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Mark Daly

Ph.D.

Director of the Finnish Institute for Molecular Medicine (FIMM)

Founding Chief of the Analytic and Translational Genetic Unit (ATGU)

Massachusetts General Hospital

Associate Professor of Medicine at Harvard Medical School

Institute member, Broad Institute of MIT and Harvard

Dr. Mark Daly is Director of the Finnish Institute for Molecular Medicine (FIMM) at the University of Helsinki, Founding Chief of the Analytic and Translational Genetic Unit (ATGU) at Massachusetts General Hospital, Associate Professor of Medicine at Harvard Medical School, and Institute member of the Broad Institute of MIT and Harvard.

His research has historically focused on the development and application of statistical methods for the discovery and interpretation of genetic variation responsible for complex human disease and with the creation of the ATGU, he and other core faculty are focused on the interpretation of genome sequence and the use of genome information in clinical settings.  At the Broad, he is an Institute Member and Co-Director of the Program in Medical and Population Genetics, where he leads many large scale genome sequencing studies in autism and inflammatory bowel disease.

In February of 2018, he was appointed Director of the Institute of Molecular Medicine Finland (FIMM), and now divides his time between Helsinki and Boston, although he maintains his primary lab and affiliations in Boston. FIMM is a translational research institute with a focus on cancer, digital diagnostics, genetics and epidemiology and is the home of landmark efforts such as the FinnGen Project.

While developing computational and statistical methods that can be broadly applied, his group has several primary medical genetics research foci.  He has extensive research program in neuropsychiatric genetics - particularly in autism, schizophrenia and ADHD – and has led large-scale GWAS and exome sequencing efforts in this area.  His lab serves as an analytic hub for the Psychiatric GWAS Consortium, an international consortium leading the largest collaborative GWAS studies in 5 major psychiatric disorders.  He also has a longstanding effort in the mapping of genes for Crohn’s disease and ulcerative colitis where he helped found and lead an international effort that has identified more than 150 genetic risk factors and pursues the functional interpretation and clinical ramifications of these continued gene discovery efforts.  He is also co-PI of the gnomAD project and committed to ensuring the output of all ATGU genomic research is maximally accessible and useful to the clinical and research communities.

Dr. Daly has received many awards and was elected to the National Academy of Medicine in 2017. 

He studied physics at MIT, and although he initially wanted to become a lawyer or poker player, he joined Eric Lander’s lab at the Whitehead Institute as a freshman to do genetics research. He received his PhD in Human Genetics from Leiden University in 2004.

Mark Daly

Ph.D.

Director of the Finnish Institute for Molecular Medicine (FIMM)

Founding Chief of the Analytic and Translational Genetic Unit (ATGU)

Massachusetts General Hospital

Associate Professor of Medicine at Harvard Medical School

Institute member, Broad Institute of MIT and Harvard

Dr. Mark Daly is Director of the Finnish Institute for Molecular Medicine (FIMM) at the University of Helsinki, Founding Chief of the Analytic and Translational Genetic Unit (ATGU) at Massachusetts General Hospital, Associate Professor of Medicine at Harvard Medical School, and Institute member of the Broad Institute of MIT and Harvard.

His research has historically focused on the development and application of statistical methods for the discovery and interpretation of genetic variation responsible for complex human disease and with the creation of the ATGU, he and other core faculty are focused on the interpretation of genome sequence and the use of genome information in clinical settings.  At the Broad, he is an Institute Member and Co-Director of the Program in Medical and Population Genetics, where he leads many large scale genome sequencing studies in autism and inflammatory bowel disease.

In February of 2018, he was appointed Director of the Institute of Molecular Medicine Finland (FIMM), and now divides his time between Helsinki and Boston, although he maintains his primary lab and affiliations in Boston. FIMM is a translational research institute with a focus on cancer, digital diagnostics, genetics and epidemiology and is the home of landmark efforts such as the FinnGen Project.

While developing computational and statistical methods that can be broadly applied, his group has several primary medical genetics research foci.  He has extensive research program in neuropsychiatric genetics - particularly in autism, schizophrenia and ADHD – and has led large-scale GWAS and exome sequencing efforts in this area.  His lab serves as an analytic hub for the Psychiatric GWAS Consortium, an international consortium leading the largest collaborative GWAS studies in 5 major psychiatric disorders.  He also has a longstanding effort in the mapping of genes for Crohn’s disease and ulcerative colitis where he helped found and lead an international effort that has identified more than 150 genetic risk factors and pursues the functional interpretation and clinical ramifications of these continued gene discovery efforts.  He is also co-PI of the gnomAD project and committed to ensuring the output of all ATGU genomic research is maximally accessible and useful to the clinical and research communities.

Dr. Daly has received many awards and was elected to the National Academy of Medicine in 2017. 

He studied physics at MIT, and although he initially wanted to become a lawyer or poker player, he joined Eric Lander’s lab at the Whitehead Institute as a freshman to do genetics research. He received his PhD in Human Genetics from Leiden University in 2004.

Recent Publications

Generalizability of proteomic risk prediction across biobanks reveals dependence on phenotype definitions

Published On 2026 Oct 10

Journal article

Advances in high-throughput proteomics technologies have enabled the assessment of dynamic health states across biobank-scale cohorts. Disease prediction models built on these data have higher accuracy than baseline clinical models for a broad range of diseases, and provide avenues to understand disease pathogenesis. However, the generalizability of these prediction models across cohorts has yet to be established at scale. Here, we train models for 15 diseases in the UK Biobank (UKB; n=53,026)...


A unified framework for local-ancestry-aware genetic association analysis across biobanks

Published On 2026 Oct 08

Journal article

Biobanks increasingly include individuals with admixed genomes, yet conventional genome-wide association study frameworks either exclude participants who cannot be confidently assigned to a discrete ancestry group or ignore ancestry-specific effects. We present FELIX, a scalable framework for local-ancestry-aware genetic analysis that retains all participants without requiring discrete ancestry assignment. FELIX combines a compact ancestry-resolved genotype representation (FELIXla) with an...