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Author Details

Genevieve L Stein-O'Brien
Johns Hopkins School of Medicine
2014
38
17
PMIDPaper TitleJournal TitlePublished Year
36881486Morphology-guided transcriptomic analysis of human pancreatic cancer organoids reveals microenvironmental signals that enhance invasion.J Clin Invest2023
37745323Digitize your Biology! Modeling multicellular systems through interpretable cell behavior.bioRxiv2023
37989764Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS.Nat Protoc2023
37885016Pumping the brakes on RNA velocity by understanding and interpreting RNA velocity estimates.Genome Biol2023
37602211Transcriptomic forecasting with neural ordinary differential equations.Patterns (N Y)2023
37316665Psychedelics reopen the social reward learning critical period.Nature2023
37080163Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces.Cell Syst2023
37067199Converging on a Cure: The Roads to Predictive Immunotherapy.Cancer Discov2023
35101061Universal prediction of cell-cycle position using transfer learning.Genome Biol2022
35358296Two-stage linked component analysis for joint decomposition of multiple biologically related data sets.Biostatistics2022
36214223Integrated T cell cytometry metrics for immune-monitoring applications in immunotherapy clinical trials.JCI Insight2022
33985562Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways.Genome Biol2021
33600760Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species.Cell Syst2021
34433496Author Correction: Community-wide hackathons to identify central themes in single-cell multi-omics.Genome Biol2021
34660940Forecasting cellular states: from descriptive to predictive biology via single-cell multiomics.Curr Opin Syst Biol2021
34796337Neoadjuvant Cabozantinib and Nivolumab Converts Locally Advanced HCC into Resectable Disease with Enhanced Antitumor Immunity.Nat Cancer2021
34353350Community-wide hackathons to identify central themes in single-cell multi-omics.Genome Biol2021
34329587From bench to bedside: Single-cell analysis for cancer immunotherapy.Cancer Cell2021
32375049Variation of Human Neural Stem Cells Generating Organizer States In Vitro before Committing to Cortical Excitatory or Inhibitory Neuronal Fates.Cell Rep2020
33113347Parallel Social Information Processing Circuits Are Differentially Impacted in Autism.Neuron2020
33219090Integrated immunological analysis of a successful conversion of locally advanced hepatocellular carcinoma to resectability with neoadjuvant therapy.J Immunother Cancer2020
32386599Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development.Dev Cell2020
32167521projectR: an R/Bioconductor package for transfer learning via PCA, NMF, correlation and clustering.Bioinformatics2020
30753828Aging-like Spontaneous Epigenetic Silencing Facilitates Wnt Activation, Stemness, and Braf<sup>V600E</sup>-Induced Tumorigenesis.Cancer Cell2019
31843893Comprehensive analysis of a mouse model of spontaneous uveoretinitis using single-cell RNA sequencing.Proc Natl Acad Sci U S A2019
31337651Differential Variation Analysis Enables Detection of Tumor Heterogeneity Using Single-Cell RNA-Sequencing Data.Cancer Res2019
31128945Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification.Neuron2019
30988181Hypoxia tolerance in the Norrin-deficient retina and the chronically hypoxic brain studied at single-cell resolution.Proc Natl Acad Sci U S A2019
31121116Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species.Cell Syst2019
31002670CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer.PLoS Comput Biol2019
29342249Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer.Bioinformatics2018
30143323Enter the Matrix: Factorization Uncovers Knowledge from Omics.Trends Genet2018
29792227Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance.Genome Med2018
28968850Epigenetic regulation of gene expression in cancer: techniques, resources and analysis.Brief Funct Genomics2018
28174896PatternMarkers &amp; GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF.Bioinformatics2017
27650546CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network.Oncotarget2016
26523645Latent tri-lineage potential of adult hippocampal neural stem cells revealed by Nf1 inactivation.Nat Neurosci2015
24233779Pattern identification in time-course gene expression data with the CoGAPS matrix factorization.Methods Mol Biol2014
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Collaborators

Johns Hopkins University School of Medicine
Co-authored papers 30
Johns Hopkins University School of Medicine
Co-authored papers 14
Convergence Institute, Johns Hopkins University
Co-authored papers 9
Johns Hopkins School of Medicine
Co-authored papers 8
Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine
Co-authored papers 6
Institute for Genome Sciences, University of Maryland School of Medicine
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Johns Hopkins University School of Medicine
Co-authored papers 4
The College of New Jersey
Co-authored papers 4
Dartmouth College Geisel School of Medicine, Princeton University, University of Colorado Anschutz Medical Campus, University of Pennsylvania Perelman School of Medicine
Co-authored papers 3
Johns Hopkins University School of Medicine.
Co-authored papers 3
Dana-Farber Cancer Institute & Harvard School of Public Health
Co-authored papers 3
Universite de Toulouse, Inserm, CNRS, Universite Toulouse III-Paul Sabatier
Co-authored papers 2
The University of Melbourne
Co-authored papers 2
Boston University School of Medicine
Co-authored papers 2
University of Wisconsin - Madison, 1300 University Ave
Co-authored papers 2
Co-authored papers 2
St. Paul's Hospital, University of British Columbia
Co-authored papers 2
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Memorial Sloan Kettering Cancer Center
Co-authored papers 2
University of California
Co-authored papers 2
University of Padova
Co-authored papers 2
Brigham and Women's Hospital, Harvard Medical School
Co-authored papers 2
University of North Carolina at Chapel Hill
Co-authored papers 2
Broad Institute of MIT and Harvard
Co-authored papers 2
McMaster University
Co-authored papers 2
University of Michigan ann arbor
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INSERM
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University of Melbourne
Co-authored papers 2
Moores Cancer Center, University of California
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European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 2