Selected Publications

 

 
Title Journal Publication Date PMID CRDC Component
Reliable Analysis of Clinical Tumor-Only Whole-Exome Sequencing Data JCO Clin Cancer Inform 4/13/21 32282230 Broad - FireCloud 
Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma. Cancer Cell 3/8/21 33417831 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 33465699 GDC
Bringing Structural Implications and Deep Learning-Based Drug Identification for KRAS Mutants J Chem Inf Model 2/22/21 33513018 GDC
TAp73β Can Promote Hepatocellular Carcinoma Dedifferentiation Cancers (Basel) 2/13/21 33668566 GDC
Proteogenomic and metabolomic characterization of human glioblastoma. Cancer Cell 2/11/21 33577785 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 33499863 GDC
Assessing single-cell transcriptomic variability through density-preserving data visualization Nature Biotechnology  1/18/21 33462509 Broad - FireCloud 
Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power Nature Genetics  1/18/21 33462486 Broad - FireCloud 
Streamlining data-intensive biology with workflow systems GigaScience 1/13/21 33438730 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 
Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer. Cell 12/23/20 33242424 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 33344254 GDC
Genomic and epigenetic aberrations of chromosome 1p36.13 have prognostic implications in malignancies Chromosome Res 12/1/20 32816122 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 33212010 PDC
Novel, abundant Drosha isoforms are deficient in miRNA processing in cancer cells RNA Biology 11/17/20 32819190 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 33086064 PDC
Genetic alterations of SUGP1 mimic mutant-SF3B1 splice pattern in lung adenocarcinoma and other cancers Oncogene 10/14/20 33057152 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 32568785 GDC
BCO App: tools for generating BioCompute Objects from next-generation sequencing workflows and computations F1000Research 9/16/20 33299553 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 32852769 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 33205130 GDC
Linked Entity Attribute Pair (LEAP): A Harmonization Framework for Data Pooling JCO Clin Cancer Inform 8/1/20 32755461 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 32719837 SB-CGC
Proteogenomic characterization of human colon and rectal cancer. Nature 7/20/20 25043054 PDC
Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma. Cell 7/9/20 32649874 PDC
Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and Progression. Cell 7/9/20 32649875 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 32764205 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 32594614 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 32742444 GDC
Identification of an Immune Score-Based Gene Panel with Prognostic Power for Oral Squamous Cell Carcinoma Med Sci Monit 6/12/20 32529991 GDC
Classification and mutation prediction based on histopathology H&E images in liver cancer using deep learning NPJ Precis Oncol 6/8/20 32550270 GDC
The road towards data integration in human genomics: players, steps and interactions Brief Bioinform 6/4/20 32496509 SB-CGC
AGO-bound mature miRNAs are oligouridylated by TUTs and subsequently degraded by DIS3L2 Nat Commun. 6/2/20 32488030 SB-CGC
Increased number of subclones in lung squamous cell carcinoma elicits overexpression of immune related genes Transl Lung Cancer Res 6/1/20 32676328 GDC
Measuring Cancer Hallmark Mediation of the TET1 Glioma Survival Effect with Linked Neural-Network Based Mediation Experiments Sci Rep 6/1/20 32483272 GDC
Modern Information Technology for Cancer Research: What’s in IT for Me? An Overview of Technologies and Approaches. Oncology 6/1/20 30439700 SB-CGC
Systematic Establishment of Robustness and Standards in Patient-Derived Xenograft Experiments and Analysis Cancer Research 6/1/20 32152150 SB-CGC
A structural variation reference for medical and population genetics Nature 5/27/20 32461652 Broad - FireCloud 
Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives Brief Bioinform 5/21/20 31263868 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 32434476 GDC
Co-occurrent Alterations of Alzheimer's Genes and Prostate Cancer Genes in Prostate Cancer Cancer Genomics Proteomics 5/1/20 32345668 GDC
Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability. Cell Reports Medicine 4/21/20 32529193 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 32324447 ISB-CGC
Automatic Staging of Cancer Tumors Using AIM Image Annotations and Ontologies J Digit Imaging 4/1/20 31396778 GDC
Whole Exome Sequencing Data Analysis Algorithms in Cancer Diagnostics Prime Archives of Cancer Research 3/27/20 31690036 SB-CGC
Microbiome analyses of blood and tissues suggest cancer diagnostic approach Nature 3/1/20 32214244 SB-CGC
Screening TCGA database for prognostic genes in lower grade glioma microenvironment Ann Transl Med 3/1/20 32309356 GDC
Genomic Characterization of Non-Invasive Differentiated-Type Gastric Cancer in the Japanese Population Cancers (Basel) 2/22/20 32098350 GDC
Proteogenomic Characterization of Endometrial Carcinoma Cell 2/20/20 32059776 PDC
The pan-cancer landscape of prognostic germline variants in 10,582 patients Genome Medicine 2/17/20 32066500 SB-CGC
Immunogenomic pathways associated with cytotoxic lymphocyte infiltration and survival in colorectal cancer BMC Cancer 2/14/20 32059711 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 31610224 GDC
Loss of Kat2a enhances transcriptional noise and depletes acute myeloid leukemia stem-like cells eLife 1/27/20 31985402 SB-CGC
Knowledge-guided analysis of “omics” data using the KnowEnG cloud platform PLoS 1/23/20 31971940 SB-CGC
Screening the Cancer Genome Atlas Database for Genes of Prognostic Value in Acute Myeloid Leukemia Front Oncol 1/21/20 32039005 GDC
Discovering the anticancer potential of non-oncology drugs by systematic viability profiling Nature Cancer 1/20/20 32613204 Broad - FireCloud 
A protein‐centric approach for exome variant aggregation enables sensitive association analysis with clinical outcomes Human Mutation 1/12/20 31930623 ISB-CGC
Building Containerized Workflows Using the BioDepot-Workflow-Builder Cell Systems 11/27/19 31521606 SB-CGC
Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma. Cell 10/31/19 31675502 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 31585088 PDC
Improved detection of gene fusions by applying statistical methods reveals oncogenic RNA cancer drivers PNAS 7/30/19 31308241 SB-CGC
Clonal replacement of tumor-specific T cells following PD-1 blockade Nature Medicine 7/29/19 31359002 Broad - FireCloud 
A cytosine deaminase for programmable single-base RNA editing Science 7/26/19 31296651 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 32038716 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 30943891 SB-CGC
The Germline Variants rs61757955 and rs34988193 Are Predictive of Survival in Lower Grade Glioma Patients Molecular Cancer Research  5/1/19 30651372 SB-CGC
Building Portable and Reproducible Cancer Informatics Workflows: An RNA Sequencing Case Study Methods Mol Biol 4/1/19 30378068 SB-CGC
Data Lakes, Clouds and Commons: A Review of Platforms for Analyzing and Sharing Genomic Data Trends in Genetics 1/25/19 30691868 DCF
Pregnancy-Associated Plasma Protein-A (PAPP-A) in Ewing Sarcoma: Role in Tumor Growth and Immune Evasion JNCI 1/20/19 30698726 ISB-CGC
Proteogenomic Characterization of Human Early-Onset Gastric Cancer. Cancer Cell 1/14/19 30645970 PDC
Structural Differences Between Pri-miRNA Paralogs Promote Alternative Drosha Cleavage and Expand Target Repertoires Cell Reports 1/8/19 30625327 SB-CGC
restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor F1000 Research 1/7/19 30828438 ISB-CGC
Maximizing the Utility of Cancer Transcriptomic Data Trends in Cancer Research 12/4/18 30470304 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 30482208 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 30388102 SB-CGC
QuagmiR: a cloud-based application for isomiR big data analytics Bioinformatics 10/9/18 30295744 SB-CGC
Using Semantic Web Technologies to Enable Cancer Genomics Discovery at Petabyte Scale. Cancer Informatics 9/28/18 30283230 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 30142341 DCF
Recurrent Tumor-Specific Regulation of Alternative Polyadenylation of Cancer-Related Genes BMC Genomics 7/13/18 30005633 ISB-CGC
Progress Towards Cancer Data Ecosystems Cancer J 5/30/18 29794537 DCF
The Immune Landscape of Cancer  Immunity 4/17/18 29628290 ISB-CGC, SB-CGC
Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images Cell Reports 4/3/18 29617659 ISB-CGC
Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines  Cell Systems 3/28/18 29596782 ISB-CGC
Using the Seven Bridges Cancer Genomics Cloud to access and analyze petabytes of cancer data  Current Protocols in Bioinformatics 12/8/17 29220078 SB-CGC
The Cancer Genomics Cloud: Collaborative, reproducible, and democratized—a new paradigm in large-scale computational research  Cancer Research 11/1/17 29092927 SB-CGC
The ISB Cancer Genomic Cloud: A Flexible Cloud-Based Platform for Cancer Genomic Research  Cancer Research 11/1/17 29092928 ISB-CGC
A Comprehensive Infrastructure for Big Data in Cancer Research: Accelerating Cancer Research and Precision Medicine Front Cell Dev Biol. 9/21/17 28983483 NCI
APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism. Nat Commun. 9/6/17 28878238 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 27372738 PDC
Proteogenomics Connects Somatic Mutations to Signalling in Breast Cancer. Nature 5/25/16 27251275 PDC
Proteomic analysis of colon and rectal carcinoma using standard and customized databases. Scientific Data 7/21/15 26110064 PDC
Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps. Nature Medicine 3/2/15 25730263 PDC