Publications
Exemplars from the Lab
Polygenic scores
Xu Y, ..., Inouye M. An atlas of genetic scores for multi-omic traits. Nature 2023.
ICDA PRS Task Force (Co-corresponding: Willer CJ*, Inouye M*). Towards responsible use of polygenic risk scores in the clinic: potential benefits, risks and gaps. Nature Medicine 2021.
Sun L, ..., Inouye M*, Di Angelantonio E*. Polygenic risk scores in cardiovascular risk prediction: a cohort study and modelling analyses. PLOS Medicine 2021.
Abraham G, ..., Inouye M*, Dichgans M*. Genomic risk score offers predictive performance comparable to clinical risk factors for ischaemic stroke. Nature Communications 2019.
Inouye M*, Abraham G*, ..., Samani NJ. Genomic risk prediction of coronary artery disease in 480,000 adults: Implications for primary prevention. Journal of the American College of Cardiology 2018.
Abraham G, ..., Ripatti S*, Inouye M*. Genomic prediction of coronary heart disease. European Heart Journal 2016.
Xu Y, ..., Inouye M. Machine learning optimized polygenic scores for blood cell traits stratify sex-specific trajectories and identify genetic correlations with disease. Cell Genomics 2022.
Abraham G, ..., Inouye M. Accurate and robust genomic prediction of celiac disease using statistical learning. PLoS Genetics 2014.
Abraham G, ..., Inouye M. Performance and robustness of penalized and unpenalized methods for genetic prediction of complex human disease. Genetic Epidemiology 2013.
Multi-omics
Ritchie SC, ..., Inouye M. Integrative analysis of the plasma proteome and polygenic risk of cardiometabolic diseases. Nature Metabolism 2021.
Foguet C, ..., Inouye M. Genetically personalised organ-specific metabolic models in health and disease. Nature Communications 2022.
Qin Y, ..., Inouye M*, Meric G*. Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort. Nature Genetics 2022.
Liu Y, ..., Inouye M. Early prediction of liver disease using conventional risk factors and gut microbiome-augmented gradient boosting. Cell Metabolism 2022.
Teo SM, ..., Inouye M. Airway microbiota dynamics identify a critical window for interplay of pathogenic bacteria and allergy in childhood respiratory disease. Cell Host & Microbe 2018.
Teo SM, ..., Holt KE*, Inouye M*. The infant airway microbiome impacts severity of lower respiratory infection and risk of asthma development. Cell Host & Microbe 2015.
Huang QQ, ..., Inouye M. Neonatal genetics of gene expression reveal the potential origins of autoimmune and allergic disease risk. Nature Communications 2020.
Ritchie SC, ..., Kettunen J*, Inouye M*. The biomarker GlycA is associated with chronic inflammation and predicts long-term risk of severe infection. Cell Systems 2015.
Methods & Tools
Lambert SA, ..., Inouye M. The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation. Nature Genetics 2021.
Wand H*, Lambert SA*, ..., Inouye M*, Wojcik GL*. Improving reporting standards for polygenic scores in risk prediction studies. Nature 2021.
Abraham G, Qiu Y, Inouye M. Flashpca2: Principal component analysis of biobank-scale genotype datasets. Bioinformatics 2017.
Ritchie SC, ..., Inouye M*. A scalable permutation approach reveals replication and preservation patterns of network modules in large datasets. Cell Systems 2016.
Inouye M, ..., Holt KE. SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Medicine 2014.
Lannelongue L*, Grealey J*, Inouye M. Green Algorithms: Quantifying the carbon emissions of computation. Advanced Science 2021.
Grealey J*, Lannelongue L*, ..., Inouye M. The carbon footprint of bioinformatics. Molecular Biology and Evolution 2022.
Pre-prints
Age-dependent topic modelling of comorbidities in UK Biobank identifies disease subtypes with differential genetic risk
Jiang X, Zhang M, Zhang Y, Inouye M, Holmes CC, Price A, McVean G
article pre-print
Using polygenic risk scores for prioritising individuals at greatest need of a CVD risk assessment
Chung R, Xu Z, Arnold M, Ip S, Harrison H, Barrett J, Pennells L, Kim LG, De Angelantonio, Paige E, Ritchie SC, Inouye M, Usher-Smith JA, Wood AM
article pre-print
Direct inference and control of genetic population structure from RNA sequencing data
Construction of in silico protein-protein interaction networks across different topologies using machine learning
Lannelongue L, Inouye M
article pre-print
Known allosteric proteins have central roles in genetic disease
Abrusan G, Ascher DB, Inouye M
article pre-print
The language of race, ethnicity, and ancestry in human genetic research
Birney E*, Inouye M*, Raff J*, Rutherford A*, Scally A*
article pre-print
Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity
Martino C, Kellman BP, Sandoval DR, Clausen TM, Marotz CA, Song SJ, Wandro S, Zaramela LS, Benitez RAS, Zhu Q, Armingol E, Vazquez-Baeza Y, McDonald R, Sorrentino JT, Taylor B, Belda-Ferre P, Liang C, Zhang Y, Schifanella L, Klatt NR, Huang S, Havulinna AS, Jousilahti P, Haiminien N, Parida L, Kim HC, Swafford AD, Zengler K, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Esko JD, Lewis NE, Knight R
article pre-print
Genome-wide association and Mendelian randomisation analysis prioritises bioactive metabolites with putative causal effects on common diseases
Qin Y, Meric G, Long T, Watrous JD, Burgess S, Havulinna AS, Ritchie SC, Brozynska M, Jousilahti P, Perola M, Lahti L, Niiranen T, Cheng S, Salomaa V, Jain M, Inouye M
article pre-print
Correcting index databases improves metagenomics studies
Meric G, Wick RR, Watts SC, Holt KE, Inouye M.
article pre-print index-databases scripts
FlashPCA: fast sparse canonical correlation analysis of genomic data
A scalable and efficient approach for explicit modeling of large multi-omic networks.
Abraham G, Kowalczyk A, and Inouye M
article pre-print pre-print-supplementary software
Exploratory analysis and error modeling of a sequencing technology
Inouye M, Small KS, Teo YY, Li H, Whiteford N, Skelly T, Abnizova I, Turner DJ, Deloukas P, Kwiatkowski DP, Brown CG, Clark TG.
All Publications
2023
An atlas of genetic scores to predict multi-omic traits
Xu Y, Ritchie SC, Liang Y, Timmers PRHJ, Pietzner M, Lannelongue L, Lambert SA, Tahir UA, May-Wilson S, Johansson A, Surendran P, Nath AP, Persyn E, Peters JE, Oliver-Williams C, Deng S, Prins B, Foguet C, Luan J, Bomba L, Soranzo N, Di Angelantonio E, Pirastu N, Tai ES, van Dam RM, Davenport EE, Paul DS, Yau C, Gerszten RE, Malarstig M, Danesh J, Sim X, Langenberg C, Wilson JF, Butterworth AS, Inouye M
Estrogen receptor α deficiency in cardiac myocytes reprograms the heart-derived extracellular vesicle proteome and induces obesity in female mice
Tham YT, Bernardo BC, Claridge B, Yildiz GS, Woon LML, Bond S, Fang H, Ooi JYY, Matsumoto A, Luo J, Tai CMK, Harmawan CA, Kiriazis H, Donner DG, Mellett NA, Abel ED, Khan SA, De Souza DP, Doomun SNE, Liu K, Xiang R, Singh M, Inouye M, Meikle PJ, Weeks KL, Drew BG, Greening DW, McMullen JR
Nature Cardiovascular Research 2023. doi:10.1038/s44161-023-00223-z. article
Carbon footprint estimation for computational research
Lannelongue L, Inouye M
Nature Reviews Methods Primers 2023. 3:9. article
African genomes hold the key to accurate genetic risk prediction
Fatumo S, Inouye M
Nature Human Behaviour 2023. doi:https://doi.org/10.1038/s41562-023-01549-1 article
The gut microbiome is a significant risk factor for future chronic lung disease
Quality control and removal of technical variation of NMR metabolic biomarker data in 120,000 UK Biobank participants
Ritchie SC, Surendran P, Karthikeyan S, Lambert SA, Bolton T, Pennells L, Danesh J, Di Angelantonio E, Butterworth AS, Inouye M
Scientific Data 2022. (accepted) article pre-print
2022
Assessing and removing the effect of unwanted technical variations in microbiome data
The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource
Sollis E, Mosaku A, Abid A, Buniello A, Cerezo M, Gil L, Groza T, Gunes O, Hall P, Hayhurst J, Ibrahim A, Ji Y, John S, Lewis E, MacArthur JAL, McMahon A, Osumi-Sutherland D, Panoutsopoulou K, Pendlington Z, Ramachandran S, Stefancsik R, Stewart J, Whetzel P, Wilson R, Hindorff L, Cunningham F, Lambert SA, Inouye M, Parkinson H, Harris LW.
Nucleic Acids Research 2022. doi:10.1093/nar/gkac1010 article
Genetically personalised organ-specific metabolic models in health and disease
Mild-to-moderate kidney dysfunction and cardiovascular disease: observational and Mendelian randomisation analyses
Gaziano L, Sun L, Arnold M, Bell S, Cho K, Kaptoge SK, Song RJ, Burgess S, Posner DC, Mosconi K, Robinson-Cohen C, Mason A, Bolton TR, Tao R, Allara E, Schubert P, Chen L, Staley JR, Staplin N, Altay S, Amiano P, Arndt V, Ärnlöv J, Barr ELM, Björkelund C, J Boer, Brenner H, Casiglia E, Chiodini P, Cooper JA, Coresh J, Cushman M, Dankner R, Davidson KW, de Jongh RT, Donfrancesco C, Engström G, Freisling H, Gómez de la Cámara A, Gudnason V, Hankey GJ, Hansson PO, Heath AK, Hoorn EJ, Imano H, Jassal SK, Kaaks R, Katzke V, Kauhanen J, Kiechl S, Koenig W, Kronmal RA, Kyrø C, Lawlor DA, Ljundberg B, MacDonald C, Masala G, Meisinger C, Melander O, Moreno Iribas C, Ninomiya T, Nitsch D, Nordestgaard BG, Onland-Moret C, Palmieri L, Dafina Petrova, Ramón Quirós Garcia J, Rosengren A, Sacerdote C, Sakurai M, Santiuste C, Schulze M, Sieri S, Sundström J, Tikhonoff V, Tjønneland A, Tong T, Tumino R, Tzoulaki I, van der Schouw YT, WM Verschuren, Völzke H, Wallace RB, S Goya Wannamethee, Weiderpass E, Willeit P, Woodward M, Yamagishi K, Zamora-Ros R, Akwo EA, Pyarajan S, Gagnon DR, Tsao PT, Muralidhar S, Edwards TL, Damrauer SM, Joseph J, Pennells L, Wilson PWF, Harrison S, Gaziano TA, Inouye M, Baigent C, Casas JP, Langenberg C, Wareham N, Riboli E, Gaziano JM, Danesh J, Hung AM, Butterworth AS, Wood AM, Di Angelantonio E
Circulation 2022. doi:10.1161/CIRCULATIONAHA.122.060700. article
Transferability of genetic loci and polygenic scores for cardiometabolic traits in British Pakistanis and Bangladeshis
New cardiovascular risk assessment techniques for primary prevention
Verma KP, Inouye M, Meikle P, Nicholls SJ, Carrington MJ, Marwick TH
Journal of the American College of Cardiology 2022. 80:373–387. article
Neurocognitive trajectory and proteomic signature of inherited risk for Alzheimer's disease
Paranjpe MD, Chaffin M, Zahid S, Ritchie SC, Rotter JI, Rich SS, Gerszten R, Guo X, Heckbert S, Tracy R, Danesh J, Lander ES, Inouye M, Kathiresan S, Butterworth AS, Khera AV
PLOS Genetics 2022. 18(9): e1010294. https://doi.org/10.1371/journal.pgen.1010294. article
Stroke genetics informs drug discovery and risk prediction across ancestries
Early prediction of liver disease using conventional risk factors and gut microbiome-augmented gradient boosting
Sex-specific survival bias and interaction modeling in coronary artery disease risk prediction
The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis
CRyPTIC Consortium, Seq&Treat Consortium
Lancet Microbe 2022. DOI:https://doi.org/10.1016/S2666-5247(21)00301-3 article
Polygenic scores in biomedical research
Kullo IJ, Lewis CM, Inouye M, Martin AR, Ripatti S, Chatterjee N
Nature Reviews Genetics 2022. doi:https://doi.org/10.1038/s41576-022-00470-z. article
The carbon footprint of bioinformatics
Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort
Qin Y, Havulinna AS, Liu Y, Jousilahti P, Ritchie SC, Tokolyi A, Sanders JG, Valsta L, Brozynska M, Zhu Q, Tripathi A, Vazquez-Baeza Y, Loomba R, Cheng S, Jain M, Niiranen T, Lahti L, Knight R, Salomaa V, Inouye M*, Meric G*
Nature Genetics 2022. doi:https://doi.org/10.1038/s41588-021-00991-z. article pre-print
Machine learning optimized polygenic scores for blood cell traits stratify sex-specific trajectories and identify genetic correlations with disease
Depression and genetic susceptibility to cardiometabolic diseases
Ritchie SC, Inouye M
Nature Cardiovascular Research 2022. doi:10.1038/s44161-021-00012-6. article
Comprehensive genetic analysis of the human lipidome identifies novel loci controlling lipid homeostasis with links to coronary artery disease
Cadby G, Giles C, Melton PE, Huynh K, Mellett NA, Duong T, Nguyen A, Cinel M, Smith A, Olshansky G, Wang T, Brozynska M, Inouye M, McCarthy NS, Ariff A, Hung J, Hui J, Beilby J, Dubé MP, Watts GF, Shah S, Wray NR, Lim WLF, Chatterjee P, Martins I, Laws SM, Porter T, Vacher M, Bush AI, Rowe CC, Villemagne VL, Ames D, Masters CL, Taddei K, Arnold M, Kastenmüller G, Nho K, Saykin AJ, Han X, Kaddurah-Daouk R, Martins RN, Blangero J, Meikle PJ, Moses EJ
Use of Coronary Computed Tomography or Polygenic Risk Scores to Prompt Action to Reduce Coronary Artery Disease Risk: The CAPAR-CAD Trial
Verma K, Marwick T, Duarte C, Meikle P, Inouye M, Carrington MJ
American Heart Journal 2022. doi:https://doi.org/10.1016/j.ahj.2022.02.007. article
Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy
Zhu Q, Huang S, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vázquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Belda-Ferre P, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Kim HC, Jain M, Inouye M, Gilbert JA, Knight R
mSystems 2022. DOI:https://doi.org/10.1128/msystems.00167-22. article pre-print
Substantial fat loss in physique competitors is characterized by increased levels of bile acids, very-long chain fatty acids, and oxylipins
Sarin VS, Hulmi JJ, Qin Y, INOUYE M, Ritchie SC, Cheng S, Watrous JD, Nguyen TTC, Lee JH, Jin Z, Terwilliger JD, Niiranen T, Havulinna A, Salomaa V, Pietiläinen KH, Isola V, Ahtiainen JP, Häkkinen K, Jain M, Perola M
Metabolites 2022. 12(10):928. article
A plasma metabolite score of three eicosanoids predicts incident type 2 diabetes – a prospective study in three independent cohorts
Gut microbiome composition is predictive of incident type 2 diabetes
2021
Genomic risk prediction of coronary artery disease in women with breast cancer: a prospective cohort study
Liou L, Kaptoge S, Dennis J, Shah M, Tyrer J, Inouye M, Easton DF, Pharoah PDP
Breast Cancer Research 2021. 23:94. article
Towards responsible use of polygenic risk scores in the clinic: potential benefits, risks and gaps
Polygenic Risk Score Task Force of the International Common Disease Alliance, Adeyemo A, Balaconis MK, Darnes DR, Fatumo S, Granados Moreno P, Hodonsky CJ, Inouye M, Kanai M, Kato K, Knoppers BM, Lewis ACF, Martin AR, McCarthy MI, Meyer MN, Okada Y, Richards JB, Richter L, Ripatti S, Rotimi CN, Sanderson SC, Sturm AC, Verdugo RA, Widen E, Willer CJ, Wojcik GL & Zhou A (Co-corresponding: Willer CJ*, Inouye M*)
Nature Medicine 2021. DOI:10.1038/s41591-021-01549-6. article
Integrative analysis of the plasma proteome and polygenic risk of cardiometabolic diseases
Ritchie SC, Lambert SA, Arnold M, Teo SM, Lim S, Scepanovic P, Marten J, Zahid S, Chaffin M, Liu Y, Abraham G, Ouwehand WH, Roberts DJ, Watkins NA, Drew B, Calkin AC, Di Angelantonio E, Soranzo N, Burgess S, Chapman M, Kathiresan S, Khera AV, Danesh J, Butterworth AS, Inouye M
Nature Metabolism 2021. https://doi.org/10.1038/s42255-021-00478-5. article pre-print
SFPhD: efficient computation of Faith’s phylogenetic diversity with applications in characterizing microbiomes
Armstrong G, Cantrell K, Huang S, McDonald D, Haiminen N, Carrieri AP, Zhu Q, Gonzalez A, McGrath I, Beck KL, Hakim D, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Jain M, Inouye M, Swafford AD, Kim HC, Parida L, Vázquez-Baeza Y, Knight R.
Genome Research 2021. DOI:10.1101/gr.275777.121. article
Risk prediction using polygenic risk scores for prevention of stroke and other cardiovascular diseases
Prognostic Value of a Polygenic Risk Score for Coronary Heart Disease in Individuals Aged 70 Years and Older
Predictive performance of a polygenic risk score for incident ischemic stroke in a healthy older population
Neumann JT, Riaz M, Bakshi A, Polekhina G, Thao LLP, Nelson MR, Woods RL, Abraham G, Inouye M, Reid CM, Tonkin AM, Williamson JD, Donnan GA, Brodtmann A, Cloud GC, McNeil JJ, Lacaze P
Stroke 2021. https://doi.org/10.1161/STROKEAHA.120.033670 article
Polygenic risk scores in cardiovascular risk prediction: a cohort study and modelling analyses
Sun L, Pennells L, Kaptoge S, Nelson CP, Ritchie SC, Abraham G, Arnold M, Bell S, Bolton T, Burgess S, Dudbridge F, Sofianopoulou E, Stevens D, Thompson JR, Butterworth AS, Wood A, Danesh J, Samani NJ, Inouye M*, Di Angelantonio E*
PLOS Medicine 2021. doi:https://doi.org/10.1371/journal.pmed.1003498. article pre-print integrated-risk-model
The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation
Improving reporting standards for polygenic scores in risk prediction studies
Wand H*, Lambert SA*, Tamburro C, Iacocca MA, O'Sullivan JW, Sillari C, Kullo IJ, Rowley R, Brockman D, Venner E, McCarthy MI, Antoniou AC, Easton DF, Hegele RA, Khera AV, Chatterjee N, Kooperberg C, Edwards K, Vlessis KR, Kinnear K, Danesh JN, Parkinson H, Ramos EM, Roberts MC, Ormond KE, Khoury MJ, Janssens ACJW, Goddard KAB, Kraft P, MacArthur JAL, Inouye M*, Wojcik GL*
Green Algorithms: Quantifying the carbon emissions of computation
Lannelongue L*, Grealey J*, Inouye M
Advanced Science 2021. https://doi.org/10.1002/advs.202100707. article pre-print emissions calculator
10 simple rules to make your computing more environmentally sustainable
Lannelongue L, Grealey J, Bateman AG, Inouye M
PLOS Computational Biology 2021. DOI:10.1371/journal.pcbi.1009324. article
Taxonomic signatures of cause-specific mortality risk in human gut microbiota
The intersection of genetics, environment and microbiota in asthma: Perspectives and challenges
Tang HHF, Teo SM, Sly PD, Holt PG, Inouye M
Journal of Allergy and Clinical Immunology 2021. 147:781-93.. article
Associations of healthy food choices with gut microbiota profiles
Koponen KK, Salosensaari A, Ruuskanen MO, Havulinna AS, Mannisto S, Jousilhati P, Palmu J, Salido R, Sanders K, Brennan C, Humphrey GC, Sanders JG, Meric G, Cheng S, Inouye M, Jain M, Niiranen T, Valsta LM, Knight R, Salomaa V
American Journal of Clinical Nutrition 2021. https://doi.org/10.1093/ajcn/nqab077. article
Links between gut microbiome composition and fatty liver disease in a large population sample
A Versatile Big Data Health System for Australia: Driving Improvements in Cardiovascular Health
Paige E, Doyle K, Jorm L, Banks E, Hsu MP, Nedkoff L, Briffa T, Cadilhac DA, Mahoney R, Verjans JW, Dwivedi G, Inouye M, Figtree GA
Heart, Lung and Circulation 2021. https://doi.org/10.1016/j.hlc.2021.04.023 article
Loss of the Long Non-coding RNA OIP5-AS1 Exacerbates Heart Failure in a Sex-Specific Manner
Zhuang A, Calkin AC, Lau S, Kiriazis H, Donner DG, Liu Y, Bond ST, Moody SC, Gould EAM, Colgan TD, Carmona SR, Inouye M, de Aguiar Vallim TQ, Tarling EJ, Quaife-Ryan GA, Hudson JE, Porrello ER, Gregorevic P, Gao XM, Du XJ, McMullen JR, Drew BG
iScience 2021. https://doi.org/10.1016/j.isci.2021.102537 article
Deletion of Trim28 in Committed Adipocytes Promotes Obesity but Preserves Glucose Tolerance
Bond S, King E, Henstridge D, Tran A, Moody S, Yang C, Liu Y, Mellett N, Nath AP, Inouye M, Tarling E, Vallim T, Meikle P, Calkin A, Drew B
Nature Communications 2021. 12:74. article
Workshop proceedings: GWAS summary statistics standards and sharing
MacArthur JAL, Buniello A, Harris LW, Hayhurst J, McMahon A, Sollis E, Cerezo M, Hall P, Whetzel PL, Bahcall O, Barroso I, Carroll RJ, Inouye M, Manolio TA, Rich SS, Hindorff LA, Wiley K, Parkinson H
Cell Genomics 2021. https://doi.org/10.1016/j.xgen.2021.100004 article
2020
Development patterns in the nasopharyngeal microbiome during infancy are associated with asthma risk
Tang HHF, Lang A, Teo SM, Judd LM, Gangnon R, Evans MD, Lee KE, Vrtis R, Holt PG, Lemanske RF, Jackson DJ, Holt KE, Inouye M, Gern JE
Journal of Allergy and Clinical Immunology 2020. DOI:https://doi.org/10.1016/j.jaci.2020.10.009. article
The polygenic and monogenic basis of blood cell traits and diseases
Vuckovic D, Bao EL, Akbari P, Lareau CA, Mousas A, Jiang T, Chen MH, Raffield LM, Tardaguila M, Huffman JE, Ritchie SC, Megy K, Ponsting H, Penkett CJ, Albers PK, Wigdor EM, Sakaue S, Moscati A, Manansala R, Lo KS, Qian H, Akiyama M, Bartz TM, Ben-Shlomo Y, Beswick A, Bork-Jensen J, Bottinger EP, Brody JA, van Rooij FJA, Chitrala KN, Cho K, Choquet H, Correa A, Danesh J, De Angelantonio E, Dimou N, Ding J, Elliott P, Esko T, Evans MK, Felix SB, Floyd JS, Broer L, Grarup N, Guo MH, Greinacher A, Haessler J, Hansen T, Howson JMM, Huang W, Jorgenson E, Kacprowski T, Kahonen M, Kamatani Y, Kanai M, Karthikeyan S, Koskeridis F, Lange LA, Lehtimaki T, Linneberg A, Liu Y, Lyytikainen LP, Manichaikul A, Matsuda K, Mohlke KL, Mononen N, Murakami Y, Nadkami GH, Nikus K, Pankratz N, Pedersen O, Preuss M, Psaty BM, Raitiakari OT, Rich SS, Rodriguez BAT, Rosen JD, Rotter JI, Schubert P, Spracklen CN, Surendran P, Tang H, Tardif JC, Ghanbari M, Volker U, Volzke H, Watkins NA, Weiss S, Cai N, Kundu K, Watt SB, Walter K, Zonderman AB, Wilson PWF, Li Y, Loos RJF, Knight J, Georges M, Stegle O, Evangelou E, Okada Y, Roberts DJ, Inouye M, Johnson AD, Auer PL, Astle WJ, Reiner AP, Butterworth AS, Ouwehand WH, Lettre G, Sankaran VG, Soranzo N
Genomic risk scores for juvenile idiopathic arthritis and its subtypes
GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure
Neonatal genetics of gene expression reveal the potential origins of autoimmune and allergic disease risk
Validation of a genome-wide polygenic score for coronary artery disease in South Asians
Wang M, Menon R, Mishra S, Patel AP, Chaffin M, Deepak T, Deshmukh M, Mathew O, Apte S, Devanboo CS, Sundaram S, Samson PL, Murugan S, Sharma KK, Karthikeyan R, Santhosh S, Rajesh T, Ahamed H, Balegadde AV, Alexander T, Swaminathan K, Gupta R, Mullasari AS, Sigamani A, Kanchi M, Peterson AS, Butterworth AS, Danesh J, Di Angelantonio E, Naheed A, Inouye M, Chowdhury R, Ramprasad VL, Kathiresan S, Gupta R, Khera AV
Journal of the American College of Cardiology 2020. 76(6):703-714. article
Eicosanoid inflammatory mediators are robustly associated with blood pressure in the general population
Association between the gut microbiota and blood pressure in a population cohort of 6953 individuals
Palmu J, Salosensaari A, Havulinna A, Cheng S, Inouye M, Jain M, Salido R, Sanders K, Brennan C, Humphrey G, Sanders J, Vartiainen E, Laatikainen T, Jousilahti P, Salomaa V, Knight R, Lahti L, and Niiranen T
Journal of the American Heart Association 2020. 9(15):e016641. article
Luminal Microbiota related to Crohn’s disease recurrence after surgery
Hamilton AL, Kamm MA, Cruz PD, Wright EK, Feng H, Wagner J, Sung JJY, Kirkwood CD, Inouye M, Teo SM.
Gut Microbes 2020. https://doi.org/10.1080/19490976.2020.1778262. article
Reference exome data for Australian Aboriginal populations to support health-based research
Weeks AL, D’Antoine HA, McKinnon M, Syn G, Bessarab D, Brown N, Tong SYC, Reményi B, Steer A, Gray LA, Inouye M, Carapetis JR, Blackwell JM, Lassmann T
Scientific Data 2020. 7:129. article
2019
Genomic risk score offers predictive performance comparable to clinical risk factors for ischaemic stroke
Systems biology and big data in asthma and allergy: recent discoveries and emerging challenges
Elevated alpha-1 antitrypsin is a major component of GlycA-associated risk for future morbidity and mortality
Multivariate genome-wide association analysis of a cytokine network reveals variants with widespread immune, haematological and cardiometabolic pleiotropy
Nath AP, Ritchie SC, Grinberg NF, Tang HHF, Huang QQ, Teo SM, Ahola-Olli AV, Würtz P, Havulinna AS, Aalto K, Pitkänen N, Lehtimäki T, Kähönen M, Lyytikäinen LP, Raitoharju E, Seppälä I, Sarin AP, Ripatti S, Palotie A, Perola M, Viikari JS, Jalkanen S, Maksimow M, Salmi M, Wallace C, , Raitakari OT, Salomaa V, Abraham G, Kettunen J, Inouye M.
American Journal of Human Genetics 2019. 105(6):1076-90. article pre-print
Towards clinical utility of polygenic risk scores
Gene regulatory networks to explain coronary artery disease susceptibility
Inouye M, Lannelongue L
Journal of the American College of Cardiology 2019. 73:23. article
Acute effects of active breaks during prolonged sitting on subcutaneous adipose tissue gene expression: an ancillary analysis of a randomized controlled trial
Grace M, Formosa M, Bozaoglu K, Bergouignan A, Brozynska M, Carey A, Veiga C, Sethi P, Dillon F, Bertovic D, Inouye M, Owen N, Dunstan D, Kingwell B
Scientific Reports 2019. in press. article
Comparative analysis reveals a role of TGF-β in shaping the residency-related transcriptional signature in tissue-resident memory CD8+ T cells
Nath AP*, Braun A*, Ritchie SC, Carbone FR, MacKay L, Gebhardt T*, Inouye M*.
PLoS ONE 2019. 14(2): e0210495. article
2018
Genomic risk prediction of coronary artery disease in 480,000 adults: Implications for primary prevention
Inouye M*, Abraham G*, Nelson CP, Wood AM, Sweeting MJ, Dudbridge F, Lai FY, Kaptoge S, Brozynska M, Wang T, Ye S, Webb TR, Rutter MK, Tzoulaki I, Patel RS, Loos RJF, Keavney B, Hemingway H, Thompson J, Watkins H, Deloukas P, Di Angelantonio E, Butterworth AS, Danesh J, Samani NJ* for The UK Biobank CardioMetabolic Consortium CHD Working Group
Journal of the American College of Cardiology 2018. 72(16):1883-93. article pre-print metaGRS
Trajectories of childhood immune development and respiratory health relevant to asthma and allergy
Biomarker glycoprotein acetyls is associated with the risk of a wide spectrum of incident diseases and stratifies mortality risk in angiography patients
Power, false discovery rate and Winner's Curse in eQTL studies
Identification of expression quantitative trait loci associated with schizophrenia and affective disorders in normal brain tissue
Airway microbiota dynamics identify a critical window for interplay of pathogenic bacteria and allergy in childhood respiratory disease
FastSpar: Rapid and scalable correlation estimation for compositional data
Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam
Genome-wide association studies and risk scores for coronary artery disease: Sex biases
Byars SG, Inouye M
Adv Exp Med Biol 2018. 1065:627-642. article
2017
A genome-wide association study of genetic risk factors for rheumatic heart disease in Aboriginal Australians provides support for pathogenic molecular mimicry
Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy
Flashpca2: Principal component analysis of biobank-scale genotype datasets
Experimental and human evidence for Lipocalin-2 (NGAL) in the development of cardiac hypertrophy and failure
Marques FZ, Prestes PR, Byars SG, Ritchie SC, Wurtz P, Patel SK, Booth SA, Rana I, Minoda Y, Berzins SP, Curl C, Bell JR, Wai B, Srivastava PM, Kangas AJ, Soininen P, Ruohonen S, Kahonen M, Lehtimaki T, Raitoharju E, Havulinna A, Perola M, Raitakari O, Salomaa V, Ala-Korpela M, Kettunen J, McGlynn M, Kelly J, Wlodek ME, Lewandowski PA, Delbridge LM, Burrell LM, Inouye M*, Harrap SB*, Charchar FJ*.
Journal of the American Heart Association 2017. 6:e005971. article
An interaction map of circulating metabolites, immune gene networks and their genetic regulation
Nath AP, Ritchie SC, Byars SG, Fearnley LG, Havulinna AS, Joensuu A, Kangas AJ, Soininen P, Wennerstrom A, Milani L, Metspalu A, Mannisto S, Wurtz P, Kettunen J, Raitoharju E, Kahonen M, Juonala M, Palotie A, Ala-Korpela M, Ripatti S, Lehtimaki T, Abraham G, Raitakari O, Salomaa V, Perola M, Inouye M.
An exposome perspective: Early life events and immune development in a changing world
Renz H, Holt PG, Inouye M, Logan A, Prescott S, Sly PD
Journal of Allergy and Clinical Immunology 2017. 140(1):24-40. article
Interactions within the MHC contribute to the genetic architecture of celiac disease
Metabolomics in cardiovascular research
Salomaa V, Inouye M
Encyclopedia of Cardiovascular Research and Medicine 2017. Elsevier ISBN: 9780128096574.
2016
Mergeomics: Integration of diverse genomics resources to identify pathogenic perturbations to biological systems
Genomic prediction of coronary heart disease
Abraham G, Havulinna AS, Bhalala OG, Byars SG, De Livera AM, Yetukuri L, Tikkanen E, Perola M, Schunkert H, Sijbrands EJ, Palotie A, Samani NJ, Salomaa V, Ripatti S*, Inouye M*
European Heart Journal 2016. 37(43):3267-3278. article pre-print predictive_model
A scalable permutation approach reveals replication and preservation patterns of network modules in large datasets
In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages
Microbial factors associated with post-operative Crohn's disease recurrence
Wright EK, Kamm MA, Wagner J, Teo SM, De Cruz P, Hamilton AL, Ritchie KJ, Inouye M*, Kirkwood CD*
Journal of Crohn's and Colitis 2016. jjw136. article
Metabolomics in epidemiology: From metabolite concentrations to integrative reaction networks
Fearnley LG, Inouye M
International Journal of Epidemiology 2016. dyw046. article
Vitamin D over the first decade and susceptibility to childhood allergy and asthma
Hollams EM, Teo SM, Kusel M, Holt BJ, Holt KE, Inouye M, de Klerk NH, Zhang G, Sly PD, Hart PH, Holt PG.
Journal of Allergy and Clinical Immunology 2016. 139(2):472-81. article
2015
Recovery from severe H7N9 disease is associated with diverse response mechanisms dominated by CD8+ T cells.
Wang Z, Wan Y, Qiu C, Zhu Z, Quinones-Parra S, Loh L, Ren Y, Hu Y, Zhang X, Inouye M, Doherty PC, Kedzierska K, Xu J.
Nature Communications 2015. 6:6833. article
The biomarker GlycA is associated with chronic inflammation and predicts long-term risk of severe infection
Ritchie SC, Würtz P, Nath AP, Abraham G, Havulinna AS, Fearnley LG, Sarin AP, Kangas AJ, Soininen P, Aalto K, Seppälä I, Raitoharju E, Salmi M, Maksimow M, Männistö S, Kähönen M, Juonala M, Ripatti S, Lehtimäki T, Jalkanen S, Perola M, Raitakari O, Salomaa V, Ala-Korpela M, Kettunen J*, Inouye M*
Recent advances in characterizing the gastrointestinal microbiome in Crohn's disease: A systematic review
Wright EK, Kamm MA, Teo SM, Inouye M, Wagner J, Kirkwood C
Inflammatory Bowel Disease 2015. 21(6):1219-28. article
Genomic prediction of celiac disease targeting HLA-positive individuals
The infant airway microbiome impacts severity of lower respiratory infection and risk of asthma development
Transcriptional profiling of mouse B cell terminal differentiation defines a signature of antibody-secreting plasma cells
Shi W, Liao Y, Willis SN, Taubenheim N, Inouye M, Tarlinton DM, Smyth GK, Hodgkin PD, Nutt SL, Corcoran LM
Nature Immunology 2015. 16(6):663-73. article
Genomic risk prediction of complex human disease and its clinical application
Abraham G and Inouye M
Current Opinion in Genetics & Development 2015. 33:10-16. article
Post-infectious group A streptococcal autoimmune syndromes and the heart
Martin WJ, Steer AC, Smeesters PR, Keeble J, Inouye M, Carapetis JR, Wicks IP
Autoimmunity Reviews 2015. 14(8):710-725. article
High performance computing enabling exhaustive analysis of higher order single nucleotide polymorphism interaction in genome wide association studies
Goudey B, Abedini M, Hopper JL, Inouye M, Makalic E, Schmidt DF, Wagner J, Zhou Z, Zobel J, Reumann M
Health Information Science and Systems. 2015 Feb 24;3:S3 article
2014
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
Distribution and Medical Impact of Loss-of-Function Variants in the Finnish Founder Population
Lim ET, Würtz P, Havulinna AS, Palta P, Tukiainen T, Rehnström K, Esko T, Mägi R, Inouye M, Lappalainen T, Sim X, Manning A, Ladenvall C, Bumpstead S, Hämäläinen E, Aalto K, Maksimow M, Salmi M, Blankenberg S, Ardissino D, Shah S, Horne B, McPherson R, Hovingh GK, Reilly MP, Watkins H, Goel A, Farrall M, Girelli D, Reiner AP, Stitziel NO, Kathiresan S, Gabriel S, Barrett JC, Lehtimäki T, Laakso M, Groop L, Kaprio J, Perola M, McCarthy MI, Boehnke M, Altshuler DM, Lindgren CM, Hirschhorn JN, Metspalu A, Freimer NB, Zeller T, Jalkanen S, Koskinen S, Raitakari OT, Durbin R, MacArthur DG, Salomaa V, Ripatti S, Daly MJ, Palotie A, for the Sequencing Initiative Suomi (SISu) Project.
PLoS Genetics 2014 10(7):e1004494. article
Elucidation of pathways in asthma pathogenesis: Development of a systems-level analytic strategy
Walker ML, Holt KE, Anderson GP, Teo SM, Sly P, Holt PG, Inouye M
Frontiers in Immunology 2014. 5:447. article
Accurate and robust genomic prediction of celiac disease using statistical learning
Abraham G, Tye-Din JA, Bhalala OG, Kowalczyk A, Zobel J, Inouye M
PLoS Genetics 2014. 10(2): e1004137. article pre-print predictive_model
The transcription factors IRF8 and PU.1 negatively regulate plasma cell differentiation
Carotta S, Willis SN, Hasbold J, Inouye M, Pang SHM, Emslie D, Light A, Chopin M, Shi W, Wang H, Morse HC, Tarlinton DM, Corcoran LM, Hodgkin PD, Nutt SL.
Journal of Experimental Medicine 2014. 211(11):2169-81. article
Fast principal component analysis of large-scale genome-wide data
Towards a molecular systems model of coronary artery disease.
2013
The development pathway for CD103+CD8+ tissue-resident memory T cells (Trm) of skin
MacKay L, Rahimpour A, Ma JZ, Collins N, Stock AT, Hafon ML, Vega-Ramos J, Lauzurica P, Stefanovic T, Tscharke D, Heath WR, Inouye M, Carbone F, Gebhardt T.
Nature Immunology 2013 14(12):1294-301. article
Performance and robustness of penalized and unpenalized methods for genetic prediction of complex human disease
Abraham G, Kowalczyk A, Zobel J, Inouye M
Genetic Epidemiology 2013. 37(2):184-95. article
Meta-Analysis of genome-wide association studies in 5 cohorts reveals common variants in RBFOX1, a regulator of tissue-specific splicing, associated with refractive error
Stambolian D, Wojciechowski R, Oexle K, Pirastu M, Li X, Raffel L, Cotch MF, Chew E, Klein BEK, Klein R, Wong TY, Simpson CL, Klaver CCW, van Duijn CM, Verhoeven VJM, Baird PN, Vitart V, Paterson AD, Mitchell P, Saw SM, Fossarello M, Kazmierkiewicz K, Murgia F, Portas L, Schache M, Richardson AJ, Xie J, Wang JJ, Rochtchina E, DCCT/EDIC Research Group, Viswanathan AC, Hayward C, Wright A, Polasek O, Campbell H, Rudan I, Oostra BA, Uitterlinden AG, Hofman A, Rivadeneira F, Amin A, Karssen LC, Vingerling J, Hosseini SM, DoringA, Bettecken T, Vatavuk Z, Gieger C, Wichmann HE, Wilson JF, Fleck B, Foster PJ, Topouzis F, McGuffin P, Sim X, Inouye M, Holliday EG, Attia J, Scott RJ,, Rotter JI, Meitinger T, Bailey-Wilson JE.
Human Molecular Genetics. 2013 22(13): 2754-2764. article
GWIS - Model-free, fast and exhaustive search for epistatic interactions in GWAS data
Look, no hands! Spectral biomarkers from genetic association studies
Inouye M and Abraham G
Genome Medicine 2013. 5:14. article
Insights into the genetic architecture of early stage age-related macular degeneration: a genome-wide association study meta-analysis
Holliday EG, Smith AV, Cornes BK, Buitendijk GH, Jensen RA, Sim X, Aspelund T, Aung T, Baird PN, Boerwinkle E, Cheng CY, van Duijn CM, Eiriksdottir G, Gudnason V, Harris T, Hewitt AW, Inouye M, Jonasson F, Klein BE, Launer L, Li X, Liew G, Lumley T, McElduff P, McKnight B, Mitchell P, Psaty BM, Rochtchina E, Rotter JI, Scott RJ, Tay W, Taylor K, Teo YY, Uitterlinden AG, Viswanathan A, Xie S; Wellcome Trust Case Control Consortium 2, Vingerling JR, Klaver CC, Tai ES, Siscovick D, Klein R, Cotch MF, Wong TY, Attia J, Wang JJ.
PLoS ONE. 2013 8(1):e53830. article
Genetic Loci for retinal arteriolar microcirculation
Sim X, Jensen RA, Ikram MK, Cotch MF, Li X, Macgregor S, Xie J, Smith AV, Boerwinkle E, Mitchell P, Klein R, Klein BE, Glazer NL, Lumley T, McKnight B, Psaty BM, de Jong PT, Hofman A, Rivadeneira F, Uitterlinden AG, van Duijn CM, Aspelund T, Eiriksdottir G, Harris TB, Jonasson F, Launer LJ; Wellcome Trust Case Control Consortium 2, Attia J, Baird PN, Harrap S, Holliday EG, Inouye M, Rochtchina E, Scott RJ, Viswanathan A; Global BPGen Consortium, Li G, Smith NL, Wiggins KL, Kuo JZ, Taylor KD, Hewitt AW, Martin NG, Montgomery GW, Sun C, Young TL, Mackey DA, van Zuydam NR, Doney AS, Palmer CN, Morris AD, Rotter JI, Tai ES, Gudnason V, Vingerling JR, Siscovick DS, Wang JJ, Wong TY.
PLoS ONE. 2013 Jun 12;8(6):e65804. article
2012
Novel loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis
Inouye M, Ripatti S, Kettunen J, Lyytikainen LP, Oksala N, Laurila PP, Kangas AJ, Soininen P, Savolainen MJ, Viikari J, Kahonen M, Perola M, Salomaa V, Raitakari O, Lehtimaki T, Taskinen MR, Jarvelin MR, Ala-Korpela M, Palotie A, de Bakker PIW.
PLoS Genetics 2012. 8(8):e1002907. article
Genome-wide association study identifies multiple loci influencing human serum metabolite levels.
Kettunen J, Tukiainen T, Sarin AP, Ortega-Alonso A, Tikkanen E, Lyytikäinen LP, Kangas AJ, Soininen P, Würtz P, Silander K, Dick DM, Rose RJ, Savolainen MJ, Viikari J, Kähönen M, Lehtimäki T, Pietiläinen KH, Inouye M, McCarthy MI, Jula A, Eriksson J, Raitakari OT, Salomaa V, Kaprio J, Järvelin MR, Peltonen L, Perola M, Freimer NB, Ala-Korpela M, Palotie A, Ripatti S.
Nature Genetics 2012. 44:269–276. article
Short Read Sequence Typing (SRST): multi-locus sequence types from short reads.
Supercomputing Enabling Exhaustive Statistical Analysis of Genome Wide Association Study Data: Preliminary Results.
Reumann M, Makalic E, Goudey B, Inouye M, Bickerstaffe AC, Bui M, Park D, Kapuscinski M, Schmidt DF, Zhou Z, Qian G, Zobel J, Wagner J, Hopper J.
Proceedings of IEEE Engineering in Medicine and Biology 2012. article
SparSNP: Fast and memory efficient analysis of all SNPs for phenotype prediction.
2011
Genome-wide association studies and systems biology: Together at last.
Ala-Korpela M, Kangas AJ, Inouye M.
Trends in Genetics 2011. 27(12): 493-498. article
Design of multiple sequence alignment algorithms on parallel, distributed memory supercomputers.
Church PC, Goscinski A, Holt KE, Inouye M, Ghoting A, Makarychev K, Reumann M.
Proceedings of IEEE Engineering in Medicine and Biology 2011. article
Genotype calling.
Inouye M and Teo YY.
Analysis of Complex Disease Association Studies. Editors: Zeggini E and Morris AP. Elsevier 2011, ISBN: 978-0-12-375142-3. book
2010
Metabonomic, transcriptomic, and genomic variation of a population cohort.
Inouye M*, Kettunen J*, Soininen P, Silander K, Ripatti S, Kumpula LS, Hamalainen E, Jousilahti P, Kangas AJ, Mannisto S, Saolainen MJ, Jula A, Leiviska J, Palotie A, Salomaa V, Perola M, Ala-Korpela M, Peltonen L.
Molecular Systems Biology 2010. 6:441. article
Genome-wide association study of migraine implicates a common susceptibility variant on 8q22.1.
Anttila V, Stefansson H, Kallela M, Todt U, Terwindt GM, Calafato MS, Nyholt DR, Dimas AS, Freilinger T, Müller-Myhsok B, Artto V, Inouye M, Alakurtti K, Kaunisto MA, Hämäläinen E, de Vries B, Stam AH, Weller CM, Heinze A, Heinze-Kuhn K, Goebel I, Borck G, Göbel H, Steinberg S, Wolf C, Björnsson A, Gudmundsson G, Kirchmann M, Hauge A, Werge T, Schoenen J, Eriksson JG, Hagen K, Stovner L, Wichmann HE, Meitinger T, Alexander M, Moebus S, Schreiber S, Aulchenko YS, Breteler MM, Uitterlinden AG, Hofman A, van Duijn CM, Tikka-Kleemola P, Vepsäläinen S, Lucae S, Tozzi F, Muglia P, Barrett J, Kaprio J, Färkkilä M, Peltonen L, Stefansson K, Zwart JA, Ferrari MD, Olesen J, Daly M, Wessman M, van den Maagdenberg AM, Dichgans M, Kubisch C, Dermitzakis ET, Frants RR, Palotie A for the International Headache Genetics Consortium.
Nature Genetics 2010. 42: 869 - 873. article
Genetic determinants of major blood lipids in Pakistanis compared with Europeans.
Saleheen D, Soranzo N, Rasheed A, Scharnagl H, Gwilliam R, Alexander M, Inouye M, Zaidi M, Potter S, Haycock P, Bumpstead S, Kaptoge S, Angelantonio ED, Sarwar N, Hunt SE, Sheikh N, Shah N, Samuel M, Haider SR, Murtaza M, Tompson A, Gobin R, Butterworth A, Ahmad U, Hakeem A, Zaman KS, Kundi A, Yaqoob Z, Cheema LA, Qamar N, Faruqui A, Mallick NH, Azhar M, Samad A, Ishaq M, Rasheed SZ Jooma R, Niazi JH, Gardezi AR, Memon NA, Ghaffar A, Rehman F, Hoffmann MM, Renner W, Kleber M, Grammer TB, Stephens J, Attwood A, Kock K, Hussain M, Kumar K, Saleem A, Kumar K, Daood MS, Gul AA, Abbas S, Zafar J, Shahid F, Bhatti SM, Ali SS, Fahim M, Sagoo G, Bray S, McGinnis RE, Dudbridge F, Winkelmann BR, Bohm B, Thompson S, Ouwehand W, Marz W, Frossard P, Danesh J, Deloukas P.
Circulation: Cardiovascular Genetics 2010. 3(4):348-57. article
An immune response network associated with blood lipid levels.
Inouye M, Silander K, Hamalainen E, Salomaa V, Harald K, Jousilahti P, Mannisto S, Eriksson J, Saarela J, Ripatti S, Perola M, van Ommen GJB, Taskinen MR, Palotie A, Dermitzakis ET, Peltonen L.
PLoS Genetics 2010. 6(9): e1001113. article
Founder population-specific HapMap panel increases power in GWA studies through improved imputation accuracy and CNV tagging.
Surakka I, Kristiansson K, Anttila V, Inouye M, Barnes C, Moutsianas L, Salomaa V, Daly MJ, Palotie A, Peltonen L, Ripatti S.
Genome Research 2010. 20:1344 - 1351. article
Integrating rare and common genetic variation in diverse human populations.
International HapMap 3 Consortium (Inouye M co-led genotyping/integration/QC of the HM3 dataset).
Nature 2010. 467:52-58. article
Genetic variants influencing circulating lipid levels and risk of coronary artery disease.
Waterworth DM, Ricketts SL, Song K, Chen L, Zhao JH, Ripatti S, Aulchenko YS, Zhang W, Yuan X, Lim N, Luan J, Ashford S, Wheeler E, Young EH, Hadley D, Thompson JR, Braund PS, Johnson T, Struchalin M, Surakka I, Luden R, Khaw KT, Rodwell SA, Loos RJF, Boekholdt M, Inouye M, Deloukas P, Elliot P, Schlessinger D, Sanna S, Scuteri A , Jackson A, Mohlke K, Tuomilehto J, Roberts R, Stewart A, Kesaniemi Y, Mahley RW, Grundy SM, Hofman A, WTCCC, McArdle W, Cardon L, Waeber G, Vollenwelder P, Chambers JC, Boehnke M, Abecasis GR, Salomaa V, Jarvelin MR, Barroso I, Epstein SE, Hakonarson H, Rader DJ, Reilly MP, Witteman J, Hall AS, Samani NJ, Strachan DP, Barter P, van Duijn C, Kooner JS, Peltonen L, Wareham NJ, McPherson R, Mooser V, Sandhu MS.
Arteriosclerosis, Thrombosis, and Vascular Biology 2010. 30(11): 2264-76. article
Visualizing chromosome mosaicism and detecting ethnic outliers by the method of “rare” heterozygotes and homozygotes (RHH).
McGinnis RE, Deloukas P, McLaren WM, Inouye M.
Human Molecular Genetics 2010. 19(13):2539-53. article
2009
Genome-wide and fine-resolution association analysis of malaria in West Africa.
Jallow M, Teo YY, Small KS, Rockett KA, Deloukas P, Clark TG, Kivinen K, Bojang KA, Conway DJ, Pinder M, Sirugo G, Sisay-Joof F, Usen S, Auburn S, Bumpstead SJ, Campino S, Coffey A, Dunham A, Fry AE, Green A, Gwilliam R, Hunt SE, Inouye M, Jeffreys AE, Mendy A, Palotie A, Potter S, Ragoussis J, Rogers J, Rowlands K, Somaskantharajah E, Whittaker P, Widden C, Donnelly P, Howie B, Marchini J, Morris A, Sanjoaquin M, Achidi EA, Agbenyega T, Allen A, Amodu O, Corran P, Djimde A, Dolo A, Doumbo OK, Drakeley C, Dunstan S, Evans J, Farrar J, Fernando D, Hien TT, Horstmann RD, Ibrahim M, Karunaweera N, Kokwaro G, Koram KA, Lemnge M, Makani J, Marsh K, Michon P, Modiano D, Molyneux ME, Mueller I, Parker M, Peshu N, Plowe CV, Puijalon O, Reeder J, Reyburn H, Riley EM, Sakuntabhai A, Singhasivanon P, Sirima S, Tall A, Taylor TE, Thera M, Troye-Blomberg M, Williams TN, Wilson M, Kwiatkowski DP; Wellcome Trust Case Control Consortium; Malaria Genomic Epidemiology Network.
Nature Genetics 2009. 41: 657-665. article
A genome-wide study reveals that ataxin 2 binding protein 1 gene is associated with hand osteoarthritis: the Treat-OA program.
Zhai G, van Meurs JB, Livshits G, Meulenbelt I, Valdes AM, Soranzo N, Hart D, Zhang F, Kato BS, Richards JB, Williams FM, Inouye M, Kloppenburg M, Deloukas P, Slagboom E, Uitterlinden A, Spector TD.
Journal of Medical Genetics 2009. Sep;46(9):614-6. article
Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size.
Soranzo N, Rivadeneira F, Chinappen-Horsley U, Malkina I, Richards JB, Hammond N, Stolk L, Nica A, Inouye M, Hofman A, Stephens J, Wheeler E, Arp P, Gwilliam R, Jhamai PM, Potter S, Chaney A, Ghori MJ, Ravindrarajah R, Ermakov S, Estrada K, Pols HA, Williams FM, McArdle WL, van Meurs JB, Loos RJ, Dermitzakis ET, Ahmadi KR, Hart DJ, Ouwehand WH, Wareham NJ, Barroso I, Sandhu MS, Strachan DP, Livshits G, Spector TD, Uitterlinden AG, Deloukas P.
PLoS Genetics 2009. 5(4):e1000445. article
Variants in the melatonin receptor 1B gene (MTNR1B) influence fasting glucose levels and risk of type 2 diabetes.
Prokopenko I, Langenberg C, Florez JC, Saxena R, Soranzo N, Thorleifsson G, Loos RJ, Manning AK, Jackson AU, Aulchenko Y, Potter SC, Erdos MR, Sanna S, Hottenga JJ, Wheeler E, Kaakinen M, Lyssenko V, Chen WM, Ahmadi K, Beckmann JS, Bergman RN, Bochud M, Bonnycastle LL, Buchanan TA, Cao A, Cervino A, Coin L, Collins FS, Crisponi L, de Geus EJ, Dehghan A, Deloukas P, Doney AS, Elliott P, Freimer N, Gateva V, Herder C, Hofman A, Hughes TE, Hunt S, Illig T, Inouye M, Isomaa B, Johnson T, Kong A, Krestyaninova M, Kuusisto J, Laakso M, Lim N, Lindblad U, Lindgren CM, McCann OT, Mohlke KL, Morris AD, Naitza S, Orrù M, Palmer CN, Pouta A, Randall J, Rathmann W, Saramies J, Scheet P, Scott LJ, Scuteri A, Sharp S, Sijbrands E, Smit JH, Song K, Steinthorsdottir V, Stringham HM, Tuomi T, Tuomilehto J, Uitterlinden AG, Voight BF, Waterworth D, Wichmann HE, Willemsen G, Witteman JC, Yuan X, Zhao JH, Zeggini E, Schlessinger D, Sandhu M, Boomsma DI, Uda M, Spector TD, Penninx BW, Altshuler D, Vollenweider P, Jarvelin MR, Lakatta E, Waeber G, Fox CS, Peltonen L, Groop LC, Mooser V, Cupples LA, Thorsteinsdottir U, Boehnke M, Barroso I, Van Duijn C, Dupuis J, Watanabe RM, Stefansson K, McCarthy MI, Wareham NJ, Meigs JB, Abecasis GR.
Nature Genetics 2009. 41: 78-81. article
2008
Bone mineral density, osteoporosis, and osteoporotic fractures: A genome-wide association study.
Richards JB*, Rivadeneira F*, Inouye M*, Pastinen TM, Soranzo N, Wilson SG, Andrew T, Falchi M, Gwilliam R, Ahmadi KR, Valdes AM, Arp P, Whittaker P, Verlaan DJ, Jhamai M, Kumanduri V, Moorhouse M, van Meurs JB, Hofman A, Pols HA, Hart D, Zhai G, Kato BS, Mullin BH, Zhang F, Deloukas P, Uitterlinden AG, Spector TD.
The Lancet 2008. 371: 1505-1512. article
The diploid genome sequence of an Asian individual.
Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Zhang J, Guo Y, Feng B, Li H, Lu Y, Fang X, Liang H, Du Z, Li D, Zhao Y, Hu Y, Yang Z, Zheng H, Hellmann I, Inouye M, Pool J, Yi X, Zhao J, Duan J, Zhou Y, Qin J, Ma L, Li G, Yang Z, Zhang G, Yang B, Yu C, Liang F, Li W, Li S, Li D, Ni P, Ruan J, Li Q, Zhu H, Liu D, Lu Z, Li N, Guo G, Zhang J, Ye J, Fang L, Hao Q, Chen Q, Liang Y, Su Y, San A, Ping C, Yang S, Chen F, Li L, Zhou K, Zheng H, Ren Y, Yang L, Gao Y, Yang G, Li Z, Feng X, Kristiansen K, Wong GK, Nielsen R, Durbin R, Bolund L, Zhang X, Li S, Yang H, Wang J.
Nature 2008. 456: 60-65. article
Whole genome amplified DNA: Insights and imputation.
Teo YY*, Inouye M*, Small KS, Fry AE, Potter SC, Dunstan SJ, Seielstad M, Barroso I, Wareham NJ, Rockett KA, Kwiatkowski DP, Deloukas P.
Nature Methods 2008. 5(4): 279-80. article
New genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn’s disease.
Fisher SA, Tremelling M, Anderson CA, Gwilliam R, Bumpstead S, Prescott NJ, Nimmo ER, Massey D, Berzuini C, Johnson C, Barrett JC, Cummings FR, Drummond H, Lees CW, Onnie CM, Hanson CE, Blaszczyk K, Inouye M, Ewels P, Ravindrarajah R, Keniry A, Hunt S, Carter M, Watkins N, Ouwehand W, Lewis CM, Cardon L; Wellcome Trust Case Control Consortium, Lobo A, Forbes A, Sanderson J, Jewell DP, Mansfield JC, Deloukas P, Mathew CG, Parkes M, Satsangi J.
Nature Genetics 2008. 40(6): 710-2. article
Association studies involving over 90,000 samples demonstrate that common variants near to MC4R influence fat mass, weight and risk of obesity.
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Nature Genetics 2008. 40(5): 575-83. article
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A genome-wide association study for coeliac disease identifies risk variants in the region harboring IL2 and IL21.
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Nature Genetics 2007. 39: 827-829. article
A genotype calling algorithm for the Illumina BeadArray platform.
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Bioinformatics 2007. 23(20): 2741-2746. article
Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants.
Wellcome Trust Case Control Consortium and Australo-Anglo-American Spondylitis Consortium.
Nature Genetics 2007. 39: 1329-1337. article
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
Wellcome Trust Case Control Consortium.
Nature 2007. 447: 661-678. article
2006
A knowledge-based scoring function based on residue triplets for protein structure prediction.
Ngan SC, Inouye M, Samudrala R.
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