Select Publications

CRDC lists peer-reviewed publications that showcase the breadth and depth of research using CRDC data and resources.

TitleJournalPublication DataCRDC Component
Enrichment of Lung Cancer Computed Tomography Collections with AI-Derived AnnotationsNature Scientific Data1/24/24IDC
The NCI Imaging Data Commons as a Platform for Reproducible Research in Computational PathologyComputer Methods and Programs in Biomedicine12/23IDC
National Cancer Institute Imaging Data Commons: Toward Transparency, Reproducibility, and Scalability in Imaging Artificial IntelligenceRadioGraphics11/24/23IDC
A Proteogenomics Data-Driven Knowledge Base of Human Cancer Cell Systems9/20/23PDC
Integrative Multi-Omic Cancer Profiling Reveals DNA Methylation Patterns Associated with Therapeutic Vulnerability and Cell-of-OriginCancer Cell9/11/23PDC
Deep Learning Integrates Histopathology and Proteogenomics at a Pan-Cancer LevelCancer Cell9/11/23PDC
Pan-Cancer Proteogenomics Connects Oncogenic Drivers to Functional StatesCell8/14/23PDC
Deep Learning Integrates Histopathology and Proteogenomics at a Pan-Cancer LevelCell Reports Medicine8/14/23PDC
Pan-Cancer Analysis of Post-Translational Modifications Reveals Shared Patterns of Protein RegulationCell8/14/23PDC
Proteogenomic Data and Resources for Pan-Cancer AnalysisCancer Cell8/14/23PDC
Transparent and Reproducible AI-based Medical Imaging Pipelines Using the CloudResearch Square7/21/23IDC
Enrichment of the NLST and NSCLC-Radiomics Computed Tomography Collections with AI-Derived AnnotationsArXiv5/21/23IDC
Integrated Glycoproteomic Characterization of Clear Cell Renal Cell CarcinomaCell Reports Medicine4/18/23PDC
Interoperable Slide Microscopy Viewer and Annotation Tool for Imaging Data Science and Computational PathologyNature Communications3/22/23IDC
Proteogenomic Landscape of Human Pancreatic Ductal Adenocarcinoma in an Asian Population Reveals Tumor Cell-Enriched and Immune-Rich SubtypesNature Cancer12/22/22PDC
Histopathologic and Proteogenomic Heterogeneity Reveals Features of Clear Cell Renal Cell Carcinoma AggressivenessCancer Cell12/22/22PDC
Proteogenomic Analysis of Lung Adenocarcinoma Reveals Tumor Heterogeneity, Survival Determinants, and Therapeutically Relevant PathwaysCell Reports Medicine11/15/22PDC
Proteogenomic Markers of Chemotherapy Resistance and Response in Triple Negative Breast CancerCancer Discovery11/2/22PDC
Neoplastic Cell Enrichment of Tumor Tissues Using Coring and Laser Microdissection for Proteomic and Genomic Analyses of Pancreatic Ductal AdenocarcinomaClinical Proteomics10/20/22PDC
Genetic Subgroups Inform on Pathobiology in Adult and Pediatric Burkitt LymphomaBlood10/6/22GDC
The Genomic Landscape of Pediatric Acute Lymphoblastic LeukemiaNature Genetics9/01/22GDC
Highdicom: a Python Library for Standardized Encoding of Image Annotations and Machine Learning Model Outputs in Pathology and RadiologyJournal of Digital Imaging8/22/22IDC
Integrative Analysis of Drug Response and Clinical Outcome in Acute Myeloid LeukemiaCancer Cell8/8/22GDC
Proteomic and Phosphoproteomic Measurements Enhance Ability to Predict Ex Vivo Drug Response in AMLClinical Proteomics7/27/22PDC
Genetic Changes Associated with Relapse in Favorable Histology Wilms tumor: A Children's Oncology Group AREN03B2 StudyCell Reports Medicine6/21/22GDC
Combinatorial and Machine Learning Approaches for Improved Somatic Variant Calling from Formalin-Fixed Paraffin-Embedded Genome Sequence DataFrontiers in Genetics4/27/22GDC
The AIMI Initiative: AI-Generated Annotations for Imaging Data Commons CollectionsArXiv11/21/21IDC
Transcriptomic Profiling in Canines and Humans Reveals Cancer Specific Gene Modules and Biological Mechanisms Common to Both SpeciesPLOS Computational Biology9/27/21ICDC
Proteogenomic Characterization of Pancreatic Ductal AdenocarcinomaCell9/16/21PDC
NCI Imaging Data CommonsCancer Research8/15/21IDC
A Proteogenomic Portrait of Lung Squamous Cell CarcinomaCell8/5/21PDC
Canine Tumor Mutational Burden is Correlated with TP53 Mutation Across Tumor Types and BreedsNature Communications8/3/21ICDC
The AML Microenvironment Catalyzes a Step-Wise Evolution to Gilteritinib ResistanceCancer Cell6/24/21PDC
Adjuvant Sirolimus Does Not Improve Outcome in Pet Dogs Receiving Standard-of-Care Therapy for Appendicular Osteosarcoma: A Prospective, Randomized Trial of 324 DogsAACR6/1/21ICDC
Reliable Analysis of Clinical Tumor-Only Whole-Exome Sequencing DataJCO Clin Cancer Inform4/13/21Broad - FireCloud 
Proteogenomic and Metabolomic Characterization of Human GlioblastomaCancer Cell4/12/21PDC
Proteogenomic Insights into the Biology and Treatment of HPV-Negative Head and Neck Squamous Cell CarcinomaCancer Cell3/8/21PDC
RNA Splicing and Aggregate Gene Expression Differences in Lung Squamous Cell Carcinoma Between Patients of West African and European AncestryLung Cancer3/1/21GDC
Bringing Structural Implications and Deep Learning-Based Drug Identification for KRAS MutantsJ Chem Inf Model2/22/21GDC
The NCI Genomic Data CommonsNature Genetics2/22/21GDC
Uniform Genomic Data Analysis in the NCI Genomic Data CommonsNature Communications2/22/21GDC
TAp73β Can Promote Hepatocellular Carcinoma DedifferentiationCancers (Basel)2/13/21GDC
Proteogenomic and Metabolomic Characterization of Human GlioblastomaCancer Cell2/11/21PDC
Genotyping Common, Large Structural Variations in 5,202 Genomes Using Pangenomes, the Giraffe Mapper, and the VG ToolkitbioRxiv2/2/21Broad - FireCloud 
A cross-disorder dosage sensitivity map of the human genomemedRxiv1/28/21Broad - FireCloud 
Expression and Gene Regulatory Network of SNHG1 in Hepatocellular CarcinomaBMC Med Genomics1/26/21GDC
Assessing single-cell transcriptomic variability through density-preserving data visualizationNature Biotechnology 1/18/21Broad - FireCloud 
Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost powerNature Genetics 1/18/21Broad - FireCloud 
Streamlining data-intensive biology with workflow systemsGigaScience1/13/21Broad - FireCloud 
BinomiRare: A carriers-only test for association of rare genetic variants with a binary outcome for mixed models and any case-control proportionMedRxiv1/9/21Broad - FireCloud 
Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinomaCancer Cell1/7/2021PDC
Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain CancerCell12/23/20PDC
The first insight into the genetic structure of the population of modern SerbiabioRxiv12/18/20SB-CGC
Ace2 expression is higher in intestines and liver while being tightly regulated in development and disease in zebrafishbioRxiv12/14/20SB-CGC
Metabolism-Associated Molecular Classification of Colorectal CancerFront Oncol12/4/20GDC
Genomic and epigenetic aberrations of chromosome 1p36.13 have prognostic implications in malignanciesChromosome Res12/1/20GDC
Transcriptional Landscape of Hepatocellular Carcinoma Reveals that Patient Ethnic-Origin Influences Patterns of ExpressionbioRxiv12/1/20SB-CGC
Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted TherapyCell11/25/20PDC
Novel, abundant Drosha isoforms are deficient in miRNA processing in cancer cellsRNA Biology11/17/20SB-CGC
Strengthening the BioCompute Standard by Crowdsourcing on PrecisionFDAbioRxiv11/2/20SB-CGC
Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian CarcinomaCell Reports Medicine10/20/20PDC
Genetic alterations of SUGP1 mimic mutant-SF3B1 splice pattern in lung adenocarcinoma and other cancersOncogene10/14/20SB-CGC
Alzheimer Gene BIN1 may Simultaneously Influence Dementia Risk and Androgen Deprivation Therapy Dosage in Prostate CancerAm J Clin Oncol10/1/20GDC
BCO App: tools for generating BioCompute Objects from next-generation sequencing workflows and computationsF1000Research9/16/20SB-CGC
OpenGDC: Unifying, Modeling, Integrating Cancer Genomic Data and Clinical MetadataApplied Sciences9/12/20SB-CGC
Developing and Using a Data Commons for Understanding the Molecular Characteristics of Germ Cell TumorsMethods Mol Biol8/28/20GDC
Integrated Analysis of Germ Cell TumorsTesticular Germ Cell Tumors8/28/20Broad - FireCloud 
The Veterans Affairs Precision Oncology Data Repository, a Clinical, Genomic, and Imaging Research DatabasePatterns (N Y)8/17/20GDC
Linked Entity Attribute Pair (LEAP): A Harmonization Framework for Data PoolingJCO Clin Cancer Inform8/1/20GDC
Scalability and cost-effectiveness analysis of whole genome-wide association studies on Google Cloud Platform and Amazon Web ServicesJ am Med Inform Assoc.7/27/20SB-CGC
Proteogenomic characterization of human colon and rectal cancerNature7/20/20PDC
Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma.Cell7/9/20PDC
Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and Progression.Cell7/9/20PDC
Oncogenic Features in Histologically Normal Mucosa: Novel Insights Into Field Effect From a Mega-Analysis of Colorectal TranscriptomesClin Transl Gastroenterol7/1/20GDC
LINE-1 expression in cancer correlates with DNA damage response, copy number variation, and cell cycle progressionbioRxiv6/28/20SB-CGC
Type 3 innate lymphoid cells are associated with a successful intestinal transplantAm J Transplant6/28/20SB-CGC
Identification of the key genes and characterizations of Tumor Immune Microenvironment in Lung Adenocarcinoma (LUAD) and Lung Squamous Cell Carcinoma (LUSC)J Cancer6/16/20GDC
Identification of an Immune Score-Based Gene Panel with Prognostic Power for Oral Squamous Cell CarcinomaMed Sci Monit6/12/20GDC
Classification and mutation prediction based on histopathology H&E images in liver cancer using deep learningNPJ Precis Oncol6/8/20GDC
The road towards data integration in human genomics: players, steps and interactionsBrief Bioinform6/4/20SB-CGC
AGO-bound mature miRNAs are oligouridylated by TUTs and subsequently degraded by DIS3L2Nat Commun.6/2/20SB-CGC
Increased number of subclones in lung squamous cell carcinoma elicits overexpression of immune related genesTransl Lung Cancer Res6/1/20GDC
Measuring Cancer Hallmark Mediation of the TET1 Glioma Survival Effect with Linked Neural-Network Based Mediation ExperimentsSci Rep6/1/20GDC
Modern Information Technology for Cancer Research: What’s in IT for Me? An Overview of Technologies and ApproachesOncology6/1/20SB-CGC
Systematic Establishment of Robustness and Standards in Patient-Derived Xenograft Experiments and AnalysisCancer Research6/1/20SB-CGC
A structural variation reference for medical and population geneticsNature5/27/20Broad - FireCloud 
Implementing the FAIR Data Principles in precision oncology: review of supporting initiativesBrief Bioinform5/21/20GDC
An integrative investigation on significant mutations and their down-stream pathways in lung squamous cell carcinoma reveals CUL3/KEAP1/NRF2 relevant subtypesMol Med5/20/20GDC
Co-occurrent Alterations of Alzheimer's Genes and Prostate Cancer Genes in Prostate CancerCancer Genomics Proteomics5/1/20GDC
Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability.Cell Reports Medicine4/21/20PDC
Open Health Imaging Foundation Viewer: An Extensible Open-Source Framework for Building Web-Based Imaging Applications to Support Cancer ResearchJCO Clin Cancer Inform4/4/20ISB-CGC
Automatic Staging of Cancer Tumors Using AIM Image Annotations and OntologiesJ Digit Imaging4/1/20GDC
Whole Exome Sequencing Data Analysis Algorithms in Cancer DiagnosticsPrime Archives of Cancer Research3/27/20SB-CGC
Microbiome analyses of blood and tissues suggest cancer diagnostic approachNature3/1/20SB-CGC
Screening TCGA database for prognostic genes in lower grade glioma microenvironmentAnn Transl Med3/1/20GDC
Genomic Characterization of Non-Invasive Differentiated-Type Gastric Cancer in the Japanese PopulationCancers (Basel)2/22/20GDC
Proteogenomic Characterization of Endometrial CarcinomaCell2/20/20PDC
The Pan-Cancer Landscape of Prognostic Germline Variants in 10,582 PatientsGenome Medicine2/17/20SB-CGC
Immunogenomic Pathways Associated with Cytotoxic Lymphocyte Infiltration and Survival in Colorectal CancerBMC Cancer2/14/20Broad - FireCloud 
Steroid Enzyme and Receptor Expression and Regulations in Breast Tumor Samples - A Statistical Evaluation of Public DataJ Steroid Biochem Mol Biol2/1/20GDC
Loss of Kat2a Enhances Transcriptional Noise and Depletes Acute Myeloid Leukemia Stem-Like CellseLife1/27/20SB-CGC
Knowledge-Guided Analysis of “Omics” Data Using the KnowEnG Cloud PlatformPLoS1/23/20SB-CGC
Screening the Cancer Genome Atlas Database for Genes of Prognostic Value in Acute Myeloid LeukemiaFront Oncol1/21/20GDC
Discovering the Anticancer Potential of Non-Oncology Drugs by Systematic Viability ProfilingNature Cancer1/20/20Broad - FireCloud 
A Protein‐Centric Approach for Exome Variant Aggregation Enables Sensitive Association Analysis with Clinical OutcomesHuman Mutation1/12/20ISB-CGC
Building Containerized Workflows Using the BioDepot-Workflow-BuilderCell Systems11/27/19SB-CGC
Integrated Proteogenomic Characterization of Clear Cell Renal Cell CarcinomaCell10/31/19PDC
Somatic Truth Data from Cell LineagebioRxiv10/31/19Broad - FireCloud 
Cumulus: a cloud-based data analysis framework for large-scale single-cell and single-nucleus RNA-seqbioRxiv10/30/19Broad - FireCloud 
Identifying Epigenetic Signature of Breast Cancer with Machine Learning arXiv10/12/19ISB-CGC
CellBender remove-background: a deep generative model for unsupervised removal of background noise from scRNA-seq datasetsbioRxiv10/3/19Broad - FireCloud 
Integrated Proteogenomic Characterization of HBV-Related Hepatocellular CarcinomaCell10/3/19PDC
Improved detection of gene fusions by applying statistical methods reveals oncogenic RNA cancer driversPNAS7/30/19SB-CGC
Clonal replacement of tumor-specific T cells following PD-1 blockadeNature Medicine7/29/19Broad - FireCloud 
A cytosine deaminase for programmable single-base RNA editingScience7/26/19Broad - FireCloud 
Read Mapping and Transcript Assembly: A Scalable and High-Throughput Workflow for the Processing and Analysis of Ribonucleic Acid Sequencing DataFrontiers in Genetics6/24/19SB-CGC
Achieving reproducibility and accuracy in cancer mutation detection with whole-genome and whole-exome sequencingbioRxiv6/2/19SB-CGC
SNP2SIM: a modular workflow for standardizing molecular simulation and functional analysis of protein variantsBMC Bioinformatics 5/1/19SB-CGC
The Germline Variants rs61757955 and rs34988193 Are Predictive of Survival in Lower Grade Glioma PatientsMolecular Cancer Research 5/1/19SB-CGC
Building Portable and Reproducible Cancer Informatics Workflows: An RNA Sequencing Case StudyMethods Mol Biol4/1/19SB-CGC
Data Lakes, Clouds and Commons: A Review of Platforms for Analyzing and Sharing Genomic DataTrends in Genetics1/25/19DCF
Pregnancy-Associated Plasma Protein-A (PAPP-A) in Ewing Sarcoma: Role in Tumor Growth and Immune EvasionJNCI1/20/19ISB-CGC
Proteogenomic Characterization of Human Early-Onset Gastric Cancer.Cancer Cell1/14/19PDC
Structural Differences Between Pri-miRNA Paralogs Promote Alternative Drosha Cleavage and Expand Target RepertoiresCell Reports1/8/19SB-CGC
restfulSE: A semantically rich interface for cloud-scale genomics with BioconductorF1000 Research1/7/19ISB-CGC
Maximizing the Utility of Cancer Transcriptomic DataTrends in Cancer Research12/4/18SB-CGC
Personal Genome Project UK (PGP-UK): a research and citizen science hybrid project in support of personalized medicineBMC Med Genomics11/27/18SB-CGC
Lack of detectable neoantigen depletion in the untreated cancer genomebioRxiv11/26/18Broad - FireCloud 
Association analysis using somatic mutationsPLOS Genetics11/2/18SB-CGC
QuagmiR: a cloud-based application for isomiR big data analyticsBioinformatics10/9/18SB-CGC
Using Semantic Web Technologies to Enable Cancer Genomics Discovery at Petabyte ScaleCancer Informatics9/28/18SB-CGC
Multiplatform Integrative Analysis of Immunogenomic Data for Biomarker DiscoveryBiomarkers for Immunotherapy of Cancer9/10/18ISB-CGC
Identification of rare-disease genes in diverse undiagnosed cases using whole blood transcriptome sequencing and large control cohortsbioRxiv9/4/18Broad - FireCloud 
Data Harmonization for a Molecularly Driven Health SystemCell8/23/18DCF
Recurrent Tumor-Specific Regulation of Alternative Polyadenylation of Cancer-Related GenesBMC Genomics7/13/18ISB-CGC
Progress Towards Cancer Data EcosystemsCancer J5/30/18DCF
The Immune Landscape of Cancer Immunity4/17/18ISB-CGC, SB-CGC
Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology ImagesCell Reports4/3/18ISB-CGC
Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines Cell Systems3/28/18ISB-CGC
Using the Seven Bridges Cancer Genomics Cloud to access and analyze petabytes of cancer data Current Protocols in Bioinformatics12/8/17SB-CGC
The Cancer Genomics Cloud: Collaborative, reproducible, and democratized—a new paradigm in large-scale computational research Cancer Research11/1/17SB-CGC
The ISB Cancer Genomic Cloud: A Flexible Cloud-Based Platform for Cancer Genomic Research Cancer Research11/1/17ISB-CGC
A Comprehensive Infrastructure for Big Data in Cancer Research: Accelerating Cancer Research and Precision MedicineFront Cell Dev Biol.9/21/17NCI
APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphismNat Commun.9/6/17PDC
Precise, pan-cancer discovery of gene fusions reveals a signature of selection in primary tumorsbioRxiv8/18/17SB-CGC
Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian CancerCell7/28/16PDC
Proteogenomics Connects Somatic Mutations to Signalling in Breast Cancer.Nature5/25/16PDC
Proteomic analysis of colon and rectal carcinoma using standard and customized databasesScientific Data7/21/15PDC
Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome mapsNature Medicine3/2/15PDC