| Enrichment of Lung Cancer Computed Tomography Collections with AI-Derived Annotations | Nature Scientific Data | 1/24/24 | IDC |
| The NCI Imaging Data Commons as a Platform for Reproducible Research in Computational Pathology | Computer Methods and Programs in Biomedicine | 12/23 | IDC |
| National Cancer Institute Imaging Data Commons: Toward Transparency, Reproducibility, and Scalability in Imaging Artificial Intelligence | RadioGraphics | 11/24/23 | IDC |
| A Proteogenomics Data-Driven Knowledge Base of Human Cancer | Cell Systems | 9/20/23 | PDC |
| Integrative Multi-Omic Cancer Profiling Reveals DNA Methylation Patterns Associated with Therapeutic Vulnerability and Cell-of-Origin | Cancer Cell | 9/11/23 | PDC |
| Deep Learning Integrates Histopathology and Proteogenomics at a Pan-Cancer Level | Cancer Cell | 9/11/23 | PDC |
| Pan-Cancer Proteogenomics Connects Oncogenic Drivers to Functional States | Cell | 8/14/23 | PDC |
| Deep Learning Integrates Histopathology and Proteogenomics at a Pan-Cancer Level | Cell Reports Medicine | 8/14/23 | PDC |
| Pan-Cancer Analysis of Post-Translational Modifications Reveals Shared Patterns of Protein Regulation | Cell | 8/14/23 | PDC |
| Proteogenomic Data and Resources for Pan-Cancer Analysis | Cancer Cell | 8/14/23 | PDC |
| Transparent and Reproducible AI-based Medical Imaging Pipelines Using the Cloud | Research Square | 7/21/23 | IDC |
| Enrichment of the NLST and NSCLC-Radiomics Computed Tomography Collections with AI-Derived Annotations | ArXiv | 5/21/23 | IDC |
| Integrated Glycoproteomic Characterization of Clear Cell Renal Cell Carcinoma | Cell Reports Medicine | 4/18/23 | PDC |
| Interoperable Slide Microscopy Viewer and Annotation Tool for Imaging Data Science and Computational Pathology | Nature Communications | 3/22/23 | IDC |
| Proteogenomic Landscape of Human Pancreatic Ductal Adenocarcinoma in an Asian Population Reveals Tumor Cell-Enriched and Immune-Rich Subtypes | Nature Cancer | 12/22/22 | PDC |
| Histopathologic and Proteogenomic Heterogeneity Reveals Features of Clear Cell Renal Cell Carcinoma Aggressiveness | Cancer Cell | 12/22/22 | PDC |
| Proteogenomic Analysis of Lung Adenocarcinoma Reveals Tumor Heterogeneity, Survival Determinants, and Therapeutically Relevant Pathways | Cell Reports Medicine | 11/15/22 | PDC |
| Proteogenomic Markers of Chemotherapy Resistance and Response in Triple Negative Breast Cancer | Cancer Discovery | 11/2/22 | PDC |
| Neoplastic Cell Enrichment of Tumor Tissues Using Coring and Laser Microdissection for Proteomic and Genomic Analyses of Pancreatic Ductal Adenocarcinoma | Clinical Proteomics | 10/20/22 | PDC |
| Genetic Subgroups Inform on Pathobiology in Adult and Pediatric Burkitt Lymphoma | Blood | 10/6/22 | GDC |
| The Genomic Landscape of Pediatric Acute Lymphoblastic Leukemia | Nature Genetics | 9/01/22 | GDC |
| Highdicom: a Python Library for Standardized Encoding of Image Annotations and Machine Learning Model Outputs in Pathology and Radiology | Journal of Digital Imaging | 8/22/22 | IDC |
| Integrative Analysis of Drug Response and Clinical Outcome in Acute Myeloid Leukemia | Cancer Cell | 8/8/22 | GDC |
| Proteomic and Phosphoproteomic Measurements Enhance Ability to Predict Ex Vivo Drug Response in AML | Clinical Proteomics | 7/27/22 | PDC |
| Genetic Changes Associated with Relapse in Favorable Histology Wilms tumor: A Children's Oncology Group AREN03B2 Study | Cell Reports Medicine | 6/21/22 | GDC |
| Combinatorial and Machine Learning Approaches for Improved Somatic Variant Calling from Formalin-Fixed Paraffin-Embedded Genome Sequence Data | Frontiers in Genetics | 4/27/22 | GDC |
| The AIMI Initiative: AI-Generated Annotations for Imaging Data Commons Collections | ArXiv | 11/21/21 | IDC |
| Transcriptomic Profiling in Canines and Humans Reveals Cancer Specific Gene Modules and Biological Mechanisms Common to Both Species | PLOS Computational Biology | 9/27/21 | ICDC |
| Proteogenomic Characterization of Pancreatic Ductal Adenocarcinoma | Cell | 9/16/21 | PDC |
| NCI Imaging Data Commons | Cancer Research | 8/15/21 | IDC |
| A Proteogenomic Portrait of Lung Squamous Cell Carcinoma | Cell | 8/5/21 | PDC |
| Canine Tumor Mutational Burden is Correlated with TP53 Mutation Across Tumor Types and Breeds | Nature Communications | 8/3/21 | ICDC |
| The AML Microenvironment Catalyzes a Step-Wise Evolution to Gilteritinib Resistance | Cancer Cell | 6/24/21 | PDC |
| Adjuvant Sirolimus Does Not Improve Outcome in Pet Dogs Receiving Standard-of-Care Therapy for Appendicular Osteosarcoma: A Prospective, Randomized Trial of 324 Dogs | AACR | 6/1/21 | ICDC |
| Reliable Analysis of Clinical Tumor-Only Whole-Exome Sequencing Data | JCO Clin Cancer Inform | 4/13/21 | Broad - FireCloud |
| Proteogenomic and Metabolomic Characterization of Human Glioblastoma | Cancer Cell | 4/12/21 | PDC |
| Proteogenomic Insights into the Biology and Treatment of HPV-Negative Head and Neck Squamous Cell Carcinoma | Cancer Cell | 3/8/21 | PDC |
| RNA Splicing and Aggregate Gene Expression Differences in Lung Squamous Cell Carcinoma Between Patients of West African and European Ancestry | Lung Cancer | 3/1/21 | GDC |
| Bringing Structural Implications and Deep Learning-Based Drug Identification for KRAS Mutants | J Chem Inf Model | 2/22/21 | GDC |
| The NCI Genomic Data Commons | Nature Genetics | 2/22/21 | GDC |
| Uniform Genomic Data Analysis in the NCI Genomic Data Commons | Nature Communications | 2/22/21 | GDC |
| TAp73β Can Promote Hepatocellular Carcinoma Dedifferentiation | Cancers (Basel) | 2/13/21 | GDC |
| Proteogenomic and Metabolomic Characterization of Human Glioblastoma | Cancer Cell | 2/11/21 | PDC |
| Genotyping Common, Large Structural Variations in 5,202 Genomes Using Pangenomes, the Giraffe Mapper, and the VG Toolkit | bioRxiv | 2/2/21 | Broad - FireCloud |
| A cross-disorder dosage sensitivity map of the human genome | medRxiv | 1/28/21 | Broad - FireCloud |
| Expression and Gene Regulatory Network of SNHG1 in Hepatocellular Carcinoma | BMC Med Genomics | 1/26/21 | GDC |
| Assessing single-cell transcriptomic variability through density-preserving data visualization | Nature Biotechnology | 1/18/21 | Broad - FireCloud |
| Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power | Nature Genetics | 1/18/21 | Broad - FireCloud |
| Streamlining data-intensive biology with workflow systems | GigaScience | 1/13/21 | Broad - FireCloud |
| BinomiRare: A carriers-only test for association of rare genetic variants with a binary outcome for mixed models and any case-control proportion | MedRxiv | 1/9/21 | Broad - FireCloud |
| Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma | Cancer Cell | 1/7/2021 | PDC |
| Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer | Cell | 12/23/20 | PDC |
| The first insight into the genetic structure of the population of modern Serbia | bioRxiv | 12/18/20 | SB-CGC |
| Ace2 expression is higher in intestines and liver while being tightly regulated in development and disease in zebrafish | bioRxiv | 12/14/20 | SB-CGC |
| Metabolism-Associated Molecular Classification of Colorectal Cancer | Front Oncol | 12/4/20 | GDC |
| Genomic and epigenetic aberrations of chromosome 1p36.13 have prognostic implications in malignancies | Chromosome Res | 12/1/20 | GDC |
| Transcriptional Landscape of Hepatocellular Carcinoma Reveals that Patient Ethnic-Origin Influences Patterns of Expression | bioRxiv | 12/1/20 | SB-CGC |
| Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy | Cell | 11/25/20 | PDC |
| Novel, abundant Drosha isoforms are deficient in miRNA processing in cancer cells | RNA Biology | 11/17/20 | SB-CGC |
| Strengthening the BioCompute Standard by Crowdsourcing on PrecisionFDA | bioRxiv | 11/2/20 | SB-CGC |
| Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian Carcinoma | Cell Reports Medicine | 10/20/20 | PDC |
| Genetic alterations of SUGP1 mimic mutant-SF3B1 splice pattern in lung adenocarcinoma and other cancers | Oncogene | 10/14/20 | SB-CGC |
| Alzheimer Gene BIN1 may Simultaneously Influence Dementia Risk and Androgen Deprivation Therapy Dosage in Prostate Cancer | Am J Clin Oncol | 10/1/20 | GDC |
| BCO App: tools for generating BioCompute Objects from next-generation sequencing workflows and computations | F1000Research | 9/16/20 | SB-CGC |
| OpenGDC: Unifying, Modeling, Integrating Cancer Genomic Data and Clinical Metadata | Applied Sciences | 9/12/20 | SB-CGC |
| Developing and Using a Data Commons for Understanding the Molecular Characteristics of Germ Cell Tumors | Methods Mol Biol | 8/28/20 | GDC |
| Integrated Analysis of Germ Cell Tumors | Testicular Germ Cell Tumors | 8/28/20 | Broad - FireCloud |
| The Veterans Affairs Precision Oncology Data Repository, a Clinical, Genomic, and Imaging Research Database | Patterns (N Y) | 8/17/20 | GDC |
| Linked Entity Attribute Pair (LEAP): A Harmonization Framework for Data Pooling | JCO Clin Cancer Inform | 8/1/20 | GDC |
| Scalability and cost-effectiveness analysis of whole genome-wide association studies on Google Cloud Platform and Amazon Web Services | J am Med Inform Assoc. | 7/27/20 | SB-CGC |
| Proteogenomic characterization of human colon and rectal cancer | Nature | 7/20/20 | PDC |
| Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma. | Cell | 7/9/20 | PDC |
| Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and Progression. | Cell | 7/9/20 | PDC |
| Oncogenic Features in Histologically Normal Mucosa: Novel Insights Into Field Effect From a Mega-Analysis of Colorectal Transcriptomes | Clin Transl Gastroenterol | 7/1/20 | GDC |
| LINE-1 expression in cancer correlates with DNA damage response, copy number variation, and cell cycle progression | bioRxiv | 6/28/20 | SB-CGC |
| Type 3 innate lymphoid cells are associated with a successful intestinal transplant | Am J Transplant | 6/28/20 | SB-CGC |
| Identification of the key genes and characterizations of Tumor Immune Microenvironment in Lung Adenocarcinoma (LUAD) and Lung Squamous Cell Carcinoma (LUSC) | J Cancer | 6/16/20 | GDC |
| Identification of an Immune Score-Based Gene Panel with Prognostic Power for Oral Squamous Cell Carcinoma | Med Sci Monit | 6/12/20 | GDC |
| Classification and mutation prediction based on histopathology H&E images in liver cancer using deep learning | NPJ Precis Oncol | 6/8/20 | GDC |
| The road towards data integration in human genomics: players, steps and interactions | Brief Bioinform | 6/4/20 | SB-CGC |
| AGO-bound mature miRNAs are oligouridylated by TUTs and subsequently degraded by DIS3L2 | Nat Commun. | 6/2/20 | SB-CGC |
| Increased number of subclones in lung squamous cell carcinoma elicits overexpression of immune related genes | Transl Lung Cancer Res | 6/1/20 | GDC |
| Measuring Cancer Hallmark Mediation of the TET1 Glioma Survival Effect with Linked Neural-Network Based Mediation Experiments | Sci Rep | 6/1/20 | GDC |
| Modern Information Technology for Cancer Research: What’s in IT for Me? An Overview of Technologies and Approaches | Oncology | 6/1/20 | SB-CGC |
| Systematic Establishment of Robustness and Standards in Patient-Derived Xenograft Experiments and Analysis | Cancer Research | 6/1/20 | SB-CGC |
| A structural variation reference for medical and population genetics | Nature | 5/27/20 | Broad - FireCloud |
| Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives | Brief Bioinform | 5/21/20 | GDC |
| An integrative investigation on significant mutations and their down-stream pathways in lung squamous cell carcinoma reveals CUL3/KEAP1/NRF2 relevant subtypes | Mol Med | 5/20/20 | GDC |
| Co-occurrent Alterations of Alzheimer's Genes and Prostate Cancer Genes in Prostate Cancer | Cancer Genomics Proteomics | 5/1/20 | GDC |
| Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability. | Cell Reports Medicine | 4/21/20 | PDC |
| Open Health Imaging Foundation Viewer: An Extensible Open-Source Framework for Building Web-Based Imaging Applications to Support Cancer Research | JCO Clin Cancer Inform | 4/4/20 | ISB-CGC |
| Automatic Staging of Cancer Tumors Using AIM Image Annotations and Ontologies | J Digit Imaging | 4/1/20 | GDC |
| Whole Exome Sequencing Data Analysis Algorithms in Cancer Diagnostics | Prime Archives of Cancer Research | 3/27/20 | SB-CGC |
| Microbiome analyses of blood and tissues suggest cancer diagnostic approach | Nature | 3/1/20 | SB-CGC |
| Screening TCGA database for prognostic genes in lower grade glioma microenvironment | Ann Transl Med | 3/1/20 | GDC |
| Genomic Characterization of Non-Invasive Differentiated-Type Gastric Cancer in the Japanese Population | Cancers (Basel) | 2/22/20 | GDC |
| Proteogenomic Characterization of Endometrial Carcinoma | Cell | 2/20/20 | PDC |
| The Pan-Cancer Landscape of Prognostic Germline Variants in 10,582 Patients | Genome Medicine | 2/17/20 | SB-CGC |
| Immunogenomic Pathways Associated with Cytotoxic Lymphocyte Infiltration and Survival in Colorectal Cancer | BMC Cancer | 2/14/20 | Broad - FireCloud |
| Steroid Enzyme and Receptor Expression and Regulations in Breast Tumor Samples - A Statistical Evaluation of Public Data | J Steroid Biochem Mol Biol | 2/1/20 | GDC |
| Loss of Kat2a Enhances Transcriptional Noise and Depletes Acute Myeloid Leukemia Stem-Like Cells | eLife | 1/27/20 | SB-CGC |
| Knowledge-Guided Analysis of “Omics” Data Using the KnowEnG Cloud Platform | PLoS | 1/23/20 | SB-CGC |
| Screening the Cancer Genome Atlas Database for Genes of Prognostic Value in Acute Myeloid Leukemia | Front Oncol | 1/21/20 | GDC |
| Discovering the Anticancer Potential of Non-Oncology Drugs by Systematic Viability Profiling | Nature Cancer | 1/20/20 | Broad - FireCloud |
| A Protein‐Centric Approach for Exome Variant Aggregation Enables Sensitive Association Analysis with Clinical Outcomes | Human Mutation | 1/12/20 | ISB-CGC |
| Building Containerized Workflows Using the BioDepot-Workflow-Builder | Cell Systems | 11/27/19 | SB-CGC |
| Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma | Cell | 10/31/19 | PDC |
| Somatic Truth Data from Cell Lineage | bioRxiv | 10/31/19 | Broad - FireCloud |
| Cumulus: a cloud-based data analysis framework for large-scale single-cell and single-nucleus RNA-seq | bioRxiv | 10/30/19 | Broad - FireCloud |
| Identifying Epigenetic Signature of Breast Cancer with Machine Learning | arXiv | 10/12/19 | ISB-CGC |
| CellBender remove-background: a deep generative model for unsupervised removal of background noise from scRNA-seq datasets | bioRxiv | 10/3/19 | Broad - FireCloud |
| Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma | Cell | 10/3/19 | PDC |
| Improved detection of gene fusions by applying statistical methods reveals oncogenic RNA cancer drivers | PNAS | 7/30/19 | SB-CGC |
| Clonal replacement of tumor-specific T cells following PD-1 blockade | Nature Medicine | 7/29/19 | Broad - FireCloud |
| A cytosine deaminase for programmable single-base RNA editing | Science | 7/26/19 | Broad - FireCloud |
| Read Mapping and Transcript Assembly: A Scalable and High-Throughput Workflow for the Processing and Analysis of Ribonucleic Acid Sequencing Data | Frontiers in Genetics | 6/24/19 | SB-CGC |
| Achieving reproducibility and accuracy in cancer mutation detection with whole-genome and whole-exome sequencing | bioRxiv | 6/2/19 | SB-CGC |
| SNP2SIM: a modular workflow for standardizing molecular simulation and functional analysis of protein variants | BMC Bioinformatics | 5/1/19 | SB-CGC |
| The Germline Variants rs61757955 and rs34988193 Are Predictive of Survival in Lower Grade Glioma Patients | Molecular Cancer Research | 5/1/19 | SB-CGC |
| Building Portable and Reproducible Cancer Informatics Workflows: An RNA Sequencing Case Study | Methods Mol Biol | 4/1/19 | SB-CGC |
| Data Lakes, Clouds and Commons: A Review of Platforms for Analyzing and Sharing Genomic Data | Trends in Genetics | 1/25/19 | DCF |
| Pregnancy-Associated Plasma Protein-A (PAPP-A) in Ewing Sarcoma: Role in Tumor Growth and Immune Evasion | JNCI | 1/20/19 | ISB-CGC |
| Proteogenomic Characterization of Human Early-Onset Gastric Cancer. | Cancer Cell | 1/14/19 | PDC |
| Structural Differences Between Pri-miRNA Paralogs Promote Alternative Drosha Cleavage and Expand Target Repertoires | Cell Reports | 1/8/19 | SB-CGC |
| restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor | F1000 Research | 1/7/19 | ISB-CGC |
| Maximizing the Utility of Cancer Transcriptomic Data | Trends in Cancer Research | 12/4/18 | SB-CGC |
| Personal Genome Project UK (PGP-UK): a research and citizen science hybrid project in support of personalized medicine | BMC Med Genomics | 11/27/18 | SB-CGC |
| Lack of detectable neoantigen depletion in the untreated cancer genome | bioRxiv | 11/26/18 | Broad - FireCloud |
| Association analysis using somatic mutations | PLOS Genetics | 11/2/18 | SB-CGC |
| QuagmiR: a cloud-based application for isomiR big data analytics | Bioinformatics | 10/9/18 | SB-CGC |
| Using Semantic Web Technologies to Enable Cancer Genomics Discovery at Petabyte Scale | Cancer Informatics | 9/28/18 | SB-CGC |
| Multiplatform Integrative Analysis of Immunogenomic Data for Biomarker Discovery | Biomarkers for Immunotherapy of Cancer | 9/10/18 | ISB-CGC |
| Identification of rare-disease genes in diverse undiagnosed cases using whole blood transcriptome sequencing and large control cohorts | bioRxiv | 9/4/18 | Broad - FireCloud |
| Data Harmonization for a Molecularly Driven Health System | Cell | 8/23/18 | DCF |
| Recurrent Tumor-Specific Regulation of Alternative Polyadenylation of Cancer-Related Genes | BMC Genomics | 7/13/18 | ISB-CGC |
| Progress Towards Cancer Data Ecosystems | Cancer J | 5/30/18 | DCF |
| The Immune Landscape of Cancer | Immunity | 4/17/18 | ISB-CGC, SB-CGC |
| Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images | Cell Reports | 4/3/18 | ISB-CGC |
| Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines | Cell Systems | 3/28/18 | ISB-CGC |
| Using the Seven Bridges Cancer Genomics Cloud to access and analyze petabytes of cancer data | Current Protocols in Bioinformatics | 12/8/17 | SB-CGC |
| The Cancer Genomics Cloud: Collaborative, reproducible, and democratized—a new paradigm in large-scale computational research | Cancer Research | 11/1/17 | SB-CGC |
| The ISB Cancer Genomic Cloud: A Flexible Cloud-Based Platform for Cancer Genomic Research | Cancer Research | 11/1/17 | ISB-CGC |
| A Comprehensive Infrastructure for Big Data in Cancer Research: Accelerating Cancer Research and Precision Medicine | Front Cell Dev Biol. | 9/21/17 | NCI |
| APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism | Nat Commun. | 9/6/17 | PDC |
| Precise, pan-cancer discovery of gene fusions reveals a signature of selection in primary tumors | bioRxiv | 8/18/17 | SB-CGC |
| Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer | Cell | 7/28/16 | PDC |
| Proteogenomics Connects Somatic Mutations to Signalling in Breast Cancer. | Nature | 5/25/16 | PDC |
| Proteomic analysis of colon and rectal carcinoma using standard and customized databases | Scientific Data | 7/21/15 | PDC |
| Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps | Nature Medicine | 3/2/15 | PDC |