List of works - Mark Joseph Daly

PLINK: a tool set for whole-genome association and population-based linkage analyses

scientific article

Haploview: analysis and visualization of LD and haplotype maps

scientific article (publication date: 15 January 2005)

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

scientific article (publication date: September 2010)

A framework for variation discovery and genotyping using next-generation DNA sequencing data

scientific article (publication date: May 2011)

Analysis of protein-coding genetic variation in 60,706 humans

scientific article (publication date: 17 August 2016)

PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes

scientific article (publication date: July 2003)

Initial sequencing and comparative analysis of the mouse genome

scientific article

A second generation human haplotype map of over 3.1 million SNPs

scientific article

The structure of haplotype blocks in the human genome

scientific article

MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations

scientific article (publication date: October 1987)

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

scientific article

The landscape of somatic copy-number alteration across human cancers

scientific article

Integrating common and rare genetic variation in diverse human populations

scientific article (publication date: 2 September 2010)

Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels

scientific article (publication date: June 2007)

A genome-wide association study identifies IL23R as an inflammatory bowel disease gene

scientific article

Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease

scientific article

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci

scientific article

A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms

scientific article (publication date: 15 February 2001)

Genome-wide detection and characterization of positive selection in human populations

scientific article

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis

scientific article

Genome sequence, comparative analysis and haplotype structure of the domestic dog

scientific article

Genome-wide association studies for common diseases and complex traits

scientific article (publication date: February 2005)

Efficiency and power in genetic association studies

scientific article

A mutation in Orai1 causes immune deficiency by abrogating CRAC channel function

scientific article

Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes

scientific article

Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs

scientific article

Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis

scientific article

Patterns and rates of exonic de novo mutations in autism spectrum disorders

scientific article

Parametric and nonparametric linkage analysis: a unified multipoint approach

scientific article (publication date: June 1996)

Association between microdeletion and microduplication at 16p11.2 and autism

scientific article

An atlas of genetic correlations across human diseases and traits

scientific article published on 28 September 2015

Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis

scientific article

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

scientific article published on 2 February 2015

Synaptic, transcriptional and chromatin genes disrupted in autism

scientific article

Plasma HDL cholesterol and risk of myocardial infarction: a mendelian randomisation study

scientific article (publication date: 11 August 2012)

Risk alleles for multiple sclerosis identified by a genomewide study

scientific article (publication date: 30 August 2007)

Efficient control of population structure in model organism association mapping

scientific article published on March 2008

Replicating genotype-phenotype associations

scientific article (publication date: 7 June 2007)

Genetic mapping in human disease

scientific article (publication date: 7 November 2008)

Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47

scientific journal article

High-resolution haplotype structure in the human genome

article

The common PPARgamma Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes

scientific article

Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants

scientific article

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

scientific article published on 20 July 2015

Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder

scientific article

Genetic and epigenetic fine mapping of causal autoimmune disease variants

scientific article

A mega-analysis of genome-wide association studies for major depressive disorder

scientific article

Schizophrenia risk from complex variation of complement component 4

scientific article

Genetic architectures of psychiatric disorders: the emerging picture and its implications

scientific article

Integrated detection and population-genetic analysis of SNPs and copy number variation

scientific article (publication date: October 2008)

List of works by Mark Joseph Daly

PLINK: a tool set for whole-genome association and population-based linkage analyses

Haploview: analysis and visualization of LD and haplotype maps

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

A framework for variation discovery and genotyping using next-generation DNA sequencing data

Analysis of protein-coding genetic variation in 60,706 humans

PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes

Initial sequencing and comparative analysis of the mouse genome

A second generation human haplotype map of over 3.1 million SNPs

The structure of haplotype blocks in the human genome

MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations

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

The landscape of somatic copy-number alteration across human cancers

Integrating common and rare genetic variation in diverse human populations

Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels

A genome-wide association study identifies IL23R as an inflammatory bowel disease gene

Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci

A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms

Genome-wide detection and characterization of positive selection in human populations

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis

Genome sequence, comparative analysis and haplotype structure of the domestic dog

Genome-wide association studies for common diseases and complex traits

Efficiency and power in genetic association studies

A mutation in Orai1 causes immune deficiency by abrogating CRAC channel function

Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes

Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs

Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis

Patterns and rates of exonic de novo mutations in autism spectrum disorders

Parametric and nonparametric linkage analysis: a unified multipoint approach

Association between microdeletion and microduplication at 16p11.2 and autism

An atlas of genetic correlations across human diseases and traits

Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

Synaptic, transcriptional and chromatin genes disrupted in autism

Plasma HDL cholesterol and risk of myocardial infarction: a mendelian randomisation study

Risk alleles for multiple sclerosis identified by a genomewide study

Efficient control of population structure in model organism association mapping

Replicating genotype-phenotype associations

Genetic mapping in human disease

Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47

High-resolution haplotype structure in the human genome

The common PPARgamma Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes

Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder

Genetic and epigenetic fine mapping of causal autoimmune disease variants

A mega-analysis of genome-wide association studies for major depressive disorder

Schizophrenia risk from complex variation of complement component 4

Genetic architectures of psychiatric disorders: the emerging picture and its implications

Integrated detection and population-genetic analysis of SNPs and copy number variation