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Author Details

Ziv Bar-Joseph
Carnegie Mellon University
2001
142
43
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
38092041Modelling post-implantation human development to yolk sac blood emergence.Nature2024
36762475Using single cell atlas data to reconstruct regulatory networks.Nucleic Acids Res2023
37387167Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis.Bioinformatics2023
36945593Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways.bioRxiv2023
37400722Spatial mapping of cellular senescence: emerging challenges and opportunities.Nat Aging2023
37398391Modelling Human Post-Implantation Development via Extra-Embryonic Niche Engineering.bioRxiv2023
37398213SCS: cell segmentation for high-resolution spatial transcriptomics.bioRxiv2023
37429992SCS: cell segmentation for high-resolution spatial transcriptomics.Nat Methods2023
34623423Clustering spatial transcriptomics data.Bioinformatics2022
35799304scSTEM: clustering pseudotime ordered single-cell data.Genome Biol2022
35764397Unsupervised cell functional annotation for single-cell RNA-seq.Genome Res2022
35422106Membrane marker selection for segmenting single cell spatial proteomics data.Nat Commun2022
35422041Interactive single-cell data analysis using Cellar.Nat Commun2022
36452867Multiset multicover methods for discriminative marker selection.Cell Rep Methods2022
36036832UNIFAN: A Tool for Unsupervised Single-Cell Clustering and Annotation.J Comput Biol2022
36064772De novo construction of T cell compartment in humanized mice engrafted with iPSC-derived thymus organoids.Nat Methods2022
36265464What are the keys to succeeding as a computational biologist in today's research climate?Cell Syst2022
35102309Temporal modelling using single-cell transcriptomics.Nat Rev Genet2022
35255944TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data.Genome Biol2022
35183765Integrating longitudinal clinical and microbiome data to predict growth faltering in preterm infants.J Biomed Inform2022
30768159Dhaka: variational autoencoder for unmasking tumor heterogeneity from single cell genomic data.Bioinformatics2021
35474899Computational tools for analyzing single-cell data in pluripotent cell differentiation studies.Cell Rep Methods2021
33876191Deep learning of gene relationships from single cell time-course expression data.Brief Bioinform2021
33785573Dynamic Bayesian Networks for Integrating Multi-omics Time Series Microbiome Data.mSystems2021
33470876Supervised Adversarial Alignment of Single-Cell RNA-seq Data.J Comput Biol2021
32886099Identifying signaling genes in spatial single-cell expression data.Bioinformatics2021
32170290Integrated multi-omics framework of the plant response to jasmonic acid.Nat Plants2020
32069291Inferring TF activation order in time series scRNA-Seq studies.PLoS Comput Biol2020
32004478Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors.Cell Stem Cell2020
33108369Iterative point set registration for aligning scRNA-seq data.PLoS Comput Biol2020
33303016GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data.Genome Biol2020
32546686Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data.Nat Commun2020
30285311Construction of integrated microRNA and mRNA immune cell signatures to predict survival of patients with breast and ovarian cancer.Genes Chromosomes Cancer2019
31822622Deep learning for inferring gene relationships from single-cell expression data.Proc Natl Acad Sci U S A2019
32457940Integration of Heterogeneous Experimental Data Improves Global Map of Human Protein Complexes.ACM BCB2019
31432713Integrating multiomics longitudinal data to reconstruct networks underlying lung development.Am J Physiol Lung Cell Mol Physiol2019
31600171Transcriptional regulatory model of fibrosis progression in the human lung.JCI Insight2019
31597755Control of cytokinesis by β-adrenergic receptors indicates an approach for regulating cardiomyocyte endowment.Sci Transl Med2019
30742607Network-guided prediction of aromatase inhibitor response in breast cancer.PLoS Comput Biol2019
31127043Adjustment in tumbling rates improves bacterial chemotaxis on obstacle-laden terrains.Proc Natl Acad Sci U S A2019
31014259Protein interaction disruption in cancer.BMC Cancer2019
31038684Continuous-state HMMs for modeling time-series single-cell RNA-Seq data.Bioinformatics2019
30940197Dynamic interaction network inference from longitudinal microbiome data.Microbiome2019
30820578Cell lineage inference from SNP and scRNA-Seq data.Nucleic Acids Res2019
29317474Reconstructing differentiation networks and their regulation from time series single-cell expression data.Genome Res2018
30124947Hercules: a profile HMM-based hybrid error correction algorithm for long reads.Nucleic Acids Res2018
30425249A web server for comparative analysis of single-cell RNA-seq data.Nat Commun2018
30290179Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation.Cell Stem Cell2018
30532261Predicting protein targets for drug-like compounds using transcriptomics.PLoS Comput Biol2018
29538379iDREM: Interactive visualization of dynamic regulatory networks.PLoS Comput Biol2018
  • 1 - 50 of 142

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Collaborators

Jason Ernst
Co-authored papers 11
Anthony Gitter
University of Wisconsin
Co-authored papers 10
Guy Zinman
Lane Center for Computational Biology, Carnegie Mellon University
Co-authored papers 7
Zolt??n N Oltvai
University of Rochester
Co-authored papers 7
Judith Klein-Seetharaman
School of Molecular Sciences & College of Health Solutions, Arizona State University
Co-authored papers 7
Yanjun Qi
University of Virginiagrid.27755.32
Co-authored papers 6
Tommi S Jaakkola
Massachusetts Institute of Technology
Co-authored papers 5
Shan Zhong
Co-authored papers 5
Roni Rosenfeld
Carnegie Mellon University
Co-authored papers 5
Mohammad R Ebrahimkhani
Co-authored papers 4
Joseph R Ecker
The Salk Institute for Biological Studies
Co-authored papers 4
Namasivayam Ambalavanan
University of Alabama at Birmingham
Co-authored papers 4
Joseph R Nery
The Salk Institute for Biological Studies
Co-authored papers 3
Huaming Chen
The Salk Institute for Biological Studies
Co-authored papers 3
Panayiotis V Benos
University of Florida
Co-authored papers 3
Robert F Murphy
Carnegie Mellon University
Co-authored papers 3
Shao-Shan Carol Huang
Salk Institute for Biological Studies
Co-authored papers 3
Jeremy J Velazquez
Co-authored papers 3
Timothy R Hughes
University of Toronto
Co-authored papers 2
Dwight Kuo
University of California
Co-authored papers 2
Trey Ideker (CM4AI)
University of California San Diego
Co-authored papers 2
Albert-L??szl?? Barab??si
Network Science Institute, Northeastern University
Co-authored papers 2
Peter Huggins
Carnegie Mellon University
Co-authored papers 2
Abdullah Ercument Cicek
Co-authored papers 2
Fran??ois Robert
Institut de recherches cliniques de Montreal
Co-authored papers 2
Bing Ren
Center for Epigenomics, University of California San Diego
Co-authored papers 2
David Benjamin Gordon
Co-authored papers 2
Ernest Fraenkel
Co-authored papers 2
Hyunju Lee
Gwangju Institute of Science and Technology
Co-authored papers 1
Yuliang Wang
Nanjing Medical University
Co-authored papers 1
Release 1.2