Ziv Bar-Joseph | Academic Influence

Ziv Bar-Joseph's AcademicInfluence.com Rankings

Ziv Bar-Joseph

Biology

#4371

World Rank

#6525

Historical Rank

Systems Biology

#34

World Rank

#34

Historical Rank

Computational Biology

#130

World Rank

#130

Historical Rank

biology Degrees

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Biology

Ziv Bar-Joseph's Degrees

PhD Computer Science Stanford University
Bachelors Computer Science Tel Aviv University

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Why Is Ziv Bar-Joseph Influential?

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According to Wikipedia, Ziv Bar-Joseph is an Israeli computational biologist and Professor in the Computational Biology Department and the Machine Learning Department at the Carnegie Mellon School of Computer Science. Education Bar-Joseph studied computer science at Bachelor of Science and Master of Science level, both at the Hebrew University of Jerusalem. He gained his PhD from the Massachusetts Institute of Technology in computer science in 2003, under the supervision of David K. Gifford and Tommi S. Jaakkola. Following this, he was a postdoctoral associate at the MIT Computer Science and Artificial Intelligence Laboratory and the Whitehead Institute.

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Ziv Bar-Joseph's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

Transcriptional Regulatory Networks in Saccharomyces cerevisiae (2002) (3179)
STEM: a tool for the analysis of short time series gene expression data (2006) (1186)
The sirtuin SIRT6 regulates lifespan in male mice (2012) (774)
Computational discovery of gene modules and regulatory networks (2003) (660)
Clustering short time series gene expression data (2005) (522)
Analyzing time series gene expression data (2004) (479)
Fast optimal leaf ordering for hierarchical clustering (2001) (465)
Studying and modelling dynamic biological processes using time-series gene expression data (2012) (419)
Evaluation of different biological data and computational classification methods for use in protein interaction prediction (2006) (403)
Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis (2013) (332)
Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity (2007) (324)
A transcription factor hierarchy defines an environmental stress response network (2016) (319)
Continuous Representations of Time-Series Gene Expression Data (2003) (285)
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program (2019) (265)
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence (2008) (261)
Texture Mixing and Texture Movie Synthesis Using Statistical Learning (2001) (258)
Reconstructing dynamic regulatory maps (2007) (231)
A new approach to analyzing gene expression time series data (2002) (229)
Random Forest Similarity for Protein-Protein Interaction Prediction from Multiple Sources (2004) (200)
Future directions in idiopathic pulmonary fibrosis research. An NHLBI workshop report. (2014) (193)
Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation. (2018) (170)
Using neural networks for reducing the dimensions of single-cell RNA-Seq data (2017) (164)
Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells (2008) (155)
Gene expression in relation to exhaled nitric oxide identifies novel asthma phenotypes with unique biomolecular pathways. (2014) (152)
A Biological Solution to a Fundamental Distributed Computing Problem (2011) (151)
Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes (2003) (141)
K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data (2002) (137)
Algorithms in nature: the convergence of systems biology and computational thinking (2011) (127)
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data (2012) (126)
Protein complex identification by supervised graph local clustering (2008) (121)
A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coli (2008) (113)
Integrating multiple evidence sources to predict transcription factor binding in the human genome. (2010) (113)
Probabilistic error correction for RNA sequencing (2013) (111)
Cross species analysis of microarray expression data (2009) (109)
Distributed information processing in biological and computational systems (2014) (108)
Beeping a maximal independent set (2011) (106)
Impact of the solvent capacity constraint on E. coli metabolism (2008) (106)
Deep learning for inferring gene relationships from single-cell expression data (2018) (105)
Discovering pathways by orienting edges in protein interaction networks (2010) (103)
Backup in gene regulatory networks explains differences between binding and knockout results (2009) (90)
Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors. (2020) (90)
Modeling spatial and temporal variation in motion data (2009) (88)
Transcriptional regulatory model of fibrosis progression in the human lung. (2019) (86)
Integrated Multi-omic Framework of the Plant Response to Jasmonic Acid (2019) (85)
Synthesizing Sound Textures through Wavelet Tree Learning (2002) (83)
Linking the signaling cascades and dynamic regulatory networks controlling stress responses (2013) (79)
Alignment and classification of time series gene expression in clinical studies (2008) (72)
A mixture of feature experts approach for protein-protein interaction prediction (2007) (72)
A probabilistic generative model for GO enrichment analysis (2008) (69)
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 (2013) (68)
Reconstructing dynamic microRNA-regulated interaction networks (2013) (67)
Deconvolving cell cycle expression data with complementary information (2004) (63)
Validating a 52-gene risk profile for outcome prediction in Idiopathic Pulmonary Fibrosis: an international multicentre cohort study (2017) (61)
Comparative Expression Profile of miRNA and mRNA in Primary Peripheral Blood Mononuclear Cells Infected with Human Immunodeficiency Virus (HIV-1) (2011) (58)
GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data (2020) (57)
A tight lower bound for randomized synchronous consensus (1998) (54)
Control of cytokinesis by β-adrenergic receptors indicates an approach for regulating cardiomyocyte endowment (2019) (52)
Budding yeast SSD1-V regulates transcript levels of many longevity genes and extends chronological life span in purified quiescent cells. (2009) (50)
DECOD: fast and accurate discriminative DNA motif finding (2011) (50)
Combined analysis reveals a core set of cycling genes (2007) (45)
A web server for comparative analysis of single-cell RNA-seq data (2018) (44)
Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation (2013) (44)
Biological interaction networks are conserved at the module level (2011) (44)
Discriminative Motif Finding for Predicting Protein Subcellular Localization (2011) (43)
Decreasing-Rate Pruning Optimizes the Construction of Efficient and Robust Distributed Networks (2015) (43)
Dynamic interaction network inference from longitudinal microbiome data (2018) (42)
Predicting protein targets for drug-like compounds using transcriptomics (2018) (40)
Extracting Dynamics from Static Cancer Expression Data (2008) (40)
Reconstructing differentiation networks and their regulation from time series single-cell expression data (2018) (37)
Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering (2010) (35)
Inferring pairwise regulatory relationships from multiple time series datasets (2007) (34)
Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data (2019) (34)
A Network-based Approach for Predicting Missing Pathway Interactions (2012) (34)
Combined static and dynamic analysis for determining the quality of time-series expression profiles (2005) (33)
Identifying proteins controlling key disease signaling pathways (2013) (32)
ExpressionBlast: mining large, unstructured expression databases (2013) (32)
TASIC: determining branching models from time series single cell data (2017) (32)
Predicting tissue specific transcription factor binding sites (2013) (31)
Topological properties of robust biological and computational networks (2014) (31)
Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data (2017) (31)
Hercules: a profile HMM-based hybrid error correction algorithm for long reads (2017) (30)
Sound-by-numbers: motion-driven sound synthesis (2003) (29)
Early-Delivery Dynamic Atomic Broadcast (2002) (29)
Cross-species queries of large gene expression databases (2010) (28)
Identifying signaling genes in spatial single cell expression data (2020) (28)
Tradeoffs between Dense and Replicate Sampling Strategies for High-Throughput Time Series Experiments. (2016) (28)
Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data (2018) (27)
Selecting the most appropriate time points to profile in high-throughput studies (2017) (26)
Identifying cycling genes by combining sequence homology and expression data (2006) (26)
Network Design and the Brain (2018) (25)
Granular Synthesis of Sound Textures Using Statistical Learning (1999) (25)
Active learning for sampling in time-series experiments with application to gene expression analysis (2005) (24)
iDREM: Interactive visualization of dynamic regulatory networks (2018) (23)
Systematic prediction of human membrane receptor interactions (2009) (23)
Temporal modelling using single-cell transcriptomics (2022) (22)
Cell lineage inference from SNP and scRNA-Seq data (2018) (22)
Cross Species Expression Analysis of Innate Immune Response (2009) (21)
A high-throughput framework to detect synapses in electron microscopy images (2013) (21)
A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors (2008) (20)
Synthesis of Sound Textures by Learning and Resampling of Wavelet Trees (20)
A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies (2006) (20)
Continuous hidden process model for time series expression experiments (2007) (18)
Integrating multi-omics longitudinal data to reconstruct networks underlying lung development. (2019) (18)
Inferring Interaction Networks using the IBP applied to microRNA Target Prediction (2011) (18)
Unbiased, High-Throughput Electron Microscopy Analysis of Experience-Dependent Synaptic Changes in the Neocortex (2015) (18)
Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells (2013) (17)
SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data (2015) (17)
Temporal transcriptional response to latency reversing agents identifies specific factors regulating HIV-1 viral transcriptional switch (2015) (16)
Clustering spatial transcriptomics data (2021) (15)
Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu (2014) (14)
Supervised Adversarial Alignment of Single-Cell RNA-seq Data (2020) (14)
Hierarchical Context‐based Pixel Ordering (2003) (13)
Dynamic Bayesian networks for integrating multi-omics time-series microbiome data (2019) (12)
Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle-phase meiosis genes (2010) (12)
De novo ChIP-seq analysis (2015) (12)
IL-3 and Oncogenic Abl Regulate the Myeloblast Transcriptome by Altering mRNA Stability (2009) (12)
ModuleBlast: identifying activated sub-networks within and across species (2014) (12)
Adjustment in tumbling rates improves bacterial chemotaxis on obstacle-laden terrains (2019) (11)
GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data (2020) (11)
cDREM: Inferring Dynamic Combinatorial Gene Regulation (2015) (11)
Genome-Wide Epigenetic Modifications as a Shared Memory Consensus Problem (2020) (11)
Reconstructing the temporal progression of HIV-1 immune response pathways (2016) (10)
QoS Preserving Totally Ordered Multicast (2000) (10)
Cross Species Expression Analysis using a Dirichlet Process Mixture Model with Latent Matchings (2010) (10)
MethRaFo: MeDIP‐seq methylation estimate using a Random Forest Regressor (2017) (10)
Inferring TF activation order in time series scRNA-Seq studies (2020) (10)
Analysis of time-series regulatory networks (2020) (10)
Computational methods for analyzing dynamic regulatory networks. (2010) (9)
Construction of integrated microRNA and mRNA immune cell signatures to predict survival of patients with breast and ovarian cancer (2018) (9)
Transcriptome analyses identify key cellular factors associated with HIV-1-associated neuropathogenesis in infected men (2017) (9)
Deep learning of gene relationships from single cell time-course expression data (2020) (7)
GCNG: Graph convolutional networks for inferring cell-cell interactions (2019) (7)
Genome wide predictions of miRNA regulation by transcription factors (2016) (7)
Integrated multi-omics framework of the plant response to jasmonic acid (2020) (7)
CNNC: Convolutional Neural Networks for Co-Expression Analysis (2018) (6)
Learning of protein interaction networks (2008) (6)
De novo construction of T cell compartment in humanized mice engrafted with iPSC-derived thymus organoids (2022) (6)
Protein interaction disruption in cancer (2019) (5)
Matching experiments across species using expression values and textual information (2012) (5)
Distributed Gradient Descent in Bacterial Food Search (2016) (5)
Retraction: Comparative Expression Profile of miRNA and mRNA in Primary Peripheral Blood Mononuclear Cells Infected with Human Immunodeficiency Virus (HIV-1) (2012) (5)
Dynamic interaction network inference from longitudinal microbiome data (2019) (5)
Network-guided prediction of aromatase inhibitor response in breast cancer (2019) (5)
A Mixture of Experts Approach for Protein-Protein Interaction Prediction (2005) (4)
Interactive single-cell data analysis using Cellar (2022) (4)
Cell Type Assignments for Spatial Transcriptomics Data (2021) (4)
A bacterial based distributed gradient descent model for mass scale evacuations (2019) (4)
The SDREM Method for Reconstructing Signaling and Regulatory Response Networks: Applications for Studying Disease Progression. (2016) (4)
MassExodus: modeling evolving networks in harsh environments (2015) (4)
The Epigenetic Consensus Problem (2021) (4)
Membrane marker selection for segmenting single cell spatial proteomics data (2022) (4)
Reconstructing cancer drug response networks using multitask learning (2017) (4)
Using Neural Networks to Improve Single Cell RNA-Seq Data Analysis (2017) (3)
Iterative point set registration for aligning scRNA-seq data (2020) (3)
Totally Ordered Multicast with Bounded Delays and Variable Rates (2000) (3)
Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs (2011) (3)
scQuery: a web server for comparative analysis of single-cell RNA-seq data (2018) (3)
Integrating longitudinal clinical and microbiome data to predict growth faltering in preterm infants (2022) (3)
TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data (2021) (3)
Computational tools for analyzing single-cell data in pluripotent cell differentiation studies (2021) (3)
Cardiac differentiation at single cell resolution reveals a requirement of hypertrophic signaling for HOPX transcription (2018) (2)
Cellar: Interactive single cell data annotation tool (2021) (2)
A computational framework for the analysis of multi-species microarray data (2008) (2)
Unsupervised cell functional annotation for single-cell RNA-seq (2021) (2)
Dynamic Bayesian Networks for Integrating Multi-omics Time Series Microbiome Data (2021) (2)
Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data (2020) (2)
Inferring interactions, expression programs and regulatory networks from high throughput biological data (2003) (1)
A unified analysis of atlas single cell data (2022) (1)
TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data (2022) (1)
BIOINFORMATICS Cross species analysis of microarray expression data (2009) (1)
Synthesizing Sound Textures through (2002) (1)
Proteome-scale detection of drug-target interactions using correlations in transcriptomic perturbations (2018) (1)
Reconstructed signaling and regulatory networks identify potential drugs for SARS-CoV-2 infection (2020) (1)
Cardiac directed differentiation using small molecule Wnt modulation at single-cell resolution (2017) (1)
Temporal transcriptional response to latency reversing agents identifies specific factors regulating HIV-1 viral transcriptional switch (2015) (1)
Modeling Variation in Motion Data (2008) (1)
CINS: Cell Interaction Network inference from Single cell expression data (2021) (1)
scSTEM: clustering pseudotime ordered single-cell data (2022) (1)
Preface: RECOMB Conference on Systems Biology, Regulatory Genomics, and DREAM Challenges 2010 special issue. (2011) (1)
Supplementary Results For : Combining Static and Time Series Data to Determine the Quality of Expression Profiles in Time Series Experiments (2005) (1)
Causal inference using deep neural networks (2020) (1)
Integration of Heterogeneous Experimental Data Improves Global Map of Human Protein Complexes (2019) (1)
Single-cell time-series mapping of cell fate trajectories reveals an expanded developmental potential for human PSC-derived distal lung progenitors (2019) (1)
ISMB 2010 Organization (2010) (0)
2011 Reviewers List (2012) (0)
MIS on the fly (2011) (0)
Early-Delivery Dynamic Atomic Broadcast (Extended Abstract) (2002) (0)
Author response: Selecting the most appropriate time points to profile in high-throughput studies (2016) (0)
RECOMB Conference on Systems Biology, Regulatory Genomics, and DREAM Challenges 2010 Special Issue, Preface (2011) (0)
Special issue focused on regulatory genomics (2020) (0)
IL-3 Coordination of the Myeloblast Transcriptome by Modulating mRNA Stability (2008) (0)
Leveraging Cell-Specific Disease Signatures to Predict New Drug Therapies for Idiopathic Pulmonary Fibrosis (2022) (0)
Proceedings of the sixth IASTED International Conference on Computational Intelligence and Bioinformatics, held November 7-9, 2011, in Pittsburgh, USA . Proceedings of the IASTED International Conference on Modelling, Simulation, and Identification, held November 7-9, 2011 in Pittsburgh, USA (2011) (0)
Using single cell atlas data to reconstruct regulatory networks (2023) (0)
Beeping a maximal independent set (2012) (0)
Cell segmentation for high-resolution spatial transcriptomics (2023) (0)
Protein interaction disruption in cancer (2019) (0)
Predicting tissue specific transcription factor binding sites (2013) (0)
Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways (2023) (0)
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 (2007) (0)
A 52-gene signature predicts mortality and transplant-free survival in Idiopathic Pulmonary Fibrosis (2017) (0)
Beeping an MIS (2011) (0)
Probabilistic Models for Error Correction of Nonuniform Sequencing Data (2017) (0)
What are the keys to succeeding as a computational biologist in today's research climate? (2022) (0)
Protein Interaction Disruption in Cancer ( Supplementary Material ) (2019) (0)
OP-NARE130215 1..11 (2013) (0)
scSTEM: clustering pseudotime ordered single-cell data (2022) (0)
De novo ChIP-seq analysis (2015) (0)
MassExodus: modeling evolving networks in harsh environments (2015) (0)
Schools anxiously await NRC program rankings. (2009) (0)
2008 Reviewers List (2009) (0)
Supplements to MethRaFo : MeDIP-Seq methylation estimate using Random Forest (2017) (0)
A Fault-Tolerant Dynami Atomi Broad ast Algorithm with QoS Guarantees (2019) (0)
Shall We Dense? Comparing Design Strategies for Time Series Expression Experiments (2016) (0)
Supplement for Target Predictions using LINCS Data (2016) (0)
Single-Cell Transcriptomic Analysis of Type 2 Alveolar Epithelial Cell Differentiation from Induced Pluripotent Stem Cells: An Emerging Tool to Model Interstitial Lung Diseases (2019) (0)
D C ] 1 0 Ju n 20 11 MIS on the fly ( Extended Abstract ) (2011) (0)
Preface (2011) (0)
A Probabilistic Graphical Model for Understanding Cellular Dynamics in Idiopathic Pulmonary Fibrosis Progression (2022) (0)
Genetic networks modulating cell fate specification and contributing to cardiac disease risk in hiPSC-derived cardiomyocytes at single cell resolution (2018) (0)
Single Nuclei RNA Sequencing of Differentially Affected Regions in IPF Lungs Suggests a Central Role of Aberrant Basaloid Cells in Disease Progression (2022) (0)
Multiset multicover methods for discriminative marker selection (2022) (0)
Publisher Correction: Integrated multi-omics framework of the plant response to jasmonic acid (2020) (0)
The Short Time-series Expression Miner (STEM) (2005) (0)
IL-3 and Oncogenic Abl Regulate the Myeloblast Transcriptome by Alt= Stability (2009) (0)
A web server for comparative analysis of single-cell RNA-seq data (2018) (0)
The diverse effects of the plant hormone ethylene on development and growth are shaped by the actions of a master regulator of transcription, EIN3. (2013) (0)
UNIFAN: A Tool for Unsupervised Single-Cell Clustering and Annotation (2022) (0)

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What Schools Are Affiliated With Ziv Bar-Joseph?

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