Discovery of stimulation-responsive immune enhancers with CRISPR activation

Fine-mapping inflammatory bowel disease loci to single-variant resolution

(2017) Hailiang Huang et al.   NATURE

Therapeutic anti-CD3 monoclonal antibodies: from bench to bedside

(2016) Chantal Kuhn et al.   Immunotherapy

High-throughput mapping of regulatory DNA

(2016) Nisha Rajagopal et al.   NATURE BIOTECHNOLOGY

Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9

(2016) Gozde Korkmaz et al.   NATURE BIOTECHNOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers

(2015) Denes Hnisz et al.   MOLECULAR CELL

New insights on the transcriptional regulation of CD69 gene through a potent enhancer located in the conserved non-coding sequence 2

(2015) Teresa Laguna et al.   MOLECULAR IMMUNOLOGY

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver et al.   NATURE

Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers

(2015) Suna Onengut-Gumuscu et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

Genetic and epigenetic fine mapping of causal autoimmune disease variants

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

Functional genomics platform for pooled screening and generation of mammalian genetic interaction maps

(2014) Martin Kampmann et al.   Nature Protocols

Intersection of population variation and autoimmunity genetics in human T cell activation

(2014) C. J. Ye et al.   SCIENCE

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Human IL2RA null mutation mediates immunodeficiency with lymphoproliferation and autoimmunity

(2013) Kevin Goudy et al.   CLINICAL IMMUNOLOGY

1000 Genomes-based imputation identifies novel and refined associations for the Wellcome Trust Case Control Consortium phase 1 Data

(2012) Jie Huang et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

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

(2011) Jason Ernst et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS