An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder

The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology

(2017) Eugene J. Gardner et al.   GENOME RESEARCH

Prevalence and architecture of de novo mutations in developmental disorders

(2017)   NATURE

Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease

(2017) Katrina M de Lange et al.   NATURE GENETICS

Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands

(2017) Sheng Chih Jin et al.   NATURE GENETICS

Whole genome sequencing in psychiatric disorders: the WGSPD consortium

(2017) Stephan J. Sanders et al.   NATURE NEUROSCIENCE

Improving genetic diagnosis in Mendelian disease with transcriptome sequencing

(2017) Beryl B. Cummings et al.   Science Translational Medicine

Indexcov: fast coverage quality control for whole-genome sequencing

(2017) Brent S Pedersen et al.   GigaScience

Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA

(2016) Tychele N. Turner et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

(2016) William J. Astle et al.   CELL

Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior

(2016) Ryan N. Doan et al.   CELL

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

(2016) Monkol Lek et al.   NATURE

The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

(2016) Claire Redin et al.   NATURE GENETICS

Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects

(2016) Christian R Marshall et al.   NATURE GENETICS

Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia

(2016) Giulio Genovese et al.   NATURE NEUROSCIENCE

The Cellular and Molecular Landscapes of the Developing Human Central Nervous System

(2016) John C. Silbereis et al.   NEURON

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

(2016) Zhongwu Lai et al.   NUCLEIC ACIDS RESEARCH

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

(2016) Jacqueline MacArthur et al.   NUCLEIC ACIDS RESEARCH

Paired-Duplication Signatures Mark Cryptic Inversions and Other Complex Structural Variation

(2015) Harrison Brand et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

A Genome-wide Association Study of Autism Using the Simons Simplex Collection: Does Reducing Phenotypic Heterogeneity in Autism Increase Genetic Homogeneity?

(2015) Pauline Chaste et al.   BIOLOGICAL PSYCHIATRY

Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data

(2015) Caroline F Wright et al.   LANCET

Evaluating historical candidate genes for schizophrenia

(2015) M S Farrell et al.   MOLECULAR PSYCHIATRY

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

Large multiallelic copy number variations in humans

(2015) Robert E Handsaker et al.   NATURE GENETICS

Whole-genome sequencing of quartet families with autism spectrum disorder

(2015) Ryan K C Yuen et al.   NATURE MEDICINE

The PsychENCODE project

(2015) Schahram Akbarian et al.   NATURE NEUROSCIENCE

Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR

(2015) Hui Yang et al.   Nature Protocols

Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci

(2015) Stephan J. Sanders et al.   NEURON

From trans to cis: transcriptional regulatory networks in neocortical development

(2015) Mikihito Shibata et al.   TRENDS IN GENETICS

The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment

(2015) Justin Cotney et al.   Nature Communications

Wham: Identifying Structural Variants of Biological Consequence

(2015) Zev N. Kronenberg et al.   PLoS Computational Biology

A Bayesian framework for de novo mutation calling in parents-offspring trios

(2014) Qiang Wei et al.   BIOINFORMATICS

Toward better understanding of artifacts in variant calling from high-coverage samples

(2014) Heng Li   BIOINFORMATICS

A polygenic burden of rare disruptive mutations in schizophrenia

(2014) Shaun M. Purcell et al.   NATURE

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

The contribution of de novo coding mutations to autism spectrum disorder

(2014) Ivan Iossifov et al.   NATURE

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

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

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Accurate de novo and transmitted indel detection in exome-capture data using microassembly

(2014) Giuseppe Narzisi et al.   NATURE METHODS

CHD8regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors

(2014) Aarathi Sugathan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

Coexpression Networks Implicate Human Midfetal Deep Cortical Projection Neurons in the Pathogenesis of Autism

(2013) A. Jeremy Willsey et al.   CELL

DeNovoGear: de novo indel and point mutation discovery and phasing

(2013) Avinash Ramu et al.   NATURE METHODS

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

Sequencing Chromosomal Abnormalities Reveals Neurodevelopmental Loci that Confer Risk across Diagnostic Boundaries

(2012) Michael E. Talkowski et al.   CELL

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Patterns and rates of exonic de novo mutations in autism spectrum disorders

(2012) Benjamin M. Neale et al.   NATURE

De novo mutations revealed by whole-exome sequencing are strongly associated with autism

(2012) Stephan J. Sanders et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Rate of de novo mutations and the importance of father’s age to disease risk

(2012) Augustine Kong et al.   NATURE

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

(2012) Brian J. O’Roak et al.   NATURE

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

(2012) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

Fecundity of Patients With Schizophrenia, Autism, Bipolar Disorder, Depression, Anorexia Nervosa, or Substance Abuse vs Their Unaffected Siblings

(2012) Robert A. Power et al.   JAMA Psychiatry

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism

(2011) Jennifer C. Darnell et al.   CELL

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Characterization of the proteome, diseases and evolution of the human postsynaptic density

(2010) Àlex Bayés et al.   NATURE NEUROSCIENCE

The Simons Simplex Collection: A Resource for Identification of Autism Genetic Risk Factors

(2010) Gerald D. Fischbach et al.   NEURON

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Why Most Discovered True Associations Are Inflated

(2008) John P. A. Ioannidis   EPIDEMIOLOGY

Estimation of significance thresholds for genomewide association scans

(2008) Frank Dudbridge et al.   GENETIC EPIDEMIOLOGY