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Author Details

Elana J Fertig
Johns Hopkins University School of Medicine
2010
136
35
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36712023Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence.bioRxiv2023
38087458Age-associated Senescent - T Cell Signaling Promotes Type 3 Immunity that Inhibits the Biomaterial Regenerative Response.Adv Mater2023
38086385Systems immunology spanning tumors, lymph nodes, and periphery.Cell Rep Methods2023
37904980Immune landscape of tertiary lymphoid structures in hepatocellular carcinoma (HCC) treated with neoadjuvant immune checkpoint blockade.bioRxiv2023
38063199CD4 T cell-activating neoantigens enhance personalized cancer vaccine efficacy.JCI Insight2023
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
37878417Antibody dependent cell-mediated cytotoxicity selection pressure induces diverse mechanisms of resistance.Cancer Biol Ther2023
37776855Barcoding intracellular reverse transcription enables high-throughput phenotype-coupled T cell receptor analyses.Cell Rep Methods2023
37645761Informing virtual clinical trials of hepatocellular carcinoma with spatial multi-omics analysis of a human neoadjuvant immunotherapy clinical trial.bioRxiv2023
37602211Transcriptomic forecasting with neural ordinary differential equations.Patterns (N Y)2023
37723590Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence.Genome Med2023
36947820Multiomics Empowers Predictive Pancreatic Cancer Immunotherapy.J Immunol2023
37080163Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces.Cell Syst2023
37079217Transfer learning in a biomaterial fibrosis model identifies in vivo senescence heterogeneity and contributions to vascularization and matrix production across species and diverse pathologies.Geroscience2023
37067199Converging on a Cure: The Roads to Predictive Immunotherapy.Cancer Discov2023
37473725What do you most hope spatial molecular profiling will help us understand? Part 2.Cell Syst2023
37398136Boosting Single-Cell RNA Sequencing Analysis with Simple Neural Attention.bioRxiv2023
36881486Morphology-guided transcriptomic analysis of human pancreatic cancer organoids reveals microenvironmental signals that enhance invasion.J Clin Invest2023
35201318Entinostat Decreases Immune Suppression to Promote Antitumor Responses in a HER2+ Breast Tumor Microenvironment.Cancer Immunol Res2022
35841152Engineered bispecific antibodies targeting the interleukin-6 and -8 receptors potently inhibit cancer cell migration and tumor metastasis.Mol Ther2022
36439024A Random Forest Genomic Classifier for Tumor Agnostic Prediction of Response to Anti-PD1 Immunotherapy.Cancer Inform2022
36524718Generating colorblind-friendly scatter plots for single-cell data.Elife2022
36214223Integrated T cell cytometry metrics for immune-monitoring applications in immunotherapy clinical trials.JCI Insight2022
36075912Model-informed experimental design recommendations for distinguishing intrinsic and acquired targeted therapeutic resistance in head and neck cancer.NPJ Syst Biol Appl2022
36306792Multi-omic analyses of changes in the tumor microenvironment of pancreatic adenocarcinoma following neoadjuvant treatment with anti-PD-1 therapy.Cancer Cell2022
35921474Triple-negative breast cancer metastasis involves complex epithelial-mesenchymal transition dynamics and requires vimentin.Sci Transl Med2022
36052016Interrogation of T Cell-Enriched Tumors Reveals Prognostic and Immunotherapeutic Implications of Polyamine Metabolism.Cancer Res Commun2022
35016036The use of machine learning to discover regulatory networks controlling biological systems.Mol Cell2022
35121989A tumor-derived type III collagen-rich ECM niche regulates tumor cell dormancy.Nat Cancer2022
33408119Newly Identified Members of FGFR1 Splice Variants Engage in Cross-talk with AXL/AKT Axis in Salivary Adenoid Cystic Carcinoma.Cancer Res2021
35474897Spatial correlation statistics enable transcriptome-wide characterization of RNA structure binding.Cell Rep Methods2021
33600760Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species.Cell Syst2021
33509790Antitumor T-cell Immunity Contributes to Pancreatic Cancer Immune Resistance.Cancer Immunol Res2021
35330848Forecasting cancer: from precision to predictive medicine.Med2021
34737215DPP inhibition alters the CXCR3 axis and enhances NK and CD8+ T cell infiltration to improve anti-PD1 efficacy in murine models of pancreatic ductal adenocarcinoma.J Immunother Cancer2021
34708216Integrating single cell sequencing with a spatial quantitative systems pharmacology model spQSP for personalized prediction of triple-negative breast cancer immunotherapy response.Immunoinformatics (Amst)2021
34433496Author Correction: Community-wide hackathons to identify central themes in single-cell multi-omics.Genome Biol2021
34788629Evaluating the impact of age on immune checkpoint therapy biomarkers.Cell Rep2021
34433020Evaluating the impact of age on immune checkpoint therapy biomarkers.Cell Rep2021
34376232Transfer learning between preclinical models and human tumors identifies a conserved NK cell activation signature in anti-CTLA-4 responsive tumors.Genome Med2021
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
33985562Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways.Genome Biol2021
34341534Computational reconstruction of the signalling networks surrounding implanted biomaterials from single-cell transcriptomics.Nat Biomed Eng2021
34283806Systemic inhibition of PTPN22 augments anticancer immunity.J Clin Invest2021
32164487Chromatin structure regulates cancer-specific alternative splicing events in primary HPV-related oropharyngeal squamous cell carcinoma.Epigenetics2020
31855578Multipanel mass cytometry reveals anti-PD-1 therapy-mediated B and T cell compartment remodeling in tumor-draining lymph nodes.JCI Insight2020
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Collaborators

Ludmila Danilova
Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine
Co-authored papers 30
Elizabeth M Jaffee
Convergence Institute, Johns Hopkins University
Co-authored papers 30
Genevieve L Stein-O'Brien
Johns Hopkins School of Medicine
Co-authored papers 30
Daria A Gaykalova
Institute for Genome Sciences, University of Maryland School of Medicine
Co-authored papers 29
Alexander V Favorov
Johns Hopkins School of Medicine
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Michael J Considine
Johns Hopkins University School of Medicine
Co-authored papers 26
Joseph A Califano
University of California
Co-authored papers 20
Michael F Ochs
The College of New Jersey
Co-authored papers 15
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Moores Cancer Center, University of California
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Justin A Bishop
UT Southwestern Medical Center
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William H Westra
Icahn School of Medicine at Mount Sinai Hospital.
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Loyal A Goff
Johns Hopkins University School of Medicine
Co-authored papers 8
Srinivasan Yegnasubramanian
Johns Hopkins University School of Medicine
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Wayne M Koch
Johns Hopkins University School of Medicine
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Luigi Marchionni
Weill-Cornell School of Medicine
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Patrick K Ha
University of California San Francisco
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Sarah J Wheelan
National Human Genome Research Institute, National Institutes of Health
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Jason D Howard
a Vaccinogen Inc.
Co-authored papers 6
Zubair Khan
University of Texas at Houston Health Science Center
Co-authored papers 6
Akihiro Sakai
Tokai University
Co-authored papers 5
Shuling Ren
Beijing Friendship Hospital, Capital Medical University
Co-authored papers 4
Trey Ideker (CM4AI)
University of California San Diego
Co-authored papers 4
Mizuo Ando
University of Tokyo
Co-authored papers 4
Donald Geman
Johns Hopkins University
Co-authored papers 4
Takahito Fukusumi
Osaka University Graduate School of Medicine
Co-authored papers 4
Chao Liu
Xiangya Hospital, Central South University
Co-authored papers 4
Kathleen M Fisch
Center for Computational Biology and Bioinformatics, University of California
Co-authored papers 3
Guorong Xu
Chinese University of Hong Kong
Co-authored papers 3
Sunny Haft
Moores Cancer Center, University of California
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