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. 

• Lannelongue L*, ..., Inouye M. GREENER principles for environmentally sustainable computational science. Nature Computational Science 2023.

All Publications

2023

• • Realistic evaluations of polygenic risk scores show potential utility

    • Lambert SA, Antoniou AC, Brown M, Duncan EL, Easton D, Ferrat L, Inouye M, Kim L, Lewis CM, Oram R, Parkes M, Pashayan N, Pennells L, Pharoah P, Ritchie SC, Simard J, Visscher P, Wray N

    • article

  • Imputation of plasma lipid species to facilitate integration of lipidomic datasets

    • Dakic A, Wu J, Wang TT, Huynh K, Mellett N, Duong T, Beyene HB, Magliano DJ, Shaw JE, Carrington MJ, Inouye M, Yang JY, Figtree GA, Simes J, LIPID Study Investigators, Giles C, Meikle P

    • Nature Communications 2023. (in press)    article

  • 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

    • Nature Genetics 2023. doi:10.1038/s41588-023-01522-8.    article    pre-print 

  • Evolution and transmission of antibiotic resistance is driven by Beijing lineage Mycobacterium tuberculosis in Vietnam

    • Silcocks M, Chang X, Thuong TNT, Qin Y, Minh HDT, Khac TPV, Vijay S, Anh TDD, Ngoc HVT, Ngoc NH, Huu LN, Quynh NNT, Edwards D, Nath AP, Pham K, Duc BN, Hong CTT, Thwaites G, Heemskerk D, Khor CC, Teo YY, Inouye M, Ong RTH, Caws M, Holt KE, Dunstan S

    • Microbiology Spectrum 2023.    article    pre-print

  • Life expectancy associated with different ages at diagnosis of type 2 diabetes in high-income countries: 23 million person-years of observation

    • Kaptoge S, Seshasai SRK, Sun L, Walker M, Bolton T, Spackman S, Ataklte F, Willeit P, Bell S, Burgess S, Pennells L, S Altay, G Assmann, Y Ben-Shlomo, LG Best, C Björkelund, DG Blazer, H Brenner, EJ Brunner, GR Dagenais, JA Cooper, C Cooper, CJ Crespo, M Cushman, RB D'Agostino Sr, M Daimon, LB Daniels, R Danker, KW Davidson, RT de Jongh, C Donfrancesco, P Ducimetiere, PJM Elders, G Engström, I Ford, I Gallacher, SJL Bakker, U Goldbourt, G de La Cámara, S Grimsgaard, V Gudnason, PO Hansson, H Imano, JW Jukema, C Kabrhel, J Kauhanen, M Kavousi, S Kiechl, MW Knuiman, D Kromhout, HM Krumholz, LH Kuller, T Laatikainen, DA Lowler, HE Meyer, K Mukamal, PJ Nietert, T Ninomiya, D Nitsch, BG Nordestgaard, L Palmieri, JF Price, PM Ridker, Q Sun, A Rosengren, R Roussel, M Sakurai, V Salomaa, B Schöttker, JE Shaw, TE Strandberg, J Sundström, H Tolonen, A Tverdal, WMM Verschuren, H Völzke, L Wagenknecht, RB Wallace, SG Wannamethee, Wareham NJ, Wassertheil-Smoller S, Yamagishi K, Yeap BB, Harrison S, Inouye M, Griffin S, Butterworth AS, Wood AM, Thompson SG, Sattar N, Danesh J, Di Angelantonio E

    • Lancet Diabetes and Endocrinology 2023. https://doi.org/10.1016/S2213-8587(23)00223-1.    article

  • Direct inference and control of genetic population structure from RNA sequencing data 

    • Fachrul M, Karkey A, Shakya M, Judd L, Harshegyi T, Sim KS, Tonks S, Dongol S, Shrestha R, Salim A, STRATAA study group, Baker S, Pollard AJ, Khor CC, Dolecek C, Basnyat B, Dunstan SJ, Holt KE, Inouye M

    • Communications Biology 2023. 6:804.    article    pre-print    software

  • 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

    • Journal of the American Heart Association 2023. 12:e029296.    article    pre-print

  • GREENER principles for environmentally sustainable computational science

    • Lannelongue L, Aronson HEG, Bateman A, Birney E, Caplan T, Juckes M, McEntyre J, Morris AD, Reilly G, Inouye M

    • Nature Computational Science 2023. 3:514-521.    article

  • Greengenes2 unifies microbial data in a single reference tree

    • McDonald D, Jiang Y, Balaban M, Cantrell K, Zhu Q, Gonzalez A, Morton JT, Nicolaou G, Parks DH, Karst S, Albertsen M, Hugenholtz P, DeSantis T, Song SJ, Bartko A, Havulinna A, Jousilahti P, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Lahti L, Mirarab S, Knight R

    • Nature Biotechnology 2023. https://doi.org/10.1038/s41587-023-01845-1.    article

  • 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, Foguet C, Johansson A, Surendran P, Nath AP, Persyn E, Peters JE, Oliver-Williams C, Deng S, Prins B, 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

    • Nature 2023. doi:https://doi.org/10.1038/s41586-023-05844-9     article    pre-print    OmicsPred

  • Gut microbiome and atrial fibrillation – results from a large population-based study

    • Palmu J, Borschel CS, Ortega-Alonso A, Marko L, Inouye M, Jousilahti P, Salido RA, Sanders K, Brennan C, Humphrey GC, Sanders JG, Gutmann F, Linz D, Salomaa V, Havulinna A, Forslund SK, Knight R, Lahti L, Niiranen T, Schnabel RB

    • eBioMedicine 2023. doi:https://doi.org/10.1016/j.ebiom.2023.1045833    article

  • 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

    • Liu Y, Teo SM, Meric G, Tang HHF, Zhu Q, Sanders JG, Vazquez-Baeza Y, Verspoor K, Vartiainen VA, Jousilahti P, Lahti L, Niiranen T, Havulinna AS, Knight R, Salomaa V, Inouye M

    • Journal of Allergy and Clinical Immunology 2023. doi:https://doi.org/10.1016/j.jaci.2022.12.810    article    pre-print

  • 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. 10:64.    article    pre-print

2022

• • Assessing and removing the effect of unwanted technical variations in microbiome data

    • Fachrul M, Meric G, Inouye M, Pamp SJ, Salim A

    • Scientific Reports 2022. 12:22236.    article    pre-print

  • 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

    • Foguet C, Xu Y, Ritchie SC, Lambert SA, Persyn E, Nath AP, Davenport EE, Roberts DJ, Paul DS, Di Angelantonio E, Danesh J, Butterworth AS, Yau C, Inouye M

    • Nature Communications 2022. 13:7356.    article    pre-print

  • 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

    • Huang QQ, Sallah N, Dunca D, Trivedi B, Hunt KA, Hodgson S, Lambert SA, Arciero E, Genes & Health Research team, Wright J, Griffiths C, Trembath RC, Hemingway H, Inouye M, Finer S, van Heel DA, Lumbers T, Martin HC, Kuchenbaecker K

    • Nature Communications 2022. 13:4664.    article    pre-print

  • 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

    • GIGASTROKE Consortium (corresponding: Debette S, Dichgans M)

    • Nature 2022. doi:10.1038/s41586-022-05165-3.    article    pre-print

  • Early prediction of liver disease using conventional risk factors and gut microbiome-augmented gradient boosting

    • Liu Y, Meric G, Havulinna AS, Teo SM, Ruuskanen M, Sanders J, Zhu Q, Tripathi A, Verspoor K, Cheng S, Jain M, Jousilahti P, Vazquez-Baeza Y, Loomba R, Lahti L, Niiranen T, Salomaa V, Knight R, Inouye M

    • Cell Metabolism 2022. DOI:https://doi.org/10.1016/j.cmet.2022.03.002.    article    pre-print

  • Sex-specific survival bias and interaction modeling in coronary artery disease risk prediction

    • Surakka I, Wolford BN, Ritchie SC, Hornsby WE, Sutton NR, Gabrielsen ME, Skogholt AH, Thomas L, Inouye M, Hveem K, Willer CJ

    • Circulation: Genomic and Precision Medicine 2022. doi:10.1161/CIRCGEN.121.003542.    article    pre-print

  • 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

    • Grealey JG*, Lannelongue L*, Saw WY, Marten J, Meric G, Ruiz-Carmona S, Inouye M

    • Molecular Biology and Evolution 2022. doi:https://doi.org/10.1093/molbev/msac034.    article    pre-print

  • 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

    • Xu Y, Vuckovic D, Ritchie SC, Akbari P, Jiang T, Grealey J, Butterworth AS, Ouwehand WH, Roberts DJ, Di Angelantonio E, Danesh J, Soranzo N, Inouye M

    • Cell Genomics 2022. DOI:https://doi.org/10.1016/j.xgen.2021.100086.     article    pre-print

  • Known allosteric proteins have central roles in genetic disease

    • Abrusan G, Ascher DB, Inouye M

    • PLOS Computational Biology 2022. 18(2): e1009806.    article    pre-print

  • 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

    • Nature Communications 2022. 13:3124.    article    pre-print

  • 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

    • Tuomisto K, Palmu J, Long T, Watrous JD, Mercader K, Lagerborg KA, Andres A, Salmi M, Jalkanen S, Vasan RS, Inouye M, Havulinna AS, Jousilahti P, Niiranen TJ, Cheng S, Jain M, Salomaa V

    • BMJ Open Diabetes Research and Care 2022. doi:http://dx.doi.org/10.1136/bmjdrc-2021-002519.    article    pre-print

  • Gut microbiome composition is predictive of incident type 2 diabetes

    • Ruuskanen MO, Erawijantari PP, Havulinna AS, Liu Y, Méric G, Inouye M, Jousilahti P, Salomaa V, Jain M, Knight R, Lahti L, Niiranen TJ

    • Diabetes Care 2022. dc212358.    article    pre-print

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

    • Abraham G, Rutten-Jacobs L, Inouye M   

    • Stroke 2021. 52:2983–2991.    article    pdf

  • Prognostic Value of a Polygenic Risk Score for Coronary Heart Disease in Individuals Aged 70 Years and Older

    • Neumann JT, Riaz M, Bakshi A, Polekhina G, Thao LLP, Nelson MR, Woods RL, Abraham G, Inouye M, Reid CM, Tonkin AM, McNeil JJ, Lacaze P

    • Circulation: Genomic and Precision Medicine 2021. https://doi.org/10.1161/CIRCGEN.121.003429.    article    pre-print

  • 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

    • Lambert SA, Gil L, Jupp S, Ritchie SC, Xu Y, Buniello A, McMahon A, Abraham G, Chapman M, Parkinson H, Danesh J, MacArthur JAL, Inouye M

    • Nature Genetics 2021. https://doi.org/10.1038/s41588-021-00783-5.    article    pre-print    catalog

  • 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*

    • Nature 2021. 591:211-219.    article    pre-print

  • 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

    • Salosensaari A, Laitinen V, Havulinna AS, Meric G, Cheng S, Perola M, Valsta L, Alfthan G, Inouye M, Watrous JD, Long T, Salido R, Sanders K, Brennan C, Humphrey GC, Sanders JG, Jousilahti P, Salomaa V, Knight R, Lahti L, Niiranen T.

    • Nature Communications 2021. 12:2671.    article    pre-print

  • 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

    • Ruuskanen M, Aberg F, Mannisto V, Havulinna A, Meric G, Liu Y, Loomba R, Vazquez-Baeza Y, Tripathi A, Valsta LM, Inouye M, Jousilahti P, Salomaa V, Jain M, Knight R, Lahti L, Niiranen T

    • Gut Microbes 2021. doi:10.1080/19490976.2021.1888673.    article    pre-print

  • 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 

    • Cell 2020. 182(5):1214-1231.    article    pre-print

  • Genomic risk scores for juvenile idiopathic arthritis and its subtypes

    • Canovas R, Cobb J, Brozynska M, Bowes J, Li YR, Smith SL, Hakonarson H, Thomson W, Ellis J, Abraham G, Munro J*, Inouye M*

    • Annals of the Rheumatic Diseases 2020. doi: 10.1136/annrheumdis-2020-217421.    article     pre-print

  • GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure

    • Wan Y, Wick RR, Zobel J, Ingle DJ, Inouye M, Holt KE

    • BMC Genomics 2020. 21:658.    article    pre-print

  • Neonatal genetics of gene expression reveal the potential origins of autoimmune and allergic disease risk

    • Huang QQ, Tang HHF, Teo SM, Mok D, Ritchie SC, Nath AP, Brozynska M, Salim A, Bakshi A, Holt BJ, Khor CC, Sly PD, Holt PG, Holt KE, Inouye M. 

    • Nature Communications 2020. 11:3761.    article    pre-print

  • 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

    • Palmu J, Watrous JD, Mercader K, Havulinna AS, Lagerborg KA, Salosensaari A, Inouye M, Larson MG, Rong J, Vasan RS, Lahti L, Andres A, Cheng S, Jousilahti P, Salomaa V, Jain M, Niiranen T.

    • Journal of the American Heart Association 2020. https://doi.org/10.1161/JAHA.120.017598.    article    pre-print

  • 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

    • Abraham G, Malik R, Yonova-Doing E, Salim A, Wang TT, Danesh J, Butterworth AS, Howson JMM, Inouye M*, Dichgans M*

    • Nature Communications 2019. 10:5819.    article    pre-print    metaGRS

  • Systems biology and big data in asthma and allergy: recent discoveries and emerging challenges

    • Tang HHF, Sly PD, Holt PG, Holt KE, Inouye M.

    • European Respiratory Journal 2019. DOI:10.1183/13993003.00844-2019.    article    pdf

  • Elevated alpha-1 antitrypsin is a major component of GlycA-associated risk for future morbidity and mortality

    • Ritchie SC, Kettunen J, Brozynska M, Nath AP, Havulinna, Mannisto S, Perola M, Salomaa V, Ala-Korpela M, Abraham G, Wurtz P, Inouye M.

    • PLoS ONE 2019. 14(10):e0223692.   article    pre-print

  • 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

    • Lambert SA, Abraham G, Inouye M

    • Human Molecular Genetics 2019. ddz187.    article    preprint   

  • 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

    • Tang HHF, Teo SM, Belgrave DCM, Evans MD, Jackson DJ, Brozynska M, Kusel MMH, Johnston SL, Gern JE, Lemanske RF, Simpson A, Custovic A, Sly PD, Holt PG, Holt KE, Inouye M

    • eLife 2018. 7:e35856.    article    pre-print

  • Biomarker glycoprotein acetyls is associated with the risk of a wide spectrum of incident diseases and stratifies mortality risk in angiography patients

    • Kettunen J*, Ritchie SC*, Anufrieva O, Lyytikainen LP, Hernesniemi J, Karhunen PJ, Kuukasjarvi P, Laurikka J, Kahonen M, Lehtimaki T, Havulinna A, Salomaa V, Mannisto S, Ala-Korpela M, Perola M, Inouye M*, Wurtz P*

    • Circulation: Genomic and Precision Medicine 2018. 11:e002234.    article    pre-print

  • Power, false discovery rate and Winner's Curse in eQTL studies

    • Huang QQ, Ritchie SC, Brozynska M, Inouye M

    • Nucleic Acids Research 2018. gky780.    article    pre-print

  • Identification of expression quantitative trait loci associated with schizophrenia and affective disorders in normal brain tissue

    • Bhalala OG, Nath AP, UK Brain Expression Consortium, Inouye M, Sibley CR

    • PLOS Genetics 2018. 14(8):e1007607.    article    pre-print

  • Airway microbiota dynamics identify a critical window for interplay of pathogenic bacteria and allergy in childhood respiratory disease

    • Teo SM, Tang HHF, Mok D, Judd LM, Watts SC, Pham K, Holt BJ, Kusel M, Serralha M, Troy N, Bochkov YA, Grindle K, Lemanske RM, Johnston SL, Gern JE, Sly PD, Holt PG, Holt KE*, Inouye M*

    • Cell Host & Microbe 2018. 24(3):341-352.    article    pre-print

  • FastSpar: Rapid and scalable correlation estimation for compositional data

    • Watts SC, Ritchie SC, Inouye M, Holt KE

    • Bioinformatics 2018. bty734.    article    pre-print

  • Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam

    • Holt KE, McAdam P, Phan VKT, Nguyen TTT, Dang TMH, Nguyen NL, Nguyen HL, Nguyen TQN, Hoang TH, Vu TNH, Thwaites G, Edwards DJ, Nath AP, Pham K, Ascher DB, Farrar JJ, Khor CC, Teo YY, Inouye M, Caws M, Dunstan SJ.

    • Nature Genetics 2018. 50:849–856.    article    pre-print

  • 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

    • Gray LA, D'Antoine HA, Tong SYC, McKinnon M, Bessarab D, Brown N, Remenyi B, Steer A, Syn G, Blackwell JM*, Inouye M*, Carapetis JR*

    • Journal of Infectious Diseases 2017. jix497.    article    pre-print       

  • Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy

    • Byars SG, Huang QQ, Gray LA, Bakshi A, Ripatti S, Abraham G, Stearns SC, Inouye M

    • PLoS Genetics 2017. 13(6):e1006328.    article    pre-print

  • Flashpca2: Principal component analysis of biobank-scale genotype datasets

    • Abraham G, Qiu Y, Inouye M.

    • Bioinformatics 2017. btx299.    article    pre-print    software

  • 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.

    • Genome Biology 2017. 18:146.    article    pre-print

  • 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

    • Goudey B, Abraham G, Kikianty E, Wang Q, Rawlinson D, Shi F, Haviv I, Stern L, Kowalczyk A*, Inouye M*

    • PLoS ONE 2017. 12(3): e0172826.    article    pre-print

  • 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

    • Shu L, Zhao Y, Kurt Z, Byars SG, Tukiainen T, Kettunen J, Orozco LD, Pellegrini M, Lusis AJ, Ripatti S, Zhang B, Inouye M, Makinen VP, Yang X

    • BMC Genomics 2016. 17:874.     article     pre-print

  • 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

    • Ritchie SC, Watts S, Fearnley LG, Holt KE, Abraham G, Inouye M. 

    • Cell Systems 2016. 3(1):71-82.    article    pre-print    software

  • 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

    • Ingle D, Valcanis M, Kuzevski A, Tauschek M, Inouye M, Stinear T, Levine MM, Robins-Browne RM, Holt KE

    • Microbial Genomics 2016. doi:10.1099/mgen.0.000064.     article     pre-print

  • 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*

    • Cell Systems 2015. 1(4):293-301.     article    pre-print

  • 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

    • Abraham G, Rohmer A, Jason Tye-Din*, Inouye M*

    • Genome Medicine 2015. 7:72.    article     pre-print

  • The infant airway microbiome impacts severity of lower respiratory infection and risk of asthma development

    • Teo SM, Mok D, Pham K, Kusel M, Serralha M, Troy N, Holt BJ, Hales B, Walker ML, Hollams E, Bochkov YH, Grindle K, Johnston SL, Gern JE, Sly PD, Holt PG, Holt KE*, Inouye M*

    • Cell Host & Microbe 2015. 17:1-12.     article     pre-print   OTU-table

  • 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

    • Inouye M, Dashnow H, Raven L, Schultz M, Pope BJ, Tomita T, Zobel J, Holt KE.

    • Genome Medicine 2014. 6:90.    article    pre-print    software   

  • 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

    • Abraham G and Inouye M

    • PLoS ONE 2014. 9(4):e93766.    article    pre-print    software

  • Towards a molecular systems model of coronary artery disease.

    • Abraham G, Bhalala OG, de Bakker PIW, Ripatti S, Inouye M

    • Current Cardiology Reports 2014. 16:488.    article    pre-print

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

    • Goudey B, Rawlinson D, Wang Q, Shi F, Ferra H, Campbell RM, Stern L, Inouye M, Ong CS, Kowalczyk A. 

    • BMC Genomics. 2013 14(Suppl 3):S10.    article    software

  • 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.

    • Inouye M, Conway T, Zobel J, and Holt KE.

    • BMC Genomics 2012. 13:338.    article    software

  • 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.

    • Abraham G, Kowalczyk A, Zobel J, Inouye M. 

    • BMC Bioinformatics 2012. 13:88.    article     software

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.

    • Loos RJ, Lindgren CM, Li S, Wheeler E, Zhao JH, Prokopenko I, Inouye M, Freathy RM, Attwood AP, Beckmann JS, Berndt SI; Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial, Jacobs KB, Chanock SJ, Hayes RB, Bergmann S, Bennett AJ, Bingham SA, Bochud M, Brown M, Cauchi S, Connell JM, Cooper C, Smith GD, Day I, Dina C, De S, Dermitzakis ET, Doney AS, Elliott KS, Elliott P, Evans DM, Sadaf Farooqi I, Froguel P, Ghori J, Groves CJ, Gwilliam R, Hadley D, Hall AS, Hattersley AT, Hebebrand J, Heid IM; KORA, Lamina C, Gieger C, Illig T, Meitinger T, Wichmann HE, Herrera B, Hinney A, Hunt SE, Jarvelin MR, Johnson T, Jolley JD, Karpe F, Keniry A, Khaw KT, Luben RN, Mangino M, Marchini J, McArdle WL, McGinnis R, Meyre D, Munroe PB, Morris AD, Ness AR, Neville MJ, Nica AC, Ong KK, O'Rahilly S, Owen KR, Palmer CN, Papadakis K, Potter S, Pouta A, Qi L; Nurses' Health Study, Randall JC, Rayner NW, Ring SM, Sandhu MS, Scherag A, Sims MA, Song K, Soranzo N, Speliotes EK; Diabetes Genetics Initiative, Syddall HE, Teichmann SA, Timpson NJ, Tobias JH, Uda M; SardiNIA Study, Vogel CI, Wallace C, Waterworth DM, Weedon MN; Wellcome Trust Case Control Consortium, Willer CJ; FUSION, Wraight, Yuan X, Zeggini E, Hirschhorn JN, Strachan DP, Ouwehand WH, Caulfield MJ, Samani NJ, Frayling TM, Vollenweider P, Waeber G, Mooser V, Deloukas P, McCarthy MI, Wareham NJ, Barroso I, Jacobs KB, Chanock SJ, Hayes RB, Lamina C, Gieger C, Illig T, Meitinger T, Wichmann HE, Kraft P, Hankinson SE, Hunter DJ, Hu FB, Lyon HN, Voight BF, Ridderstrale M, Groop L, Scheet P, Sanna S, Abecasis GR, Albai G, Nagaraja R, Schlessinger D, Jackson AU, Tuomilehto J, Collins FS, Boehnke M, Mohlke KL.

    • Nature Genetics 2008. 40(6): 768-75.    article

  • Genome-wide association analysis identifies 20 loci that influence adult height.

    • Weedon MN, Lango H, Lindgren CM, Wallace C, Evans DM, Mangino M, Freathy RM, Perry JR, Stevens S, Hall AS, Samani NJ, Shields B, Prokopenko I, Farrall M, Dominiczak A; Diabetes Genetics Initiative; Wellcome Trust Case Control Consortium, Johnson T, Bergmann S, Beckmann JS, Vollenweider P, Waterworth DM, Mooser V, Palmer CN, Morris AD, Ouwehand WH; Cambridge GEM Consortium, Zhao JH, Li S, Loos RJ, Barroso I, Deloukas P, Sandhu MS, Wheeler E, Soranzo N, Inouye M, Wareham NJ, Caulfield M, Munroe PB, Hattersley AT, McCarthy MI, Frayling TM. 

    • Nature Genetics 2008. 40(5): 575-83.    article

  • LDL-cholesterol concentrations: a genome-wide association study. 

    • Sandhu MS, Waterworth DM, Debenham SL, Wheeler E, Papadakis K, Zhao JH, Song K, Yuan X, Johnson T, Ashford S, Inouye M, Luben R, Sims M, Hadley D, McArdle W, Barter P, Kesäniemi YA, Mahley RW, McPherson R, Grundy SM; Wellcome Trust Case Control Consortium, Bingham SA, Khaw KT, Loos RJ, Waeber G, Barroso I, Strachan DP, Deloukas P, Vollenweider P, Wareham NJ, Mooser V. 

    • The Lancet 2008. 371: 483-491.    article

2007

• • A genome-wide association study for coeliac disease identifies risk variants in the region harboring IL2 and IL21. 

    • van Heel DA, Franke L, Hunt KA, Gwilliam R, Zhernakova A, Inouye M, Wapenaar MC, Barnardo MC, Bethel G, Holmes GK, Feighery C, Jewell D, Kelleher D, Kumar P, Travis S, Walters JR, Sanders DS, Howdle P, Swift J, Playford RJ, McLaren WM, Mearin ML, Mulder CJ, McManus R, McGinnis R, Cardon LR, Deloukas P, Wijmenga C. 

    • Nature Genetics 2007. 39: 827-829.    article

  • A genotype calling algorithm for the Illumina BeadArray platform.

    • Teo YY*, Inouye M*, Small KS, Gwilliam R, Deloukas P, Kwiatkowski DP, Clark TG.

    • 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. 

    • Protein Engineering, Design and Selection 2006. 19:187-193.    article