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Author Details

Sean Davis
Johns Hopkins School of Medicine, National Cancer Institute, Princeton University, University of Colorado Anschutz Medical Campus, University of Pittsburgh, University of Washington
0000-0002-8991-6458
1974
114
54
PMIDPaper TitleJournal TitlePublished Year
37745420<i>bamSliceR</i>: cross-cohort variant and allelic bias analysis for rare variants and rare diseases.bioRxiv2023
34717047Infantile-onset myoclonic developmental and epileptic encephalopathy: A new RARS2 phenotype.Epilepsia Open2022
35760813GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases.Nat Commun2022
35143491Ten simple rules for large-scale data processing.PLoS Comput Biol2022
32026945Toward a gold standard for benchmarking gene set enrichment analysis.Brief Bioinform2021
32823322From Patient Engagement to Precision Oncology: Leveraging Informatics to Advance Cancer Care.Yearb Med Inform2020
31949145Melanoblast transcriptome analysis reveals pathways promoting melanoma metastasis.Nat Commun2020
30828438restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor.F1000Res2019
31249680BiocPkgTools: Toolkit for mining the <i>Bioconductor</i> package ecosystem.F1000Res2019
29489755Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours.Nature2018
30473781Orchestrating a community-developed computational workshop and accompanying training materials.F1000Res2018
29092936Software for the Integration of Multiomics Experiments in Bioconductor.Cancer Res2017
28114280RARRES2 functions as a tumor suppressor by promoting β-catenin phosphorylation/degradation and inhibiting p38 phosphorylation in adrenocortical carcinoma.Oncogene2017
28407484Autoreactive T Cells and Chronic Fungal Infection Drive Esophageal Carcinogenesis.Cell Host Microbe2017
28935813ASXL3 Is a Novel Pluripotency Factor in Human Respiratory Epithelial Cells and a Potential Therapeutic Target in Small Cell Lung Cancer.Cancer Res2017
28975082Resources for Interpreting Variants in Precision Genomic Oncology Applications.Front Oncol2017
27005934caOmicsV: an R package for visualizing multidimensional cancer genomic data.BMC Bioinformatics2016
26463000Public data and open source tools for multi-assay genomic investigation of disease.Brief Bioinform2016
27694491Upregulation of IFN-Inducible and Damage-Response Pathways in Chronic Graft-versus-Host Disease.J Immunol2016
27626441On the Selective Packaging of Genomic RNA by HIV-1.Viruses2016
27132513TNF-α modulates genome-wide redistribution of οNp63α/TAp73 and NF-κB cREL interactive binding on TP53 and AP-1 motifs to promote an oncogenic gene program in squamous cancer.Oncogene2016
26962861Whole Genome Sequencing of Newly Established Pancreatic Cancer Lines Identifies Novel Somatic Mutation (c.2587G&gt;A) in Axon Guidance Receptor Plexin A1 as Enhancer of Proliferation and Invasion.PLoS One2016
27087319Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant.Am J Hum Genet2016
25488748miR30a inhibits LOX expression and anaplastic thyroid cancer progression.Cancer Res2015
26084801A Genome-Wide Scan Identifies Variants in NFIB Associated with Metastasis in Patients with Osteosarcoma.Cancer Discov2015
25944801Inhibition of Survivin with YM155 Induces Durable Tumor Response in Anaplastic Thyroid Cancer.Clin Cancer Res2015
25940539Dual inhibition of HDAC and EGFR signaling with CUDC-101 induces potent suppression of tumor growth and metastasis in anaplastic thyroid cancer.Oncotarget2015
25633503Orchestrating high-throughput genomic analysis with Bioconductor.Nat Methods2015
25629959Antagonistic cross-regulation between Sox9 and Sox10 controls an anti-tumorigenic program in melanoma.PLoS Genet2015
25686607Super-enhancers delineate disease-associated regulatory nodes in T cells.Nature2015
25764003Characterization of genomic alterations in radiation-associated breast cancer among childhood cancer survivors, using comparative genomic hybridization (CGH) arrays.PLoS One2015
25773928Integrated analysis of DNA methylation, immunohistochemistry and mRNA expression, data identifies a methylation expression index (MEI) robustly associated with survival of ER-positive breast cancer patients.Breast Cancer Res Treat2015
24241536High prevalence of MAP2K1 mutations in variant and IGHV4-34-expressing hairy-cell leukemias.Nat Genet2014
25032700NCI-60 whole exome sequencing and pharmacological CellMiner analyses.PLoS One2014
25030697Lineage of origin in rhabdomyosarcoma informs pharmacological response.Genes Dev2014
24292683Downregulation of IGFBP2 is associated with resistance to IGF1R therapy in rhabdomyosarcoma.Oncogene2014
24423287Genome-wide methylation patterns in papillary thyroid cancer are distinct based on histological subtype and tumor genotype.J Clin Endocrinol Metab2014
22935230Harnessing genomics to identify environmental determinants of heritable disease.Mutat Res2013
24274149Rb1 loss modifies but does not initiate alveolar rhabdomyosarcoma.Skelet Muscle2013
24247619Prohibitin expression is associated with high grade breast cancer but is not a driver of amplification at 17q21.33.Pathology2013
24267888A polymorphism in IRF4 affects human pigmentation through a tyrosinase-dependent MITF/TFAP2A pathway.Cell2013
23856246The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology.Cancer Res2013
23901115Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma.Proc Natl Acad Sci U S A2013
23940108Oncogenic ETS fusions deregulate E2F3 target genes in Ewing sarcoma and prostate cancer.Genome Res2013
23937229RCircos: an R package for Circos 2D track plots.BMC Bioinformatics2013
23577124Whole genome and transcriptome sequencing of a B3 thymoma.PLoS One2013
23193258NCBI GEO: archive for functional genomics data sets--update.Nucleic Acids Res2013
23271725Chromothripsis and focal copy number alterations determine poor outcome in malignant melanoma.Cancer Res2013
23323543SRAdb: query and use public next-generation sequencing data from within R.BMC Bioinformatics2013
21765476CHEK2 genomic and proteomic analyses reveal genetic inactivation or endogenous activation across the 60 cell lines of the US National Cancer Institute.Oncogene2012
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Collaborators

Susan R Davis
Co-authored papers 114
Paul S Meltzer
Center for Cancer Research, National Cancer Institute, National Institutes of Health
Co-authored papers 61
Robert L Walker
Center for Cancer Research, National Cancer Institute, National Institutes of Health
Co-authored papers 23
Sven Bilke
Center for Cancer Research, National Cancer Institute, National Institutes of Health
Co-authored papers 9
Yidong Chen
Zhujiang Hospital, Southern Medical University
Co-authored papers 9
Jonathan K Killian
From Foundation Medicine
Co-authored papers 8
Martin Morgan
Roswell Park Comprehensive Cancer Center
Co-authored papers 7
Vincent J Carey
Brigham and Women's Hospital, Harvard Medical School
Co-authored papers 7
Daniel E Weeks
Co-authored papers 7
Levi Waldron
City University of New York School of Public Health
Co-authored papers 7
Francis S Collins
University of Michigan ann arbor
Co-authored papers 6
Gregory E Crawford
Center for Genomic & Computational Biology, Duke University
Co-authored papers 6
Marbin Pineda
Center for Cancer Research, National Cancer Institute
Co-authored papers 6
Marcel Ramos
Graduate School of Public Health and Health Policy, City University of New York
Co-authored papers 5
Lisa Zhang
National Institute of Child Health and Development
Co-authored papers 5
Electron Kebebew
Stanford University School of Medicine
Co-authored papers 5
Yuelin J Zhu
National Cancer Institute, National Institutes of Health
Co-authored papers 5
Glenn Merlino
Center for Cancer Research, National Cancer Institute, National Institutes of Health
Co-authored papers 5
William C Reinhold
Center for Cancer Research, National Cancer Institute
Co-authored papers 5
Xiaomu Wei
Cornell University
Co-authored papers 4
M Raza Zaidi
Northwell Health Cancer Institute
Co-authored papers 4
Yves Pommier
Center for Cancer Research, National Cancer Institute
Co-authored papers 4
Myriem Boufraqech
The University of Texas at Austin
Co-authored papers 4
Elliott H Margulies
National Human Genome Research Institute, National Institutes of Health
Co-authored papers 4
Yonghong Wang
Center for Cancer Research, National Cancer Institute, National Institutes of Health
Co-authored papers 4
Robert Cornelison
University of Virginia
Co-authored papers 4
Theresa Guo
Moores Cancer Center, University of California
Co-authored papers 4
Yardena Samuels
Weizmann Institute of Science
Co-authored papers 4
Ogan D Abaan
Illumina Inc.
Co-authored papers 4
Steven A Rosenberg
University of Colorado School of Medicine
Co-authored papers 4
Release 1.2