Z. Bar-Joseph

发表

Computational discovery of gene modules and regulatory networks

Nicola J. Rinaldi, T. Jaakkola, D. Gifford, 2003, Nature Biotechnology.

Transcriptional Regulatory Networks in Saccharomyces cerevisiae

Nicola J. Rinaldi, John J. Wyrick, I. Simon, 2002, Science.

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

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

Continuous Representations of Time-Series Gene Expression Data

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

Fast optimal leaf ordering for hierarchical clustering

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

Studying and modelling dynamic biological processes using time-series gene expression data

I. Simon, Z. Bar-Joseph, A. Gitter, 2012, Nature Reviews Genetics.

Integrating multiple evidence sources to predict transcription factor binding in the human genome.

Jason B. Ernst, I. Simon, Z. Bar-Joseph, 2010, Genome research.

Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes

T. Jaakkola, I. Simon, D. Gifford, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Combined static and dynamic analysis for determining the quality of time-series expression profiles

I. Simon, Z. Bar-Joseph, J. Ernst, 2005, Nature Biotechnology.

Reconstructing dynamic regulatory maps

I. Simon, C. T. Harbison, Z. Bar-Joseph, 2007, Molecular systems biology.

Discovering pathways by orienting edges in protein interaction networks

Anupam Gupta, J. Klein-Seetharaman, Z. Bar-Joseph, 2010, Nucleic acids research.

Using neural networks for reducing the dimensions of single-cell RNA-Seq data

Z. Bar-Joseph, C. Lin, Siddhartha Jain, 2017, Nucleic acids research.

Analyzing time series gene expression data

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

Texture Mixing and Texture Movie Synthesis Using Statistical Learning

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

Modeling spatial and temporal variation in motion data

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

Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity

M. A. de Menezes, A. Barabasi, Z. Oltvai, 2007, Proceedings of the National Academy of Sciences.

Protein complex identification by supervised graph local clustering

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

Algorithms in nature: the convergence of systems biology and computational thinking

Z. Bar-Joseph, S. Navlakha, Saket Navlakha, 2011, Molecular systems biology.

ExpressionBlast: mining large, unstructured expression databases

Guy E. Zinman, Z. Bar-Joseph, S. Naiman, 2013, Nature Methods.

Distributed information processing in biological and computational systems

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

Backup in gene regulatory networks explains differences between binding and knockout results

I. Simon, Z. Bar-Joseph, A. Gitter, 2009, Molecular systems biology.

Topological properties of robust biological and computational networks

C. Faloutsos, Z. Bar-Joseph, S. Navlakha, 2014, Journal of The Royal Society Interface.

Linking the signaling cascades and dynamic regulatory networks controlling stress responses

Z. Bar-Joseph, N. Barkai, A. Gitter, 2013, Genome research.

Adjustment in tumbling rates improves bacterial chemotaxis on obstacle-laden terrains

Z. Oltvai, Z. Bar-Joseph, S. Navlakha, 2019, Proceedings of the National Academy of Sciences.

A transcription factor hierarchy defines an environmental stress response network

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

De novo ChIP-seq analysis

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

Reconstructing dynamic microRNA-regulated interaction networks

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

Predicting tissue specific transcription factor binding sites

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

Combined analysis reveals a core set of cycling genes

I. Simon, R. Rosenfeld, Z. Bar-Joseph, 2007, Genome Biology.

Probabilistic error correction for RNA sequencing

Marcel H. Schulz, H. Le, Z. Bar-Joseph, 2013, Nucleic acids research.

Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells

I. Simon, R. Eils, Z. Bar-Joseph, 2008, Proceedings of the National Academy of Sciences.

Modeling Variation in Motion Data

J. Kuffner, Z. Bar-Joseph, Manfred Lau, 2008 .

Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation.

Z. Bar-Joseph, H. Ruohola-Baker, J. Han, 2018, Cell stem cell.

Protein interaction disruption in cancer

Z. Bar-Joseph, Matthew Ruffalo, 2019, BMC Cancer.

Predicting protein targets for drug-like compounds using transcriptomics

Nicolas A. Pabon, Z. Bar-Joseph, C. Camacho, 2018, bioRxiv.

Integrated Multi-omic Framework of the Plant Response to Jasmonic Acid

Natalie M. Clark, Mathew G. Lewsey, Z. Bar-Joseph, 2020, Nature Plants.

Integrating multi-omics longitudinal data to reconstruct networks underlying lung development.

Z. Bar-Joseph, N. Kaminski, N. Ambalavanan, 2019, American journal of physiology. Lung cellular and molecular physiology.

Reconstructing differentiation networks and their regulation from time series single-cell expression data

Z. Bar-Joseph, B. Aronow, N. Kaminski, 2018, Genome research.

Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors.

Ignacio S. Caballero, Z. Bar-Joseph, F. Camargo, 2020, Cell stem cell.

Reconstructed signaling and regulatory networks identify potential drugs for SARS-CoV-2 infection

Z. Bar-Joseph, Jose Lugo-Martinez, D. Kotton, 2020, bioRxiv : the preprint server for biology.

Single-cell time-series mapping of cell fate trajectories reveals an expanded developmental potential for human PSC-derived distal lung progenitors

Ignacio S. Caballero, Z. Bar-Joseph, F. Camargo, 2019, bioRxiv.

Cell lineage inference from SNP and scRNA-Seq data

Z. Bar-Joseph, C. Lin, Jun Ding, 2018, bioRxiv.

Cell lineage inference from SNP and scRNA-Seq data

Z. Bar-Joseph, C. Lin, Jun Ding, 2018, bioRxiv.

Cardiac differentiation at single cell resolution reveals a requirement of hypertrophic signaling for HOPX transcription

Z. Bar-Joseph, J. Han, J. Powell, 2018 .

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, bioRxiv.

A probabilistic generative model for GO enrichment analysis

I. Simon, R. Rosenfeld, Z. Bar-Joseph, 2008, Nucleic acids research.

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.

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

C. Alkan, Z. Bar-Joseph, A. E. Cicek, 2017, bioRxiv.

cDREM: Inferring Dynamic Combinatorial Gene Regulation

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

Beeping an MIS

N. Alon, Z. Bar-Joseph, Y. Afek, 2011 .

Identifying signaling genes in spatial single cell expression data.

Z. Bar-Joseph, Jun Ding, Dongshunyi Li, 2020, Bioinformatics.

Deconvolving cell cycle expression data with complementary information

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

Unbiased, High-Throughput Electron Microscopy Analysis of Experience-Dependent Synaptic Changes in the Neocortex

Alison L. Barth, Z. Bar-Joseph, A. Barth, 2015, The Journal of Neuroscience.

GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data

Z. Bar-Joseph, Ye Yuan, 2020, Genome Biology.

Inferring pairwise regulatory relationships from multiple time series datasets

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

Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data

Z. Bar-Joseph, C. Lin, Hamim Zafar, 2020, Nature Communications.

Reconstructing cancer drug response networks using multitask learning

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

Integrated Multi-omic Framework of the Plant Response to Jasmonic Acid

Natalie M. Clark, Mathew G. Lewsey, Z. Bar-Joseph, 2019, Nature Plants.

Network-guided prediction of aromatase inhibitor response in breast cancer

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

Budding yeast SSD1-V regulates transcript levels of many longevity genes and extends chronological life span in purified quiescent cells.

Z. Bar-Joseph, L. Qin, L. Breeden, 2009, Molecular biology of the cell.

Proteome-scale detection of drug-target interactions using correlations in transcriptomic perturbations

Nicolas A. Pabon, Z. Bar-Joseph, C. Camacho, 2018 .

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

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

Totally Ordered Multicast with Bounded Delays and Variable Rates

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

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

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

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

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

Granular Synthesis of Sound Textures Using Statistical Learning

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

Reconstructing the temporal progression of HIV-1 immune response pathways

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

Transcriptome analyses identify key cellular factors associated with HIV-1-associated neuropathogenesis in infected men

Narasimhan J. Venkatachari, Z. Bar-Joseph, J. Becker, 2017, AIDS.

Inferring TF activation order in time series scRNA-Seq studies

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

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

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

DECOD: fast and accurate discriminative DNA motif finding

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

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..

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

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

Genome wide predictions of miRNA regulation by transcription factors

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

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

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

Supplements to MethRaFo : MeDIP-Seq methylation estimate using Random Forest

Z. Bar-Joseph, Jun Ding, 2017 .

Transcriptional regulatory model of fibrosis progression in the human lung.

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

A unified analysis of atlas single cell data

Nam D. Nguyen, Z. Bar-Joseph, Hao Chen, 2022, bioRxiv.

Systematic prediction of human membrane receptor interactions

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

Temporal transcriptional response to latency reversing agents identifies specific factors regulating HIV-1 viral transcriptional switch

Narasimhan J. Venkatachari, Z. Bar-Joseph, Siddhartha Jain, 2015, Retrovirology.

Intracellular crowding of macromolecules defines the mode and sequence of substrate uptake by E . coli and constrains its metabolic activity and growth Supporting Information , Part 2 : Experimental protocols and microarray analyses

A. Barabasi, Z. Oltvai, Z. Bar-Joseph, 2007 .

BIOINFORMATICS Cross species analysis of microarray expression data

Z. Bar-Joseph, Yong Lu, P. Huggins, 2009 .

IL-3 and Oncogenic Abl Regulate the Myeloblast Transcriptome by Altering mRNA Stability

Jason L. Brown, Z. Bar-Joseph, J. Ernst, 2009, PloS one.

Multiset multicover methods for discriminative marker selection

B. Póczos, Z. Bar-Joseph, A. Alavi, 2022, Cell reports methods.

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

Z. Bar-Joseph, Jun Ding, Dongshunyi Li, 2022, J. Comput. Biol..

De novo construction of T cell compartment in humanized mice engrafted with iPSC-derived thymus organoids

Z. Bar-Joseph, I. Banerjee, M. Trucco, 2022, Nature Methods.

OP-NARE130215 1..11

Marcel H. Schulz, H. Le, Z. Bar-Joseph, 2013 .

MassExodus: modeling evolving networks in harsh environments

C. Faloutsos, Z. Bar-Joseph, Saket Navlakha, 2015, Data Mining and Knowledge Discovery.

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

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

Cellar: Interactive single cell data annotation tool

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

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

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

Interactive single-cell data analysis using Cellar

Z. Bar-Joseph, Jun Ding, A. Sarathi, 2022, Nature Communications.

Unsupervised cell functional annotation for single-cell RNA-seq

Z. Bar-Joseph, Jun Ding, Dongshunyi Li, 2021, bioRxiv.

Iterative point set registration for aligning scRNA-seq data

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

Comparative Expression Profile of miRNA and mRNA in Primary Peripheral Blood Mononuclear Cells Infected with Human Immunodeficiency Virus (HIV-1)

H. Le, Z. Bar-Joseph, A. Thalamuthu, 2011, PloS one.

scSTEM: clustering pseudotime ordered single-cell data

Z. Bar-Joseph, Qi Song, Jingtao Wang, 2022, Genome Biology.

scSTEM: clustering pseudotime ordered single-cell data

Z. Bar-Joseph, Qi Song, Jingtao Wang, 2022, Genome biology.

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.

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

Z. Bar-Joseph, Matthew Ruffalo, A. Alavi, 2018, Nature Communications.

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..

Temporal modelling using single-cell transcriptomics

Z. Bar-Joseph, Jun Ding, N. Sharon, 2022, Nature Reviews Genetics.

Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs

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

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 .

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

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

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

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

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

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

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

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

Identifying signaling genes in spatial single cell expression data

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

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.

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

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

Identifying cycling genes by combining sequence homology and expression data

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

Clustering short time series gene expression data

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

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

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

A new approach to analyzing gene expression time series data

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

TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data

Z. Bar-Joseph, Jun Ding, Dongshunyi Li, 2022, Genome Biology.

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

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

CINS: Cell Interaction Network inference from Single cell expression data

Z. Bar-Joseph, N. Kaminski, N. Xylourgidis, 2021, bioRxiv.

Supervised Adversarial Alignment of Single-Cell RNA-seq Data

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

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

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

Construction of integrated microRNA and mRNA immune cell signatures to predict survival of patients with breast and ovarian cancer

Z. Bar-Joseph, Matthew Ruffalo, Mondira Ray, 2018, Genes, chromosomes & cancer.

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.

The sirtuin SIRT6 regulates lifespan in male mice

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

Distributed Gradient Descent in Bacterial Food Search

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

A Network-based Approach for Predicting Missing Pathway Interactions

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

MicroRNA regulation and its effects on cellular transcriptome in Human Immunodeficiency Virus-1 (HIV-1) infected individuals with distinct viral load and CD4 cell counts

H. Le, Z. Bar-Joseph, A. Thalamuthu, 2013, BMC Infectious Diseases.

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

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

Inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data

Z. Bar-Joseph, Jun Ding, Dongshunyi Li, 2021, bioRxiv.

Learning of protein interaction networks

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

Predicting protein targets for drug-like compounds using transcriptomics

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

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.

Cross species analysis of microarray expression data

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

Biological interaction networks are conserved at the module level

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

Cross-species queries of large gene expression databases

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

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

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

Dynamic interaction network inference from longitudinal microbiome data

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

Future directions in idiopathic pulmonary fibrosis research. An NHLBI workshop report.

H. Collard, K. Anstrom, F. Martinez, 2014, American journal of respiratory and critical care medicine.

Membrane marker selection for segmenting single cell spatial proteomics data

Z. Bar-Joseph, C. Wasserfall, Maigan A. Brusko, 2022, Nature Communications.

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

Z. Bar-Joseph, Jose Lugo-Martinez, G. Narasimhan, 2021, mSystems.

iDREM: Interactive visualization of dynamic regulatory networks

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

The Epigenetic Consensus Problem

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

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

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

Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data

Z. Bar-Joseph, C. Lin, Hamim Zafar, 2019, bioRxiv.

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

Michael I. Jordan, William Stafford Noble, Gert R. G. Lanckriet, 2008, Genome Biology.

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

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

GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data

Z. Bar-Joseph, Ye Yuan, 2020, Genome biology.

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

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

IL-3 and Oncogenic Abl Regulate the Myeloblast Transcriptome by Alt= Stability

Jason L. Brown, Z. Bar-Joseph, J. Ernst, 2009 .

Cell segmentation for high-resolution spatial transcriptomics

Z. Bar-Joseph, Hao Chen, Dongshunyi Li, 2023, bioRxiv.

Cell Type Assignments for Spatial Transcriptomics Data

Z. Bar-Joseph, Ye Yuan, Haotian Teng, 2021, bioRxiv.

GCNG: Graph convolutional networks for inferring cell-cell interactions

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

Using single cell atlas data to reconstruct regulatory networks

Z. Bar-Joseph, Qi Song, Matthew Ruffalo, 2023, Nucleic acids research.

Control of cytokinesis by β-adrenergic receptors indicates an approach for regulating cardiomyocyte endowment

Z. Bar-Joseph, Junhyong Kim, J. Eberwine, 2019, Science Translational Medicine.

Validating a 52-gene risk profile for outcome prediction in Idiopathic Pulmonary Fibrosis: an international multicentre cohort study

Hongyu Zhao, I. Noth, Z. Bar-Joseph, 2017, The Lancet. Respiratory medicine.

A 52-gene signature predicts mortality and transplant-free survival in Idiopathic Pulmonary Fibrosis

Hongyu Zhao, I. Noth, Z. Bar-Joseph, 2017 .

Deconvolving cell cycle expression data with complementary information

I. Simon, D. Gifford, Z. Bar-Joseph, 2004, ISMB/ECCB.

TASIC: determining branching models from time series single cell data

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

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.

Clustering spatial transcriptomics data

Z. Bar-Joseph, Ye Yuan, Haotian Teng, 2021, Bioinform..

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.

Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways

Natalie M. Clark, Mathew G. Lewsey, Z. Bar-Joseph, 2023, bioRxiv.

A tight lower bound for randomized synchronous consensus

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

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

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

Fast optimal leaf ordering for hierarchical clustering

T. Jaakkola, D. Gifford, Z. Bar-Joseph, 2001, ISMB.

CNNC: Convolutional Neural Networks for Co-Expression Analysis

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

Hierarchical Context‐based Pixel Ordering

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

ModuleBlast: identifying activated sub-networks within and across species

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

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

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

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

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

Integrated multi-omics framework of the plant response to jasmonic acid

Natalie M. Clark, Mathew G. Lewsey, Z. Bar-Joseph, 2020, Nature Plants.

Beeping a maximal independent set

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

A Biological Solution to a Fundamental Distributed Computing Problem

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

Cardiac directed differentiation using small molecule Wnt modulation at single-cell resolution

Z. Bar-Joseph, T. Bruxner, Angelika N. Christ, 2017, bioRxiv.

Identifying proteins controlling key disease signaling pathways

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

Protein interaction disruption in cancer

Z. Bar-Joseph, Matthew Ruffalo, 2019, BMC Cancer.

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.

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

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

ISMB 2010 Organization

Roger L. Chang, S. Batzoglou, L. Cowen, 2010, Bioinformatics.

Extracting Dynamics from Static Cancer Expression Data

A. Gupta, Z. Bar-Joseph, Anupam Gupta, 2008, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Impact of the solvent capacity constraint on E. coli metabolism

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

Temporal transcriptional response to latency reversing agents identifies specific factors regulating HIV-1 viral transcriptional switch

Narasimhan J. Venkatachari, Z. Bar-Joseph, Siddhartha Jain, 2015, Retrovirology.

SCS: cell segmentation for high-resolution spatial transcriptomics

Z. Bar-Joseph, Hao Chen, Dongshunyi Li, 2023, bioRxiv.

Cross Species Expression Analysis of Innate Immune Response

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

Spatial mapping of cellular senescence: emerging challenges and opportunities

Jeffrey H. Chuang, Andrew C. Nelson, Z. Bar-Joseph, 2023, Nature Aging.

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

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

SCS: cell segmentation for high-resolution spatial transcriptomics

Z. Bar-Joseph, Hao Chen, Dongshunyi Li, 2023, Nature Methods.

Analysis of time-series regulatory networks

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

The SDREM Method for Reconstructing Signaling and Regulatory Response Networks: Applications for Studying Disease Progression.

Z. Bar-Joseph, A. Gitter, 2016, Methods in molecular biology.

A unified analysis of atlas single cell data

Nam D. Nguyen, Z. Bar-Joseph, Hao Chen, 2023, bioRxiv.

Supporting online material for : Transcriptional Regulatory Networks in Saccharomyces cerevisiae

Nicola J. Rinaldi, John J. Wyrick, I. Simon, 2002 .

Continuous hidden process model for time series expression experiments

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

Inferring Interaction Networks using the IBP applied to microRNA Target Prediction

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

Alignment and classification of time series gene expression in clinical studies

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

Deep Batch Active Learning for Drug Discovery

Z. Bar-Joseph, C. Grebner, H. Matter, 2023, bioRxiv.

Optimal transport for mapping senescent cells in spatial transcriptomics

Nam D. Nguyen, Z. Bar-Joseph, Jose Lugo-Martinez, 2023, bioRxiv.

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

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

A Mixture of Experts Approach for Protein-Protein Interaction Prediction

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

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

Z. Bar-Joseph, Jose Lugo-Martinez, J. Neu, 2022, J. Biomed. Informatics.

Early-Delivery Dynamic Atomic Broadcast

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

Matching experiments across species using expression values and textual information

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

Impact of the solvent capacity constraint on E. coli metabolism

Z. Oltvai, Z. Bar-Joseph, A. Vazquez, 2008, BMC Systems Biology.

Supplementary Material: Spatial feature extraction for enhancing cancer survival analysis in spatial proteomics imaging data

Alexandro E. Trevino, Z. Bar-Joseph, U. Duvvuri, 2023 .

The diverse effects of the plant hormone ethylene on development and growth are shaped by the actions of a master regulator of transcription, EIN3.

Z. Bar-Joseph, S. Brady, M. Urich, 2013 .

Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation.

Z. Bar-Joseph, H. Ruohola-Baker, J. Han, 2018, Cell stem cell.

A Biological Solution to a Fundamental Distributed Computing Problem

N. Alon, Z. Bar-Joseph, N. Barkai, 2011, Science.

Backup in gene regulatory networks explains differences between binding and knockout results

I. Simon, Z. Bar-Joseph, A. Gitter, 2009, Molecular systems biology.

Distributed Gradient Descent in Bacterial Food Search

Z. Oltvai, Z. Bar-Joseph, S. Rashid, 2016, RECOMB 2016.

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

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

Impact of the solvent capacity constraint on E. coli metabolism

Z. Oltvai, Z. Bar-Joseph, A. Vazquez, 2008, BMC Systems Biology.

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

Jason B. Ernst, Krin A. Kay, Z. Oltvai, 2008, PLoS Comput. Biol..

Publisher Correction: Integrated multi-omics framework of the plant response to jasmonic acid

Mathew G. Lewsey, Z. Bar-Joseph, Mark Zander, 2020, Nature Plants.

Computational methods for analyzing dynamic regulatory networks.

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

Deep Batch Active Learning for Drug Discovery

Z. Bar-Joseph, C. Grebner, H. Matter, 2023, bioRxiv.

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

Paula M. Mabee, Sushma A. Akoju, Jocelyn Y. Kishi, 2019, Nature.

Discriminative Motif Finding for Predicting Protein Subcellular Localization

Z. Bar-Joseph, Tien-ho Lin, R. F. Murphy, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

scResolve: Recovering single cell expression profiles from multi-cellular spatial transcriptomics

Z. Bar-Joseph, Jose Lugo-Martinez, Jose A. Ovando, 2023, bioRxiv.

Bioinformatics Identifying Cycling Genes by Combining Sequence Homology and Expression Data

Z. Bar-Joseph, Yong Lu, Roni Rosenfeld, 2022 .

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

Marcel H. Schulz, William E. Devanny, Z. Bar-Joseph, 2012, BMC Systems Biology.

Causal inference using deep neural networks pdf

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

Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes

T. Jaakkola, I. Simon, D. Gifford, 2003, Proceedings of the National Academy of Sciences of the United States of America.