Paper Info
Title
Public data and open source tools for multi-assay genomic investigation of disease.
Abstract
Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have generated extensive and freely available multi-assay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent. We review multi-assay genomic data resources in the areas of clinical oncology, pharmacogenomics and other perturbation experiments, population genomics and regulatory genomics and other areas, and tools for data acquisition. Finally, we review bioinformatic tools that are explicitly geared toward integrative genomic data visualization and analysis. This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods.
Year
DOI
Venue
2016
10.1093/bib/bbv080
BRIEFINGS IN BIOINFORMATICS
Keywords
Field
DocType
multiple assays (multi-assays),public data,bioconductor,integrative genomics,cancer,pharmacogenomics,omics
Data science,Population genomics,Data mining,Data visualization,Proteomics,Profiling (computer programming),Computer science,Bioconductor,Genomics,DNA sequencing,Bioinformatics,Pharmacogenomics
Journal
Volume
Issue
ISSN
17
SP4
1467-5463
Citations 
PageRank 
References 
4
0.43
26
Authors
15
Name
Order
Citations
PageRank
Lavanya Kannan1223.10
Marcel Ramos241.11
Angela Re3574.21
Nehme Hachem4364.60
Zhaleh Safikhani540.43
Deena M A Gendoo6172.48
Sean Davis755240.63
David Gomez-Cabrero8698.38
Robert Castelo91318.24
Kasper D. Hansen1019317.73
Vincent J Carey1120917.35
Martin Morgan1241.44
Aedín C Culhane1340.43
Benjamin Haibe-Kains1412419.97
Levi Waldron15516.96