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List of works by Patrick M Gaffney

A 10-gene classifier for distinguishing head and neck squamous cell carcinoma and lung squamous cell carcinoma

scientific article published on 01 May 2007

A comprehensive analysis of shared loci between systemic lupus erythematosus (SLE) and sixteen autoimmune diseases reveals limited genetic overlap

scientific article

A functional haplotype of UBE2L3 confers risk for systemic lupus erythematosus

scientific article

A genome-wide search for susceptibility genes in human systemic lupus erythematosus sib-pair families

scientific article (publication date: 8 December 1998)

A missense variant in NCF1 is associated with susceptibility to multiple autoimmune diseases

scientific article

A novel polymorphism of the human CD40 receptor with enhanced function

scientific article published on 30 June 2008

A plausibly causal functional lupus-associated risk variant in the STAT1-STAT4 locus

scholarly article by Zubin Patel published in April 2018

A polymorphism within IL21R confers risk for systemic lupus erythematosus

scientific article published on August 2009

A20-Binding Inhibitor of NF-κB Activation 1 is a Physiologic Inhibitor of NF-κB: A Molecular Switch for Inflammation and Autoimmunity

scientific article

ABIN1 Determines Severity of Glomerulonephritis via Activation of Intrinsic Glomerular Inflammation

scientific article

ABIN1 dysfunction as a genetic basis for lupus nephritis

scientific article published on 22 August 2013

Activating mutations in STIM1 and ORAI1 cause overlapping syndromes of tubular myopathy and congenital miosis

scientific article

Admixture mapping in lupus identifies multiple functional variants within IFIH1 associated with apoptosis, inflammation, and autoantibody production

scientific article

Allelic heterogeneity in NCF2 associated with systemic lupus erythematosus (SLE) susceptibility across four ethnic populations

scientific article published on 26 October 2013

An enhancer element harboring variants associated with systemic lupus erythematosus engages the TNFAIP3 promoter to influence A20 expression

scientific article (publication date: 2013)

Analysis of autosomal genes reveals gene-sex interactions and higher total genetic risk in men with systemic lupus erythematosus

scientific article published on 21 November 2011

Analysis of maternal-offspring HLA compatibility, parent-of-origin effects, and noninherited maternal antigen effects for HLA-DRB1 in systemic lupus erythematosus

scientific article

Association of Epstein-Barr virus serological reactivation with transitioning to systemic lupus erythematosus in at-risk individuals

scientific article published on 19 June 2019

Association of IFIH1 and pro-inflammatory mediators: Potential new clues in SLE-associated pathogenesis

scientific article

Association of Natural Killer Cell Ligand Polymorphism HLA-C Asn80Lys With the Development of Anti-SSA/Ro-Associated Congenital Heart Block.

scientific article

Association of PPP2CA polymorphisms with systemic lupus erythematosus susceptibility in multiple ethnic groups

scientific article

Association of a functional variant downstream of TNFAIP3 with systemic lupus erythematosus

scientific article

Association of genetic variants in complement factor H and factor H-related genes with systemic lupus erythematosus susceptibility

scientific article

Association of two independent functional risk haplotypes in TNIP1 with systemic lupus erythematosus

scientific article

CSK regulatory polymorphism is associated with systemic lupus erythematosus and influences B-cell signaling and activation

scientific article published on 7 October 2012

Chromatin Looping Links Target Genes with Genetic Risk Loci for Dermatological Traits

scientific article published in 2021

Combined role of vitamin D status and CYP24A1 in the transition to systemic lupus erythematosus

scientific article published on 9 June 2016

Complement receptor 2 polymorphisms associated with systemic lupus erythematosus modulate alternative splicing

scientific article published on 23 April 2009

Contributions of mass spectrometry-based proteomics to defining cellular mechanisms and diagnostic markers for systemic lupus erythematosus.

scientific article

Correction: Identification and replication of RNA-Seq gene network modules associated with depression severity

scientific article published on 12 August 2020

Decreased SMG7 expression associates with lupus-risk variants and elevated antinuclear antibody production

scientific article published on 18 January 2016

Deep sequencing reveals a DAP1 regulatory haplotype that potentiates autoimmunity in systemic lupus erythematosus

scientific article published on 19 November 2020

Defining a new molecular basis of systemic lupus erythematosus through transcriptional profiling

scientific article published on 01 November 2007

Dense genotyping of immune-related disease regions identifies 14 new susceptibility loci for juvenile idiopathic arthritis.

scientific article

Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production

scientific article

Disease mechanisms in rheumatology--tools and pathways: defining functional genetic variants in autoimmune diseases

scientific article

Effects of IRF5 lupus risk haplotype on pathways predicted to influence B cell functions

scientific article published on 22 February 2012

Encore: Genetic Association Interaction Network centrality pipeline and application to SLE exome data

scientific article

Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks

scientific article published in Nature Communications

Erratum: Complement receptor 2 polymorphisms associated with systemic lupus erythematosus modulate alternative splicing

article

Erratum: Genetic associations of LYN with systemic lupus erythematosus

article

European population substructure is associated with mucocutaneous manifestations and autoantibody production in systemic lupus erythematosus

scientific article published on August 2009

Evaluation of TRAF6 in a large multiancestral lupus cohort

scientific article

Evaluation of imputation-based association in and around the integrin-alpha-M (ITGAM) gene and replication of robust association between a non-synonymous functional variant within ITGAM and systemic lupus erythematosus (SLE).

scientific article

Evaluation of the TREX1 gene in a large multi-ancestral lupus cohort

scientific article

Evidence for gene-gene epistatic interactions among susceptibility loci for systemic lupus erythematosus

scientific article published on February 2012

Exon 6 variants carried on systemic lupus erythematosus (SLE) risk haplotypes modulate IRF5 function.

scientific article published on 9 August 2010

Expression and methylation data from SLE patient and healthy control blood samples subdivided with respect to ARID3a levels

scientific article

Expression levels for many genes in human peripheral blood cells are highly sensitive to ex vivo incubation

scientific article published in August 2004

F.20. Delineating SLE Susceptibility Polymorphisms at the OX40L Locus

Familial aggregation and linkage analysis of autoantibody traits in pedigrees multiplex for systemic lupus erythematosus

article

Fatal acute lymphoblastic leukemia in mice transgenic for B cell-restricted bcl-xL and c-myc.

scientific article published in June 2004

Fine mapping chromosome 16q12 in a collection of 231 systemic lupus erythematosus sibpair and multiplex families.

scientific article published in February 2005

Fine mapping of Xq28: both MECP2 and IRAK1 contribute to risk for systemic lupus erythematosus in multiple ancestral groups

scientific article published on 17 August 2012

Fine-mapping and transethnic genotyping establish IL2/IL21 genetic association with lupus and localize this genetic effect to IL21

scientific article

Fine-mapping chromosome 20 in 230 systemic lupus erythematosus sib pair and multiplex families: evidence for genetic epistasis with chromosome 16q12.

scientific article

Forward genetic screening identifies a small molecule that blocks Toxoplasma gondii growth by inhibiting both host- and parasite-encoded kinases

scientific article (publication date: June 2014)

From association to mechanism in complex disease genetics: the role of the 3D genome

article

Functional activation of PPARγ in human upper aerodigestive cancer cell lines.

scientific article published on 21 March 2016

GWAS identifies novel SLE susceptibility genes and explains the association of the HLA region

scientific journal article

Gene expression profiling in human autoimmunity.

scientific article

Genes associated with early development, apoptosis and cell cycle regulation define a gene expression profile of adenoid cystic carcinoma.

scientific article published on 9 June 2006

Genetic analyses of interferon pathway-related genes reveal multiple new loci associated with systemic lupus erythematosus

scientific article

Genetic and physical interaction of the B-cell systemic lupus erythematosus-associated genes BANK1 and BLK.

scientific article published on 6 October 2011

Genetic association of CD247 (CD3ζ) with SLE in a large-scale multiethnic study.

scientific article

Genetic association of the R620W polymorphism of protein tyrosine phosphatase PTPN22 with human SLE.

scientific article

Genetic associations of LYN with systemic lupus erythematosus

scientific article published on 16 April 2009

Genetic associations of leptin-related polymorphisms with systemic lupus erythematosus

scientific article

Genetic fine mapping of systemic lupus erythematosus MHC associations in Europeans and African Americans

scholarly article by Ken B Hanscombe published in November 2018

Genetic linkage and transmission disequilibrium of marker haplotypes at chromosome 1q41 in human systemic lupus erythematosus

scientific article

Genetic variants at the 16p13 locus confer risk for eosinophilic esophagitis

article

Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus

scientific journal article

Genome scan of human systemic lupus erythematosus by regression modeling: evidence of linkage and epistasis at 4p16-15.2.

scientific article

Genome screening in human systemic lupus erythematosus: results from a second Minnesota cohort and combined analyses of 187 sib-pair families

scientific article

Genome-Wide Association Study in an Amerindian Ancestry Population Reveals Novel Systemic Lupus Erythematosus Risk Loci and the Role of European Admixture

scientific article published on 25 November 2015

Genome-wide association meta-analysis in Chinese and European individuals identifies ten new loci associated with systemic lupus erythematosus

scientific article published on 11 July 2016

Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci

scientific article

High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions

scientific article published in October 2009

High-density genotyping of STAT4 reveals multiple haplotypic associations with systemic lupus erythematosus in different racial groups

scientific article published on April 2009

Human effector B lymphocytes express ARID3a and secrete interferon alpha

scientific article

IRF5 haplotypes demonstrate diverse serological associations which predict serum interferon alpha activity and explain the majority of the genetic association with systemic lupus erythematosus

scientific article

Identification and replication of RNA-Seq gene network modules associated with depression severity

article

Identification of IRAK1 as a risk gene with critical role in the pathogenesis of systemic lupus erythematosus

scholarly article

Identification of IRF8, TMEM39A, and IKZF3-ZPBP2 as susceptibility loci for systemic lupus erythematosus in a large-scale multiracial replication study

scientific article published on 29 March 2012

Identification of a New Susceptibility Locus for Systemic Lupus Erythematosus on Chromosome 12 in Individuals of European Ancestry

scientific article published on 28 August 2015

Identification of a Sjögren's syndrome susceptibility locus at OAS1 that influences isoform switching, protein expression, and responsiveness to type I interferons

scientific article

Identification of a Systemic Lupus Erythematosus Risk Locus Spanning ATG16L2, FCHSD2, and P2RY2 in Koreans

scientific article published on 14 December 2015

Identification of a systemic lupus erythematosus susceptibility locus at 11p13 between PDHX and CD44 in a multiethnic study

scientific article

Identification of new SLE-associated genes with a two-step Bayesian study design.

scientific article

Identification of novel coding mutation in C1qA gene in an African-American pedigree with lupus and C1q deficiency

scientific article

Identification of novel genetic susceptibility loci in African American lupus patients in a candidate gene association study

scientific article

Impact of genetic ancestry and sociodemographic status on the clinical expression of systemic lupus erythematosus in American Indian-European populations

scientific article

Infinium assay for large-scale SNP genotyping applications.

scientific article

Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus

scientific article (publication date: 4 March 2003)

Keys to unlocking the mysteries of rheumatic autoimmune disease.

scientific article published on May 2004

Latent autoimmunity across disease-specific boundaries in at-risk first-degree relatives of SLE and RA patients

Lupus Risk Variant Increases pSTAT1 Binding and Decreases ETS1 Expression

scientific article

Lupus nephritis susceptibility loci in women with systemic lupus erythematosus

scientific article

Lupus risk variants in the PXK locus alter B-cell receptor internalization

scientific article

Lupus-associated causal mutation in neutrophil cytosolic factor 2 (NCF2) brings unique insights to the structure and function of NADPH oxidase

scientific article published on 27 December 2011

MHC associations with clinical and autoantibody manifestations in European SLE.

scientific article

Meta-analysis and imputation identifies a 109 kb risk haplotype spanning TNFAIP3 associated with lupus nephritis and hematologic manifestations

scientific article published on 23 April 2009

Meta-analysis of genome-wide linkage studies of systemic lupus erythematosus

scientific article published on 14 September 2006

MicroRNA-3148 modulates allelic expression of toll-like receptor 7 variant associated with systemic lupus erythematosus

scientific article

MicroRNA-3148 modulates differential gene expression of the SLE-associated TLR7 variant.

scientific article

Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly.

scientific article published on 14 August 2017

Nearest-Neighbor Projected Distance Regression for Epistasis Detection in GWAS With Population Structure Correction

scientific article published on 22 July 2020

OP0020 Identification of Multiple Sjögren’s Syndrome Susceptibility Loci

PARP alleles and SLE: failure to confirm association with disease susceptibility

scientific article published on 01 June 2000

PPARγ targeted oral cancer treatment and additional utility of genomics analytic techniques.

scientific article published on 29 November 2016

PTPN22 association in systemic lupus erythematosus (SLE) with respect to individual ancestry and clinical sub-phenotypes

scientific article

Periostin promotes invasion and anchorage-independent growth in the metastatic process of head and neck cancer.

scientific article published on July 2006

Peripheral blood gene expression profiling in Sjögren's syndrome

scientific article published on 30 April 2009

Phenotypic associations of genetic susceptibility loci in systemic lupus erythematosus

scientific article published on 30 June 2011

Polygenic risk assessment reveals pleiotropy between sarcoidosis and inflammatory disorders in the context of genetic ancestry

scientific article published on 9 March 2017

Polymorphism at the TNF superfamily gene TNFSF4 confers susceptibility to systemic lupus erythematosus

scientific article published on 02 December 2007

Preferential association of a functional variant in complement receptor 2 with antibodies to double-stranded DNA.

scientific article

Preferential binding to Elk-1 by SLE-associated IL10 risk allele upregulates IL10 expression

scientific article

Progress towards understanding the genetic pathogenesis of systemic lupus erythematosus

scientific article

RBPJ mutations identified in two families affected by Adams-Oliver syndrome

scientific article

Recent advances in the genetics of systemic lupus erythematosus

scientific article published on 01 February 2002

Regulatory polymorphisms modulate the expression of HLA class II molecules and promote autoimmunity.

scientific article published on 16 February 2016

Replication of the BANK1 genetic association with systemic lupus erythematosus in a European-derived population

scientific article published on 02 April 2009

Risk alleles for systemic lupus erythematosus in a large case-control collection and associations with clinical subphenotypes

scientific article

Role of MYH9 and APOL1 in African and non-African populations with lupus nephritis

scientific article published on 22 December 2011

Role of Systemic Lupus Erythematosus Risk Variants With Opposing Functional Effects as a Driver of Hypomorphic Expression of TNIP1 and Other Genes Within a Three-Dimensional Chromatin Network

scientific article published on 05 December 2019

Sa.54. Positional Identification of Integrin- αMβ2 (ITGAM) as a Susceptibility Gene for Systematic Lupus Erythematosus (SLE)

article

Sex chromosome aneuploidies among men with systemic lupus erythematosus

scientific article published on 6 December 2011

Site-1 protease deficiency causes human skeletal dysplasia due to defective inter-organelle protein trafficking

scientific article published on 26 July 2018

Specific combinations of HLA-DR2 and DR3 class II haplotypes contribute graded risk for disease susceptibility and autoantibodies in human SLE

scientific article published on 04 April 2007

Subsistence strategies in traditional societies distinguish gut microbiomes

scientific article

TALEN-mediated enhancer knockout influences TNFAIP3 gene expression and mimics a molecular phenotype associated with systemic lupus erythematosus

scientific article published on 28 January 2016

The IRF5-TNPO3 association with systemic lupus erythematosus has two components that other autoimmune disorders variably share

scientific article

The effect of inversion at 8p23 on BLK association with lupus in Caucasian population

scientific article

The genetics of human systemic lupus erythematosus

scientific article published on 01 December 1998

The genomics of autoimmune disease in the era of genome-wide association studies and beyond

scientific article published on 07 October 2011

The role of genetic variation near interferon-kappa in systemic lupus erythematosus

scientific article

The rs4774 CIITA missense variant is associated with risk of systemic lupus erythematosus.

scientific article

The use of microarrays to study autoimmunity.

scientific article published on January 2004

Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus

scholarly article

Trans-ancestral studies fine map the SLE-susceptibility locus TNFSF4.

scientific article

Transancestral mapping and genetic load in systemic lupus erythematosus

scientific article published on 17 July 2017

Two functional lupus-associated BLK promoter variants control cell-type- and developmental-stage-specific transcription

scientific article published on April 2014

Unraveling Multiple MHC Gene Associations with Systemic Lupus Erythematosus: Model Choice Indicates a Role for HLA Alleles and Non-HLA Genes in Europeans.

scientific article published on 3 September 2015

Unraveling multiple MHC gene associations with systemic lupus erythematosus: model choice indicates a role for HLA alleles and non-HLA genes in Europeans

scientific article

Use of next-generation DNA sequencing to analyze genetic variants in rheumatic disease

scientific article published on January 2014

Variable association of reactive intermediate genes with systemic lupus erythematosus in populations with different African ancestry

scientific article

Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjögren's syndrome

scientific article published on 6 October 2013

Variants within MECP2, a key transcription regulator, are associated with increased susceptibility to lupus and differential gene expression in patients with systemic lupus erythematosus

scientific article published on April 2009

Variation in the ATP-binding cassette transporter 2 gene is a separate risk factor for systemic lupus erythematosus within the MHC.

scientific article

Variation in the ICAM1-ICAM4-ICAM5 locus is associated with systemic lupus erythematosus susceptibility in multiple ancestries

scientific article

Variation in the upstream region of P-Selectin (SELP) is a risk factor for SLE

scientific article

Visualizing human leukocyte antigen class II risk haplotypes in human systemic lupus erythematosus.

scientific article published on 26 July 2002

WITHDRAWN: A female autoimmunity gene exists: DDX3X.

retracted scientific article published on 20 August 2012

X Chromosome Dose and Sex Bias in Autoimmune Diseases: Increased Prevalence of 47,XXX in Systemic Lupus Erythematosus and Sjögren's Syndrome

scientific article published on 29 December 2015

c-kit expression in adenoid cystic carcinoma does not have an impact on local or distant tumor recurrence

scientific article published on 01 December 2005

βIV Spectrinopathies Cause Profound Intellectual Disability, Congenital Hypotonia, and Motor Axonal Neuropathy

scientific article published on 31 May 2018