List of works - Ziv Bar-Joseph

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

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

article

A biological solution to a fundamental distributed computing problem

scientific article published in January 2011

A combined expression-interaction model for inferring the temporal activity of transcription factors

scientific article published on August 2009

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

scientific article

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

scientific article published on July 2013

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

scientific article

A network-based approach for predicting missing pathway interactions

scientific article

A patient-gene model for temporal expression profiles in clinical studies

scientific article published in April 2007

A probabilistic generative model for GO enrichment analysis

scientific article published on August 2008

A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli

scientific article

A transcription factor hierarchy defines an environmental stress response network

scientific article

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

scientific article published in Nature Communications

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

scientific article published on 24 May 2019

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

scientific article

Alignment and classification of time series gene expression in clinical studies

scientific article published in July 2008

Analyzing time series gene expression data

scientific article

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

scientific article published on 16 June 2009

Beeping a Maximal Independent Set

Beeping a maximal independent set

article published in 2012

Biological interaction networks are conserved at the module level

scientific article

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

scientific article published on July 2009

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

scientific article

Cell lineage inference from SNP and scRNA-Seq data

scientific article published on 01 June 2019

Clustering short time series gene expression data

scientific article

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

scientific article

Combined analysis reveals a core set of cycling genes

scientific article published on January 2007

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

scientific article published in December 2005

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

scientific article published on 21 August 2003

Computational discovery of gene modules and regulatory networks

scientific article published on 12 October 2003

Computational methods for analyzing dynamic regulatory networks

scientific article published on January 2010

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

scientific article

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

scientific article published on 18 November 2018

Continuous hidden process model for time series expression experiments

scientific article

Continuous representations of time-series gene expression data

scientific article

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

scientific article published on 01 November 2019

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

scientific article published on 01 October 2019

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

scientific article published on August 29, 2012

Cross Species Expression Analysis of Innate Immune Response

Cross species analysis of microarray expression data

scientific article

Cross species expression analysis of innate immune response

scientific article published on March 2010

Cross-species queries of large gene expression databases

scientific article

DECOD: fast and accurate discriminative DNA motif finding

scientific article

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

scientific article

De novo ChIP-seq analysis

scientific article

Deconvolving cell cycle expression data with complementary information

scientific article

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

scientific article (publication date: July 2015)

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

scientific article published on 10 December 2019

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

scientific article published on 15 February 2019

Discovering pathways by orienting edges in protein interaction networks

scientific article

Discriminative motif finding for predicting protein subcellular localization

scientific article

Distributed information processing in biological and computational systems

Dynamic interaction network inference from longitudinal microbiome data

scientific article published on 02 April 2019

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

scientific article

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

scientific article

ExpressionBlast: mining large, unstructured expression databases

Extracting dynamics from static cancer expression data

scientific article

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

scientific article published on January 2014

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

scientific article published on 10 December 2020

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

scientific article

Genome wide predictions of miRNA regulation by transcription factors

scientific article

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

scholarly article

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

scientific article published on 01 November 2018

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

Hierarchical Context-based Pixel Ordering

IL-3 and oncogenic Abl regulate the myeloblast transcriptome by altering mRNA stability

scientific article

Identifying cycling genes by combining sequence homology and expression data

scientific article

Identifying proteins controlling key disease signaling pathways ⬇️

scientific article published on July 1, 2013

Identifying signaling genes in spatial single cell expression data

scientific article published on 04 September 2020

Impact of the solvent capacity constraint on E. coli metabolism

scientific article

Inferring TF activation order in time series scRNA-Seq studies

scientific article published on 18 February 2020

Inferring pairwise regulatory relationships from multiple time series datasets

scientific article published on 19 January 2007

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

scientific article published on 13 March 2020

Integrating multiomics longitudinal data to reconstruct networks underlying lung development

scientific article published on 21 August 2019

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

scientific article

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

scientific article

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

scientific article published on 01 September 2019

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

scholarly article

Iterative point set registration for aligning scRNA-seq data

scientific article published on 27 October 2020

K-ary clustering with optimal leaf ordering for gene expression data

scientific article

Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque

scientific article

Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs

Learning cellular sorting pathways using protein interactions and sequence motifs

scientific article published on 14 October 2011

Linking the signaling cascades and dynamic regulatory networks controlling stress responses

scientific article published on 11 October 2012

MassExodus: modeling evolving networks in harsh environments

Matching experiments across species using expression values and textual information

scientific article

Membrane marker selection for segmenting single cell spatial proteomics data

scientific article published in 2022

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

scientific article published on 13 July 2017

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

scientific article

Modeling spatial and temporal variation in motion data

ModuleBlast: identifying activated sub-networks within and across species

scientific article

Multitask learning of signaling and regulatory networks with application to studying human response to flu

scientific article published on 18 December 2014

Network Design and the Brain

scientific article published on 17 October 2017

Network-guided prediction of aromatase inhibitor response in breast cancer

scientific article published on 11 February 2019

Predicting protein targets for drug-like compounds using transcriptomics

scientific article published on 07 December 2018

Predicting tissue specific transcription factor binding sites

scientific article

Preface

scholarly article by Manolis Kellis published in February 2011

Probabilistic error correction for RNA sequencing

scientific article (publication date: May 2013)

Protein complex identification by supervised graph local clustering

scientific article published on July 2008

Protein interaction disruption in cancer

scientific article published on 23 April 2019

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

scientific article published on 21 July 2020

Random forest similarity for protein-protein interaction prediction from multiple sources.

scientific article published in January 2005

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

scientific article published on 30 January 2020

Reconstructing SARS-CoV-2 response signaling and regulatory networks

scientific article published on 13 October 2020

Reconstructing cancer drug response networks using multitask learning.

scientific article published on 10 October 2017

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

scientific article published on 9 January 2018

Reconstructing dynamic microRNA-regulated interaction networks

scientific article published on 28 August 2013

Reconstructing dynamic regulatory maps

scientific article published on 16 January 2007

Reconstructing the temporal progression of HIV-1 immune response pathways

scientific article published on June 2016

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

retracted article

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

scientific article

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

scientific article

Schools anxiously await NRC program rankings

scientific article

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

scientific article published on 26 January 2017

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

scientific article published on 01 October 2018

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

scientific article published on 16 June 2020

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

scientific article published on July 18, 2012

Synthesizing sound textures through wavelet tree learning

Systematic prediction of human membrane receptor interactions

scientific article

TASIC: Determining branching models from time series single cell data

scientific article

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

scientific article published on 11 June 2013

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

scientific article

Texture mixing and texture movie synthesis using statistical learning

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

scientific article published on January 2016

The sirtuin SIRT6 regulates lifespan in male mice

scientific article

Topological properties of robust biological and computational networks

scientific article

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

scientific article published on 20 July 2016

Transcriptional regulatory model of fibrosis progression in the human lung

scientific article published on 14 November 2019

Transcriptional regulatory networks in Saccharomyces cerevisiae

scientific article

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

scientific article

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

scientific article

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

scientific article published on September 2017

Validation of a 52-gene risk profile for outcome prediction in patients with idiopathic pulmonary fibrosis: an international, multicentre, cohort study.

scientific article published on 20 September 2017

cDREM: inferring dynamic combinatorial gene regulation

scientific article

iDREM: Interactive visualization of dynamic regulatory networks.

scientific article published on 14 March 2018

List of works by Ziv Bar-Joseph

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

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

A biological solution to a fundamental distributed computing problem

A combined expression-interaction model for inferring the temporal activity of transcription factors

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

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

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

A network-based approach for predicting missing pathway interactions

A patient-gene model for temporal expression profiles in clinical studies

A probabilistic generative model for GO enrichment analysis

A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli

A transcription factor hierarchy defines an environmental stress response network

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

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

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

Alignment and classification of time series gene expression in clinical studies

Analyzing time series gene expression data

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

Beeping a Maximal Independent Set

Beeping a maximal independent set

Biological interaction networks are conserved at the module level

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

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

Cell lineage inference from SNP and scRNA-Seq data

Clustering short time series gene expression data

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

Combined analysis reveals a core set of cycling genes

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

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

Computational discovery of gene modules and regulatory networks

Computational methods for analyzing dynamic regulatory networks

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

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

Continuous hidden process model for time series expression experiments

Continuous representations of time-series gene expression data

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

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

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

Cross Species Expression Analysis of Innate Immune Response

Cross species analysis of microarray expression data

Cross species expression analysis of innate immune response

Cross-species queries of large gene expression databases

DECOD: fast and accurate discriminative DNA motif finding

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

De novo ChIP-seq analysis

Deconvolving cell cycle expression data with complementary information

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

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

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

Discovering pathways by orienting edges in protein interaction networks

Discriminative motif finding for predicting protein subcellular localization

Distributed information processing in biological and computational systems

Dynamic interaction network inference from longitudinal microbiome data

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

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

ExpressionBlast: mining large, unstructured expression databases

Extracting dynamics from static cancer expression data

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

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

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

Genome wide predictions of miRNA regulation by transcription factors

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

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

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

Hierarchical Context-based Pixel Ordering

IL-3 and oncogenic Abl regulate the myeloblast transcriptome by altering mRNA stability

Identifying cycling genes by combining sequence homology and expression data

Identifying proteins controlling key disease signaling pathways ⬇️

Identifying signaling genes in spatial single cell expression data

Impact of the solvent capacity constraint on E. coli metabolism

Inferring TF activation order in time series scRNA-Seq studies

Inferring pairwise regulatory relationships from multiple time series datasets

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

Integrating multiomics longitudinal data to reconstruct networks underlying lung development

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

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

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

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

Iterative point set registration for aligning scRNA-seq data