A Tight Lower Bound for Randomized Synchronous Consensus. - Ziv Bar-Joseph; Michael Ben-Or (PODC, 1998)

Granular Synthesis of Sound Textures Using Statistical Learning. - Ziv Bar-Joseph; Dani Lischinski; Michael Werman; Shlomo Dubnov; Ran El-Yaniv (ICMC, 1999)

Totally Ordered Multicast with Bounded Delays and Variable Rates. - Ziv Bar-Joseph; Idit Keidar; Tal Anker; Nancy A. Lynch (OPODIS, 2000)

Fast optimal leaf ordering for hierarchical clustering. - Ziv Bar-Joseph; David K. Gifford; Tommi S. Jaakkola (ISMB (Supplement of Bioinformatics), 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)

A new approach to analyzing gene expression time series data. - Ziv Bar-Joseph; Georg K. Gerber; David K. Gifford; Tommi S. Jaakkola; Itamar Simon (RECOMB, 2002)

Early-Delivery Dynamic Atomic Broadcast. - Ziv Bar-Joseph; Idit Keidar; Nancy A. Lynch (DISC, 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)

Sound-by-numbers: motion-driven sound synthesis. - Marc Cardle; Stephen Brooks; Ziv Bar-Joseph; Peter Robinson 001 (Symposium on Computer Animation, 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)

Hierarchical Context-based Pixel Ordering. - Ziv Bar-Joseph; Daniel Cohen-Or (Comput. Graph. Forum, 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)

Inferring interactions, expression programs and regulatory networks from high throughput biological data. - Ziv Bar-Joseph (2003)

Deconvolving cell cycle expression data with complementary information. - Ziv Bar-Joseph; Shlomit Farkash; David K. Gifford; Itamar Simon; Roni Rosenfeld (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Analyzing time series gene expression data. - Ziv Bar-Joseph (Bioinform., 2004)

Active learning for sampling in time-series experiments with application to gene expression analysis. - Rohit Singh 001; Nathan P. Palmer; David K. Gifford; Bonnie Berger; Ziv Bar-Joseph (ICML, 2005)

Clustering short time series gene expression data. - Jason Ernst; Gerard J. Nau; Ziv Bar-Joseph (ISMB (Supplement of Bioinformatics), 2005)

Random Forest Similarity for Protein-Protein Interaction Prediction from Multiple Sources. - Yanjun Qi; Judith Klein-Seetharaman; Ziv Bar-Joseph (Pacific Symposium on Biocomputing, 2005)

Identifying cycling genes by combining sequence homology and expression data. - Yong Lu; Ronald Rosenfeld; Ziv Bar-Joseph (ISMB (Supplement of Bioinformatics), 2006)

STEM: a tool for the analysis of short time series gene expression data. - Jason Ernst; Ziv Bar-Joseph (BMC Bioinform., 2006)

Continuous hidden process model for time series expression experiments. - Yanxin Shi; Michael Klutstein; Itamar Simon; Tom M. Mitchell; Ziv Bar-Joseph (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Inferring pairwise regulatory relationships from multiple time series datasets. - Yanxin Shi; Tom M. Mitchell; Ziv Bar-Joseph (Bioinform., 2007)

A mixture of feature experts approach for protein-protein interaction prediction. - Yanjun Qi; Judith Klein-Seetharaman; Ziv Bar-Joseph (BMC Bioinform., 2007)

A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies. - Naftali Kaminski; Ziv Bar-Joseph (J. Comput. Biol., 2007)

Alignment and classification of time series gene expression in clinical studies. - Tien-ho Lin; Naftali Kaminski; Ziv Bar-Joseph (ISMB, 2008)

Protein complex identification by supervised graph local clustering. - Yanjun Qi; Fernanda Balem; Christos Faloutsos; Judith Klein-Seetharaman; Ziv Bar-Joseph (ISMB, 2008)

A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors. - Yanxin Shi; Itamar Simon; Tom M. Mitchell; Ziv Bar-Joseph (RECOMB, 2008)

Impact of the solvent capacity constraint on E. coli metabolism. - Alexei Vázquez; 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 Semi-Supervised Method for Predicting Transcription Factor-Gene Interactions in Escherichia coli. - Jason Ernst; Qasim K. Beg; Krin A. Kay; Gábor Balázsi; Zoltán N. Oltvai; Ziv Bar-Joseph (PLoS Comput. Biol., 2008)

Extracting Dynamics from Static Cancer Expression Data. - Anupam Gupta 001; Ziv Bar-Joseph (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

Cross species analysis of microarray expression data. - Yong Lu; Peter Huggins; Ziv Bar-Joseph (Bioinform., 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)

Modeling spatial and temporal variation in motion data. - Manfred Lau; Ziv Bar-Joseph; James Kuffner (ACM Trans. Graph., 2009)

Cross Species Expression Analysis using a Dirichlet Process Mixture Model with Latent Matchings. - Hai-Son Le; Ziv Bar-Joseph (NIPS, 2010)

Cross-species queries of large gene expression databases. - Hai-Son Le; Zoltán N. Oltvai; Ziv Bar-Joseph (Bioinform., 2010)

Cross Species Expression Analysis of Innate Immune Response. - Yong Lu; Roni Rosenfeld; Gerard J. Nau; Ziv Bar-Joseph (J. Comput. Biol., 2010)

Inferring Interaction Networks using the IBP applied to microRNA Target Prediction. - Hai-Son Le; Ziv Bar-Joseph (NIPS, 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)

Biological interaction networks are conserved at the module level. - Guy E. Zinman; Shan Zhong; Ziv Bar-Joseph (BMC Syst. Biol., 2011)

MIS on the fly - Yehuda Afek; Noga Alon; Ziv Bar-Joseph (CoRR, 2011)

Preface. - Manolis Kellis; Andrea Califano; Ziv Bar-Joseph (J. Comput. Biol., 2011)

Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs. - Tien-ho Lin; Ziv Bar-Joseph; Robert F. Murphy (J. Comput. Biol., 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)

Matching experiments across species using expression values and textual information. - Aaron Wise; Zoltán N. Oltvai; Ziv Bar-Joseph (Bioinform., 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)

A Network-based Approach for Predicting Missing Pathway Interactions. - Saket Navlakha; Anthony Gitter; Ziv Bar-Joseph (PLoS Comput. Biol., 2012)

Identifying proteins controlling key disease signaling pathways. - Anthony Gitter; 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)

A high-throughput framework to detect synapses in electron microscopy images. - Saket Navlakha; Joseph Suhan; Alison L. Barth; Ziv Bar-Joseph (Bioinform., 2013)

Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells. - Yi Zhou; Alexei Vázquez; Aaron Wise; Tomoko Warita; Katsuhiko Warita; Ziv Bar-Joseph; Zoltán N. Oltvai (BMC Syst. Biol., 2013)

Beeping a maximal independent set. - Yehuda Afek; Noga Alon; Ziv Bar-Joseph; Alejandro Cornejo; Bernhard Haeupler; Fabian Kuhn (Distributed Comput., 2013)

Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu. - Siddhartha Jain 001; Anthony Gitter; Ziv Bar-Joseph (PLoS Comput. Biol., 2014)

SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data. - Aaron Wise; Ziv Bar-Joseph (Bioinform., 2015)

Distributed information processing in biological and computational systems. - Saket Navlakha; Ziv Bar-Joseph (Commun. ACM, 2015)

MassExodus: modeling evolving networks in harsh environments. - Saket Navlakha; Christos Faloutsos; Ziv Bar-Joseph (Data Min. Knowl. Discov., 2015)

cDREM: Inferring Dynamic Combinatorial Gene Regulation. - Aaron Wise; Ziv Bar-Joseph (J. Comput. Biol., 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)

Shall We Dense? Comparing Design Strategies for Time Series Expression Experiments. - Emre Sefer; Ziv Bar-Joseph (RECOMB, 2016)

Distributed Gradient Descent in Bacterial Food Search. - Shashank Singh 005; Sabrina Rashid; Saket Navlakha; Ziv Bar-Joseph (RECOMB, 2016)

Reconstructing the temporal progression of HIV-1 immune response pathways. - Siddhartha Jain 001; Joel Arrais; Narasimhan J. Venkatachari; Velpandi Ayyavoo; Ziv Bar-Joseph (Bioinform., 2016)

Genome wide predictions of miRNA regulation by transcription factors. - Matthew Ruffalo; Ziv Bar-Joseph (Bioinform., 2016)

Probabilistic Models for Error Correction of Nonuniform Sequencing Data. - Marcel H. Schulz; Ziv Bar-Joseph (Algorithms for Next-Generation Sequencing Data, 2017)

MethRaFo: MeDIP-seq methylation estimate using a Random Forest Regressor. - Jun Ding; Ziv Bar-Joseph (Bioinform., 2017)

TASIC: determining branching models from time series single cell data. - Sabrina Rashid; Darrell N. Kotton; Ziv Bar-Joseph (Bioinform., 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)

iDREM: Interactive visualization of dynamic regulatory networks. - Jun Ding; James S. Hagood; Namasivayam Ambalavanan; Naftali Kaminski; Ziv Bar-Joseph (PLoS Comput. Biol., 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)

Integration of Heterogeneous Experimental Data Improves Global Map of Human Protein Complexes. - Jose Lugo-Martinez; Jörn Dengjel; Ziv Bar-Joseph; Robert F. Murphy (BCB, 2019)

Continuous-state HMMs for modeling time-series single-cell RNA-Seq data. - Chieh Lin; Ziv Bar-Joseph (Bioinform., 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; et al. (Nat., 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)

Deep learning for inferring gene relationships from single-cell expression data. - Ye Yuan; Ziv Bar-Joseph (Proc. Natl. Acad. Sci. USA, 2019)

A bacterial based distributed gradient descent model for mass scale evacuations. - Sabrina Rashid; Shashank Singh 005; Saket Navlakha; Ziv Bar-Joseph (Swarm Evol. Comput., 2019)

Genome-Wide Epigenetic Modifications as a Shared Memory Consensus Problem. - Sabrina Rashid; Gadi Taubenfeld; Ziv Bar-Joseph (CoRR, 2020)

Causal inference using deep neural networks. - Ye Yuan; Xueying Ding; Ziv Bar-Joseph (CoRR, 2020)

Iterative point set registration for aligning scRNA-seq data. - Amir Alavi; Ziv Bar-Joseph (PLoS Comput. Biol., 2020)

Inferring TF activation order in time series scRNA-Seq studies. - Chieh Lin; Jun Ding; Ziv Bar-Joseph (PLoS Comput. Biol., 2020)

The Epigenetic Consensus Problem. - Sabrina Rashid; Gadi Taubenfeld; Ziv Bar-Joseph (SIROCCO, 2021)

Deep learning of gene relationships from single cell time-course expression data. - Ye Yuan; Ziv Bar-Joseph (Briefings Bioinform., 2021)

Identifying signaling genes in spatial single-cell expression data. - Dongshunyi Li; Jun Ding; Ziv Bar-Joseph (Bioinform., 2021)

Dhaka: variational autoencoder for unmasking tumor heterogeneity from single cell genomic data. - Sabrina Rashid; Sohrab Shah; Ziv Bar-Joseph; Ravi Pandya (Bioinform., 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., 2021)

Unsupervised Cell Functional Annotation for Single-Cell RNA-Seq. - Dongshunyi Li; Jun Ding; Ziv Bar-Joseph (RECOMB, 2022)

Clustering spatial transcriptomics data. - Haotian Teng; Ye Yuan; Ziv Bar-Joseph (Bioinform., 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; et al. (J. Biomed. Informatics, 2022)

UNIFAN: A Tool for Unsupervised Single-Cell Clustering and Annotation. - Dongshunyi Li; Jun Ding; Ziv Bar-Joseph (J. Comput. Biol., 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., 2022)

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 (BCB, 2023)

Deriving spatial features from in situ 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)

Integrating patients in time series clinical transcriptomics data. - Euxhen Hasanaj; Sachin Mathur; Ziv Bar-Joseph (Bioinform., 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)

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; et al. (CoRR, 2024)

Recovering Time-Varying Networks From Single-Cell Data. - Euxhen Hasanaj; Barnabás Póczos; Ziv Bar-Joseph (CoRR, 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)

Predicting lung aging using scRNA-Seq data. - Qi Song; Alex Singh; John E. McDonough; Taylor Sterling Adams; Robin Vos; Ruben De Man; Greg Myers; Laurens J. Ceulemans; Bart M. Vanaudenaerde; Wim A. Wuyts; Xiting Yan; Jonas Schupp; et al. (PLoS Comput. Biol., 2024)

Constrained Pseudo-Time Ordering for Clinical Transcriptomics Data. - Sachin Mathur; Hamid Mattoo; Ziv Bar-Joseph (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

Active Learning for Protein Structure Prediction. - Zexin Xue; Michael Bailey; Abhinav Gupta; Ruijiang Li; Alejandro Corrochano-Navarro; Sizhen Li; Lorenzo Kogler-Anele; Qui Yu; Ziv Bar-Joseph; Sven Jager (RECOMB, 2025)