Discovery of potential causative mutations in human coding and noncoding genome with the interactive software BasePlayer

VIPER: a web application for rapid expert review of variant calls

(2018) Marius Wöste et al.   BIOINFORMATICS

Exome-wide somatic mutation characterization of small bowel adenocarcinoma

(2018) Ulrika A. Hänninen et al.   PLoS Genetics

Candidate susceptibility variants for esophageal squamous cell carcinoma

(2017) Iikki Donner et al.   GENES CHROMOSOMES & CANCER

Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing

(2017) Barun Pradhan et al.   Scientific Reports

The genetics and pathology of mitochondrial disease

(2016) Charlotte L Alston et al.   JOURNAL OF PATHOLOGY

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity

(2016) Karthik A Jagadeesh et al.   NATURE GENETICS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Clonal hematopoiesis of indeterminate potential and its distinction from myelodysplastic syndromes

(2015) D. P. Steensma et al.   BLOOD

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

CTCF/cohesin-binding sites are frequently mutated in cancer

(2015) Riku Katainen et al.   NATURE GENETICS

Next-generation diagnostics and disease-gene discovery with the Exomiser

(2015) Damian Smedley et al.   Nature Protocols

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing

(2015) Tyler S. Alioto et al.   Nature Communications

Rare-Variant Association Analysis: Study Designs and Statistical Tests

(2014) Seunggeung Lee et al.   AMERICAN JOURNAL OF HUMAN GENETICS

DANN: a deep learning approach for annotating the pathogenicity of genetic variants

(2014) Daniel Quang et al.   BIOINFORMATICS

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

The Next-Generation Sequencing Revolution and Its Impact on Genomics

(2013) Daniel C. Koboldt et al.   CELL

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Rare-disease genetics in the era of next-generation sequencing: discovery to translation

(2013) Kym M. Boycott et al.   NATURE REVIEWS GENETICS

Loss of SUFU Function in Familial Multiple Meningioma

(2012) Mervi Aavikko et al.   AMERICAN JOURNAL OF HUMAN GENETICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

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

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

(2011) T. Carver et al.   BIOINFORMATICS

Tabix: fast retrieval of sequence features from generic TAB-delimited files

(2011) H. Li   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Chipster: user-friendly analysis software for microarray and other high-throughput data

(2011) M Aleksi Kallio et al.   BMC GENOMICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

GenomeView: a next-generation genome browser

(2011) T. Abeel et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

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

MOODS: fast search for position weight matrix matches in DNA sequences

(2009) J. Korhonen et al.   BIOINFORMATICS

Tablet--next generation sequence assembly visualization

(2009) I. Milne et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS