ArticlePLoS computational biology2015
Genome Modeling System: A Knowledge Management Platform for Genomics.
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Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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64citing papers in PubMed
–field-weighted citation impact
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
64 citing papers in PubMed.
- Immunogenomic profiling and pathological response results from a clinical trial of docetaxel and carboplatin in triple-negative breast cancer.Breast cancer research and treatment · 2021Trial
- Yap1 Mediates Trametinib Resistance in Head and Neck Squamous Cell Carcinomas.Clinical cancer research : an official journal of the American Association for Cancer Research · 2021Trial
- Neoadjuvant and Adjuvant Pembrolizumab in Resectable Locally Advanced, Human Papillomavirus-Unrelated Head and Neck Cancer: A Multicenter, Phase II Trial.Clinical cancer research : an official journal of the American Association for Cancer Research · 2020Trial
- Single-agent ibrutinib in relapsed or refractory follicular lymphoma: a phase 2 consortium trial.Blood · 2018Trial
- A Phase II Trial of Neoadjuvant MK-2206, an AKT Inhibitor, with Anastrozole in Clinical Stage II or IIIClinical cancer research : an official journal of the American Association for Cancer Research · 2017Trial
- NeoPalAna: Neoadjuvant Palbociclib, a Cyclin-Dependent Kinase 4/6 Inhibitor, and Anastrozole for Clinical Stage 2 or 3 Estrogen Receptor-Positive Breast Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2017Trial
- Surveying the Genomic Landscape of Mantle Cell Lymphoma Indicates the Importance of Multimodal Genomic and Transcriptomic Exploration.medRxiv : the preprint server for health sciences · 2026Article
- Whole Exome Sequencing of Feline Oral Squamous Cell Carcinoma Reveals Genomic Parallels With Human Head and Neck Squamous Cell Carcinoma.Veterinary and comparative oncology · 2026Article
- Exome sequencing of Hodgkin and non-Hodgkin composite lymphomas identifies shared somatic mutations indicative of common founding precursors.Cancer genetics · 2026Article
- ImmunoNX: a robust bioinformatics workflow to support personalized neoantigen vaccine trials.ArXiv · 2025Article
- Large B cell lymphoma microenvironment archetype profiles.Cancer cell · 2025Article
- pVACview: an interactive visualization tool for efficient neoantigen prioritization and selection.Genome medicine · 2024Article
- Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma.Cancer research communications · 2023Article
- Endothelial cells are a key target of IFN-g during response to combined PD-1/CTLA-4 ICB treatment in a mouse model of bladder cancer.iScience · 2023Article
- Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303.Blood advances · 2023Article
- Donor-Derived Follicular Lymphoma After Kidney Transplantation: A Case Report.JCO precision oncology · 2023Article
- Genetic characterization of primary and metastatic high-grade serous ovarian cancer tumors reveals distinct features associated with survival.Communications biology · 2023Article
- Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer.Nature communications · 2023Article
- Personalized ctDNA micro-panels can monitor and predict clinical outcomes for patients with triple-negative breast cancer.Scientific reports · 2022Article
- Integrating LASSO Feature Selection and Soft Voting Classifier to Identify Origins of Replication Sites.Current genomics · 2022Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
64 authors.
Malachi GriffithThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America.
Obi L GriffithThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America.
Scott M SmithThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Avinash RamuThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Matthew B CallawayThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Anthony M BrummettThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Michael J KiwalaThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Adam C CoffmanThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Allison A RegierThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Ben J OberkfellThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Gabriel E SandersonThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Thomas P MooneyThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Nathaniel G NutterThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Edward A BelterThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Feiyu DuThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Robert L LongThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Travis E AbbottThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Ian T FergusonThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
David L MortonThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Mark M BurnettThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
James V WeibleThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Joshua B PeckThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Adam DukesThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Joshua F McMichaelThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Justin T LolofieThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Brian R DericksonThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Jasreet HundalThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Zachary L SkidmoreThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Benjamin J AinscoughThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Nathan D DeesThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
William S SchierdingThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Cyriac KandothThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Kyung H KimThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Charles LuThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Christopher C HarrisThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Nicole MaherDepartment of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America.
Christopher A MaherThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America; Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America.
Vincent J MagriniThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America.
Benjamin S AbbottThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Ken ChenThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Eric ClarkThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Indraniel DasThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Xian FanThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Amy E HawkinsThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Todd G HeplerThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Todd N WylieThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Shawn M LeonardThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
William E SchroederThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Xiaoqi ShiThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Lynn K CarmichaelThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Matthew R WeilThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Richard W WohlstadterThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Gary StiehrThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Michael D McLellanThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Craig S PohlThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Christopher A MillerThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Daniel C KoboldtThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Jason R WalkerThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
James M EldredThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
David E LarsonThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America.
David J DoolingThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Li DingThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America; Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America.
Elaine R MardisThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America; Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America.
Richard K WilsonThe Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America; Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America.
Funding
Large Scale Genome SequencingU54HG003079 · NHGRI · WASHINGTON UNIVERSITY · PI DUTCHER, SUSAN K · 2004 to 2016
$445.7MMOLECULAR ONCOLOGY TRAINING GRANTT32CA113275 · NCI · WASHINGTON UNIVERSITY · PI Matthew J Walter · 2006 to 2026
$5.7MA Turnkey System for High-throughput Variant Discovery and InterpretationU01HG006517 · NHGRI · WASHINGTON UNIVERSITY · PI DING, LI · 2012 to 2015
$3.0MCANCER SUSCEPTIBILITY VARIANT DISCOVERY IN HIGH THROUGHPUT SEQUENCING DATAR01CA180006 · NCI · WASHINGTON UNIVERSITY · PI DING, LI · 2013 to 2016
$1.1MDEFINING THE REGULATORY, NON-CODING, MUTATIONAL LANDSCAPE OF BREAST CANCERK22CA188163 · NCI · WASHINGTON UNIVERSITY · PI GRIFFITH, OBI L. · 2014 to 2016
$515kNCI NIH HHS K22 CA188163NCI NIH HHS R01 CA180006NCI NIH HHS T32 CA113275NHGRI NIH HHS U01 HG006517NHGRI NIH HHS U54 HG003079
Abstract
In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395) and matched lymphoblastoid line (HCC1395BL). These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms.
Indexed as
Knowledge BasesModels, GeneticUser-Computer InterfaceAlgorithmsChromosome MappingComputer SimulationDatabase Management SystemsDatabases, GeneticGenome, HumanHumansSequence AlignmentSequence Analysis, DNA
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LicenceCC BY
Read underepoch 390
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.