Orchestrating high-throughput genomic analysis with Bioconductor
Bioconductor is an open-source, open-development software project for the analysis and
comprehension of high-throughput data in genomics and molecular biology. The project …
comprehension of high-throughput data in genomics and molecular biology. The project …
ceRNA in cancer: possible functions and clinical implications
Competing endogenous RNAs (ceRNAs) are transcripts that can regulate each other at post-
transcription level by competing for shared miRNAs. CeRNA networks link the function of …
transcription level by competing for shared miRNAs. CeRNA networks link the function of …
[HTML][HTML] A global reference for human genetic variation
1000 Genomes Project Consortium - Nature, 2015 - ncbi.nlm.nih.gov
Abstract The 1000 Genomes Project set out to provide a comprehensive description of
common human genetic variation by applying whole-genome sequencing to a diverse set of …
common human genetic variation by applying whole-genome sequencing to a diverse set of …
An integrated map of structural variation in 2,504 human genomes
Structural variants are implicated in numerous diseases and make up the majority of varying
nucleotides among human genomes. Here we describe an integrated set of eight structural …
nucleotides among human genomes. Here we describe an integrated set of eight structural …
A comprehensive 1000 Genomes–based genome-wide association meta-analysis of coronary artery disease
Nature genetics, 2015 - nature.com
Existing knowledge of genetic variants affecting risk of coronary artery disease (CAD) is
largely based on genome-wide association study (GWAS) analysis of common SNPs …
largely based on genome-wide association study (GWAS) analysis of common SNPs …
Predicting effects of noncoding variants with deep learning–based sequence model
J Zhou, OG Troyanskaya - Nature methods, 2015 - nature.com
Identifying functional effects of noncoding variants is a major challenge in human genetics.
To predict the noncoding-variant effects de novo from sequence, we developed a deep …
To predict the noncoding-variant effects de novo from sequence, we developed a deep …
The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans
Understanding the functional consequences of genetic variation, and how it affects complex
human disease and quantitative traits, remains a critical challenge for biomedicine. We …
human disease and quantitative traits, remains a critical challenge for biomedicine. We …
Single-cell chromatin accessibility reveals principles of regulatory variation
JD Buenrostro, B Wu, UM Litzenburger, D Ruff… - Nature, 2015 - nature.com
Cell-to-cell variation is a universal feature of life that affects a wide range of biological
phenomena, from developmental plasticity, to tumour heterogeneity. Although recent …
phenomena, from developmental plasticity, to tumour heterogeneity. Although recent …
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
Methods used to sequence the transcriptome often produce more than 200 million short
sequences. We introduce StringTie, a computational method that applies a network flow …
sequences. We introduce StringTie, a computational method that applies a network flow …
[HTML][HTML] Integrative analysis of 111 reference human epigenomes
The reference human genome sequence set the stage for studies of genetic variation and its
association with human disease, but epigenomic studies lack a similar reference. To …
association with human disease, but epigenomic studies lack a similar reference. To …