Systems Biology Group - Carnegie Mellon University (original) (raw)
Publications
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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, 2023M. 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, 2023S. 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). , 2023H. Chen, D. Li and Z. Bar-Joseph
SCS: Cell Segmentation for High-Resolution Spatial Transcriptomics
Nature Methods , 20(8):1237-1243, 2023A. 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, 2023M. 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, 2023H. 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, 2023Q. Song, M. Ruffalo and Z Bar-Joseph
Using single cell atlas data to reconstruct regulatory networks
Nucleic Acids Research , 51 (7), e38-e38, 20232022
Q. Song, J. Wang and Z. Bar-Joseph
scSTEM: clustering pseudotime ordered single-cell data
Genome Biology. , 23, 150 2022E. Hasanaj, A. Alavi, A. Gupta, B. Poczos and Z Bar-Joseph
Multiset multicover methods for discriminative marker selection
Cell Reports Methods. , 100332, 2022B. 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, 2022E. Hasanaj, J. Wang, A. Sarathi, J. Ding and Z. Bar-Joseph
Interactive single-cell data analysis using Cellar
Nature Communications. , 13 (1), 1-6, 2022Y. 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, 2022A. 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, 2022J. 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, 2022D. Li, J. Ding, Z, Bar-Joseph
UNIFAN: A Tool for Unsupervised Single-Cell Clustering and Annotation
Journal of Computational Biology, in press, 2022D. 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, 2022P. 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, 2022D. 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, 2022M.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, 2022J. Ding, N. Sharon, Z. Bar-Joseph
Temporal modelling using single-cell transcriptomics.
Nat Rev Gene. , 23 (6), 355-368, 20222021
S. Rashid, G. Taubenfeld, Z. Bar-Joseph
The Epigenetic Consensus Problem.
International Colloquium on Structural Information and Communication Complexity (SIROCCO). , pp 146-163, 2021H. Teng, Y. Yuan, Z. Bar-Joseph
Clustering Spatial Transcriptomics Data.
Bioinformatics. , 38(4):997-1004, 2021J. 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), 2021Y Yuan, Z Bar-Joseph.
Deep learning of gene relationships from single cell time-course expression data.
Briefings in Bioinformatics. , 22(5), 2021S. 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, 2018D. 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 authorsD. Li, J. Ding, Z. Bar-Joseph
Identifying signaling genes in spatial single cell expression data.
Bioinformatics , 37(7), Pages 968-975, 2021G. 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, 20202020
Y. Yuan, Z. Bar-Joseph
GCNG: Graph convolutional networks for inferring cell-cell interactions
Genome Biology , 21(1):300, 2020A. Alavi, Z. Bar-Joseph.
Iterative point set registration for aligning scRNA-seq data.
PLoS Comput Biol. , 16(10):e1007939, 2020J Ding, Z Bar-Joseph.
Analysis of time series regulatory networks .
Current Opinion in Systems Biology. , 21, Pages 16-24, 2020H. Zafar, C. Lin, Z. Bar-Joseph.
Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data
Nature Communications , 11:3055, 2020C. Lin, J. Ding, Z. Bar-Joseph.
Inferring TF activation order in time series scRNA-Seq studies
PLoS Comput Biol. , 16(2):e1007644, 2020Z. Bar-Joseph, I. Simon.
Introduction to Special Issue Focused on Regulatory Genomics
Current Opinion in Systems Biology. , to appear, 2020K. 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, 2020M. 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, 20202019
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 GitHubJ. 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 websiteM.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 authorJ. 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, 2019S. 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 strideM. Ruffalo and Z. Bar-Joseph Z.
Protein interaction disruption in cancer.
BMC Cancer, 19(1):370, 2019J.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], 2019H. 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), 2019C. Lin and Z. Bar-Joseph
Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data.
Bioinformatics, epub ahead of print, 2019J. Ding C. Lin and Z. Bar-Joseph
Cell lineage inference from SNP and scRNA-Seq data
Nucleic Acids Res., 47(10):e56 of print, 2019J. Lugo-Martinez, D. Ruiz-Perez, G. Narasimhan and Ziv Bar-Joseph
Dynamic interaction network inference from longitudinal microbiome data
Microbiome , 7(1):54, 2019S. 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, 2019M. 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, 2019M. 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, 20192018
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 websiteC. 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 websiteC.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, 2018A. 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 websiteJ. 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 websiteS. 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, 2018S. Navlakha, Z. Bar-Joseph, A.L. Barth.
Network Design and the Brain.
Trends Cogn Sci., 22(1):64-78, 2018S. Rashid, G. Taubenfeld, and Z. Bar-Joseph
Genome Wide Epigenetic Modifications as a Shared Memory Consensus Problem
6th Workshop on Biological Distributed Algorithms , 20182017
J. Ding, Z. Bar-Joseph.
MethRaFo: MeDIP-seq methylation estimate using a Random Forest Regressor
Bioinformatics , 33(21):3477-3479, 2017
Supporting websiteM. 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 websiteJ.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, 2017C. 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 websiteS. Rashid, D.N. Kotton, Z. Bar-Joseph.
TASIC: Determining branching models from time series single cell data.
Bioinformatics , 33(16):2504-2512, 2017
Supporting websiteM. 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 websiteN.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, 2017M.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, 20172016
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, 2016E. 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 websiteM. 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 websiteS. 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 websiteE. 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 websiteS. 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 website2015
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 websiteS. 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 issueN.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, 2015S. 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, 2015S. 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 issueS. Navlakha, C. Faloutsos and Z. Bar-Joseph.
MASSEXODUS: Modeling evolving networks in adversarial environments
Data Mining and Knowledge Discovery (DAMI), 29(5): 1211-1232, 2015A. 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, 2015A. 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 Genomics2014
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 websiteS. 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), 2014A. 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 brainG.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 websiteB.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, 2014S. Navlakha, X. He, C. Faloutsos, and Z. Bar-Joseph.
Topological Properties of Robust Biological and Computational Networks
J. R. Soc. Interface, 11(96):20140283, 20142013
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 websiteM.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 websiteS. Zhong, X. He and Z. Bar-Joseph.
Predicting tissue specific transcription factor binding sites.
BMC Genomics. 14(1):796, 2013.
Supporting websiteY. 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 websiteH.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 websiteS. 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, 2013A. 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, 2013H.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, 2013K.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, 2013K. 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, 20132012
S. Navlakha, A. Gitter, Z. Bar-Joseph
A network-based approach for predicting missing pathway interactions
PLoS Computational Biology, 8:8, 2012Z. Bar-Joseph, A. Gitter, I. Simon
Studying and modelling dynamic biological processes using time-series gene expression data
Nature Reviews Genetics, 13, 552-564, 2012M.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 websiteY. Afek, N. Alon, Z. Bar-Joseph, A. Cornejo, B. Haeupler, F. Kuhn
Beeping a maximal independent set
Ditributed Computing , in press, 2012A. 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 websiteY. 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, 20122011
S. Navlakha, Z. Bar-Joseph
Algorithms in nature: the convergence of systems biology and computational thinking
Nature-EMBO Molecular Systems Biology, 7:546, 2011Y. 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 CellH.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, 2011H.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 websiteG.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 authorsG. 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 authorsP. 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 authorsY. 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, 2011A. 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 websiteH.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 website2010
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, 2010H.S. Le, Z.N. Oltvai, Z. Bar-Joseph
Cross Species Queries of Large Gene Expression Databases
Bioinformatics, 26(19):2416-23, 2010
Supporting websiteM. 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, 2010D. 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 informationJ. 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 websiteY. 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, 2010A. 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., 20102009
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 websiteM. 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 websiteA. 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 informationZ. Bar-Joseph
Schools Anxiously Await NRC Program Rankings
Science, 324(5931):1140-1, 2009Y. Lu, P. Huggins, Z. Bar-Joseph
Cross species analysis of microarray expression data
Bioinformatics, 25(12), pp. 1476-1483, 2009L. 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, 2009J. 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, 2009Y. 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 websiteY. 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, 20092008
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 websiteT.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 websiteY. 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 websiteL. Pe�a-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, 2008Y. 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, 2008J. Ernst, Q.K. Beg, K.A. Kay, G. Bal�zsi, 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 websiteZ. 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 websiteY. 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 websiteA. Vazquez, Q.K. Beg, M.A. de Menezes, J. Ernst, Z. Bar-Joseph, A.-L. Barab�si, 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 website2007
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 websiteQ.K. Beg, A. Vazquez, J. Ernst, M.A. de Menezes, Z. Bar-Joseph, A.-L. Barab�si, 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 InformationY. 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 websiteY. 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 websiteJ. 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 websiteN. 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 websiteY. Shi, T. Mitchell and Z. Bar-Joseph
Inferring Gene Regulatory Relationships from Multiple Time Series Datasets
Bioinformatics, 23(6), pp. 755-63, 2007
Supporting website2006
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, 2006J. Ernst, Z. Bar-Joseph
STEM: a tool for the analysis of short time series gene expression data.
BMC Bioinformatics, 7:191, 2006
Supporting websiteY. 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, 2006N. 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, 20062005
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 ResultsJ. 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 websiteY. 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 2005R 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 websiteY. 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 websiteZ. Bar-Joseph
Analyzing time series gene expression data
Bioinformatics, 20(16), pp 2493-2503, 20042003
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 websiteZ. 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
AppendixZ. 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, 2003Ziv 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, 2003Z. Bar-Joseph and D. Cohen-Or.
Hierarchical Context-based Pixel Ordering.
Computer Graphics Forum (Proceedings of Eurographics) 22(3), pp. 349-358, 2003M. Cardle, S. Brooks, Z. Bar-Joseph and P. Robinson
Sound-by-Numbers: Motion-Driven Sound Synthesis.
SIGGRAPH Symposium on Computer Animation (SCA), 20032002
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 websiteS. 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, 2002Z. 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, 2002Z. 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, 20021998-2001
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, 2001Z. 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
SoftwareZ. 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, 2000Z. 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, 1999Z. 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