A semi-supervised approach for predicting cell-type specific functional consequences of non-coding variation using MPRAs

FUN-LDA: A Latent Dirichlet Allocation Model for Predicting Tissue-Specific Functional Effects of Noncoding Variation: Methods and Applications

(2018) Daniel Backenroth et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data

(2017) Yi-Fei Huang et al.   NATURE GENETICS

Predicting regulatory variants with composite statistic

(2016) Mulin Jun Li et al.   BIOINFORMATICS

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

(2016) Ryan Tewhey et al.   CELL

Variable Selection With Prior Information for Generalized Linear Models via the Prior LASSO Method

(2016) Yuan Jiang et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

A spectral approach integrating functional genomic annotations for coding and noncoding variants

(2016) Iuliana Ionita-Laza et al.   NATURE GENETICS

Integrative Tissue-Specific Functional Annotations in the Human Genome Provide Novel Insights on Many Complex Traits and Improve Signal Prioritization in Genome Wide Association Studies

(2016) Qiongshi Lu et al.   PLoS Genetics

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

(2015) Matthew T Maurano et al.   NATURE GENETICS

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity

(2015) Slavé Petrovski et al.   PLoS Genetics

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Rare-Variant Association Analysis: Study Designs and Statistical Tests

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

A Rare Functional Noncoding Variant at the GWAS-Implicated MIR137 / MIR2682 Locus Might Confer Risk to Schizophrenia and Bipolar Disorder

(2014) Jubao Duan 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

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

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

(2014) Martin Kircher et al.   NATURE GENETICS

A framework for the interpretation of de novo mutation in human disease

(2014) Kaitlin E Samocha et al.   NATURE GENETICS

Functional annotation of noncoding sequence variants

(2014) Graham R S Ritchie et al.   NATURE METHODS

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Role for Noncoding Variation in Schizophrenia

(2014) Panos Roussos et al.   Cell Reports

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

(2013) P. Kheradpour et al.   GENOME RESEARCH

BLUEPRINT: mapping human blood cell epigenomes

(2013) J. H. A. Martens et al.   HAEMATOLOGICA

Discovery and refinement of loci associated with lipid levels

(2013) Cristen J Willer et al.   NATURE GENETICS

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Integrative Modeling of eQTLs and Cis-Regulatory Elements Suggests Mechanisms Underlying Cell Type Specificity of eQTLs

(2013) Christopher D. Brown et al.   PLoS Genetics

Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes

(2013) Slavé Petrovski et al.   PLoS Genetics

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The Metabochip, a Custom Genotyping Array for Genetic Studies of Metabolic, Cardiovascular, and Anthropometric Traits

(2012) Benjamin F. Voight et al.   PLoS Genetics

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Genetic Mapping in Human Disease

(2008) D. Altshuler et al.   SCIENCE