Ziv Bar-Joseph

According to our database, Ziv Bar-Joseph authored at least 93 papers between 1998 and 2024.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of two.

2024

Proxy endpoints - bridging clinical trials and real world data.

Maxim Kryukov, Kathleen P. Moriarty, Macarena Villamea, Ingrid O'dwyer, Ohn Chow, Flavio Dormont, Ramon Hernandez, Ziv Bar-Joseph, Brandon Rufino

J. Biomed. Informatics, 2024

Recovering Time-Varying Networks From Single-Cell Data.

Euxhen Hasanaj, Barnabás Póczos, Ziv Bar-Joseph

CoRR, 2024

Many-Shot In-Context Learning for Molecular Inverse Design.

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

CoRR, 2024

Identifying indications for novel drugs using electronic health records.

Lukas Adamek, Greg Padiasek, Chaorui Zhang, Ingrid O'dwyer, Nicolas Capit, Flavio Dormont, Ramon Hernandez, Ziv Bar-Joseph, Brandon Rufino

Comput. Biol. Medicine, 2024

2023

Deriving spatial features from <i>in situ</i> proteomics imaging to enhance cancer survival analysis.

Monica T. Dayao, Alexandro Trevino, Honesty Kim, Matthew Ruffalo, H. Blaize D'angio, Ryan Preska, Umamaheswar Duvvuri, Aaron T. Mayer, Ziv Bar-Joseph

Bioinform., 2023

Deep-Learning Based Cell Segmentation and Deconvolution in Spatial Transcriptomics.

Mena Soliman Asaad Kamel, Amrut Sarangi, Cindy Qin, Het Barot, Pavel Senin, Sergio Villordo, Sunaal Mathew, Albert Pla Planas, Ziv Bar-Joseph

Proceedings of the 14th ACM International Conference on Bioinformatics, 2023

2022

CINS: Cell Interaction Network inference from Single cell expression data.

Ye Yuan, Carlos Cosme, Taylor Sterling Adams, Jonas Schupp, Koji Sakamoto, Nikos Xylourgidis, Matthew Ruffalo, Jiachen Li, Naftali Kaminski, Ziv Bar-Joseph

PLoS Comput. Biol., September, 2022

UNIFAN: A Tool for Unsupervised Single-Cell Clustering and Annotation.

Dongshunyi Li, Jun Ding, Ziv Bar-Joseph

J. Comput. Biol., 2022

Integrating longitudinal clinical and microbiome data to predict growth faltering in preterm infants.

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

J. Biomed. Informatics, 2022

Clustering spatial transcriptomics data.

Haotian Teng, Ye Yuan, Ziv Bar-Joseph

Bioinform., 2022

Unsupervised Cell Functional Annotation for Single-Cell RNA-Seq.

Dongshunyi Li, Jun Ding, Ziv Bar-Joseph

Proceedings of the Research in Computational Molecular Biology, 2022

2021

Supervised Adversarial Alignment of Single-Cell RNA-seq Data.

Songwei Ge, Haohan Wang, Amir Alavi, Eric P. Xing, Ziv Bar-Joseph

J. Comput. Biol., May, 2021

Dhaka: variational autoencoder for unmasking tumor heterogeneity from single cell genomic data.

Sabrina Rashid, Sohrab Shah, Ziv Bar-Joseph, Ravi Pandya

Bioinform., 2021

Identifying signaling genes in spatial single-cell expression data.

Dongshunyi Li, Jun Ding, Ziv Bar-Joseph

Bioinform., 2021

Deep learning of gene relationships from single cell time-course expression data.

Ye Yuan, Ziv Bar-Joseph

Briefings Bioinform., 2021

The Epigenetic Consensus Problem.

Sabrina Rashid, Gadi Taubenfeld, Ziv Bar-Joseph

Proceedings of the Structural Information and Communication Complexity, 2021

2020

Inferring TF activation order in time series scRNA-Seq studies.

Chieh Lin, Jun Ding, Ziv Bar-Joseph

PLoS Comput. Biol., 2020

Iterative point set registration for aligning scRNA-seq data.

Amir Alavi, Ziv Bar-Joseph

PLoS Comput. Biol., 2020

Causal inference using deep neural networks.

Ye Yuan, Xueying Ding, Ziv Bar-Joseph

CoRR, 2020

Genome-Wide Epigenetic Modifications as a Shared Memory Consensus Problem.

Sabrina Rashid, Gadi Taubenfeld, Ziv Bar-Joseph

CoRR, 2020

2019

A bacterial based distributed gradient descent model for mass scale evacuations.

Sabrina Rashid, Shashank Singh, Saket Navlakha, Ziv Bar-Joseph

Swarm Evol. Comput., 2019

Deep learning for inferring gene relationships from single-cell expression data.

Ye Yuan, Ziv Bar-Joseph

Proc. Natl. Acad. Sci. USA, 2019

Network-guided prediction of aromatase inhibitor response in breast cancer.

Matthew Ruffalo, Roby Thomas, Jian Chen, Adrian V. Lee, Steffi Oesterreich, Ziv Bar-Joseph

PLoS Comput. Biol., 2019

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.

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 P. de Caestecker, 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 Anand 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

Nat., 2019

Continuous-state HMMs for modeling time-series single-cell RNA-Seq data.

Chieh Lin, Ziv Bar-Joseph

Bioinform., 2019

Integration of Heterogeneous Experimental Data Improves Global Map of Human Protein Complexes.

Jose Lugo-Martinez, Jörn Dengjel, Ziv Bar-Joseph, Robert F. Murphy

Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

2018

Predicting protein targets for drug-like compounds using transcriptomics.

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

PLoS Comput. Biol., 2018

iDREM: Interactive visualization of dynamic regulatory networks.

Jun Ding, James S. Hagood, Namasivayam Ambalavanan, Naftali Kaminski, Ziv Bar-Joseph

PLoS Comput. Biol., 2018

2017

Reconstructing cancer drug response networks using multitask learning.

Matthew Ruffalo, Petar Stojanov, Venkata Krishna Pillutla, Rohan Varma, Ziv Bar-Joseph

BMC Syst. Biol., 2017

TASIC: determining branching models from time series single cell data.

Sabrina Rashid, Darrell N. Kotton, Ziv Bar-Joseph

Bioinform., 2017

MethRaFo: MeDIP-seq methylation estimate using a Random Forest Regressor.

Jun Ding, Ziv Bar-Joseph

Bioinform., 2017

Probabilistic Models for Error Correction of Nonuniform Sequencing Data.

Marcel H. Schulz, Ziv Bar-Joseph

Proceedings of the Algorithms for Next-Generation Sequencing Data, Techniques, 2017

2016

Genome wide predictions of miRNA regulation by transcription factors.

Matthew Ruffalo, Ziv Bar-Joseph

Bioinform., 2016

Reconstructing the temporal progression of HIV-1 immune response pathways.

Siddhartha Jain, Joel Arrais, Narasimhan J. Venkatachari, Velpandi Ayyavoo, Ziv Bar-Joseph

Bioinform., 2016

Distributed Gradient Descent in Bacterial Food Search.

Shashank Singh, Sabrina Rashid, Saket Navlakha, Ziv Bar-Joseph

Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

Shall We Dense? Comparing Design Strategies for Time Series Expression Experiments.

Emre Sefer, Ziv Bar-Joseph

Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

2015

Decreasing-Rate Pruning Optimizes the Construction of Efficient and Robust Distributed Networks.

Saket Navlakha, Alison L. Barth, Ziv Bar-Joseph

PLoS Comput. Biol., 2015

cDREM: Inferring Dynamic Combinatorial Gene Regulation.

Aaron Wise, Ziv Bar-Joseph

J. Comput. Biol., 2015

MassExodus: modeling evolving networks in harsh environments.

Saket Navlakha, Christos Faloutsos, Ziv Bar-Joseph

Data Min. Knowl. Discov., 2015

Distributed information processing in biological and computational systems.

Saket Navlakha, Ziv Bar-Joseph

Commun. ACM, 2015

SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data.

Aaron Wise, Ziv Bar-Joseph

Bioinform., 2015

2014

Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu.

Siddhartha Jain, Anthony Gitter, Ziv Bar-Joseph

PLoS Comput. Biol., 2014

2013

Beeping a maximal independent set.

Yehuda Afek, Noga Alon, Ziv Bar-Joseph, Alejandro Cornejo, Bernhard Haeupler, Fabian Kuhn

Distributed Comput., 2013

Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells.

Yi Zhou, Alexei Vazquez, Aaron Wise, Tomoko Warita, Katsuhiko Warita, Ziv Bar-Joseph, Zoltán N. Oltvai

BMC Syst. Biol., 2013

A high-throughput framework to detect synapses in electron microscopy images.

Saket Navlakha, Joseph Suhan, Alison L. Barth, Ziv Bar-Joseph

Bioinform., 2013

Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation.

Hai-Son Le, Ziv Bar-Joseph

Bioinform., 2013

Identifying proteins controlling key disease signaling pathways.

Anthony Gitter, Ziv Bar-Joseph

Bioinform., 2013

2012

A Network-based Approach for Predicting Missing Pathway Interactions.

Saket Navlakha, Anthony Gitter, Ziv Bar-Joseph

PLoS Comput. Biol., 2012

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data.

Marcel H. Schulz, William E. Devanny, Anthony Gitter, Shan Zhong, Jason Ernst, Ziv Bar-Joseph

BMC Syst. Biol., 2012

Matching experiments across species using expression values and textual information.

Aaron Wise, Zoltán N. Oltvai, Ziv Bar-Joseph

Bioinform., 2012

2011

Discriminative Motif Finding for Predicting Protein Subcellular Localization.

Tien-ho Lin, Robert F. Murphy, Ziv Bar-Joseph

IEEE ACM Trans. Comput. Biol. Bioinform., 2011

Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs.

Tien-ho Lin, Ziv Bar-Joseph, Robert F. Murphy

J. Comput. Biol., 2011

Preface.

Manolis Kellis, Andrea Califano, Ziv Bar-Joseph

J. Comput. Biol., 2011

MIS on the fly

Yehuda Afek, Noga Alon, Ziv Bar-Joseph

CoRR, 2011

Biological interaction networks are conserved at the module level.

Guy E. Zinman, Shan Zhong, Ziv Bar-Joseph

BMC Syst. Biol., 2011

DECOD: fast and accurate discriminative DNA motif finding.

Peter Huggins, Shan Zhong, Idit Shiff, Rachel Beckerman, Oleg Laptenko, Carol Prives, Marcel H. Schulz, Itamar Simon, Ziv Bar-Joseph

Bioinform., 2011

Inferring Interaction Networks using the IBP applied to microRNA Target Prediction.

Hai-Son Le, Ziv Bar-Joseph

Proceedings of the Advances in Neural Information Processing Systems 24: 25th Annual Conference on Neural Information Processing Systems 2011. Proceedings of a meeting held 12-14 December 2011, 2011

2010

Cross Species Expression Analysis of Innate Immune Response.

Yong Lu, Roni Rosenfeld, Gerard J. Nau, Ziv Bar-Joseph

J. Comput. Biol., 2010

Cross-species queries of large gene expression databases.

Hai-Son Le, Zoltán N. Oltvai, Ziv Bar-Joseph

Bioinform., 2010

Cross Species Expression Analysis using a Dirichlet Process Mixture Model with Latent Matchings.

Hai-Son Le, Ziv Bar-Joseph

Proceedings of the Advances in Neural Information Processing Systems 23: 24th Annual Conference on Neural Information Processing Systems 2010. Proceedings of a meeting held 6-9 December 2010, 2010

2009

Modeling spatial and temporal variation in motion data.

Manfred Lau, Ziv Bar-Joseph, James Kuffner

ACM Trans. Graph., 2009

A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors.

Yanxin Shi, Michael Klutstein, Itamar Simon, Tom M. Mitchell, Ziv Bar-Joseph

J. Comput. Biol., 2009

Cross species analysis of microarray expression data.

Yong Lu, Peter Huggins, Ziv Bar-Joseph

Bioinform., 2009

2008

Extracting Dynamics from Static Cancer Expression Data.

Anupam Gupta, Ziv Bar-Joseph

IEEE ACM Trans. Comput. Biol. Bioinform., 2008

A Semi-Supervised Method for Predicting Transcription Factor-Gene Interactions in <i>Escherichia coli</i>.

Jason Ernst, Qasim K. Beg, Krin A. Kay, Gábor Balázsi, Zoltán N. Oltvai, Ziv Bar-Joseph

PLoS Comput. Biol., 2008

Impact of the solvent capacity constraint on E. coli metabolism.

Alexei Vazquez, Qasim K. Beg, Marcio A. de Menezes, Jason Ernst, Ziv Bar-Joseph, Albert-László Barabási, László G. Boros, Zoltán N. Oltvai

BMC Syst. Biol., 2008

A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors.

Yanxin Shi, Itamar Simon, Tom M. Mitchell, Ziv Bar-Joseph

Proceedings of the Research in Computational Molecular Biology, 2008

Protein complex identification by supervised graph local clustering.

Yanjun Qi, Fernanda Balem, Christos Faloutsos, Judith Klein-Seetharaman, Ziv Bar-Joseph

Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

Alignment and classification of time series gene expression in clinical studies.

Tien-ho Lin, Naftali Kaminski, Ziv Bar-Joseph

Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

2007

A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies.

Naftali Kaminski, Ziv Bar-Joseph

J. Comput. Biol., 2007

A mixture of feature experts approach for protein-protein interaction prediction.

Yanjun Qi, Judith Klein-Seetharaman, Ziv Bar-Joseph

BMC Bioinform., 2007

Inferring pairwise regulatory relationships from multiple time series datasets.

Yanxin Shi, Tom M. Mitchell, Ziv Bar-Joseph

Bioinform., 2007

Continuous hidden process model for time series expression experiments.

Yanxin Shi, Michael Klutstein, Itamar Simon, Tom M. Mitchell, Ziv Bar-Joseph

Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

2006

STEM: a tool for the analysis of short time series gene expression data.

Jason Ernst, Ziv Bar-Joseph

BMC Bioinform., 2006

Identifying cycling genes by combining sequence homology and expression data.

Yong Lu, Ronald Rosenfeld, Ziv Bar-Joseph

Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2005

Random Forest Similarity for Protein-Protein Interaction Prediction from Multiple Sources.

Yanjun Qi, Judith Klein-Seetharaman, Ziv Bar-Joseph

Proceedings of the Biocomputing 2005, 2005

Clustering short time series gene expression data.

Jason Ernst, Gerard J. Nau, Ziv Bar-Joseph

Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

Active learning for sampling in time-series experiments with application to gene expression analysis.

Rohit Singh, Nathan P. Palmer, David K. Gifford, Bonnie Berger, Ziv Bar-Joseph

Proceedings of the Machine Learning, 2005

2004

Analyzing time series gene expression data.

Ziv Bar-Joseph

Bioinform., 2004

Deconvolving cell cycle expression data with complementary information.

Ziv Bar-Joseph, Shlomit Farkash, David K. Gifford, Itamar Simon, Roni Rosenfeld

Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

2003

Inferring interactions, expression programs and regulatory networks from high throughput biological data.

Ziv Bar-Joseph

PhD thesis, 2003

Continuous Representations of Time-Series Gene Expression Data.

Ziv Bar-Joseph, Georg K. Gerber, David K. Gifford, Tommi S. Jaakkola, Itamar Simon

J. Comput. Biol., 2003

Hierarchical Context-based Pixel Ordering.

Ziv Bar-Joseph, Daniel Cohen-Or

Comput. Graph. Forum, 2003

K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data.

Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Nathan Srebro, Angèle M. Hamel, Tommi S. Jaakkola

Bioinform., 2003

Sound-by-numbers: motion-driven sound synthesis.

Marc Cardle, Stephen Brooks, Ziv Bar-Joseph, Peter Robinson

Proceedings of the 2003 ACM SIGGRAPH/Eurographics Symposium on Computer Animation, 2003

2002

Synthesizing Sound Textures through Wavelet Tree Learning.

Shlomo Dubnov, Ziv Bar-Joseph, Ran El-Yaniv, Dani Lischinski, Michael Werman

IEEE Computer Graphics and Applications, 2002

Early-Delivery Dynamic Atomic Broadcast.

Ziv Bar-Joseph, Idit Keidar, Nancy A. Lynch

Proceedings of the Distributed Computing, 16th International Conference, 2002

A new approach to analyzing gene expression time series data.

Ziv Bar-Joseph, Georg K. Gerber, David K. Gifford, Tommi S. Jaakkola, Itamar Simon

Proceedings of the Sixth Annual International Conference on Computational Biology, 2002

2001

Texture Mixing and Texture Movie Synthesis Using Statistical Learning.

Ziv Bar-Joseph, Ran El-Yaniv, Dani Lischinski, Michael Werman

IEEE Trans. Vis. Comput. Graph., 2001

Fast optimal leaf ordering for hierarchical clustering.

Ziv Bar-Joseph, David K. Gifford, Tommi S. Jaakkola

Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001

2000

Totally Ordered Multicast with Bounded Delays and Variable Rates.

Ziv Bar-Joseph, Idit Keidar, Tal Anker, Nancy A. Lynch

Proceedings of the Procedings of the 4th International Conference on Principles of Distributed Systems, 2000

1999

Granular Synthesis of Sound Textures Using Statistical Learning.

Ziv Bar-Joseph, Dani Lischinski, Michael Werman, Shlomo Dubnov, Ran El-Yaniv

Proceedings of the 1999 International Computer Music Conference, 1999

1998

A Tight Lower Bound for Randomized Synchronous Consensus.

Ziv Bar-Joseph, Michael Ben-Or

Proceedings of the Seventeenth Annual ACM Symposium on Principles of Distributed Computing, 1998