Mark J. Daly

OpenAlex profile · ORCID

Selected research works

Up to 100 selected research works. Source updated 2026-10-28T19:34:48+00:00.

1. PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses · 2007 · 34,078 citations
2. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data · 2010 · 27,868 citations
3. A global reference for human genetic variation · 2015 · 18,231 citations
4. Haploview: analysis and visualization of LD and haplotype maps · 2004 · 14,532 citations
5. A framework for variation discovery and genotyping using next-generation DNA sequencing data · 2011 · 11,479 citations
6. PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes · 2003 · 10,177 citations
7. Analysis of protein-coding genetic variation in 60,706 humans · 2016 · 9,587 citations
8. The mutational constraint spectrum quantified from variation in 141,456 humans · 2020 · 9,417 citations
9. Biological insights from 108 schizophrenia-associated genetic loci · 2014 · 7,575 citations
10. Initial sequencing and comparative analysis of the mouse genome · 2002 · 7,180 citations
11. MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations · 1987 · 6,657 citations
12. The International HapMap Project · 2003 · 6,058 citations
13. The Structure of Haplotype Blocks in the Human Genome · 2002 · 5,864 citations
14. LD Score regression distinguishes confounding from polygenicity in genome-wide association studies · 2015 · 5,559 citations
15. Common polygenic variation contributes to risk of schizophrenia and bipolar disorder · 2009 · 4,811 citations
16. Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease · 2012 · 4,719 citations
17. A second generation human haplotype map of over 3.1 million SNPs · 2007 · 4,437 citations
18. An atlas of genetic correlations across human diseases and traits · 2015 · 4,255 citations
19. FinnGen provides genetic insights from a well-phenotyped isolated population · 2023 · 4,230 citations
20. The landscape of somatic copy-number alteration across human cancers · 2010 · 4,017 citations
21. A Genome-Wide Association Study Identifies IL23R as an Inflammatory Bowel Disease Gene · 2006 · 3,041 citations
22. Integrating common and rare genetic variation in diverse human populations · 2010 · 3,017 citations
23. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms · 2001 · 2,976 citations
24. Mapping genomic loci implicates genes and synaptic biology in schizophrenia · 2022 · 2,952 citations
25. Parametric and nonparametric linkage analysis: a unified multipoint approach. · 1996 · 2,883 citations
26. Genome-wide association studies for common diseases and complex traits · 2005 · 2,865 citations
27. Genome-Wide Association Analysis Identifies Loci for Type 2 Diabetes and Triglyceride Levels · 2007 · 2,843 citations
28. Clinical use of current polygenic risk scores may exacerbate health disparities · 2019 · 2,806 citations
29. Synaptic, transcriptional and chromatin genes disrupted in autism · 2014 · 2,744 citations
30. Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis · 2011 · 2,698 citations
31. Partitioning heritability by functional annotation using genome-wide association summary statistics · 2015 · 2,602 citations
32. Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations · 2015 · 2,602 citations
33. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease · 2008 · 2,594 citations
34. Genome sequence, comparative analysis and haplotype structure of the domestic dog · 2005 · 2,568 citations
35. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci · 2010 · 2,520 citations
36. New insights into the genetic etiology of Alzheimer’s disease and related dementias · 2022 · 2,490 citations
37. Schizophrenia risk from complex variation of complement component 4 · 2016 · 2,429 citations
38. Identification of common genetic risk variants for autism spectrum disorder · 2019 · 2,420 citations
39. A cross-population atlas of genetic associations for 220 human phenotypes · 2021 · 2,327 citations
40. Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism · 2019 · 2,316 citations
41. A mutation in Orai1 causes immune deficiency by abrogating CRAC channel function · 2006 · 2,286 citations
42. Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs · 2013 · 2,263 citations
43. Discovery of the first genome-wide significant risk loci for attention deficit/hyperactivity disorder · 2018 · 2,204 citations
44. Genetic and epigenetic fine mapping of causal autoimmune disease variants · 2014 · 1,952 citations
45. Scaling accurate genetic variant discovery to tens of thousands of samples · 2017 · 1,938 citations
46. Analysis of shared heritability in common disorders of the brain · 2018 · 1,924 citations
47. Genome-wide association study identifies five new schizophrenia loci · 2011 · 1,919 citations
48. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes · 2008 · 1,865 citations
49. Efficient Control of Population Structure in Model Organism Association Mapping · 2008 · 1,847 citations
50. Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis · 2007 · 1,768 citations
51. The common PPARγ Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes · 2000 · 1,767 citations
52. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis · 2010 · 1,761 citations
53. Patterns and rates of exonic de novo mutations in autism spectrum disorders · 2012 · 1,735 citations
54. A genomic mutational constraint map using variation in 76,156 human genomes · 2023 · 1,723 citations
55. High-resolution haplotype structure in the human genome · 2001 · 1,717 citations
56. Efficiency and power in genetic association studies · 2005 · 1,688 citations
57. Association between Microdeletion and Microduplication at 16p11.2 and Autism · 2008 · 1,666 citations
58. The mutational constraint spectrum quantified from variation in 141,456 humans · 2019 · 1,604 citations
59. Genome-wide association study identifies 30 loci associated with bipolar disorder · 2019 · 1,519 citations
60. Rare chromosomal deletions and duplications increase risk of schizophrenia · 2008 · 1,474 citations
61. Genetic Mapping in Human Disease · 2008 · 1,452 citations
62. Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci · 2015 · 1,429 citations
63. Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis · 2019 · 1,413 citations
64. Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations · 2017 · 1,390 citations
65. Genomic Relationships, Novel Loci, and Pleiotropic Mechanisms across Eight Psychiatric Disorders · 2019 · 1,381 citations
66. Replicating genotype–phenotype associations · 2007 · 1,352 citations
67. Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4 · 2011 · 1,343 citations
68. Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47 · 2011 · 1,316 citations
69. Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores · 2015 · 1,302 citations
70. Guidelines for investigating causality of sequence variants in human disease · 2014 · 1,234 citations
71. Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder · 2008 · 1,234 citations
72. High-throughput discovery of novel developmental phenotypes · 2016 · 1,196 citations
73. Genetic architectures of psychiatric disorders: the emerging picture and its implications · 2012 · 1,177 citations
74. A mega-analysis of genome-wide association studies for major depressive disorder · 2012 · 1,119 citations
75. Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap · 2018 · 1,093 citations
76. Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants · 2009 · 1,088 citations
77. Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects · 2016 · 1,057 citations
78. The genetic architecture of type 2 diabetes · 2016 · 1,051 citations
79. HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin · 2009 · 1,047 citations
80. A structural variation reference for medical and population genetics · 2020 · 1,036 citations
81. Mapping the human genetic architecture of COVID-19 · 2021 · 984 citations
82. Rare coding variants in ten genes confer substantial risk for schizophrenia · 2022 · 979 citations
83. A framework for the interpretation of de novo mutation in human disease · 2014 · 979 citations
84. Integrated detection and population-genetic analysis of SNPs and copy number variation · 2008 · 935 citations
85. Common variants associated with plasma triglycerides and risk for coronary artery disease · 2013 · 862 citations
86. De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies · 2015 · 857 citations
87. A comprehensive genetic map of the mouse genome · 1996 · 827 citations
88. Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci · 2009 · 801 citations
89. Seven new loci associated with age-related macular degeneration · 2013 · 788 citations
90. Genome-wide analyses of ADHD identify 27 risk loci, refine the genetic architecture and implicate several cognitive domains · 2023 · 786 citations
91. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs · 2008 · 783 citations
92. Estimation of the multiple testing burden for genomewide association studies of nearly all common variants · 2008 · 783 citations
93. The ExAC browser: displaying reference data information from over 60 000 exomes · 2016 · 782 citations
94. Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study · 2015 · 782 citations
95. Genetic variation in the 5q31 cytokine gene cluster confers susceptibility to Crohn disease · 2001 · 775 citations
96. Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease · 2011 · 771 citations
97. A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC · 2006 · 766 citations
98. Guilt by association · 2000 · 762 citations
99. Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways · 2015 · 755 citations
100. Exome Sequencing, ANGPTL3 Mutations, and Familial Combined Hypolipidemia · 2010 · 754 citations