| Combinatorial and Machine Learning Approaches for Improved Somatic Variant Calling from Formalin-Fixed Paraffin-Embedded Genome Sequence Data |
Frontiers in Genetics |
4/27/22 |
35571031 |
GDC |
| Genetic changes associated with relapse in favorable histology Wilms tumor: A Children's Oncology Group AREN03B2 study |
Cell Reports Medicine |
6/21/22 |
35617957 |
GDC |
| Integrative Analysis of Drug Response and Clinical Outcome in Acute Myeloid Leukemia |
Cancer Cell |
8/8/22 |
35868306 |
GDC |
| Genetic Subgroups inform on Pathobiology in Adult and Pediatric Burkitt Lymphoma |
Blood |
10/6/22 |
36201743 |
GDC |
| Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness |
Cancer Cell |
12/22/22 |
36563681 |
PDC |
| Proteogenomic analysis of lung adenocarcinoma reveals tumor heterogeneity, survival determinants, and therapeutically relevant pathways |
Cell Reports Medicine |
11/15/22 |
36384096 |
PDC |
| Proteogenomic markers of chemotherapy resistance and response in triple negative breast cancer |
Cancer Discovery |
11/2/22 |
36001024 |
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 |
36266629 |
PDC |
| Proteomic and phosphoproteomic measurements enhance ability to predict ex vivo drug response in AML |
Clinical Proteomics |
7/27/22 |
35896960 |
PDC |
| Transcriptomic profiling in canines and humans reveals cancer specific gene modules and biological mechanisms common to both species |
PLOS Computational Biology |
9/27/21 |
25082814 |
ICDC |
| Proteogenomic Characterization of Pancreatic Ductal Adenocarcinoma |
Cell 2021 |
9/16/21 |
34171263 |
PDC |
| A proteogenomic portrait of lung squamous cell carcinoma |
Cell 2021 |
8/5/21 |
34358469 |
PDC |
| Canine tumor mutational burden is correlated with TP53 mutation across tumor types and breeds |
Nature Communications |
8/3/21 |
34570764 |
ICDC |
| The AML Microenvironment Catalyzes a Step-wise Evolution to Gilteritinib Resistance |
Cancer Cell 2021 |
6/24/21 |
34171263 |
PDC |
| NCI Imaging Data Commons |
Cancer Research |
6/15/21 |
34185678 |
IDC |
|
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 |
33753454 |
ICDC |
| Reliable Analysis of Clinical Tumor-Only Whole-Exome Sequencing Data |
JCO Clin Cancer Inform |
4/13/21 |
32282230 |
Broad - FireCloud |
| Proteogenomic and metabolomic characterization of human glioblastoma |
Cancer Cell 2021 |
4/12/21 |
33417831 |
PDC |
| 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 |
| The NCI Genomic Data Commons |
Nature Genetics |
2/22/21 |
33619384 |
GDC |
| Uniform genomic data analysis in the NCI Genomic Data Commons |
Nature Communications |
2/22/21 |
33619257 |
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 |
34337551 |
Broad - FireCloud |
| Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma |
Cancer Cell 2021 |
1/7/2021 |
33417831 |
PDC |
| 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 |
34234178 |
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 |
32852765 |
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 |
32719530 |
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 |
31768072 |
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 |
31502174 |
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 |