P. Donnelly

P. Donnelly, R. Ward, R. Bowden, 2006, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

Recombination and Population Structure in Salmonella enterica

P. Donnelly, C. Spencer, G. McVean, 2011, PLoS genetics.

An integrated map of genetic variation from 1,092 human genomes

Kenny Q. Ye, Mauricio O. Carneiro, Francisco M. De La Vega, 2012, Nature.

Common variants in the HLA-DRB1-HLA-DQA1 Class II region are associated with susceptibility to visceral leishmaniasis

M. Pirinen, P. Donnelly, C. Spencer, 2013, Nature Genetics.

Platypus and echidna genomes reveal mammalian biology and evolution

P. Donnelly, J. Korlach, A. Phillippy, 2021, Nature.

Insights into Platypus Population Structure and History from Whole-Genome Sequencing

P. Donnelly, R. Bowden, C. Moritz, 2017, bioRxiv.

Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility

Paul Weston, Robert Plomin, Elvira Bramon, 2011, Nature Genetics.

A genome-wide association study in Europeans and South Asians identifies five new loci for coronary artery disease

Mark I. McCarthy, Philippe Froguel, Paul Elliott, 2011, Nature Genetics.

Multiple rare alleles at LDLR and APOA5 confer risk for early-onset myocardial infarction

David M. Herrington, Adam Kiezun, Peter Donnelly, 2014, Nature.

Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data

Judy H. Cho, John P. Ferguson, G. Wainrib, 2019, Scientific Reports.

A Genome-wide Association Analysis of a Broad Psychosis Phenotype Identifies Three Loci for Further Investigation

M. Pirinen, P. Donnelly, C. Spencer, 2014, Biological Psychiatry.

Altering the Binding Properties of PRDM9 Partially Restores Fertility across the Species Boundary

P. Donnelly, S. Myers, Polinka Hernandez-Pliego, 2021, Molecular biology and evolution.

Factors influencing meiotic recombination revealed by whole-genome sequencing of single sperm

P. Donnelly, R. Hinch, R. Bowden, 2019, Science.

Re-engineering the zinc fingers of PRDM9 reverses hybrid sterility in mice

P. Donnelly, S. Myers, D. Biggs, 2016, Nature.

Multicohort analysis of the maternal age effect on recombination

P. Donnelly, Jared O'Connell, J. Marchini, 2015, Nature Communications.

Whole-genome sequencing of bladder cancers reveals somatic CDKN1A mutations and clinicopathological associations with mutation burden

Peter Donnelly, Gil McVean, Paolo Piazza, 2014, Nature Communications.

Coalescents and genealogical structure under neutrality.

P Donnelly, P. Donnelly, S. Tavaré, 1995, Annual review of genetics.

Assessing allele-specific expression across multiple tissues from RNA-seq read data

Matti Pirinen, Peter Donnelly, Mark I. McCarthy, 2015, Bioinform..

A polygenic resilience score moderates the genetic risk for schizophrenia

M. Pirinen, P. Donnelly, C. Spencer, 2019, Molecular Psychiatry.

Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke

M. Pirinen, P. Donnelly, C. Spencer, 2012, Nature Genetics.

Human recombination hot spots hidden in regions of strong marker association

Peter Donnelly, Simon Myers, P. Donnelly, 2005, Nature Genetics.

Experiments with the Site Frequency Spectrum

Kevin R. Thornton, P. Donnelly, G. McVean, 2011, Bulletin of mathematical biology.

The distribution and causes of meiotic recombination in the human genome.

P Donnelly, P. Donnelly, C. Spencer, 2006, Biochemical Society transactions.

Genomic Tools for Evolution and Conservation in the Chimpanzee: Pan troglodytes ellioti Is a Genetically Distinct Population

P. Donnelly, C. Freeman, S. Myers, 2012, PLoS genetics.

Genes, fossils and behaviour : an integrated approach to human evolution

Peter Donnelly, Robert A. Foley, P. Donnelly, 2001 .

Is Mate Choice in Humans MHC-Dependent?

P. Donnelly, R. Chaix, C. Cao, 2008, PLoS genetics.

A comparison of bayesian methods for haplotype reconstruction from population genotype data.

Peter Donnelly, Matthew Stephens, P. Donnelly, 2003, American journal of human genetics.

The role of ATM in response to metformin treatment and activation of AMPK.

P. Donnelly, C. Bellenguez, C. Palmer, 2012, Nature genetics.

Multiple rare alleles at LDLR and APOA5 confer risk for early-onset myocardial infarction

Andrew D. Johnson, C. Carlson, Dermot F. Reilly, 2014, Nature.

Choice of transcripts and software has a large effect on variant annotation

Jean-Baptiste Cazier, Kyle J. Gaulton, Peter Humburg, 2014, Genome Medicine.

University of Dundee Polymorphism in a lincRNA Associates with a Doubled Risk of Pneumococcal Bacteremia in Kenyan Children Rautanen,

Anne W. Ndungu, M. Pirinen, P. Donnelly, 2017 .

Genome-wide association study of intraocular pressure identifies the GLCCI1/ICA1 region as a glaucoma susceptibility locus

M. Pirinen, P. Donnelly, C. Spencer, 2013, Human molecular genetics.

A Bayesian Method for Detecting and Characterizing Allelic Heterogeneity and Boosting Signals in Genome-Wide Association Studies

Peter Donnelly, Niall Cardin, Jonathan Marchini, 2009, 1010.4670.

THE INAUGURAL EDITOR'S INVITED PAPER FOR 2002 ANCESTRAL INFERENCE IN POPULATION GENETICS MODELS WITH SELECTION

P. Donnelly, M. Stephens, 2003 .

Conditional genealogies and the age of a neutral mutant.

P. Donnelly, C. Wiuf, Peter Donnelly, 1999, Theoretical population biology.

Complement genes contribute sex-biased vulnerability in diverse illnesses

Simon C. Potter, Christopher W. Whelan, M. Pirinen, 2020, Nature.

A Genome-Wide Metabolic QTL Analysis in Europeans Implicates Two Loci Shaped by Recent Positive Selection

Peter Donnelly, Mark I. McCarthy, Kourosh R. Ahmadi, 2011, PLoS genetics.

A Greedy Homotopy Method for Regression with Nonconvex Constraints

Peter Donnelly, Fabian L. Wauthier, P. Donnelly, 2014, AISTATS.

Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett’s esophagus

Simon C. Potter, M. Pirinen, P. Donnelly, 2012, Nature Genetics.

Congenital myasthenic syndromes due to mutations in ALG2 and ALG14

Peter Donnelly, Nicola Carboni, Hanns Lochmüller, 2013, Brain : a journal of neurology.

Congenital myasthenic syndromes due to mutations in ALG 2 and ALG 14

P. Donnelly, D. Bentley, Jacqueline A Palace, 2013 .

Patterns of genetic differentiation and the footprints of historical migrations in the Iberian Peninsula

P. Donnelly, S. Myers, C. Bycroft, 2018, bioRxiv.

Germline mutations in the proofreading domains of POLE and POLD 1 predispose to colorectal adenomas and carcinomas

P. Donnelly, G. McVean, D. Bentley, 2022 .

Strong genetic evidence for a selective influence of GABAA receptors on a component of the bipolar disorder phenotype

P. Donnelly, D. Collier, D. Clair, 2008, Molecular Psychiatry.

Replicating genotype – phenotype associations What constitutes replication of a genotype – phenotype association , and how best can it be achieved ?

Peter Donnelly, Lon R. Cardon, Ellen M. Wijsman, 2007 .

Efficient computation with a linear mixed model on large-scale data sets with applications to genetic studies

Matti Pirinen, Peter Donnelly, Chris C. A. Spencer, 2012, 1207.4886.

Homozygous microdeletion of exon 5 in ZNF277 in a girl with specific language impairment

Peter Donnelly, Gillian Baird, Simon E Fisher, 2014, European Journal of Human Genetics.

Erythrocytosis associated with a novel missense mutation in the BPGM gene

Davis J. McCarthy, Lisa J. Murray, P. Donnelly, 2010, Haematologica.

High recombination rate in herpes simplex virus type 1 natural populations suggests significant co-infection.

P. Donnelly, R. Ward, R. Bowden, 2004, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

The transient behaviour of the Moran model in population genetics

Peter Donnelly, P. Donnelly, 1984, Mathematical Proceedings of the Cambridge Philosophical Society.

Application of Coalescent Methods to Reveal Fine-Scale Rate Variation and Recombination Hotspots

Peter Donnelly, Paul Fearnhead, Simon Myers, 2004, Genetics.

Quantifying the Underestimation of Relative Risks from Genome-Wide Association Studies

Peter Donnelly, Damjan Vukcevic, P. Donnelly, 2011, PLoS genetics.

Homozygous mutations in a predicted endonuclease are a novel cause of congenital dyserythropoietic anemia type I

Peter Donnelly, Gil McVean, Chris P. Ponting, 2013, Haematologica.

Microevolutionary analysis of Clostridium difficile genomes to investigate transmission

Daniel J. Wilson, P. J. Donnelly, P. Donnelly, 2012, Genome Biology.

Validation of an Integrated Risk Tool, Including Polygenic Risk Score, for Atherosclerotic Cardiovascular Disease in Multiple Ethnicities and Ancestries.

P. Donnelly, G. McVean, E. Ashley, 2021, The American journal of cardiology.

Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins

Matti Pirinen, David M. Herrington, Alex Doney, 2014, Nature Communications.

WEAK CONVERGENCE TO A MARKOV CHAIN WITH AN ENTRANCE BOUNDARY: ANCESTRAL PROCESSES IN POPULATION GENETICS'

Peter Donnelly, P. Donnelly, 1991 .

Heterogeneity of microsatellite mutations within and between loci, and implications for human demographic histories.

P Donnelly, P. Donnelly, A. Di Rienzo, 1998, Genetics.

Optimal sequencing strategies for surveying molecular genetic diversity.

P. Donnelly, A. Pluzhnikov, P. Donnelly, 1996, Genetics.

A robust clustering algorithm for identifying problematic samples in genome-wide association studies

Peter Donnelly, Amy Strange, Chris C. A. Spencer, 2011, Bioinform..

Disease Model Distortion in Association Studies

P. Donnelly, C. Spencer, Damjan Vukcevic, 2011, Genetic epidemiology.

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease

Peter Donnelly, Zamin Iqbal, Richard G. Everitt, 2012, Proceedings of the National Academy of Sciences.

Match probability calculations for multi-locus DNA profiles

P. Donnelly, 2005, Genetica.

Microsatellite mutations and inferences about human demography.

P Donnelly, P. Donnelly, A. Di Rienzo, 2000, Genetics.

Rare loss of function variants in candidate genes and risk of colorectal cancer

Taylor J. Maxwell, Jennifer G. Robinson, Andrew J. Sanford, 2018, Human Genetics.

The coalescent and its descendants

P. Donnelly, S. Leslie, 2010, 1006.1514.

Estimating the Age of the Common Ancestor of Men from the ZFY Intron

P. Donnelly, A. von Haeseler, S. Tavaré, 1996, Science.

Interpreting genetic variability: the effects of shared evolutionary history.

P. Donnelly, 1996, Ciba Foundation symposium.

Inference in Forensic Identification

Peter Donnelly, David J. Balding, P. Donnelly, 1995 .

Meta-analysis of genome-wide association studies identifies novel loci that influence cupping and the glaucomatous process

Adriana I. Iglesias, M. Pirinen, P. Donnelly, 2014, Nature Communications.

How convincing is DNA evidence?

Peter Donnelly, David J. Balding, P. Donnelly, 1994, Nature.

Genomic control to the extreme - Reply

P. Donnelly, L. Cardon, M. Phillips, 2004 .

Particle Representations for Measure-Valued Population Models

Peter Donnelly, Thomas G. Kurtz, P. Donnelly, 1999 .

Pairwise comparisons of mitochondrial DNA sequences in subdivided populations and implications for early human evolution.

P. Donnelly, P. Marjoram, P. Donnelly, 1994, Genetics.

The UK Biobank resource with deep phenotyping and genomic data

P. Donnelly, N. Allen, A. Young, 2018, Nature.

Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer

Peter Donnelly, Mark I. McCarthy, Nazneen Rahman, 2012, Nature.

Genome Sequencing of an Extended Series of NDM-Producing Klebsiella pneumoniae Isolates from Neonatal Infections in a Nepali Hospital Characterizes the Extent of Community- versus Hospital-Associated Transmission in an Endemic Setting

Daniel J. Wilson, A. J. Pollard, P. Donnelly, 2014, Antimicrobial Agents and Chemotherapy.

Identifying loci affecting trait variability and detecting interactions in genome-wide association studies

Fabian L. Wauthier, P. Donnelly, Alexander I. Young, 2018, Nature Genetics.

Continuity and weak convergence of ranked and size-biased permutations on the infinite simplex

Peter Donnelly, Paul Joyce, P. Donnelly, 1989 .

Weak Convergence of Population Genealogical Processes to the Coalescent with Ages

P. Donnelly, P. Joyce, 1992 .

Consistent ordered sampling distributions : characterization and convergence

P. Donnelly, P. Joyce, 1991 .

A genealogical approach to variable-population-size models in population genetics

P. Donnelly, 1986, Journal of Applied Probability.

Dual processes in population genetics

P. Donnelly, 1986 .

On the Functional Central Limit Theorem for the Ewens Sampling Formula

Peter Donnelly, Simon Tavaré, Thomas G. Kurtz, 1991 .

Modelling genes: mathematical and statistical challenges in genomics

P. Donnelly, 2006 .

Do Eve's alleles live on?

P. Donnelly, G. A. Watterson, 1992, Genetical research.

Consistent ordered sampling distributions: characterization and convergence

P. Donnelly, P. Joyce, 1991, Advances in Applied Probability.

The population genealogy of the infinitely-many neutral alleles model

P. Donnelly, S. Tavaré, 1987, Journal of mathematical biology.

The effect on genetic sampling distributions of correlations in reproduction

P. Donnelly, P. Marjoram, 1989 .

A genealogical description of the infinitely-many neutral alleles model

P. Donnelly, S. Tavaré, 1987 .

Likelihoods and simulation methods for a class of nonneutral population genetics models.

P Joyce, P Donnelly, P. Donnelly, 2001, Genetics.

People of the British Isles: preliminary analysis of genotypes and surnames in a UK-control population

P. Donnelly, D. Davison, T. Frayling, 2011, European Journal of Human Genetics.

The Wright-Fisher model with temporally varying selection and population size

P. Donnelly, N. Weber, 1985 .

An integrated polygenic and clinical risk tool enhances coronary artery disease prediction

Michael A Sivley, P. Donnelly, C. Spencer, 2020, medRxiv.

Assessing population structure and its effects on association studies in a genome wide SNP dataset.

P. Donnelly, J. Marchini, L. Cardon, 2002 .

Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

Taesung Park, Christian Gieger, Tien Yin Wong, 2017, Scientific Data.

Evaluating DNA profile evidence when the suspect is identified through a database search.

D J Balding, P Donnelly, P. Donnelly, 1996, Journal of forensic sciences.

The correlation between reading and mathematics ability at age twelve has a substantial genetic component

Matti Pirinen, Peter Donnelly, Robert Plomin, 2014, Nature Communications.

Discussion: Recent Common Ancestors of all Present-Day Individuals

P. Donnelly, M. Slatkin, J. Hein, 1999, Advances in Applied Probability.

Assessing association between protein truncating variants and quantitative traits

Matti Pirinen, Peter Donnelly, Mark I. McCarthy, 2013, Bioinform..

A point mutation in the ion conduction pore of AMPA receptor GRIA3 causes dramatically perturbed sleep patterns as well as intellectual disability

P. Donnelly, G. McVean, A. Bhomra, 2017, Human molecular genetics.

THE PROSECUTORS FALLACY AND DNA EVIDENCE

Peter Donnelly, Dj Balding, P. Donnelly, 1994 .

Identifying loci affecting trait variability and detecting interactions in genome-wide association studies

Fabian L. Wauthier, P. Donnelly, Alexander I. Young, 2018, Nature Genetics.

Zhou et al. reply

Peter Donnelly, Kaixin Zhou, P. Donnelly, 2012, Nature Genetics.

Alu insertion polymorphisms in humans: A review

P. Donnelly, M. Stoneking, M. Batzer, 2001 .

Gene-gene interactions in breast cancer susceptibility.

Deborah Hughes, Peter Donnelly, Jonathan Berg, 2012, Human molecular genetics.

A model-based approach to capture genetic variation for future association studies.

P. Donnelly, J. Marchini, G. McVean, 2006, Genome research.

CONSTANT PREDATOR-PREY RATIOS: AN ARITHMETICAL ARTIFACT?

Peter Donnelly, P. Donnelly, G. A. Watterson, 1993 .

Reply to Pembrey et al: ‘ZNF277 microdeletions, specific language impairment and the meiotic mismatch methylation (3M) hypothesis'

P. Donnelly, C. Francks, A. Pagnamenta, 2014, European Journal of Human Genetics.

Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility

Tanya M. Teslovich, Andrew D. Johnson, Kyle J. Gaulton, 2014 .

Genotyping and population characteristics of the China Kadoorie Biobank

Warren W. Kretzschmar, P. Donnelly, R. Collins, 2023, Cell genomics.

Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes

Tanya M. Teslovich, Andrew D. Johnson, Simon C. Potter, 2012, Nature Genetics.

Progress and promise in understanding the genetic basis of common diseases

P. Donnelly, C. Spencer, A. Price, 2015, Proceedings of the Royal Society B: Biological Sciences.

Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants.

P. Donnelly, C. Spencer, A. Silman, 2007, Nature genetics.

Genomic Dissection of Bipolar Disorder and Schizophrenia, Including 28 Subphenotypes.

John P. Rice, Simon C. Potter, Melissa J. Green, 2018, Cell.

A map of human genome variation from population-scale sequencing

P. Donnelly, R. Durbin, G. McVean, 2011, Nature.

Human metabolic profiles are stably controlled by genetic and environmental variation

P. Donnelly, T. Spector, M. McCarthy, 2011 .

APPROACH TO STATIONARITY OF THE BERNOULLI

P. Donnelly, A. Sudbury, Peter Lloyd, 1994 .

Genetic fine-mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci

Tanya M. Teslovich, Kyle J. Gaulton, Sara M. Willems, 2015, Nature Genetics.

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

M. Pirinen, P. Donnelly, C. Spencer, 2013, Nature Genetics.

Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region

Simon C. Potter, P. Donnelly, C. Spencer, 2009, Nature Genetics.

Genome-wide and fine-resolution association analysis of malaria in West Africa

P. Donnelly, P. Deloukas, J. Marchini, 2009, Nature Genetics.

Versus Hospital-associated Transmission in an Endemic Setting 3 4

Daniel J. Wilson, P. Donnelly, A. Kasarskis, 2014 .

Cross-ancestry genome-wide association analysis of corneal thickness strengthens link between complex and Mendelian eye diseases

Simon C. Potter, Adriana I. Iglesias, M. Pirinen, 2018, Nature Communications.

Schizophrenia genetic variants are not associated with intelligence

A F Terwisscha van Scheltinga, S C Bakker, N E M van Haren, 2013, Psychological Medicine.

Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants

P. Donnelly, C. Spencer, A. Silman, 2007, Nature Genetics.

A gene pathway analysis highlights the role of cellular adhesion molecules in multiple sclerosis susceptibility

Simon C. Potter, M. Pirinen, P. Donnelly, 2014, Genes and Immunity.

Molecular Systems Biology Peer Review Process File Human Metabolic Profiles Are Stably Controlled by Genetic and Environmental Variation Transaction Report

P. Donnelly, T. Spector, M. Rantalainen, 2022 .

A Genome-wide Association Analysis of a Broad Psychosis Phenotype Identifies Three Loci for Further Investigation

Simon C. Potter, M. Pirinen, P. Donnelly, 2014, Biological Psychiatry.

Schizophrenia genetic variants are not associated with intelligence

P. Donnelly, P. Visscher, H. Stefánsson, 2013, Psychological Medicine.

Genome-wide strategies for detecting multiple loci that influence complex diseases

P. Donnelly, J. Marchini, L. Cardon, 2005, Nature Genetics.

Multiple rare alleles at LDLR and APOA5 confer risk for early-onset myocardial infarction

Andrew D. Johnson, C. Carlson, Dermot F. Reilly, 2015 .

Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes

Tanya M. Teslovich, Andrew D. Johnson, Ross M. Fraser, 2012, Nature Genetics.

Dissection of the genetics of Parkinson ’ s disease identifies an additional association 5 ′ of SNCA and multiple associated haplotypes at 17 q 21 The UK Parkinson ’ s Disease

M. Pirinen, P. Donnelly, L. Peltonen, 2017 .

Particle representations for measure-valued population models 1 June 1 , 1998

P. Donnelly, T. Kurtz, 1998 .

A Fine-Scale Chimpanzee Genetic Map from Population Sequencing

P. Donnelly, A. Auton, G. McVean, 2012, Science.

HAPGEN2: simulation of multiple disease SNPs

P. Donnelly, J. Marchini, Z. Su, 2011, Bioinform..

A model-based approach to capture genetic variation for future Material Supplemental

P. Donnelly, J. Marchini, G. McVean, 2006 .

Genomic dissection of bipolar disorder and schizophrenia including 28 subphenotypes

Madeline, Melissa J. Green, Janice M. Fullerton, 2017 .

Making Sense of the Data

P. Donnelly, 2011, Science.