Epigenomic analysis of primary human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments

(2013) Matthias Lienhard et al.   BIOINFORMATICS

Global Chromatin State Analysis Reveals Lineage-Specific Enhancers during the Initiation of Human T helper 1 and T helper 2 Cell Polarization

(2013) R. David Hawkins et al.   IMMUNITY

Lung dendritic cells imprint T cell lung homing and promote lung immunity through the chemokine receptor CCR4

(2013) Zamaneh Mikhak et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

(2013) Yubo Zhang et al.   NATURE

Predicting Cell Types and Genetic Variations Contributing to Disease by Combining GWAS and Epigenetic Data

(2013) Anna Gerasimova et al.   PLoS One

Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity

(2012) Jingli A. Zhang et al.   CELL

Widespread plasticity in CTCF occupancy linked to DNA methylation

(2012) H. Wang et al.   GENOME RESEARCH

Interleukin-4 Production by Follicular Helper T Cells Requires the Conserved Il4 Enhancer Hypersensitivity Site V

(2012) Pandurangan Vijayanand et al.   IMMUNITY

Th2 Skewing by Activation of Nrf2 in CD4+ T Cells

(2012) C. E. Rockwell et al.   JOURNAL OF IMMUNOLOGY

Pathogen-induced human TH17 cells produce IFN-γ or IL-10 and are regulated by IL-1β

(2012) Christina E. Zielinski et al.   NATURE

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

(2012)   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

The ConsensusPathDB interaction database: 2013 update

(2012) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Reprogramming Factor Expression Initiates Widespread Targeted Chromatin Remodeling

(2011) Richard P. Koche et al.   Cell Stem Cell

GWAS Integrator: a bioinformatics tool to explore human genetic associations reported in published genome-wide association studies

(2011) Wei Yu et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

The Transcription Factor Myc Controls Metabolic Reprogramming upon T Lymphocyte Activation

(2011) Ruoning Wang et al.   IMMUNITY

The genetics of asthma and allergic disease: a 21st century perspective

(2011) Carole Ober et al.   IMMUNOLOGICAL REVIEWS

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

(2011) Jason Ernst et al.   NATURE

Epigenome-wide association studies for common human diseases

(2011) Vardhman K. Rakyan et al.   NATURE REVIEWS GENETICS

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

(2011) L. D. Ward et al.   NUCLEIC ACIDS RESEARCH

Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage

(2010) L. Chavez et al.   GENOME RESEARCH

Chemokine Receptor 4 Plays a Key Role in T Cell Recruitment into the Airways of Asthmatic Patients

(2010) P. Vijayanand et al.   JOURNAL OF IMMUNOLOGY

A Large-Scale, Consortium-Based Genomewide Association Study of Asthma

(2010) Miriam F. Moffatt et al.   NEW ENGLAND JOURNAL OF MEDICINE

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Global Mapping of H3K4me3 and H3K27me3 Reveals Specificity and Plasticity in Lineage Fate Determination of Differentiating CD4+ T Cells

(2009) Gang Wei et al.   IMMUNITY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Recent Advances in the Genetics of Autoimmune Disease

(2008) Peter K. Gregersen et al.   Annual Review of Immunology

ConsensusPathDB—a database for integrating human functional interaction networks

(2008) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH