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Article
Open AccessAnalysis of structural variation among inbred mouse strains
‘Long read’ sequencing methods have been used to identify previously uncharacterized structural variants that cause human genetic diseases. Therefore, we investigated whether long read sequencing could facilitate...
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Article
Open AccessX-CAP improves pathogenicity prediction of stopgain variants
Stopgain substitutions are the third-largest class of monogenic human disease mutations and often examined first in patient exomes. Existing computational stopgain pathogenicity predictors, however, exhibit po...
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Article
Avoiding genetic racial profiling in criminal DNA profile databases
DNA profiling has become an essential tool for crime solving and prevention, and CODIS (Combined DNA Index System) criminal investigation databases have flourished at the national, state and even local level. ...
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Article
Open AccessComponents of genetic associations across 2,138 phenotypes in the UK Biobank highlight adipocyte biology
Population-based biobanks with genomic and dense phenotype data provide opportunities for generating effective therapeutic hypotheses and understanding the genomic role in disease predisposition. To characteri...
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Article
Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts
It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene1. The current molecular diagnostic rate is estimated at 50%, with whol...
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Article
S-CAP extends pathogenicity prediction to genetic variants that affect RNA splicing
Exome analysis of patients with a likely monogenic disease does not identify a causal variant in over half of cases. Splice-disrupting mutations make up the second largest class of known disease-causing mutati...
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Article
M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity
Gill Bejerano and colleagues present M-CAP, a classifier that estimates variant pathogenicity in clinical exome data sets. They show that M-CAP outperforms other existing methods at all thresholds and correctl...
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Article
A family of transposable elements co-opted into developmental enhancers in the mouse neocortex
The neocortex is a mammalian-specific structure that is responsible for higher functions such as cognition, emotion and perception. To gain insight into its evolution and the gene regulatory codes that pattern...
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Article
Enhancers: five essential questions
Although enhancers are crucial and widespread gene-regulatory elements, we are far from a complete understanding of how they function or their importance in areas such as disease and evolution. Five prominent ...
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Article
Human-specific loss of regulatory DNA and the evolution of human-specific traits
A computational survey of the human genome has identified more than 500 human-specific genomic deletions that remove sequences that are highly conserved between chimpanzees and other animals. These are genomic...
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Article
GREAT improves functional interpretation of cis-regulatory regions
ChIP-Seq data are usually analyzed with approaches developed for microarrays, which only consider binding events within a few kilobases of a gene. McLean et al. present an algorithm that takes into account more d...
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Protocol
Comparative Genomic Analysis Using the UCSC Genome Browser
Comparative analysis of DNA sequence from multiple species can provide insights into the function and evolutionary processes that shape genomes. The University of California Santa Cruz (UCSC) Genome Bioinforma...
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Article
A distal enhancer and an ultraconserved exon are derived from a novel retroposon
Evidence from vertebrate genome sequences has shown that conserved noncoding regions significantly outnumber coding regions, and that these elements are mostly involved in gene regulation. The origins of these...
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Article
Computational screening of conserved genomic DNA in search of functional noncoding elements
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Article
Discriminative Feature Selection via Multiclass Variable Memory Markov Model
We propose a novel feature selection method based on a variable memory Markov (VMM) model. The VMM was originally proposed as a generative model trying to preserve the original source statistics from training ...
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Chapter and Conference Paper
A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites
A central issue in molecular biology is understanding the regulatory mechanisms that control gene expression. The recent flood of genomic and post-genomic data opens the way for computational methods elucidati...
