properties of Robust Biological and Computational Networks
  J. R. Soc. Interface, 11(96):20140283, 2014
  

• 2013

• G.E. Zinman, S. Naiman, Y. Kanfi, H. Cohen, and Z. Bar-Joseph
  ExpressionBlast: mining large, unstructured expression databases
  Nature Methods, 10: 925-926, 2013
  Supporting website
  
• M.H. Schulz, K.V. Pandit, C.L. Lino Cardenasb, N. Ambalavananc, N. Kaminski, and Z. Bar-Joseph
  Reconstructing dynamic microRNA-regulated interaction networks
  Proceedings of the National Academy of Science (PNAS), 110 (39):15686-91, 2013
  PNAS Commentary: Using machine learning to identify disease-relevant regulatory RNAs
  Supporting website
  
• S. Zhong, X. He and Z. Bar-Joseph.
  Predicting tissue specific transcription factor binding sites.
  BMC Genomics. 14(1):796, 2013.
  Supporting website
  
• Y. Zhou, A. Vazquez, A. Wise, T. Warita, K. Warita, Z. Bar-Joseph and Z.N. Oltvai .
  Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells.
  BMC Systems Biology. 7:138, 2013.
  
• T.S. Blackwell, A.M. Tager, Z. Borok, B.B. Moore, D.A. Schwartz, K.J. Anstrom, Z. Bar-Joseph, …, N. Kaminski, F.Z. Martinez, T.A. Wynn, V.J. Thannickal, J.P. Eu.
  Future Directions in Idiopathic Pulmonary Fibrosis Research: An NHLBI Workshop Report. .
  Am J Respir Crit Care Med. [Epub ahead of print] 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), 29 (13): i9-i17, 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), 29 (13): i227-i236, 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), 29 (13): i89-i97, 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, 2:e00675, 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, 13:250, 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