Ziv Bar-Joseph

ORCID

Publication Activity (10 Years)

Years Active: 1998-2024
Publications (10 Years): 38

Top Venues

Massachusetts Institute of Technology, Cambridge, MA, USA (PHD)

Education History

Massachusetts Institute of Technology, Cambridge, MA, USA

PHD

Publications

Saeed Moayedpour, Alejandro Corrochano-Navarro, Faryad Sahneh, Shahriar Noroozizadeh, Alexander Koetter, Jiri Vymetal, Lorenzo Kogler-Anele, Pablo Mas, Yasser Jangjou, Sizhen Li, Michael Bailey, Marc Bianciotto, Hans Matter, Christoph Grebner, Gerhard Hessler, Ziv Bar-Joseph, Sven Jager
Many-Shot In-Context Learning for Molecular Inverse Design. CoRR (2024)
Monica T. Dayao, Alexandro Trevino, Honesty Kim, Matthew Ruffalo, H. Blaize D'angio, Ryan Preska, Umamaheswar Duvvuri, Aaron T. Mayer, Ziv Bar-Joseph
proteomics imaging to enhance cancer survival analysis. Bioinform. 39 (Supplement-1) (2023)
Mena Soliman Asaad Kamel, Amrut Sarangi, Cindy Qin, Het Barot, Pavel Senin, Sergio Villordo, Sunaal Mathew, Albert Pla Planas, Ziv Bar-Joseph
Deep-Learning Based Cell Segmentation and Deconvolution in Spatial Transcriptomics. BCB (2023)
Dongshunyi Li, Jun Ding, Ziv Bar-Joseph
Unsupervised Cell Functional Annotation for Single-Cell RNA-Seq. RECOMB (2022)
Ye Yuan, Carlos Cosme, Taylor Sterling Adams, Jonas Schupp, Koji Sakamoto, Nikos Xylourgidis, Matthew Ruffalo, Jiachen Li, Naftali Kaminski, Ziv Bar-Joseph
CINS: Cell Interaction Network inference from Single cell expression data. PLoS Comput. Biol. 18 (9) (2022)
Jose Lugo-Martinez, Siwei Xu, Justine Levesque, Daniel Gallagher, Leslie A. Parker, Josef Neu, Christopher J. Stewart, Janet E. Berrington, Nicholas D. Embleton, Gregory Young, Katherine E. Gregory, Misty Good, Arti Tandon, David Genetti, Tracy Warren, Ziv Bar-Joseph
Integrating longitudinal clinical and microbiome data to predict growth faltering in preterm infants. J. Biomed. Informatics 128 (2022)
Dongshunyi Li, Jun Ding, Ziv Bar-Joseph
UNIFAN: A Tool for Unsupervised Single-Cell Clustering and Annotation. J. Comput. Biol. 29 (11) (2022)
Haotian Teng, Ye Yuan, Ziv Bar-Joseph
Clustering spatial transcriptomics data. Bioinform. 38 (4) (2022)
Songwei Ge, Haohan Wang, Amir Alavi, Eric P. Xing, Ziv Bar-Joseph
Supervised Adversarial Alignment of Single-Cell RNA-seq Data. J. Comput. Biol. 28 (5) (2021)
Ye Yuan, Ziv Bar-Joseph
Deep learning of gene relationships from single cell time-course expression data. Briefings Bioinform. 22 (5) (2021)
Sabrina Rashid, Gadi Taubenfeld, Ziv Bar-Joseph
The Epigenetic Consensus Problem. SIROCCO (2021)
Sabrina Rashid, Sohrab Shah, Ziv Bar-Joseph, Ravi Pandya
Dhaka: variational autoencoder for unmasking tumor heterogeneity from single cell genomic data. Bioinform. 37 (11) (2021)
Dongshunyi Li, Jun Ding, Ziv Bar-Joseph
Identifying signaling genes in spatial single-cell expression data. Bioinform. 37 (7) (2021)
Songwei Ge, Haohan Wang, Amir Alavi, Eric P. Xing, Ziv Bar-Joseph
Supervised Adversarial Alignment of Single-Cell RNA-seq Data. RECOMB (2020)
Ye Yuan, Xueying Ding, Ziv Bar-Joseph
Causal inference using deep neural networks. CoRR (2020)
Sabrina Rashid, Gadi Taubenfeld, Ziv Bar-Joseph
Genome-Wide Epigenetic Modifications as a Shared Memory Consensus Problem. CoRR (2020)
Amir Alavi, Ziv Bar-Joseph
Iterative point set registration for aligning scRNA-seq data. PLoS Comput. Biol. 16 (10) (2020)
Chieh Lin, Jun Ding, Ziv Bar-Joseph
Inferring TF activation order in time series scRNA-Seq studies. PLoS Comput. Biol. 16 (2) (2020)
Matthew Ruffalo, Roby Thomas, Jian Chen, Adrian V. Lee, Steffi Oesterreich, Ziv Bar-Joseph
Network-guided prediction of aromatase inhibitor response in breast cancer. PLoS Comput. Biol. 15 (2) (2019)
Chieh Lin, Ziv Bar-Joseph
Continuous-state HMMs for modeling time-series single-cell RNA-Seq data. Bioinform. 35 (22) (2019)
Jose Lugo-Martinez, Jörn Dengjel, Ziv Bar-Joseph, Robert F. Murphy
Integration of Heterogeneous Experimental Data Improves Global Map of Human Protein Complexes. BCB (2019)
Michael P. Snyder, Shin Lin, Amanda Posgai, Mark Atkinson, Aviv Regev, Jennifer Rood, Orit Rozenblatt-Rosen, Leslie Gaffney, Anna Hupalowska, Rahul Satija, Nils Gehlenborg, Jay Shendure, Julia Laskin, Pehr Harbury, Nicholas A. Nystrom, Jonathan C. Silverstein, Ziv Bar-Joseph, Kun Zhang, Katy Börner, Yiing Lin, Richard Conroy, Dena Procaccini, Ananda L. Roy, Ajay Pillai, Marishka Brown, Zorina S. Galis, Long Cai, Cole Trapnell, Dana Jackson, Garry P. Nolan, William James Greenleaf, Sylvia K. Plevritis, Sara Ahadi, Stephanie A. Nevins, Hayan Lee, Christian Martijn Schuerch, Sarah Black, Vishal Gautham Venkataraaman, Ed Esplin, Aaron Horning, Amir Bahmani, Xin Sun, Sanjay Jain, James S. Hagood, Gloria Pryhuber, Peter V. Kharchenko, Bernd Bodenmiller, Todd Brusko, Michael Clare-Salzler, Harry Nick, Kevin Otto, Clive Wasserfall, Marda Jorgensen, Maigan Brusko, Sergio Maffioletti, Richard M. Caprioli, Jeffrey M. Spraggins, Danielle Gutierrez, Nathan Heath Patterson, Elizabeth K. Neumann, Raymond Harris, Mark deCaestecker, Agnes B. Fogo, Raf Van de Plas, Ken Lau, Guo-Cheng Yuan, Qian Zhu, Ruben Dries, Peng Yin, Sinem K. Saka, Jocelyn Y. Kishi, Yu Wang, Isabel Goldaracena, Dong Hye Ye, Kristin E. Burnum-Johnson, Paul D. Piehowski, Charles Ansong, Ying Zhu, Tushar Desai, Jay Mulye, Peter Chou, Monica Nagendran, Sarah A. Teichmann, Benedict Paten, Robert F. Murphy, Jian Ma, Vladimir Yu. Kiselev, Carl Kingsford, Allyson Ricarte, Maria Keays, Sushma A. Akoju, Matthew Ruffalo, Margaret Vella, Chuck McCallum, Leonard E. Cross, Samuel H. Friedman, Randy W. Heiland, Bruce William Herr II, Paul Macklin, Ellen M. Quardokus, Lisel Record, James P. Sluka, Griffin M. Weber, Philip D. Blood, Alexander Ropelewski, William Shirey, Robin M. Scibek, Paula M. Mabee, W. Christopher Lenhardt, Kimberly Robasky, Stavros Michailidis, John C. Marioni, Andrew Butler, Tim Stuart, Eyal Fisher, Shila Ghazanfar, Gökcen Eraslan, Tommaso Biancalani, Eeshit D. Vaishnav, Pothur Srinivas, Aaron Pawlyk, Salvatore Sechi, Elizabeth L. Wilder, James Anderson
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nat. 574 (7777) (2019)
Sabrina Rashid, Shashank Singh, Saket Navlakha, Ziv Bar-Joseph
A bacterial based distributed gradient descent model for mass scale evacuations. Swarm Evol. Comput. 46 (2019)
Ye Yuan, Ziv Bar-Joseph
Deep learning for inferring gene relationships from single-cell expression data. Proc. Natl. Acad. Sci. USA 116 (52) (2019)
Nicolas A. Pabon, Yan Xia, Samuel K. Estabrooks, Zhaofeng Ye, Amanda K. Herbrand, Evelyn Süß, Ricardo M. Biondi, Victoria A. Assimon, Jason E. Gestwicki, Jeffrey L. Brodsky, Carlos J. Camacho, Ziv Bar-Joseph
Predicting protein targets for drug-like compounds using transcriptomics. PLoS Comput. Biol. 14 (12) (2018)
Jun Ding, James S. Hagood, Namasivayam Ambalavanan, Naftali Kaminski, Ziv Bar-Joseph
iDREM: Interactive visualization of dynamic regulatory networks. PLoS Comput. Biol. 14 (3) (2018)
Jun Ding, Ziv Bar-Joseph
MethRaFo: MeDIP-seq methylation estimate using a Random Forest Regressor. Bioinform. 33 (21) (2017)
Matthew Ruffalo, Petar Stojanov, Venkata Krishna Pillutla, Rohan Varma, Ziv Bar-Joseph
Reconstructing cancer drug response networks using multitask learning. BMC Syst. Biol. 11 (1) (2017)
Sabrina Rashid, Darrell N. Kotton, Ziv Bar-Joseph
TASIC: determining branching models from time series single cell data. Bioinform. 33 (16) (2017)
Shashank Singh, Sabrina Rashid, Saket Navlakha, Ziv Bar-Joseph
Distributed Gradient Descent in Bacterial Food Search. RECOMB (2016)
Matthew Ruffalo, Ziv Bar-Joseph
Genome wide predictions of miRNA regulation by transcription factors. Bioinform. 32 (17) (2016)
Siddhartha Jain, Joel Arrais, Narasimhan J. Venkatachari, Velpandi Ayyavoo, Ziv Bar-Joseph
Reconstructing the temporal progression of HIV-1 immune response pathways. Bioinform. 32 (12) (2016)
Emre Sefer, Ziv Bar-Joseph
Shall We Dense? Comparing Design Strategies for Time Series Expression Experiments. RECOMB (2016)
Aaron Wise, Ziv Bar-Joseph
SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data. Bioinform. 31 (8) (2015)
Saket Navlakha, Alison L. Barth, Ziv Bar-Joseph
Decreasing-Rate Pruning Optimizes the Construction of Efficient and Robust Distributed Networks. PLoS Comput. Biol. 11 (7) (2015)
Aaron Wise, Ziv Bar-Joseph
cDREM: Inferring Dynamic Combinatorial Gene Regulation. J. Comput. Biol. 22 (4) (2015)
Saket Navlakha, Christos Faloutsos, Ziv Bar-Joseph
MassExodus: modeling evolving networks in harsh environments. Data Min. Knowl. Discov. 29 (5) (2015)
Saket Navlakha, Ziv Bar-Joseph
Distributed information processing in biological and computational systems. Commun. ACM 58 (1) (2015)
Siddhartha Jain, Anthony Gitter, Ziv Bar-Joseph
Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu. PLoS Comput. Biol. 10 (12) (2014)
Saket Navlakha, Joseph Suhan, Alison L. Barth, Ziv Bar-Joseph
A high-throughput framework to detect synapses in electron microscopy images. Bioinform. 29 (13) (2013)
Yehuda Afek, Noga Alon, Ziv Bar-Joseph, Alejandro Cornejo, Bernhard Haeupler, Fabian Kuhn
Beeping a maximal independent set. Distributed Comput. 26 (4) (2013)
Hai-Son Le, Ziv Bar-Joseph
Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation. Bioinform. 29 (13) (2013)
Anthony Gitter, Ziv Bar-Joseph
Identifying proteins controlling key disease signaling pathways. Bioinform. 29 (13) (2013)
Yi Zhou, Alexei Vazquez, Aaron Wise, Tomoko Warita, Katsuhiko Warita, Ziv Bar-Joseph, Zoltán N. Oltvai
Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells. BMC Syst. Biol. 7 (2013)
Marcel H. Schulz, William E. Devanny, Anthony Gitter, Shan Zhong, Jason Ernst, Ziv Bar-Joseph
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. BMC Syst. Biol. 6 (2012)
Aaron Wise, Zoltán N. Oltvai, Ziv Bar-Joseph
Matching experiments across species using expression values and textual information. Bioinform. 28 (12) (2012)
Saket Navlakha, Anthony Gitter, Ziv Bar-Joseph
A Network-based Approach for Predicting Missing Pathway Interactions. PLoS Comput. Biol. 8 (8) (2012)
Yehuda Afek, Noga Alon, Ziv Bar-Joseph, Alejandro Cornejo, Bernhard Haeupler, Fabian Kuhn
Beeping a Maximal Independent Set CoRR (2012)
Tien-ho Lin, Ziv Bar-Joseph, Robert F. Murphy
Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs. RECOMB (2011)
Guy E. Zinman, Shan Zhong, Ziv Bar-Joseph
Biological interaction networks are conserved at the module level. BMC Syst. Biol. 5 (2011)
Yehuda Afek, Noga Alon, Ziv Bar-Joseph
MIS on the fly CoRR (2011)
Peter Huggins, Shan Zhong, Idit Shiff, Rachel Beckerman, Oleg Laptenko, Carol Prives, Marcel H. Schulz, Itamar Simon, Ziv Bar-Joseph
DECOD: fast and accurate discriminative DNA motif finding. Bioinform. 27 (17) (2011)
Tien-ho Lin, Ziv Bar-Joseph, Robert F. Murphy
Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs. J. Comput. Biol. 18 (11) (2011)
Tien-ho Lin, Robert F. Murphy, Ziv Bar-Joseph
Discriminative Motif Finding for Predicting Protein Subcellular Localization. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (2) (2011)
Yehuda Afek, Noga Alon, Ziv Bar-Joseph, Alejandro Cornejo, Bernhard Haeupler, Fabian Kuhn
Beeping a Maximal Independent Set. DISC (2011)
Manolis Kellis, Andrea Califano, Ziv Bar-Joseph
Preface. J. Comput. Biol. 18 (2) (2011)
Hai-Son Le, Ziv Bar-Joseph
Inferring Interaction Networks using the IBP applied to microRNA Target Prediction. NIPS (2011)
Yong Lu, Roni Rosenfeld, Gerard J. Nau, Ziv Bar-Joseph
Cross Species Expression Analysis of Innate Immune Response. J. Comput. Biol. 17 (3) (2010)
Hai-Son Le, Zoltán N. Oltvai, Ziv Bar-Joseph
Cross-species queries of large gene expression databases. Bioinform. 26 (19) (2010)
Hai-Son Le, Ziv Bar-Joseph
Cross Species Expression Analysis using a Dirichlet Process Mixture Model with Latent Matchings. NIPS (2010)
Yanxin Shi, Michael Klutstein, Itamar Simon, Tom M. Mitchell, Ziv Bar-Joseph
A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors. J. Comput. Biol. 16 (8) (2009)
Yong Lu, Roni Rosenfeld, Gerard J. Nau, Ziv Bar-Joseph
Cross Species Expression Analysis of Innate Immune Response. RECOMB (2009)
Yong Lu, Peter Huggins, Ziv Bar-Joseph
Cross species analysis of microarray expression data. Bioinform. 25 (12) (2009)
Manfred Lau, Ziv Bar-Joseph, James Kuffner
Modeling spatial and temporal variation in motion data. ACM Trans. Graph. 28 (5) (2009)
Alexei Vazquez, Qasim K. Beg, Marcio A. de Menezes, Jason Ernst, Ziv Bar-Joseph, Albert-László Barabási, László G. Boros, Zoltán N. Oltvai
Impact of the solvent capacity constraint on E. coli metabolism. BMC Syst. Biol. 2 (2008)
Yanjun Qi, Fernanda Balem, Christos Faloutsos, Judith Klein-Seetharaman, Ziv Bar-Joseph
Protein complex identification by supervised graph local clustering. ISMB (2008)
Yanxin Shi, Itamar Simon, Tom M. Mitchell, Ziv Bar-Joseph
A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors. RECOMB (2008)
Anupam Gupta, Ziv Bar-Joseph
Extracting Dynamics from Static Cancer Expression Data. IEEE ACM Trans. Comput. Biol. Bioinform. 5 (2) (2008)
Tien-ho Lin, Naftali Kaminski, Ziv Bar-Joseph
Alignment and classification of time series gene expression in clinical studies. ISMB (2008)
Jason Ernst, Qasim K. Beg, Krin A. Kay, Gábor Balázsi, Zoltán N. Oltvai, Ziv Bar-Joseph
. PLoS Comput. Biol. 4 (3) (2008)
Yanxin Shi, Tom M. Mitchell, Ziv Bar-Joseph
Inferring pairwise regulatory relationships from multiple time series datasets. Bioinform. 23 (6) (2007)
Naftali Kaminski, Ziv Bar-Joseph
A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies. J. Comput. Biol. 14 (3) (2007)
Yanxin Shi, Michael Klutstein, Itamar Simon, Tom M. Mitchell, Ziv Bar-Joseph
Continuous hidden process model for time series expression experiments. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Yanjun Qi, Judith Klein-Seetharaman, Ziv Bar-Joseph
A mixture of feature experts approach for protein-protein interaction prediction. BMC Bioinform. 8 (S-10) (2007)
Jason Ernst, Ziv Bar-Joseph
STEM: a tool for the analysis of short time series gene expression data. BMC Bioinform. 7 (2006)
Yong Lu, Ronald Rosenfeld, Ziv Bar-Joseph
Identifying cycling genes by combining sequence homology and expression data. ISMB (Supplement of Bioinformatics) (2006)
Naftali Kaminski, Ziv Bar-Joseph
A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies. RECOMB (2006)
Rohit Singh, Nathan P. Palmer, David K. Gifford, Bonnie Berger, Ziv Bar-Joseph
Active learning for sampling in time-series experiments with application to gene expression analysis. ICML (2005)
Jason Ernst, Gerard J. Nau, Ziv Bar-Joseph
Clustering short time series gene expression data. ISMB (Supplement of Bioinformatics) (2005)
Yanjun Qi, Judith Klein-Seetharaman, Ziv Bar-Joseph
Random Forest Similarity for Protein-Protein Interaction Prediction from Multiple Sources. Pacific Symposium on Biocomputing (2005)
Ziv Bar-Joseph
Analyzing time series gene expression data. Bioinform. 20 (16) (2004)
Ziv Bar-Joseph, Shlomit Farkash, David K. Gifford, Itamar Simon, Roni Rosenfeld
Deconvolving cell cycle expression data with complementary information. ISMB/ECCB (Supplement of Bioinformatics) (2004)
Ziv Bar-Joseph, Georg K. Gerber, David K. Gifford, Tommi S. Jaakkola, Itamar Simon
Continuous Representations of Time-Series Gene Expression Data. J. Comput. Biol. 10 (3/4) (2003)
Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Nathan Srebro, Angèle M. Hamel, Tommi S. Jaakkola
K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data. Bioinform. 19 (9) (2003)
Ziv Bar-Joseph, Daniel Cohen-Or
Hierarchical Context-based Pixel Ordering. Comput. Graph. Forum 22 (3) (2003)
Marc Cardle, Stephen Brooks, Ziv Bar-Joseph, Peter Robinson
Sound-by-numbers: motion-driven sound synthesis. Symposium on Computer Animation (2003)
Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Angèle M. Hamel, Tommi S. Jaakkola, Nathan Srebro
K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data. WABI (2002)
Shlomo Dubnov, Ziv Bar-Joseph, Ran El-Yaniv, Dani Lischinski, Michael Werman
Synthesizing Sound Textures through Wavelet Tree Learning. IEEE Computer Graphics and Applications 22 (4) (2002)
Ziv Bar-Joseph, Georg K. Gerber, David K. Gifford, Tommi S. Jaakkola, Itamar Simon
A new approach to analyzing gene expression time series data. RECOMB (2002)
Ziv Bar-Joseph, Idit Keidar, Nancy A. Lynch
Early-Delivery Dynamic Atomic Broadcast. DISC (2002)
Ziv Bar-Joseph, Ran El-Yaniv, Dani Lischinski, Michael Werman
Texture Mixing and Texture Movie Synthesis Using Statistical Learning. IEEE Trans. Vis. Comput. Graph. 7 (2) (2001)
Ziv Bar-Joseph, David K. Gifford, Tommi S. Jaakkola
Fast optimal leaf ordering for hierarchical clustering. ISMB (Supplement of Bioinformatics) (2001)
Ziv Bar-Joseph, Idit Keidar, Tal Anker, Nancy A. Lynch
Totally Ordered Multicast with Bounded Delays and Variable Rates. OPODIS (2000)
Ziv Bar-Joseph, Dani Lischinski, Michael Werman, Shlomo Dubnov, Ran El-Yaniv
Granular Synthesis of Sound Textures Using Statistical Learning. ICMC (1999)
Ziv Bar-Joseph, Michael Ben-Or
A Tight Lower Bound for Randomized Synchronous Consensus. PODC (1998)

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Publication Activity (10 Years)

Top Topics

Top Venues

Ziv Bar-Joseph