Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks

PICS2: next-generation fine mapping via probabilistic identification of causal SNPs

(2021) Kimberly E Taylor et al.   BIOINFORMATICS

The Ever-Increasing Array of Novel Inborn Errors of Immunity: an Interim Update by the IUIS Committee

(2021) Stuart G. Tangye et al.   JOURNAL OF CLINICAL IMMUNOLOGY

Restoring IL-2 to its cancer immunotherapy glory

(2021) Asher Mullard   NATURE REVIEWS DRUG DISCOVERY

Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression

(2021) Urmo Võsa et al.   NATURE GENETICS

Human Inborn Errors of Immunity: 2019 Update of the IUIS Phenotypical Classification

(2020) Aziz Bousfiha et al.   JOURNAL OF CLINICAL IMMUNOLOGY

Human Inborn Errors of Immunity: 2019 Update on the Classification from the International Union of Immunological Societies Expert Committee

(2020) Stuart G. Tangye et al.   JOURNAL OF CLINICAL IMMUNOLOGY

Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe

(2020) Xiaojie Qiu et al.   Cell Systems

CRISPR screen in regulatory T cells reveals modulators of Foxp3

(2020) Jessica T. Cortez et al.   NATURE

pyGenomeTracks: reproducible plots for multivariate genomic data sets

(2020) Lucille Lopez-Delisle et al.   BIOINFORMATICS

Dynamics in protein translation sustaining T cell preparedness

(2020) Tobias Wolf et al.   NATURE IMMUNOLOGY

Functional CRISPR dissection of gene networks controlling human regulatory T cell identity

(2020) Kathrin Schumann et al.   NATURE IMMUNOLOGY

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

Open Targets Platform: supporting systematic drug–target identification and prioritisation

(2020) David Ochoa et al.   NUCLEIC ACIDS RESEARCH

Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation

(2019) Johan Henriksson et al.   CELL

Trans Effects on Gene Expression Can Drive Omnigenic Inheritance

(2019) Xuanyao Liu et al.   CELL

Landscape of stimulation-responsive chromatin across diverse human immune cells

(2019) Diego Calderon et al.   NATURE GENETICS

Chromatin activity at GWAS loci identifies T cell states driving complex immune diseases

(2019) Blagoje Soskic et al.   NATURE GENETICS

Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility

(2019)   SCIENCE

c-Jun overexpression in CAR T cells induces exhaustion resistance

(2019) Rachel C. Lynn et al.   NATURE

The Post-GWAS Era: From Association to Function

(2018) Michael D. Gallagher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Mapping gene regulatory networks from single-cell omics data

(2018) Mark W E J Fiers et al.   Briefings in Functional Genomics

Regulatory variants at KLF14 influence type 2 diabetes risk via a female-specific effect on adipocyte size and body composition

(2018) Kerrin S. Small et al.   NATURE GENETICS

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

(2018) Hilary K. Finucane et al.   NATURE GENETICS

Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function

(2018) Eric Shifrut et al.   CELL

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks

(2018) Adam J. Rubin et al.   CELL

ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data

(2018) Shinya Oki et al.   EMBO REPORTS

Guide Swap enables genome-scale pooled CRISPR–Cas9 screening in human primary cells

(2018) Pamela Y. Ting et al.   NATURE METHODS

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Genetic wiring maps of single-cell protein states reveal an off-switch for GPCR signalling

(2017) Markus Brockmann et al.   NATURE

Discovery of stimulation-responsive immune enhancers with CRISPR activation

(2017) Dimitre R. Simeonov et al.   NATURE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes: Functional dissection of theIl2ragene locus

(2017) Peng Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BAGEL: a computational framework for identifying essential genes from pooled library screens

(2016) Traver Hart et al.   BMC BIOINFORMATICS

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

(2016) Diego Adhemar Jaitin et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson et al.   CELL

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks

(2015) Oren Parnas et al.   CELL

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

(2015) Melina Claussnitzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Generation of knock-in primary human T cells using Cas9 ribonucleoproteins

(2015) Kathrin Schumann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A validated gene regulatory network and GWAS identifies early regulators of T cell–associated diseases

(2015) Mika Gustafsson et al.   Science Translational Medicine

The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations

(2014) C. Schmidl et al.   BLOOD

Large-Scale Genetic Perturbations Reveal Regulatory Networks and an Abundance of Gene-Specific Repressors

(2014) Patrick Kemmeren et al.   CELL

Obesity-associated variants within FTO form long-range functional connections with IRX3

(2014) Scott Smemo et al.   NATURE

Genetic and epigenetic fine mapping of causal autoimmune disease variants

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

Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations

(2014) Desirée Schubert et al.   NATURE MEDICINE

Immune dysregulation in human subjects with heterozygous germline mutations in CTLA4

(2014) H. S. Kuehn et al.   SCIENCE

The Functional Consequences of Variation in Transcription Factor Binding

(2014) Darren A. Cusanovich et al.   PLoS Genetics

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Follicular bronchiolitis as phenotype associated with CD25 deficiency

(2013) L. Bezrodnik et al.   CLINICAL AND EXPERIMENTAL IMMUNOLOGY

Human IL2RA null mutation mediates immunodeficiency with lymphoproliferation and autoimmunity

(2013) Kevin Goudy et al.   CLINICAL IMMUNOLOGY

Mapping Yeast Transcriptional Networks

(2013) T. R. Hughes et al.   GENETICS

Interleukin-2 at the Crossroads of Effector Responses, Tolerance, and Immunotherapy

(2013) Wei Liao et al.   IMMUNITY

Systematic identification of trans eQTLs as putative drivers of known disease associations

(2013) Harm-Jan Westra et al.   NATURE GENETICS

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Leveraging models of cell regulation and GWAS data in integrative network-based association studies

(2012) Andrea Califano et al.   NATURE 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

T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements

(2012) Aditi Kanhere et al.   Nature Communications

Modulation of cytokine receptors by IL-2 broadly regulates differentiation into helper T cell lineages

(2011) Wei Liao et al.   NATURE IMMUNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

CTLA-4: a key protein in autoimmunity

(2009) Jagadeesh Bayry   Nature Reviews Rheumatology

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

(2009) I. Amit et al.   SCIENCE

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY