| 2025 | RECOMB | 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 |
| 2022 | RECOMB | Unsupervised Cell Functional Annotation for Single-Cell RNA-Seq. | Dongshunyi Li, Jun Ding, Ziv Bar-Joseph |
| 2021 | SIROCCO | The Epigenetic Consensus Problem. | Sabrina Rashid, Gadi Taubenfeld, Ziv Bar-Joseph |
| 2020 | RECOMB | Supervised Adversarial Alignment of Single-Cell RNA-seq Data. | Songwei Ge, Haohan Wang, Amir Alavi, Eric P. Xing, Ziv Bar-Joseph |
| 2016 | RECOMB | Shall We Dense? Comparing Design Strategies for Time Series Expression Experiments. | Emre Sefer, Ziv Bar-Joseph |
| 2016 | RECOMB | Distributed Gradient Descent in Bacterial Food Search. | Shashank Singh, Sabrina Rashid, Saket Navlakha, Ziv Bar-Joseph |
| 2011 | RECOMB | Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs. | Tien-ho Lin, Ziv Bar-Joseph, Robert F. Murphy |
| 2009 | RECOMB | Cross Species Expression Analysis of Innate Immune Response. | Yong Lu, Roni Rosenfeld, Gerard J. Nau, Ziv Bar-Joseph |
| 2008 | ISMB | Alignment and classification of time series gene expression in clinical studies. | Tien-ho Lin, Naftali Kaminski, Ziv Bar-Joseph |
| 2008 | ISMB | Protein complex identification by supervised graph local clustering. | Yanjun Qi, Fernanda Balem, Christos Faloutsos, Judith Klein-Seetharaman, Ziv Bar-Joseph |
| 2008 | RECOMB | A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors. | Yanxin Shi, Itamar Simon, Tom M. Mitchell, Ziv Bar-Joseph |
| 2007 | ISMB | Continuous hidden process model for time series expression experiments. | Yanxin Shi, Michael Klutstein, Itamar Simon, Tom M. Mitchell, Ziv Bar-Joseph |
| 2006 | ISMB | Identifying cycling genes by combining sequence homology and expression data. | Yong Lu, Ronald Rosenfeld, Ziv Bar-Joseph |
| 2006 | RECOMB | A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies. | Naftali Kaminski, Ziv Bar-Joseph |
| 2005 | ICML | 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 |
| 2005 | ISMB | Clustering short time series gene expression data. | Jason Ernst, Gerard J. Nau, Ziv Bar-Joseph |
| 2005 | PSB | Random Forest Similarity for Protein-Protein Interaction Prediction from Multiple Sources. | Yanjun Qi, Judith Klein-Seetharaman, Ziv Bar-Joseph |
| 2004 | ISMB | Deconvolving cell cycle expression data with complementary information. | Ziv Bar-Joseph, Shlomit Farkash, David K. Gifford, Itamar Simon, Roni Rosenfeld |
| 2003 | SCA | Sound-by-numbers: motion-driven sound synthesis. | Marc Cardle, Stephen Brooks, Ziv Bar-Joseph, Peter Robinson |
| 2002 | RECOMB | A new approach to analyzing gene expression time series data. | Ziv Bar-Joseph, Georg K. Gerber, David K. Gifford, Tommi S. Jaakkola, Itamar Simon |
| 2002 | WABI | K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data. | Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Angle M. Hamel, Tommi S. Jaakkola, Nathan Srebro |
| 2001 | ISMB | Fast optimal leaf ordering for hierarchical clustering. | Ziv Bar-Joseph, David K. Gifford, Tommi S. Jaakkola |
| 2000 | OPODIS | Totally Ordered Multicast with Bounded Delays and Variable Rates. | Ziv Bar-Joseph, Idit Keidar, Tal Anker, Nancy A. Lynch |
| 1998 | PODC | A Tight Lower Bound for Randomized Synchronous Consensus. | Ziv Bar-Joseph, Michael Ben-Or |