Systems Genomics‎ > ‎

Publications

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      Inouye Lab authors
      *equal contribution


Pre-prints

  • Genomic analysis of Mycobacterium tuberculosis reveals complex etiology of tuberculosis in Vietnam including frequent introduction and transmission of Beijing lineage and positive selection for EsxW Beijing variant
    • Holt KE, McAdam P, Phan VKT, Dang TMH, Nguyen NL, Nguyen HL, Nguyen TQN, Nguyen TTT, Thwaites G, Edwards DJ, Pham K, Farrar JJ, Khor CC, Teo YY, Inouye M, Caws M, Dunstan SJ.
    • 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
    • article    pre-print
  • FlashPCA: fast sparse canonical correlation analysis of genomic data
  • 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.
    • pre-print


Publications

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.    article    pre-print       
    • Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy
      • Byars SG, Huang QQ, Gray LA, 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
    • 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*, 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.    article

    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 APAbraham 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
    • 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.
      • Abraham G, Bhalala OG, de Bakker PIW, Ripatti S, and 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, and 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.
    • 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.

    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, and 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, and 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. Published by 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, and 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 41: 657 - 665. (2009)
    • 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. Sep;46(9):614-6. (2009)
    • 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. 5(4):e1000445. (2009)
    • 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 41: 78-81. (2009)


    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 456: 60-65. (2008)
    • 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 40(6): 710-2. (2008)
    • 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 40(6): 768-75. (2008)
    • 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 40(5): 575-83. (2008)
    • 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 371: 483-491. (2008)

    2007

    • A genome-wide association 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 39: 827-829. (2007)
    • 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 39: 1329-1337. (2007)
    • Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. 
      • Wellcome Trust Case Control Consortium
      • Nature 447: 661-678. (2007)

    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