Public data and open source tools for multi-assay genomic investigation of disease

In Silico Prescription of Anticancer Drugs to Cohorts of 28 Tumor Types Reveals Targeting Opportunities

(2015) Carlota Rubio-Perez et al.   CANCER CELL

Health: Make precision medicine work for cancer care

(2015) Mark A. Rubin   NATURE

A resource for cell line authentication, annotation and quality control

(2015) Mamie Yu et al.   NATURE

Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer

(2015) Kyriaki Michailidou et al.   NATURE GENETICS

The European Genome-phenome Archive of human data consented for biomedical research

(2015) Ilkka Lappalainen et al.   NATURE GENETICS

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

New database links regulatory DNA to its target genes

(2015) E. Pennisi   SCIENCE

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

The Ensembl Regulatory Build

(2015) Daniel R Zerbino et al.   GENOME BIOLOGY

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles

(2014) Bülent Arman Aksoy et al.   BIOINFORMATICS

Variable selection for generalized canonical correlation analysis

(2014) A. Tenenhaus et al.   BIOSTATISTICS

A multivariate approach to the integration of multi-omics datasets

(2014) Chen Meng et al.   BMC BIOINFORMATICS

Data integration in the era of omics: current and future challenges

(2014) David Gomez-Cabrero et al.   BMC Systems Biology

Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality

(2014) Livnat Jerby-Arnon et al.   CELL

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

(2014) Katherine A. Hoadley et al.   CELL

Characterizing Cancer Subtypes Using Dual Analysis in Caleydo StratomeX

(2014) Cagatay Turkay et al.   IEEE COMPUTER GRAPHICS AND APPLICATIONS

Changing the research landscape: the New York City Clinical Data Research Network

(2014) R. Kaushal et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Comparative analysis of regulatory information and circuits across distant species

(2014) Alan P. Boyle et al.   NATURE

Assessing the clinical utility of cancer genomic and proteomic data across tumor types

(2014) Yuan Yuan et al.   NATURE BIOTECHNOLOGY

Epiviz: interactive visual analytics for functional genomics data

(2014) Florin Chelaru et al.   NATURE METHODS

TCGA-Assembler: open-source software for retrieving and processing TCGA data

(2014) Yitan Zhu et al.   NATURE METHODS

The UCSC Cancer Genomics Browser: update 2015

(2014) Mary Goldman et al.   NUCLEIC ACIDS RESEARCH

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures

(2014) Qiaonan Duan et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

High Resolution Copy Number Variation Data in the NCI-60 Cancer Cell Lines from Whole Genome Microarrays Accessible through CellMiner

(2014) Sudhir Varma et al.   PLoS One

RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data

(2014) Mehmet Kemal Samur   PLoS One

The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data

(2014) C. Wilks et al.   Database-The Journal of Biological Databases and Curation

Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies

(2014) Glenn S Cowley et al.   Scientific Data

Sparse integrative clustering of multiple omics data sets

(2013) Ronglai Shen et al.   Annals of Applied Statistics

Genome-wide identification of Ikaros targets elucidates its contribution to mouse B-cell lineage specification and pre-B-cell differentiation

(2013) I. Ferreiros-Vidal et al.   BLOOD

An Interactive Resource to Identify Cancer Genetic and Lineage Dependencies Targeted by Small Molecules

(2013) Amrita Basu et al.   CELL

Understanding the Epigenetic Syntax for the Genetic Alphabet in the Kidney

(2013) K. Susztak   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

(2013) J. Gao et al.   Science Signaling

curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome

(2013) Benjamin Frederick Ganzfried et al.   Database-The Journal of Biological Databases and Curation

Analysis of In Vitro Insulin-Resistance Models and Their Physiological Relevance to In Vivo Diet-Induced Adipose Insulin Resistance

(2013) Kinyui Alice Lo et al.   Cell Reports

Visualizing multidimensional cancer genomics data

(2013) Michael P Schroeder et al.   Genome Medicine

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

A novel approach for biomarker selection and the integration of repeated measures experiments from two assays

(2012) Benoit Liquet et al.   BMC BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Abstract 3499: CD56 targeted chimeric antigen receptors for immunotherapy of multiple myeloma

(2012) Reuben Benjamin et al.   CANCER RESEARCH

Cancer Vulnerabilities Unveiled by Genomic Loss

(2012) Deepak Nijhawan et al.   CELL

Systematic identification of genomic markers of drug sensitivity in cancer cells

(2012) Mathew J. Garnett et al.   NATURE

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

(2012) Christina Curtis et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Savant Genome Browser 2: visualization and analysis for population-scale genomics

(2012) M. Fiume et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

CNAmet: an R package for integrating copy number, methylation and expression data

(2011) Riku Louhimo et al.   BIOINFORMATICS

COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines

(2011) J. L. Y. Koh et al.   NUCLEIC ACIDS RESEARCH

Gitools: Analysis and Visualisation of Genomic Data Using Interactive Heat-Maps

(2011) Christian Perez-Llamas et al.   PLoS One

Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer

(2011) H. W. Cheung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrating diverse genomic data using gene sets

(2011) Svitlana Tyekucheva et al.   GENOME BIOLOGY

Clinical Implications of the Cancer Genome

(2010) Laura E. MacConaill et al.   JOURNAL OF CLINICAL ONCOLOGY

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

IntOGen: integration and data mining of multidimensional oncogenomic data

(2010) Gunes Gundem et al.   NATURE METHODS

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Importing ArrayExpress datasets into R/Bioconductor

(2009) Audrey Kauffmann et al.   BIOINFORMATICS

A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis

(2009) D. M. Witten et al.   BIOSTATISTICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

(2008) Y. Zhu et al.   BIOINFORMATICS

Autoimmune diseases: insights from genome-wide association studies

(2008) G. Lettre et al.   HUMAN MOLECULAR GENETICS

Revealing the architecture of gene regulation: the promise of eQTL studies

(2008) Yoav Gilad et al.   TRENDS IN GENETICS