Ziv Bar-Joseph

发表

Learning of protein interaction networks

Ziv Bar-Joseph, Judith Klein-Seetharaman, Yanjun Qi, 2008 .

Dynamic interaction network inference from longitudinal microbiome data

Giri Narasimhan, Ziv Bar-Joseph, Jose Lugo-Martinez, 2018 .

Reconstructing cancer drug response networks using multitask learning

Ziv Bar-Joseph, Matthew Ruffalo, Petar Stojanov, 2017, BMC Systems Biology.

Iterative point set registration for aligning scRNA-seq data

Ziv Bar-Joseph, Amir Alavi, 2020, PLoS computational biology.

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

Ziv Bar-Joseph, Gadi Taubenfeld, Sabrina Rashid, 2020, ArXiv.

Probabilistic Models for Error Correction of Nonuniform Sequencing Data

Ziv Bar-Joseph, Marcel H. Schulz, Z. Bar-Joseph, 2017, Algorithms for Next-Generation Sequencing Data.

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

Ziv Bar-Joseph, Aaron Wise, Z. Bar-Joseph, 2015, Bioinform..

Continuous Representations of Time-Series Gene Expression Data

Tommi S. Jaakkola, Ziv Bar-Joseph, David K. Gifford, 2003, J. Comput. Biol..

iDREM: Interactive visualization of dynamic regulatory networks

Ziv Bar-Joseph, Jun Ding, Naftali Kaminski, 2018, PLoS Comput. Biol..

Early-Delivery Dynamic Atomic Broadcast (Extended Abstract)

Nancy A. Lynch, Idit Keidar, Ziv Bar-Joseph, 2002 .

Synthesizing Sound Textures through Wavelet Tree Learning

Dani Lischinski, Ran El-Yaniv, Michael Werman, 2002, IEEE Computer Graphics and Applications.

Extracting Dynamics from Static Cancer Expression Data

Ziv Bar-Joseph, Anupam Gupta, 2008, IEEE ACM Trans. Comput. Biol. Bioinform..

Synthesizing Sound Textures through

Ran El-Yaniv, Michael Werman, Shlomo Dubnov, 2002 .

A Network-based Approach for Predicting Missing Pathway Interactions

Ziv Bar-Joseph, Saket Navlakha, Anthony Gitter, 2012, PLoS Comput. Biol..

Iterative point set registration for aligning scRNA-seq data

Ziv Bar-Joseph, Amir Alavi, Z. Bar-Joseph, 2020, bioRxiv.

Causal inference using deep neural networks pdf

Ziv Bar-Joseph, Ye Yuan, Xueying Ding, 2020, ArXiv.

RECOMB Conference on Systems Biology, Regulatory Genomics, and DREAM Challenges 2010 Special Issue, Preface

Ziv Bar-Joseph, Manolis Kellis, Andrea Califano, 2011 .

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

Erik D. Demaine, Tommi S. Jaakkola, Ziv Bar-Joseph, 2002, WABI.

Identifying proteins controlling key disease signaling pathways

Ziv Bar-Joseph, Anthony Gitter, Z. Bar-Joseph, 2013, Bioinform..

Beeping a maximal independent set

Noga Alon, Ziv Bar-Joseph, Yehuda Afek, 2011, Distributed Computing.

Distributed Gradient Descent in Bacterial Food Search

Ziv Bar-Joseph, Shashank Singh, Saket Navlakha, 2016, RECOMB 2016.

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

Ziv Bar-Joseph, Hai-Son Le, H. Le, 2013, Bioinform..

Cross-species queries of large gene expression databases

Ziv Bar-Joseph, Hai-Son Le, Zoltán N. Oltvai, 2010, Bioinform..

A tight lower bound for randomized synchronous consensus

Ziv Bar-Joseph, Michael Ben-Or, M. Ben-Or, 1998, PODC '98.

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

Yanjun Qi, Ziv Bar-Joseph, Judith Klein-Seetharaman, 2004, Pacific Symposium on Biocomputing.

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

Ziv Bar-Joseph, Hai-Son Le, H. Le, 2010, NIPS.

Sound-by-numbers: motion-driven sound synthesis

Ziv Bar-Joseph, Stephen Brooks, Peter Robinson, 2003, SCA '03.

Fast optimal leaf ordering for hierarchical clustering

Tommi S. Jaakkola, Ziv Bar-Joseph, David K. Gifford, 2001, ISMB.

Analyzing time series gene expression data

Ziv Bar-Joseph, Z. Bar-Joseph, 2004, Bioinform..

Preface

Ziv Bar-Joseph, Manolis Kellis, Andrea Califano, 2011, J. Comput. Biol..

Genome wide predictions of miRNA regulation by transcription factors

Ziv Bar-Joseph, Matthew Ruffalo, Z. Bar-Joseph, 2016, Bioinform..

Early-Delivery Dynamic Atomic Broadcast

Nancy A. Lynch, Idit Keidar, Ziv Bar-Joseph, 2002, DISC.

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

Ziv Bar-Joseph, Saket Navlakha, Alison L. Barth, 2013, Bioinform..

Cross species analysis of microarray expression data

Ziv Bar-Joseph, Yong Lu, Peter Huggins, 2009, Bioinform..

Granular Synthesis of Sound Textures Using Statistical Learning

Dani Lischinski, Ran El-Yaniv, Michael Werman, 1999, ICMC.

Matching experiments across species using expression values and textual information

Ziv Bar-Joseph, Zoltán N. Oltvai, Aaron Wise, 2012, Bioinform..

Inferring pairwise regulatory relationships from multiple time series datasets

Tom M. Mitchell, Ziv Bar-Joseph, Yanxin Shi, 2007, Bioinform..

Computational methods for analyzing dynamic regulatory networks.

Ziv Bar-Joseph, Yong Lu, Anthony Gitter, 2010, Methods in molecular biology.

A computational framework for the analysis of multi-species microarray data

Ziv Bar-Joseph, Roni Rosenfeld, Yong Lu, 2008 .

Protein complex identification by supervised graph local clustering

Yanjun Qi, Christos Faloutsos, Ziv Bar-Joseph, 2008, ISMB.

Impact of the solvent capacity constraint on E. coli metabolism

Ziv Bar-Joseph, Albert-László Barabási, Zoltán N. Oltvai, 2008, BMC Systems Biology.

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

Ziv Bar-Joseph, Saket Navlakha, Alison L. Barth, 2015, PLoS Comput. Biol..

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

Ziv Bar-Joseph, Ye Yuan, Z. Bar-Joseph, 2019, Proceedings of the National Academy of Sciences.

Selecting the most appropriate time points to profile in high-throughput studies

Ziv Bar-Joseph, Emre Sefer, Naftali Kaminski, 2017, eLife.

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

Ziv Bar-Joseph, Judith Klein-Seetharaman, Yanjun Qi, 2007, BMC Bioinformatics.

Distributed information processing in biological and computational systems

Ziv Bar-Joseph, Saket Navlakha, Z. Bar-Joseph, 2014, Commun. ACM.

Tradeoffs between Dense and Replicate Sampling Strategies for High-Throughput Time Series Experiments.

Ziv Bar-Joseph, Emre Sefer, Michael Kleyman, 2016, Cell systems.

Hercules: a profile HMM-based hybrid error correction algorithm for long reads

Ziv Bar-Joseph, A. Ercument Cicek, Can Alkan, 2017 .

Supervised Adversarial Alignment of Single-Cell RNA-seq Data

Eric P. Xing, Ziv Bar-Joseph, Amir Alavi, 2020, RECOMB.

Using Neural Networks to Improve Single Cell RNA-Seq Data Analysis

Ziv Bar-Joseph, Siddhartha Jain, Chieh Lin, 2017, bioRxiv.

Analysis of time-series regulatory networks

Ziv Bar-Joseph, Jun Ding, Z. Bar-Joseph, 2020, Current Opinion in Systems Biology.

Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data

Ziv Bar-Joseph, Chieh Lin, Z. Bar-Joseph, 2018, bioRxiv.

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

Ziv Bar-Joseph, Jose Lugo-Martinez, Robert F. Murphy, 2019, BCB.

Alignment and classification of time series gene expression in clinical studies

Ziv Bar-Joseph, Naftali Kaminski, Tien-ho Lin, 2008, ISMB.

TASIC: determining branching models from time series single cell data

Ziv Bar-Joseph, Sabrina Rashid, Darrell N. Kotton, 2017, Bioinform..

Modeling spatial and temporal variation in motion data

Ziv Bar-Joseph, Manfred Lau, James J. Kuffner, 2009, ACM Trans. Graph..

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

Yi Zhou, Ziv Bar-Joseph, Zoltán N. Oltvai, 2013, BMC Systems Biology.

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

Tom M. Mitchell, Ziv Bar-Joseph, Yanxin Shi, 2009, J. Comput. Biol..

MethRaFo: MeDIP‐seq methylation estimate using a Random Forest Regressor

Ziv Bar-Joseph, Jun Ding, Z. Bar-Joseph, 2017, Bioinform..

Network-guided prediction of aromatase inhibitor response in breast cancer

Ziv Bar-Joseph, Matthew Ruffalo, Jian Chen, 2019, PLoS Comput. Biol..

A web server for comparative analysis of single-cell RNA-seq data

Ziv Bar-Joseph, Matthew Ruffalo, Amir Alavi, 2018, Nature Communications.

Reconstructing the temporal progression of HIV-1 immune response pathways

Ziv Bar-Joseph, Joel Arrais, Siddhartha Jain, 2016, Bioinform..

Predicting protein targets for drug-like compounds using transcriptomics

Yan Xia, Ziv Bar-Joseph, Jeffrey L Brodsky, 2018, bioRxiv.

A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coli

Ziv Bar-Joseph, Zoltán N. Oltvai, Jason Ernst, 2008, PLoS Comput. Biol..

Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs

Ziv Bar-Joseph, Robert F. Murphy, Tien-ho Lin, 2011, RECOMB.

Ieee/acm Transactions on Computational Biology and Bioinformatics Discriminative Motif Finding for Predicting Protein Subcellular Localization

Ziv Bar-Joseph, Robert F. Murphy, Tien-ho Lin, 2022 .

A Biological Solution to a Fundamental Distributed Computing Problem

Noga Alon, Ziv Bar-Joseph, Yehuda Afek, 2011, Science.

DECOD: fast and accurate discriminative DNA motif finding

Ziv Bar-Joseph, Marcel H. Schulz, Shan Zhong, 2011, Bioinform..

Continuous hidden process model for time series expression experiments

Tom M. Mitchell, Ziv Bar-Joseph, Yanxin Shi, 2007, ISMB/ECCB.

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

Ziv Bar-Joseph, Naftali Kaminski, 2007, J. Comput. Biol..

Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs

Ziv Bar-Joseph, Robert F. Murphy, Tien-ho Lin, 2011, J. Comput. Biol..

CNNC: Convolutional Neural Networks for Co-Expression Analysis

Ziv Bar-Joseph, Ye Yuan, Z. Bar-Joseph, 2018, bioRxiv.

Inferring TF activation order in time series scRNA-Seq studies

Ziv Bar-Joseph, Chieh Lin, Jun Ding, 2020, PLoS Comput. Biol..

Cross Species Expression Analysis of Innate Immune Response

Ziv Bar-Joseph, Ronald Rosenfeld, Yong Lu, 2009, J. Comput. Biol..

Beeping a Maximal Independent Set

Noga Alon, Ziv Bar-Joseph, Yehuda Afek, 2011, DISC.

The Short Time-series Expression Miner (STEM)

Ziv Bar-Joseph, Jesse Ernst, 2005 .

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

Tom M. Mitchell, Ziv Bar-Joseph, Yanxin Shi, 2008, RECOMB.

Author response: Selecting the most appropriate time points to profile in high-throughput studies

Ziv Bar-Joseph, Emre Sefer, Naftali Kaminski, 2016 .

Deconvolving cell cycle expression data with complementary information

Ziv Bar-Joseph, Ronald Rosenfeld, David K. Gifford, 2004, ISMB/ECCB.

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

Ziv Bar-Joseph, Ye Yuan, 2019 .

Inferring Interaction Networks using the IBP applied to microRNA Target Prediction

Ziv Bar-Joseph, Hai-Son Le, H. Le, 2011, NIPS.

Cross Species Expression Analysis of Innate Immune Response

Ziv Bar-Joseph, Ronald Rosenfeld, Yong Lu, 2009, RECOMB.

Biological interaction networks are conserved at the module level

Ziv Bar-Joseph, Shan Zhong, Guy E. Zinman, 2011, BMC Systems Biology.

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

Shila Ghazanfar, Yu Wang, Ziv Bar-Joseph, 2019, Nature.

Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data

Ziv Bar-Joseph, Chieh Lin, Z. Bar-Joseph, 2018, bioRxiv.

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

Erik D. Demaine, Tommi S. Jaakkola, Ziv Bar-Joseph, 2002, WABI.

Dynamic Bayesian Networks for Integrating Multi-omics Time Series Microbiome Data

Giri Narasimhan, Ziv Bar-Joseph, Jose Lugo-Martinez, 2019, mSystems.

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

Ziv Bar-Joseph, Ye Yuan, Z. Bar-Joseph, 2020, bioRxiv.

Texture Mixing and Texture Movie Synthesis Using Statistical Learning

Dani Lischinski, Ran El-Yaniv, Michael Werman, 2001, IEEE Trans. Vis. Comput. Graph..

Totally Ordered Multicast with Bounded Delays and Variable Rates

Nancy A. Lynch, Idit Keidar, Ziv Bar-Joseph, 2000, OPODIS.

Modeling spatial and temporal variation in motion data

Ziv Bar-Joseph, Manfred Lau, James J. Kuffner, 2009, SIGGRAPH 2009.

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

Ziv Bar-Joseph, Z. Bar-Joseph, 2003 .

scQuery: a web server for comparative analysis of single-cell RNA-seq data

Ziv Bar-Joseph, Matthew Ruffalo, Amir Alavi, 2018, bioRxiv.

MassExodus: modeling evolving networks in harsh environments

Christos Faloutsos, Ziv Bar-Joseph, Saket Navlakha, 2014, Data Mining and Knowledge Discovery.

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

Ziv Bar-Joseph, David K. Gifford, Nathan P. Palmer, 2005, ICML.

GCNG: Graph convolutional networks for inferring cell-cell interactions

Ziv Bar-Joseph, Ye Yuan, Z. Bar-Joseph, 2019, bioRxiv.

Supervised Adversarial Alignment of Single-Cell RNA-seq Data

Eric P. Xing, Ziv Bar-Joseph, Amir Alavi, 2020, bioRxiv.

Clustering short time series gene expression data

Ziv Bar-Joseph, Jason Ernst, Gerard J. Nau, 2005, ISMB.

Evaluation of different biological data and computational classification methods for use in protein interaction prediction

Ziv Bar-Joseph, Judith Klein-Seetharaman, Yanjun Qi, 2006, Proteins.

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

Ziv Bar-Joseph, Marcel H. Schulz, Shan Zhong, 2012, BMC Systems Biology.

A new approach to analyzing gene expression time series data

Tommi S. Jaakkola, Ziv Bar-Joseph, David K. Gifford, 2002, RECOMB '02.

Deconvolving cell cycle expression data with complementary information

Ziv Bar-Joseph, David K. Gifford, Itamar Simon, 2004, ISMB 2004.

A bacterial based distributed gradient descent model for mass scale evacuations

Ziv Bar-Joseph, Shashank Singh, Saket Navlakha, 2019, Swarm Evol. Comput..

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

Ziv Bar-Joseph, Jason Ernst, Z. Bar-Joseph, 2006, BMC Bioinformatics.

Identifying cycling genes by combining sequence homology and expression data

Ziv Bar-Joseph, Ronald Rosenfeld, Yong Lu, 2006, ISMB.

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

Ziv Bar-Joseph, Naftali Kaminski, Z. Bar-Joseph, 2006, RECOMB.

QoS Preserving Totally Ordered Multicast

Idit Keidar, Ziv Bar-Joseph, Tal Anker, 2000 .

MIS on the fly pdf

Noga Alon, Ziv Bar-Joseph, Yehuda Afek, 2011, ArXiv.

Hierarchical Context‐based Pixel Ordering

Daniel Cohen-Or, Ziv Bar-Joseph, D. Cohen-Or, 2003, Comput. Graph. Forum.

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

Ziv Bar-Joseph, Siddhartha Jain, Anthony Gitter, 2014, PLoS Comput. Biol..

cDREM: Inferring Dynamic Combinatorial Gene Regulation

Ziv Bar-Joseph, Aaron Wise, Z. Bar-Joseph, 2015, J. Comput. Biol..

Identifying signaling genes in spatial single cell expression data

Ziv Bar-Joseph, Dongshunyi Li, Jun Ding, 2020, bioRxiv.

The Epigenetic Consensus Problem

Ziv Bar-Joseph, Gadi Taubenfeld, Sabrina Rashid, 2021, SIROCCO.

Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data

Ziv Bar-Joseph, Ravi Pandya, Sabrina Rashid, 2017, bioRxiv.

Computational tools for analyzing single-cell data in pluripotent cell differentiation studies

Ziv Bar-Joseph, Amir Alavi, Jun Ding, 2021, Cell reports methods.

Cellar: Interactive single cell data annotation tool

Ziv Bar-Joseph, Jun Ding, Euxhen Hasanaj, 2021, bioRxiv.

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

Ziv Bar-Joseph, Ye Yuan, 2021, Briefings Bioinform..

Dynamic interaction network inference from longitudinal microbiome data

Giri Narasimhan, Ziv Bar-Joseph, Jose Lugo-Martinez, 2018, Microbiome.

Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis

Ziv Bar-Joseph, Bing Ren, Abdullah Jamali, 2013, eLife.

A Mixture of Experts Approach for Protein-Protein Interaction Prediction

Yanjun Qi, Ziv Bar-Joseph, Judith Klein-Seetharaman, 2005 .

Reconstructing dynamic microRNA-regulated interaction networks

Ziv Bar-Joseph, Marcel H. Schulz, Naftali Kaminski, 2013, Proceedings of the National Academy of Sciences.

Gene expression in relation to exhaled nitric oxide identifies novel asthma phenotypes with unique biomolecular pathways.

Ziv Bar-Joseph, Naftali Kaminski, Sally E. Wenzel, 2014, American journal of respiratory and critical care medicine.

Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle-phase meiosis genes

Ziv Bar-Joseph, Itamar Simon, Michael Klutstein, 2010, BMC Genomics.

De novo ChIP-seq analysis

Ziv Bar-Joseph, Marcel H. Schulz, A. Ercument Cicek, 2015, Genome Biology.

Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering

Ziv Bar-Joseph, Trey Ideker, Timothy Ravasi, 2010, Genome Biology.

Systematic prediction of human membrane receptor interactions

Yanjun Qi, Ziv Bar-Joseph, Judith Klein-Seetharaman, 2009, Proteomics.

Transcriptional regulatory model of fibrosis progression in the human lung.

Ziv Bar-Joseph, Naftali Kaminski, Xiting Yan, 2019, JCI insight.

Synthesis of Sound Textures by Learning and Resampling of Wavelet Trees

Dani Lischinski, Ran El-Yaniv, Michael Werman, .

Network Design and the Brain

Ziv Bar-Joseph, Saket Navlakha, Alison L. Barth, 2018, Trends in Cognitive Sciences.

Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data

Ziv Bar-Joseph, Ravi Pandya, Sabrina Rashid, 2017 .

ModuleBlast: identifying activated sub-networks within and across species

Ziv Bar-Joseph, Gerard J. Nau, Guy E. Zinman, 2014, Nucleic acids research.

A transcription factor hierarchy defines an environmental stress response network

Ziv Bar-Joseph, Joseph R. Ecker, Aaron Wise, 2016, Science.

Predicting tissue specific transcription factor binding sites

Ziv Bar-Joseph, Z. Bar-Joseph, Xin He, 2013, BMC Genomics.

The sirtuin SIRT6 regulates lifespan in male mice

Ziv Bar-Joseph, Gail Amir, Guy E. Zinman, 2012, Nature.