Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

Whole exome sequencing of familial hypercholesterolaemia patients negative forLDLR/APOB/PCSK9mutations

(2014) Marta Futema et al.   JOURNAL OF MEDICAL GENETICS

A 3′UTR polymorphism modulates mRNA stability of the oncogene and drug target Polo-like Kinase 1

(2014) Neval Akdeli et al.   Molecular Cancer

Choice of transcripts and software has a large effect on variant annotation

(2014) Davis J McCarthy et al.   Genome Medicine

Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation

(2013) Justin J.-L. Wong et al.   CELL

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment

(2012) Lukas Habegger et al.   BIOINFORMATICS

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome

(2012) C. Howald et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2012)   NATURE

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

A probabilistic disease-gene finder for personal genomes

(2011) M. Yandell et al.   GENOME RESEARCH

Disrupted posttranscriptional regulation of the cystic fibrosis transmembrane conductance regulator (CFTR) by a 5′UTR mutation is associated with a cftr-related disease

(2011) Samuel W. Lukowski et al.   HUMAN MUTATION

Sequence variants within the 3′-UTR of the COL5A1 gene alters mRNA stability: Implications for musculoskeletal soft tissue injuries

(2011) Mary-Jessica Laguette et al.   MATRIX BIOLOGY

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE