Genome Modeling System: A Knowledge Management Platform for Genomics.
Malachi Griffith,Obi L. Griffith,Scott M. Smith,Avinash Ramu,Matthew B. Callaway,Anthony M. Brummett,Michael J. Kiwala,Adam C. Coffman,Allison A. Regier,Benjamin J. Oberkfell,Gabriel E. Sanderson,Thomas P. Mooney,Nathaniel G. Nutter,Edward A. Belter,Feiyu Du,Robert T. L. Long,Travis E. Abbott,Ian T. Ferguson,David L. Morton,Mark M. Burnett,James V. Weible,Joshua Peck,Adam F. Dukes,Joshua F. McMichael,Justin T. Lolofie,Brian R. Derickson,Jasreet Hundal,Zachary L. Skidmore,Benjamin J. Ainscough,Nathan D. Dees,William Schierding,Cyriac Kandoth,Kyung H. Kim,Charles Lu,Chris Harris,Nicole Maher,Christopher G. Maher,Vincent Magrini,Benjamin S. Abbott,Ken Chen,Eric M. Clark,Indraniel Das,Xian Fan,Amy Hawkins,Todd G. Hepler,Todd Wylie,Shawn Leonard,William E. Schroeder,Xiaoqi Shi,Lynn K. Carmichael,Matthew R. Weil,Richard W. Wohlstadter,Gary Stiehr,Michael D. McLellan,Craig Pohl,Christopher A. Miller,Daniel C. Koboldt,Jason Walker,James M. Eldred,David E. Larson,David J. Dooling,Li Ding,Elaine R. Mardis,Richard K. Wilson +63 more
TLDR
The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines, 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.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.read more
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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update
Enis Afgan,Dannon Baker,Marius van den Beek,Daniel Blankenberg,Dave Bouvier,Martin Čech,John Chilton,Dave Clements,Nate Coraor,Carl Eberhard,Björn Grüning,Aysam Guerler,Jennifer Hillman-Jackson,Gregory Von Kuster,Eric Rasche,Nicola Soranzo,Nitesh Turaga,James Taylor,Anton Nekrutenko,Jeremy Goecks +19 more
TL;DR: Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse.
Journal ArticleDOI
MHC proteins confer differential sensitivity to CTLA-4 and PD-1 blockade in untreated metastatic melanoma
Scott J. Rodig,Scott J. Rodig,Daniel Gusenleitner,Donald G. Jackson,Evisa Gjini,Anita Giobbie-Hurder,Chelsea Jin,Han Chang,Scott B. Lovitch,Christine Horak,Jeffrey S. Weber,Jason L. Weirather,Jedd D. Wolchok,Michael A. Postow,Michael A. Postow,Anna C. Pavlick,Jason Chesney,F. Stephen Hodi +17 more
TL;DR: It is shown that MHC class I expression in advanced melanoma predicted resistance to anti–CTLA-4, but not anti-PD-1, treatment, which may need MHCclass II to be effective, which explains why patients on combined therapy do better on average, with one drug overcoming the limitations of the other.
Journal ArticleDOI
pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens.
Jasreet Hundal,Beatriz M. Carreno,Allegra A. Petti,Gerald P. Linette,Obi L. Griffith,Elaine R. Mardis,Malachi Griffith +6 more
TL;DR: A flexible, streamlined computational workflow for identification of personalized Variant Antigens by Cancer Sequencing (pVAC-Seq) that integrates tumor mutation and expression data (DNA- and RNA-Sequ) is presented.
Journal ArticleDOI
NeoPalAna: Neoadjuvant Palbociclib, a Cyclin-Dependent Kinase 4/6 Inhibitor, and Anastrozole for Clinical Stage 2 or 3 Estrogen Receptor-Positive Breast Cancer.
Cynthia X. Ma,Feng Gao,Jingqin Luo,Donald W. Northfelt,Matthew P. Goetz,Andres Forero,Jeremy Hoog,Michael Naughton,Foluso O. Ademuyiwa,Rama Suresh,Karen S. Anderson,Julie A. Margenthaler,Rebecca Aft,Timothy J. Hobday,Timothy J. Moynihan,William E. Gillanders,Amy E. Cyr,Timothy J. Eberlein,Tina J. Hieken,Helen Krontiras,Zhanfang Guo,Michelle V. Lee,Nicholas C. Spies,Zachary L. Skidmore,Obi L. Griffith,Malachi Griffith,Shana Thomas,Caroline Bumb,Kiran Vij,Cynthia Huang Bartlett,Maria Koehler,Hussam Al-Kateb,Souzan Sanati,Matthew J. Ellis +33 more
TL;DR: Palbociclib is an active antiproliferative agent for early-stage breast cancer resistant to anastrozole; however, prolonged administration may be necessary to maintain its effect.
Journal ArticleDOI
GenVisR: Genomic Visualizations in R
Zachary L. Skidmore,Alex H. Wagner,Robert Lesurf,Katie M. Campbell,Jason Kunisaki,Obi L. Griffith,Malachi Griffith +6 more
TL;DR: The GenVisR package provides a rapid and easy-to-use suite of genomic visualization tools, while maintaining a high degree of flexibility by leveraging the abilities of ggplot2 and Bioconductor.
References
More filters
Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Journal ArticleDOI
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Journal ArticleDOI
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
TL;DR: EdgeR as mentioned in this paper is a Bioconductor software package for examining differential expression of replicated count data, which uses an overdispersed Poisson model to account for both biological and technical variability and empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference.
Journal ArticleDOI
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
Aaron McKenna,Matthew Hanna,Eric Banks,Andrey Sivachenko,Kristian Cibulskis,Andrew Kernytsky,Kiran V. Garimella,David Altshuler,Stacey Gabriel,Mark J. Daly,Mark A. DePristo +10 more
TL;DR: The GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
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