Predicting the impact of non-coding variants on DNA methylation

Convolutional neural network architectures for predicting DNA–protein binding

(2016) Haoyang Zeng et al.   BIOINFORMATICS

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

Predicting CpG methylation levels by integrating Infinium HumanMethylation450 BeadChip array data

(2016) Shicai Fan et al.   GENOMICS

A pooling-based approach to mapping genetic variants associated with DNA methylation

(2015) Irene M. Kaplow et al.   GENOME RESEARCH

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

A method to predict the impact of regulatory variants from DNA sequence

(2015) Dongwon Lee et al.   NATURE GENETICS

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

(2015) Jian Zhou et al.   NATURE METHODS

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos

(2015) Hyung Joo Lee et al.   Nature Communications

Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements

(2015) Weiwei Zhang et al.   GENOME BIOLOGY

Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

(2014) Alexander Gusev et al.   AMERICAN JOURNAL OF HUMAN GENETICS

GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database

(2014) R. Leslie et al.   BIOINFORMATICS

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

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

(2014) Martin Kircher et al.   NATURE GENETICS

Functional annotation of noncoding sequence variants

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

Genome Wide Association Study of Fetal Hemoglobin in Sickle Cell Anemia in Tanzania

(2014) Siana Nkya Mtatiro et al.   PLoS One

Seven new loci associated with age-related macular degeneration

(2013) Lars G Fritsche et al.   NATURE GENETICS

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

An Erythroid Enhancer of BCL11A Subject to Genetic Variation Determines Fetal Hemoglobin Level

(2013) D. E. Bauer et al.   SCIENCE

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

(2012)   NATURE

Analysing and interpreting DNA methylation data

(2012) Christoph Bock   NATURE REVIEWS GENETICS

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Genome-Wide Association for Abdominal Subcutaneous and Visceral Adipose Reveals a Novel Locus for Visceral Fat in Women

(2012) Caroline S. Fox et al.   PLoS Genetics

Genomic Imprinting: A Mammalian Epigenetic Discovery Model

(2011) Denise P. Barlow   Annual Review of Genetics

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Prediction of methylation CpGs and their methylation degrees in human DNA sequences

(2011) Xuan Zhou et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Dnmt3/transcription factor interactions as crucial players in targeted DNA methylation

(2010) Eric Hervouet et al.   Epigenetics

From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

(2010) Kiran Musunuru et al.   NATURE

Epigenetic modifications in pluripotent and differentiated cells

(2010) Alexander Meissner   NATURE BIOTECHNOLOGY

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Common variants at 30 loci contribute to polygenic dyslipidemia

(2008) Sekar Kathiresan et al.   NATURE GENETICS