Integrative annotation of chromatin elements from ENCODE data

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

Genome-wide Epigenetic Data Facilitate Understanding of Disease Susceptibility Association Studies

(2012) Ross C. Hardison   JOURNAL OF BIOLOGICAL CHEMISTRY

Intragenic Enhancers Act as Alternative Promoters

(2012) Monika S. Kowalczyk et al.   MOLECULAR CELL

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

(2012) Kevin Y Yip et al.   GENOME BIOLOGY

A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules

(2011) Shihua Zhang et al.   BIOINFORMATICS

Exploratory analysis of genomic segmentations with Segtools

(2011) Orion J Buske et al.   BMC BIOINFORMATICS

Ending the message: poly(A) signals then and now

(2011) N. J. Proudfoot   GENES & DEVELOPMENT

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

Complete Khoisan and Bantu genomes from southern Africa

(2010) Stephan C. Schuster et al.   NATURE

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Nucleosome dynamics define transcriptional enhancers

(2010) Housheng Hansen He et al.   NATURE GENETICS

Toward a gold standard for promoter prediction evaluation

(2009) Thomas Abeel et al.   BIOINFORMATICS

Identifying novel constrained elements by exploiting biased substitution patterns

(2009) Manuel Garber et al.   BIOINFORMATICS

mGene: Accurate SVM-based gene finding with an application to nematode genomes

(2009) G. Schweikert et al.   GENOME RESEARCH

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

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

Automated mapping of large-scale chromatin structure in ENCODE

(2008) Heng Lian et al.   BIOINFORMATICS

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY