Genomic profiling of T-cell activation suggests increased sensitivity of memory T cells to CD28 costimulation

Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk

(2019) Iris E. Jansen et al.   NATURE GENETICS

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

A large electronic-health-record-based genome-wide study of serum lipids

(2018) Thomas J. Hoffmann et al.   NATURE GENETICS

Multiancestry association study identifies new asthma risk loci that colocalize with immune-cell enhancer marks

(2017) Florence Demenais et al.   NATURE GENETICS

Identification of 153 new loci associated with heel bone mineral density and functional involvement of GPC6 in osteoporosis

(2017) John P Kemp et al.   NATURE GENETICS

Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology

(2017) Manuel A Ferreira et al.   NATURE GENETICS

Oncostatin M drives intestinal inflammation and predicts response to tumor necrosis factor–neutralizing therapy in patients with inflammatory bowel disease

(2017) Nathaniel R West et al.   NATURE MEDICINE

T cell costimulatory receptor CD28 is a primary target for PD-1–mediated inhibition

(2017) Enfu Hui et al.   SCIENCE

Rescue of exhausted CD8 T cells by PD-1–targeted therapies is CD28-dependent

(2017) Alice O. Kamphorst et al.   SCIENCE

PD-L1 genetic overexpression or pharmacological restoration in hematopoietic stem and progenitor cells reverses autoimmune diabetes

(2017) Moufida Ben Nasr et al.   Science Translational Medicine

Transancestral mapping and genetic load in systemic lupus erythematosus

(2017) Carl D. Langefeld et al.   Nature Communications

Large scale meta-analysis characterizes genetic architecture for common psoriasis associated variants

(2017) Lam C. Tsoi et al.   Nature Communications

Single CD28 stimulation induces stable and polyclonal expansion of human regulatory T cells

(2017) Xuehui He et al.   Scientific Reports

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

(2016) Biola M. Javierre et al.   CELL

CD28 days later: Resurrecting costimulation for CD8+memory T cells

(2016) Verena van der Heide et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Interrupting CD28 costimulation before antigen rechallenge affects CD8+T-cell expansion and effector functions during secondary response in mice

(2016) Monika Fröhlich et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

CD28 Costimulation: From Mechanism to Therapy

(2016) Jonathan H. Esensten et al.   IMMUNITY

SNP2TFBS – a database of regulatory SNPs affecting predicted transcription factor binding site affinity

(2016) Sunil Kumar et al.   NUCLEIC ACIDS RESEARCH

Immune related adverse events associated with anti-CTLA-4 antibodies: systematic review and meta-analysis

(2015) Anne Bertrand et al.   BMC Medicine

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

ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors

(2015) Christian Schmidl et al.   NATURE METHODS

Patients with LRBA deficiency show CTLA4 loss and immune dysregulation responsive to abatacept therapy

(2015) B. Lo et al.   SCIENCE

Confusing signals: Recent progress in CTLA-4 biology

(2015) Lucy S.K. Walker et al.   TRENDS IN IMMUNOLOGY

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Understanding the CD28/CTLA-4 (CD152) Pathway and Its Implications for Costimulatory Blockade

(2014) D. Gardner et al.   AMERICAN JOURNAL OF TRANSPLANTATION

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Control of Memory CD8+ T Cell Differentiation by CD80/CD86-CD28 Costimulation and Restoration by IL-2 during the Recall Response

(2014) S. Fuse et al.   JOURNAL OF IMMUNOLOGY

Genetic and epigenetic fine mapping of causal autoimmune disease variants

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

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   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

Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

(2014) B. P. Fairfax et al.   SCIENCE

Regulation of Gene Expression in Autoimmune Disease Loci and the Genetic Basis of Proliferation in CD4+ Effector Memory T Cells

(2014) Xinli Hu et al.   PLoS Genetics

Inducible Deletion of CD28 Prior to Secondary Nippostrongylus brasiliensis Infection Impairs Worm Expulsion and Recall of Protective Memory CD4+ T Cell Responses

(2014) Hlumani Ndlovu et al.   PLoS Pathogens

CD28 expression is required after T cell priming for helper T cell responses and protective immunity to infection

(2014) Michelle A Linterman et al.   eLife

Enhanced Activity of Akt in Teff Cells From Children With Lupus Nephritis Is Associated With Reduced Induction of Tumor Necrosis Factor Receptor-Associated Factor 6 and Increased OX40 Expression

(2013) Sudhir Kshirsagar et al.   ARTHRITIS AND RHEUMATISM

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

(2013) Y. Liao et al.   BIOINFORMATICS

Genetics of rheumatoid arthritis contributes to biology and drug discovery

(2013) Yukinori Okada et al.   NATURE

Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis

(2013) Ashley H Beecham et al.   NATURE GENETICS

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

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

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

Chromatin marks identify critical cell types for fine mapping complex trait variants

(2012) Gosia Trynka et al.   NATURE GENETICS

Impaired suppression of synovial fluid CD4+CD25− T cells from patients with juvenile idiopathic arthritis by CD4+CD25+ Treg cells

(2011) Susanne Haufe et al.   ARTHRITIS AND RHEUMATISM

Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease

(2011) Gosia Trynka et al.   NATURE GENETICS

Trans-Endocytosis of CD80 and CD86: A Molecular Basis for the Cell-Extrinsic Function of CTLA-4

(2011) O. S. Qureshi et al.   SCIENCE

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Monoclonal antibody TGN1412 trial failure explained by species differences in CD28 expression on CD4+ effector memory T-cells

(2010) D Eastwood et al.   BRITISH JOURNAL OF PHARMACOLOGY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Multiple common variants for celiac disease influencing immune gene expression

(2010) Patrick C A Dubois et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

CD28 stimulation triggers NF- B activation through the CARMA1-PKC -Grb2/Gads axis

(2008) K. Takeda et al.   INTERNATIONAL IMMUNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY