The publication list below includes only publications (\(N = 113\)) where M. Pirinen is an individually-named author in the main author list of the publication. Thus, it excludes the publications where the authorship of M. Pirinen is only through a membership in a consortium.

  1. Elliott A, Walters RK, Pirinen M, Kurki M, Junna N, Goldstein JI, Reeve MP, Siirtola H, Lemmelä SM, Turley P, Lahtela E, Mehtonen J, Reis K, Elnahas AG, Reigo A, Palta P, Esko T, Mägi R; Estonian Biobank Research Team; FinnGen; Palotie A, Daly MJ, Widén E.
    Distinct and shared genetic architectures of gestational diabetes mellitus and type 2 diabetes.
    Nat Genet. 2024 Mar;56(3):377-382. DOI:10.1038/s41588-023-01607-4, PMID:38182742, PMCID:PMC10937370.

  2. Leinonen JT; FinnGen; Pirinen M, Tukiainen T.
    Disentangling the link between maternal influences on birth weight and disease risk in 36,211 genotyped mother-child pairs.
    Commun Biol. 2024 Feb 12;7(1):175. DOI:10.1038/s42003-024-05872-9, PMID:38347176, PMCID:PMC10861556.

  3. Mars N, Kerminen S, Tamlander M, Pirinen M, Jakkula E, Aaltonen K, Meretoja T, Heinävaara S, Widén E, Ripatti S; FinnGen.
    Comprehensive Inherited Risk Estimation for Risk-Based Breast Cancer Screening in Women.
    J Clin Oncol. 2024 May 1;42(13):1477-1487. DOI:10.1200/JCO.23.00295, PMID:38422475, PMCID:PMC11095905.

  4. Drouard G, Mykkänen J, Heiskanen J, Pohjonen J, Ruohonen S, Pahkala K, Lehtimäki T, Wang X, Ollikainen M, Ripatti S, Pirinen M, Raitakari O, Kaprio J.
    Exploring machine learning strategies for predicting cardiovascular disease risk factors from multi-omic data.
    BMC Med Inform Decis Mak. 2024 May 2;24(1):116. DOI:10.1186/s12911-024-02521-3, PMID:38698395, PMCID:PMC11064347.

  5. Liu A, Genovese G, Zhao Y, Pirinen M, Zekavat SM, Kentistou KA, Yang Z, Yu K, Vlasschaert C, Liu X, Brown DW, Hudjashov G, Gorman BR, Dennis J, Zhou W, Momozawa Y, Pyarajan S, Tuzov V, Pajuste FD, Aavikko M, Sipilä TP, Ghazal A, Huang WY, Freedman ND, Song L, Gardner EJ; FinnGen; Estonian Biobank Research Team; Breast Cancer Association Consortium; Million Veteran Program; Sankaran VG, Palotie A, Ollila HM, Tukiainen T, Chanock SJ, Mägi R, Natarajan P, Daly MJ, Bick A, McCarroll SA, Terao C, Loh PR, Ganna A, Perry JRB, Machiela MJ.
    Genetic drivers and cellular selection of female mosaic X chromosome loss.
    Nature. 2024 Jul;631(8019):134-141. DOI:10.1038/s41586-024-07533-7, PMID:38867047, PMCID: none.

  6. Reeve M, Kanai M, Graham D, Karjalainen J, Luo S, Kolosov N, Adams C, Ritari J, Karczewski K, Kiiskinen T, Fuller Z, Mehtonen J, Kurki M, Khan Z, Partanen J, McCarthy M, Artomov M, Tuomi T, Pirinen M, Kero J, Xavier R, Daly M, Ripatti S, Gen F.
    Autoimmune hypothyroidism GWAS reveals independent autoimmune and thyroid-specific contributions and an inverse relation with cancer risk.
    Res Sq [Preprint]. 2024 Jul 8:rs.3.rs-4626646. DOI:10.21203/rs.3.rs-4626646/v1, PMID:39041034, PMCID:PMC11261955.

  7. Rämö JT, Kiiskinen T, Seist R, Krebs K, Kanai M, Karjalainen J, Kurki M, Hämäläinen E, Häppölä P, Havulinna AS, Hautakangas H; FinnGen; Mägi R, Palta P, Esko T, Metspalu A, Pirinen M, Karczewski KJ, Ripatti S, Milani L, Stankovic KM, Mäkitie A, Daly MJ, Palotie A.
    Genome-wide screen of otosclerosis in population biobanks: 27 loci and shared associations with skeletal structure.
    Nat Commun. 2023 Jan 18;14(1):157. DOI:10.1038/s41467-022-32936-3, PMID:36653343, PMCID:PMC9849444.

  8. Saarentaus EC, Karjalainen J, Rämö JT, Kiiskinen T, Havulinna AS, Mehtonen J, Hautakangas H, Ruotsalainen S, Tamlander M, Mars N; FINNGEN; Toppila-Salmi S, Pirinen M, Kurki M, Ripatti S, Daly M, Palotie T, Mäkitie A, Palotie A.
    Inflammatory and infectious upper respiratory diseases associate with 41 genomic loci and type 2 inflammation.
    Nat Commun. 2023 Jan 18;14(1):83. DOI:10.1038/s41467-022-33626-w, PMID:36653354, PMCID:PMC9849224.

  9. Kiiskinen T, Helkkula P, Krebs K, Karjalainen J, Saarentaus E, Mars N, Lehisto A, Zhou W, Cordioli M, Jukarainen S, Rämö JT, Mehtonen J, Veerapen K, Räsänen M, Ruotsalainen S, Maasha M; FinnGen; Niiranen T, Tuomi T, Salomaa V, Kurki M, Pirinen M, Palotie A, Daly M, Ganna A, Havulinna AS, Milani L, Ripatti S.
    Genetic predictors of lifelong medication-use patterns in cardiometabolic diseases.
    Nat Med. 2023 Jan;29(1):209-218. DOI:10.1038/s41591-022-02122-5, PMID:36653479, PMCID:PMC9873570.

  10. Leinonen JT, Mars N, Lehtonen LE, Ahola-Olli A, Ruotsalainen S, Lehtimäki T, Kähönen M, Raitakari O; FinnGen Consortium; Piltonen T, Daly M, Tuomi T, Ripatti S, Pirinen M, Tukiainen T.
    Genetic analyses implicate complex links between adult testosterone levels and health and disease.
    Commun Med (Lond). 2023 Jan 18;3(1):4. DOI:10.1038/s43856-022-00226-0, PMID:36653534, PMCID:PMC9849476.

  11. Almangush A, Alabi RO, De Keukeleire S, Mäkitie AA, Pirinen M, Leivo I.
    Clinical significance of overall assessment of tumor-infiltrating lymphocytes in oropharyngeal cancer: A meta-analysis.
    Pathol Res Pract. 2023 Mar;243:154342. DOI:10.1016/j.prp.2023.154342, PMID:36758415, PMCID: none.

  12. Pirinen M.
    linemodels: clustering effects based on linear relationships.
    Bioinformatics. 2023 Mar 1;39(3):btad115. DOI:10.1093/bioinformatics/btad115, PMID:36864614, PMCID:PMC10005595.

  13. Kaivola K, Pirinen M, Laaksovirta H, Jansson L, Rautila O, Launes J, Hokkanen L, Lahti J, Eriksson JG, Strandberg TE, FinnGen, Tienari PJ.
    C9orf72 hexanucleotide repeat allele tagging SNPs: Associations with ALS risk and longevity.
    Front Genet. 2023 Mar 1;14:1087098. DOI:10.3389/fgene.2023.1087098, PMID:36936421, PMCID:PMC10014923.

  14. Kivimäki M, Livingston G, Singh-Manoux A, Mars N, Lindbohm JV, Pentti J, Nyberg ST, Pirinen M, Anderson EL, Hingorani AD, Sipilä PN.
    Estimating Dementia Risk Using Multifactorial Prediction Models.
    JAMA Netw Open. 2023 Jun 1;6(6):e2318132. DOI:10.1001/jamanetworkopen.2023.18132, PMID:37310738, PMCID:PMC10265307.

  15. Winsvold BS, Harder AVE, Ran C, Chalmer MA, Dalmasso MC, Ferkingstad E, Tripathi KP, Bacchelli E, Børte S, Fourier C, Petersen AS, Vijfhuizen LS, Magnusson SH, O’Connor E, Bjornsdottir G, Häppölä P, Wang YF, Callesen I, Kelderman T, Gallardo VJ, de Boer I, Olofsgård FJ, Heinze K, Lund N, Thomas LF, Hsu CL, Pirinen M, Hautakangas H, Ribasés M, Guerzoni S, Sivakumar P, Yip J, Heinze A, Küçükali F, Ostrowski SR, Pedersen OB, Kristoffersen ES, Martinsen AE, Artigas MS, Lagrata S, Cainazzo MM, Adebimpe J, Quinn O, Göbel C, Cirkel A, Volk AE, Heilmann-Heimbach S, Skogholt AH, Gabrielsen ME, Wilbrink LA, Danno D, Mehta D, Guðbjartsson DF; HUNT All-In Headache, The International Headache Genetics Consortium, DBDS Genomic Consortium; Rosendaal FR, Willems van Dijk K, Fronczek R, Wagner M, Scherer M, Göbel H, Sleegers K, Sveinsson OA, Pani L, Zoli M, Ramos-Quiroga JA, Dardiotis E, Steinberg A, Riedel-Heller S, Sjöstrand C, Thorgeirsson TE, Stefansson H, Southgate L, Trembath RC, Vandrovcova J, Noordam R, Paemeleire K, Stefansson K, Fann CS, Waldenlind E, Tronvik E, Jensen RH, Chen SP, Houlden H, Terwindt GM, Kubisch C, Maestrini E, Vikelis M, Pozo-Rosich P, Belin AC, Matharu M, van den Maagdenberg AMJM, Hansen TF, Ramirez A, Zwart JA; International Consortium for Cluster Headache Genetics.
    Cluster Headache Genomewide Association Study and Meta-Analysis Identifies Eight Loci and Implicates Smoking as Causal Risk Factor.
    Ann Neurol. 2023 Oct;94(4):713-726. DOI:10.1002/ana.26743, PMID:37486023, PMCID:PMC10952302.

  16. Ottensmann L, Tabassum R, Ruotsalainen SE, Gerl MJ, Klose C, Widén E; FinnGen; Simons K, Ripatti S, Pirinen M.
    Genome-wide association analysis of plasma lipidome identifies 495 genetic associations.
    Nat Commun. 2023 Oct 31;14(1):6934. DOI:10.1038/s41467-023-42532-8, PMID:37907536, PMCID:PMC10618167.

  17. Drouard G, Hagenbeek FA, Whipp AM, Pool R, Hottenga JJ, Jansen R, Hubers N, Afonin A; BIOS Consortium, BBMRI-N. L. Metabolomics Consortium; Willemsen G, de Geus EJC, Ripatti S, Pirinen M, Kanninen KM, Boomsma DI, van Dongen J, Kaprio J.
    Longitudinal multi-omics study reveals common etiology underlying association between plasma proteome and BMI trajectories in adolescent and young adult twins.
    BMC Med. 2023 Dec 21;21(1):508. DOI:10.1186/s12916-023-03198-7, PMID:38129841, PMCID:PMC10740308.

  18. Lin J, Mars N, Fu Y, Ripatti P, Kiiskinen T; FinnGen study; Tukiainen T, Ripatti S, Pirinen M.
    Integration of Biomarker Polygenic Risk Score Improves Prediction of Coronary Heart Disease.
    JACC Basic Transl Sci. 2023 Oct 4;8(12):1489-1499. DOI:10.1016/j.jacbts.2023.07.006, PMID:38205343, PMCID:PMC10774750.

  19. Wahab A, Onkamo O, Pirinen M, Almangush A, Salo T.
    The budding and depth of invasion model in oral cancer: A systematic review and meta-analysis.
    Oral Dis. 2022 Mar;28(2):275-283. DOI:10.1111/odi.13671, PMID:33031610, PMCID: none.

  20. Bahrami S, Hindley G, Winsvold BS, O’Connell KS, Frei O, Shadrin A, Cheng W, Bettella F, Rødevand L, Odegaard KJ, Fan CC, Pirinen M, Hautakangas HM; HUNT All-In Headache; Dale AM, Djurovic S, Smeland OB, Andreassen OA.
    Dissecting the shared genetic basis of migraine and mental disorders using novel statistical tools.
    Brain. 2022 Mar 29;145(1):142-153. DOI:10.1093/brain/awab267, PMID:34273149, PMCID:PMC8967089.

  21. Häppölä P, Gormley P, Nuottamo ME, Artto V, Sumelahti ML, Nissilä M, Keski-Säntti P, Ilmavirta M, Kaunisto MA, Hämäläinen EI, Ripatti S, Pirinen M, Wessman M, Palotie A, Kallela M; International Headache Genetics Consortium (IHGC).
    Polygenic risk provides biological validity for the ICHD-3 criteria among Finnish migraine families.
    Cephalalgia. 2022 Apr;42(4-5):345-356. DOI:10.1177/03331024211045651, PMID:34648375, PMCID:PMC8988286.

  22. Hautakangas H, Winsvold BS, Ruotsalainen SE, Bjornsdottir G, Harder AVE, Kogelman LJA, Thomas LF, Noordam R, Benner C, Gormley P, Artto V, Banasik K, Bjornsdottir A, Boomsma DI, Brumpton BM, Burgdorf KS, Buring JE, Chalmer MA, de Boer I, Dichgans M, Erikstrup C, Färkkilä M, Garbrielsen ME, Ghanbari M, Hagen K, Häppölä P, Hottenga JJ, Hrafnsdottir MG, Hveem K, Johnsen MB, Kähönen M, Kristoffersen ES, Kurth T, Lehtimäki T, Lighart L, Magnusson SH, Malik R, Pedersen OB, Pelzer N, Penninx BWJH, Ran C, Ridker PM, Rosendaal FR, Sigurdardottir GR, Skogholt AH, Sveinsson OA, Thorgeirsson TE, Ullum H, Vijfhuizen LS, Widén E, van Dijk KW; International Headache Genetics Consortium; HUNT All-in Headache; Danish Blood Donor Study Genomic Cohort; Aromaa A, Belin AC, Freilinger T, Ikram MA, Järvelin MR, Raitakari OT, Terwindt GM, Kallela M, Wessman M, Olesen J, Chasman DI, Nyholt DR, Stefánsson H, Stefansson K, van den Maagdenberg AMJM, Hansen TF, Ripatti S, Zwart JA, Palotie A, Pirinen M.
    Genome-wide analysis of 102,084 migraine cases identifies 123 risk loci and subtype-specific risk alleles.
    Nat Genet. 2022 Feb;54(2):152-160. DOI:10.1038/s41588-021-00990-0, PMID:35115687, PMCID:PMC8837554.

  23. Nuottamo ME, Häppölä P, Artto V, Hautakangas H, Pirinen M, Hiekkalinna T, Ellonen P, Lepistö M, Hämäläinen E; International Headache Genetics Consortium (IHGC), FinnGenConsortium; Siren A, Lehesjoki AE, Kallela M, Palotie A, Kaunisto MA, Wessman M.
    NCOR2 is a novel candidate gene for migraine-epilepsy phenotype.
    Cephalalgia. 2022 Jun;42(7):631-644. DOI:10.1177/03331024211068065, PMID:35166138, PMCID: none.

  24. Elovainio M, Lahti J, Pirinen M, Pulkki-Råback L, Malmberg A, Lipsanen J, Virtanen M, Kivimäki M, Hakulinen C.
    Association of social isolation, loneliness and genetic risk with incidence of dementia: UK Biobank Cohort Study.
    BMJ Open. 2022 Feb 23;12(2):e053936. DOI:10.1136/bmjopen-2021-053936, PMID:35197341, PMCID:PMC8867309.

  25. Tamlander M, Mars N, Pirinen M; FinnGen; Widén E, Ripatti S.
    Integration of questionnaire-based risk factors improves polygenic risk scores for human coronary heart disease and type 2 diabetes.
    Commun Biol. 2022 Feb 23;5(1):158. DOI:10.1038/s42003-021-02996-0, PMID:35197564, PMCID:PMC8866413.

  26. Trubetskoy V, Pardiñas AF, Qi T, Panagiotaropoulou G, Awasthi S, Bigdeli TB, Bryois J, Chen CY, Dennison CA, Hall LS, Lam M, Watanabe K, Frei O, Ge T, Harwood JC, Koopmans F, Magnusson S, Richards AL, Sidorenko J, Wu Y, Zeng J, Grove J, Kim M, Li Z, Voloudakis G, Zhang W, Adams M, Agartz I, Atkinson EG, Agerbo E, Al Eissa M, Albus M, Alexander M, Alizadeh BZ, Alptekin K, Als TD, Amin F, Arolt V, Arrojo M, Athanasiu L, Azevedo MH, Bacanu SA, Bass NJ, Begemann M, Belliveau RA, Bene J, Benyamin B, Bergen SE, Blasi G, Bobes J, Bonassi S, Braun A, Bressan RA, Bromet EJ, Bruggeman R, Buckley PF, Buckner RL, Bybjerg-Grauholm J, Cahn W, Cairns MJ, Calkins ME, Carr VJ, Castle D, Catts SV, Chambert KD, Chan RCK, Chaumette B, Cheng W, Cheung EFC, Chong SA, Cohen D, Consoli A, Cordeiro Q, Costas J, Curtis C, Davidson M, Davis KL, de Haan L, Degenhardt F, DeLisi LE, Demontis D, Dickerson F, Dikeos D, Dinan T, Djurovic S, Duan J, Ducci G, Dudbridge F, Eriksson JG, Fañanás L, Faraone SV, Fiorentino A, Forstner A, Frank J, Freimer NB, Fromer M, Frustaci A, Gadelha A, Genovese G, Gershon ES, et al.
    Mapping genomic loci implicates genes and synaptic biology in schizophrenia.
    Nature. 2022 Apr;604(7906):502-508. DOI:10.1038/s41586-022-04434-5, PMID:35396580, PMCID:PMC9392466.

  27. Mars N, Kerminen S, Feng YA, Kanai M, Läll K, Thomas LF, Skogholt AH, Della Briotta Parolo P; Biobank Japan Project; FinnGen; Neale BM, Smoller JW, Gabrielsen ME, Hveem K, Mägi R, Matsuda K, Okada Y, Pirinen M, Palotie A, Ganna A, Martin AR, Ripatti S.
    Genome-wide risk prediction of common diseases across ancestries in one million people.
    Cell Genom. 2022 Apr 13;2(4):None. DOI:10.1016/j.xgen.2022.100118, PMID:35591975, PMCID:PMC9010308.

  28. Jukarainen S, Kiiskinen T, Kuitunen S, Havulinna AS, Karjalainen J, Cordioli M, Rämö JT, Mars N; FinnGen; Samocha KE, Ollila HM, Pirinen M, Ganna A.
    Genetic risk factors have a substantial impact on healthy life years.
    Nat Med. 2022 Sep;28(9):1893-1901. DOI:10.1038/s41591-022-01957-2, PMID:36097220, PMCID:PMC9499866.

  29. Tabassum R, Ruotsalainen S, Ottensmann L, Gerl MJ, Klose C, Tukiainen T, Pirinen M, Simons K, Widén E, Ripatti S.
    Lipidome- and Genome-Wide Study to Understand Sex Differences in Circulatory Lipids.
    J Am Heart Assoc. 2022 Oct 4;11(19):e027103. DOI:10.1161/JAHA.122.027103, PMID:36193934, PMCID:PMC9673737.

  30. Partanen JJ, Häppölä P, Zhou W, Lehisto AA, Ainola M, Sutinen E, Allen RJ, Stockwell AD, Leavy OC, Oldham JM, Guillen-Guio B, Cox NJ, Hirbo JB, Schwartz DA, Fingerlin TE, Flores C, Noth I, Yaspan BL, Jenkins RG, Wain LV, Ripatti S, Pirinen M; International IPF Genetics Consortium; Global Biobank Meta-Analysis Initiative (GBMI); Laitinen T, Kaarteenaho R, Myllärniemi M, Daly MJ, Koskela JT.
    Leveraging global multi-ancestry meta-analysis in the study of idiopathic pulmonary fibrosis genetics.
    Cell Genom. 2022 Oct 12;2(10):100181. DOI:10.1016/j.xgen.2022.100181, PMID:36777997, PMCID:PMC9903787.

  31. COVID-19 Host Genetics Initiative.
    A first update on mapping the human genetic architecture of COVID-19.
    Nature. 2022 Aug;608(7921):E1-E10. DOI:10.1038/s41586-022-04826-7 , PMID:35922517, PMCID: none.

  32. Mars N, Kerola AM, Kauppi MJ, Pirinen M, Elonheimo O, Sokka-Isler T.
    Cluster analysis identifies unmet healthcare needs among patients with rheumatoid arthritis.
    Scand J Rheumatol. 2022 Sep;51(5):355-362. DOI:10.1080/03009742.2021.1944306 , PMID:34511040, PMCID: none.

  33. Buchwald J, Chenoweth MJ, Palviainen T, Zhu G, Benner C, Gordon S, Korhonen T, Ripatti S, Madden PAF, Lehtimäki T, Raitakari OT, Salomaa V, Rose RJ, George TP, Lerman C, Pirinen M, Martin NG, Kaprio J, Loukola A, Tyndale RF.
    Genome-wide association meta-analysis of nicotine metabolism and cigarette consumption measures in smokers of European descent.
    Mol Psychiatry. 2021 Jun;26(6):2212-2223. DOI:10.1038/s41380-020-0702-z, PMID:32157176, PMCID:PMC7483250.

  34. Ruotsalainen SE, Partanen JJ, Cichonska A, Lin J, Benner C, Surakka I; FinnGen; Reeve MP, Palta P, Salmi M, Jalkanen S, Ahola-Olli A, Palotie A, Salomaa V, Daly MJ, Pirinen M, Ripatti S, Koskela J.
    An expanded analysis framework for multivariate GWAS connects inflammatory biomarkers to functional variants and disease.
    Eur J Hum Genet. 2021 Feb;29(2):309-324. DOI:10.1038/s41431-020-00730-8, PMID:33110245, PMCID:PMC7868371.

  35. Alabi RO, Mäkitie AA, Pirinen M, Elmusrati M, Leivo I, Almangush A.
    Comparison of nomogram with machine learning techniques for prediction of overall survival in patients with tongue cancer.
    Int J Med Inform. 2021 Jan;145:104313. DOI:10.1016/j.ijmedinf.2020.104313, PMID:33142259, PMCID: none.

  36. Hassan S, Surakka I, Taskinen MR, Salomaa V, Palotie A, Wessman M, Tukiainen T, Pirinen M, Palta P, Ripatti S.
    High-resolution population-specific recombination rates and their effect on phasing and genotype imputation.
    Eur J Hum Genet. 2021 Apr;29(4):615-624. DOI:10.1038/s41431-020-00768-8, PMID:33249422, PMCID:PMC8114909.

  37. Kerminen S, Cerioli N, Pacauskas D, Havulinna AS, Perola M, Jousilahti P, Salomaa V, Daly MJ, Vyas R, Ripatti S, Pirinen M.
    Changes in the fine-scale genetic structure of Finland through the 20th century.
    PLoS Genet. 2021 Mar 4;17(3):e1009347. DOI:10.1371/journal.pgen.1009347, PMID:33661898, PMCID:PMC7932171.

  38. Ahlström S, Bergman P, Jokela R, Ottensmann L, Ahola-Olli A, Pirinen M, Olkkola KT, Kaunisto MA, Kalso E.
    First genome-wide association study on rocuronium dose requirements shows association with SLCO1A2.
    Br J Anaesth. 2021 May;126(5):949-957. DOI:10.1016/j.bja.2021.01.029, PMID:33676726, PMCID:PMC8132880.

  39. Almangush A, Alabi RO, Troiano G, Coletta RD, Salo T, Pirinen M, Mäkitie AA, Leivo I.
    Clinical significance of tumor-stroma ratio in head and neck cancer: a systematic review and meta-analysis.
    BMC Cancer. 2021 Apr 30;21(1):480. DOI:10.1186/s12885-021-08222-8, PMID:33931044, PMCID:PMC8086072.

  40. Alabi RO, Youssef O, Pirinen M, Elmusrati M, Mäkitie AA, Leivo I, Almangush A.
    Machine learning in oral squamous cell carcinoma: Current status, clinical concerns and prospects for future-A systematic review.
    Artif Intell Med. 2021 May;115:102060. DOI:10.1016/j.artmed.2021.102060, PMID:34001326, PMCID: none.

  41. Palomäki A; FinnGen Rheumatology Clinical Expert Group; Palotie A, Koskela J, Eklund KK, Pirinen M; FinnGen; Ripatti S, Laitinen T, Mars N.
    Lifetime risk of rheumatoid arthritis-associated interstitial lung disease in MUC5B mutation carriers.
    Ann Rheum Dis. 2021 Dec;80(12):1530-1536. DOI:10.1136/annrheumdis-2021-220698, PMID:34344703, PMCID:PMC8600604.

  42. Venkataraman GR, DeBoever C, Tanigawa Y, Aguirre M, Ioannidis AG, Mostafavi H, Spencer CCA, Poterba T, Bustamante CD, Daly MJ, Pirinen M, Rivas MA.
    Bayesian model comparison for rare-variant association studies.
    Am J Hum Genet. 2021 Dec 2;108(12):2354-2367. DOI:10.1016/j.ajhg.2021.11.005, PMID:34822764, PMCID:PMC8715195.

  43. Ripatti P, Rämö JT, Mars NJ, Fu Y, Lin J, Söderlund S, Benner C, Surakka I, Kiiskinen T, Havulinna AS, Palta P, Freimer NB, Widén E, Salomaa V, Tukiainen T, Pirinen M, Palotie A, Taskinen MR, Ripatti S; FinnGen†.
    Polygenic Hyperlipidemias and Coronary Artery Disease Risk.
    Circ Genom Precis Med. 2020 Apr;13(2):e002725. DOI:10.1161/CIRCGEN.119.002725, PMID:32154731, PMCID:PMC7176338.

  44. Lin J, Tabassum R, Ripatti S, Pirinen M.
    MetaPhat: Detecting and Decomposing Multivariate Associations From Univariate Genome-Wide Association Statistics.
    Front Genet. 2020 May 15;11:431. DOI:10.3389/fgene.2020.00431, PMID:32499813, PMCID:PMC7242752.

  45. Gilchrist JJ, Uyoga S, Pirinen M, Rautanen A, Mwarumba S, Njuguna P, Mturi N; Kenyan Bacteraemia Study Group; Hill AVS, Scott JAG, Williams TN.
    Risk of pneumococcal bacteremia in Kenyan children with glucose-6-phosphate dehydrogenase deficiency.
    BMC Med. 2020 Jun 15;18(1):148. DOI:10.1186/s12916-020-01604-y, PMID:32536341, PMCID:PMC7294654.

  46. Almangush A, Pirinen M, Youssef O, Mäkitie AA, Leivo I.
    Risk stratification in oral squamous cell carcinoma using staging of the eighth American Joint Committee on Cancer: Systematic review and meta-analysis.
    Head Neck. 2020 Oct;42(10):3002-3017. DOI:10.1002/hed.26344, PMID:32548858, PMCID: none.

  47. Weissbrod O, Hormozdiari F, Benner C, Cui R, Ulirsch J, Gazal S, Schoech AP, van de Geijn B, Reshef Y, Márquez-Luna C, O’Connor L, Pirinen M, Finucane HK, Price AL.
    Functionally informed fine-mapping and polygenic localization of complex trait heritability.
    Nat Genet. 2020 Dec;52(12):1355-1363. DOI:10.1038/s41588-020-00735-5, PMID:33199916, PMCID:PMC7710571.

  48. Mars N, Widén E, Kerminen S, Meretoja T, Pirinen M, Della Briotta Parolo P, Palta P; FinnGen; Palotie A, Kaprio J, Joensuu H, Daly M, Ripatti S.
    The role of polygenic risk and susceptibility genes in breast cancer over the course of life.
    Nat Commun. 2020 Dec 14;11(1):6383. DOI:10.1038/s41467-020-19966-5, PMID:33318493, PMCID:PMC7736877.

  49. Sieviläinen M, Almahmoudi R, Al-Samadi A, Salo T, Pirinen M, Almangush A.
    The prognostic value of immune checkpoints in oral squamous cell carcinoma.
    Oral Dis. 2019 Sep;25(6):1435-1445. DOI:10.1111/odi.12991, PMID:30315712, PMCID: none.

  50. Almangush A, Youssef O, Pirinen M, Sundström J, Leivo I, Mäkitie AA.
    Does evaluation of tumour budding in diagnostic biopsies have a clinical relevance? A systematic review.
    Histopathology. 2019 Mar;74(4):536-544. DOI:10.1111/his.13793, PMID:30450728, PMCID: none.

  51. Kurki MI, Saarentaus E, Pietiläinen O, Gormley P, Lal D, Kerminen S, Torniainen-Holm M, Hämäläinen E, Rahikkala E, Keski-Filppula R, Rauhala M, Korpi-Heikkilä S, Komulainen-Ebrahim J, Helander H, Vieira P, Männikkö M, Peltonen M, Havulinna AS, Salomaa V, Pirinen M, Suvisaari J, Moilanen JS, Körkkö J, Kuismin O, Daly MJ, Palotie A.
    Contribution of rare and common variants to intellectual disability in a sub-isolate of Northern Finland.
    Nat Commun. 2019 Jan 24;10(1):410. DOI:10.1038/s41467-018-08262-y, PMID:30679432, PMCID:PMC6345990.

  52. Trochet H, Pirinen M, Band G, Jostins L, McVean G, Spencer CCA.
    Bayesian meta-analysis across genome-wide association studies of diverse phenotypes.
    Genet Epidemiol. 2019 Jul;43(5):532-547. DOI:10.1002/gepi.22202, PMID:30920090, PMCID: none.

  53. Rivas MA, Avila BE, Koskela J, Huang H, Stevens C, Pirinen M, Haritunians T, Neale BM, Kurki M, Ganna A, Graham D, Glaser B, Peter I, Atzmon G, Barzilai N, Levine AP, Schiff E, Pontikos N, Weisburd B, Lek M, Karczewski KJ, Bloom J, Minikel EV, Petersen BS, Beaugerie L, Seksik P, Cosnes J, Schreiber S, Bokemeyer B, Bethge J; International IBD Genetics Consortium; NIDDK IBD Genetics Consortium; T2D-GENES Consortium; Heap G, Ahmad T, Plagnol V, Segal AW, Targan S, Turner D, Saavalainen P, Farkkila M, Kontula K, Palotie A, Brant SR, Duerr RH, Silverberg MS, Rioux JD, Weersma RK, Franke A, Jostins L, Anderson CA, Barrett JC, MacArthur DG, Jalas C, Sokol H, Xavier RJ, Pulver A, Cho JH, McGovern DPB, Daly MJ.
    Correction: Insights into the genetic epidemiology of Crohn’s and rare diseases in the Ashkenazi Jewish population.
    PLoS Genet. 2019 May 30;15(5):e1008190. DOI:10.1371/journal.pgen.1008190, PMID:31145742, PMCID:PMC6542503.

  54. Kerminen S, Martin AR, Koskela J, Ruotsalainen SE, Havulinna AS, Surakka I, Palotie A, Perola M, Salomaa V, Daly MJ, Ripatti S, Pirinen M.
    Geographic Variation and Bias in the Polygenic Scores of Complex Diseases and Traits in Finland.
    Am J Hum Genet. 2019 Jun 6;104(6):1169-1181. DOI:10.1016/j.ajhg.2019.05.001, PMID:31155286, PMCID:PMC6562021.

  55. Rämö JT, Ripatti P, Tabassum R, Söderlund S, Matikainen N, Gerl MJ, Klose C, Surma MA, Stitziel NO, Havulinna AS, Pirinen M, Salomaa V, Freimer NB, Jauhiainen M, Palotie A, Taskinen MR, Simons K, Ripatti S.
    Coronary Artery Disease Risk and Lipidomic Profiles Are Similar in Hyperlipidemias With Family History and Population-Ascertained Hyperlipidemias.
    J Am Heart Assoc. 2019 Jul 2;8(13):e012415. DOI:10.1161/JAHA.119.012415, PMID:31256696, PMCID:PMC6662358.

  56. Locke AE, Steinberg KM, Chiang CWK, Service SK, Havulinna AS, Stell L, Pirinen M, Abel HJ, Chiang CC, Fulton RS, Jackson AU, Kang CJ, Kanchi KL, Koboldt DC, Larson DE, Nelson J, Nicholas TJ, Pietilä A, Ramensky V, Ray D, Scott LJ, Stringham HM, Vangipurapu J, Welch R, Yajnik P, Yin X, Eriksson JG, Ala-Korpela M, Järvelin MR, Männikkö M, Laivuori H; FinnGen Project; Dutcher SK, Stitziel NO, Wilson RK, Hall IM, Sabatti C, Palotie A, Salomaa V, Laakso M, Ripatti S, Boehnke M, Freimer NB.
    Exome sequencing of Finnish isolates enhances rare-variant association power.
    Nature. 2019 Aug;572(7769):323-328. DOI:10.1038/s41586-019-1457-z, PMID:31367044, PMCID:PMC6697530.

  57. Almahmoudi R, Kasanen M, Sieviläinen M, Salem A, Pirinen M, Salo T, Al-Samadi A.
    Prognostic value of blood and lymphatic vessel markers in tongue cancer: A systematic review.
    Cancer Sci. 2019 Nov;110(11):3424-3433. DOI:10.1111/cas.14189, PMID:31495050, PMCID:PMC6824997.

  58. Tabassum R, Rämö JT, Ripatti P, Koskela JT, Kurki M, Karjalainen J, Palta P, Hassan S, Nunez-Fontarnau J, Kiiskinen TTJ, Söderlund S, Matikainen N, Gerl MJ, Surma MA, Klose C, Stitziel NO, Laivuori H, Havulinna AS, Service SK, Salomaa V, Pirinen M; FinnGen Project; Jauhiainen M, Daly MJ, Freimer NB, Palotie A, Taskinen MR, Simons K, Ripatti S.
    Genetic architecture of human plasma lipidome and its link to cardiovascular disease.
    Nat Commun. 2019 Sep 24;10(1):4329. DOI:10.1038/s41467-019-11954-8, PMID:31551469, PMCID:PMC6760179.

  59. Locke AE, Steinberg KM, Chiang CWK, Service SK, Havulinna AS, Stell L, Pirinen M, Abel HJ, Chiang CC, Fulton RS, Jackson AU, Kang CJ, Kanchi KL, Koboldt DC, Larson DE, Nelson J, Nicholas TJ, Pietilä A, Ramensky V, Ray D, Scott LJ, Stringham HM, Vangipurapu J, Welch R, Yajnik P, Yin X, Eriksson JG, Ala-Korpela M, Järvelin MR, Männikkö M, Laivuori H; FinnGen Project; Dutcher SK, Stitziel NO, Wilson RK, Hall IM, Sabatti C, Palotie A, Salomaa V, Laakso M, Ripatti S, Boehnke M, Freimer NB.
    Author Correction: Exome sequencing of Finnish isolates enhances rare-variant association power.
    Nature. 2019 Nov;575(7783):E4. DOI:10.1038/s41586-019-1726-x, PMID:31686056, PMCID: none.

  60. Mars NJ, Kerola AM, Kauppi MJ, Pirinen M, Elonheimo O, Sokka-Isler T.
    Healthcare costs and outcomes in adult patients with juvenile idiopathic arthritis: a population-based study.
    Scand J Rheumatol. 2019 Mar;48(2):114-120. DOI:10.1080/03009742.2018.1475580 , PMID:30070935, PMCID: none.

  61. Mars NJ, Kerola AM, Kauppi MJ, Pirinen M, Elonheimo O, Sokka-Isler T.
    Patients with rheumatic diseases share similar patterns of healthcare resource utilization.
    Scand J Rheumatol. 2019 Jul;48(4):300-307. DOI:10.1080/03009742.2018.1559878 , PMID:30836033, PMCID: none.

  62. Almangush A, Pirinen M, Heikkinen I, Mäkitie AA, Salo T, Leivo I.
    Tumour budding in oral squamous cell carcinoma: a meta-analysis.
    Br J Cancer. 2018 Feb 20;118(4):577-586. DOI:10.1038/bjc.2017.425, PMID:29190636, PMCID:PMC5830589.

  63. Gilchrist JJ, Rautanen A, Fairfax BP, Mills TC, Naranbhai V, Trochet H, Pirinen M, Muthumbi E, Mwarumba S, Njuguna P, Mturi N, Msefula CL, Gondwe EN, MacLennan JM, Chapman SJ, Molyneux ME, Knight JC, Spencer CCA, Williams TN, MacLennan CA, Scott JAG, Hill AVS.
    Risk of nontyphoidal Salmonella bacteraemia in African children is modified by STAT4.
    Nat Commun. 2018 Mar 9;9(1):1014. DOI:10.1038/s41467-017-02398-z, PMID:29523850, PMCID:PMC5844948.

  64. Gilchrist JJ, Mentzer AJ, Rautanen A, Pirinen M, Mwarumba S, Njuguna P, Mturi N; Wellcome Trust Case-Control Consortium 2; Kenyan Bacteraemia Study Group; Williams TN, Scott JAG, Hill AVS.
    Genetic variation in VAC14 is associated with bacteremia secondary to diverse pathogens in African children.
    Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):E3601-E3603. DOI:10.1073/pnas.1802071115, PMID:29588414, PMCID:PMC5910872.

  65. Martin AR, Karczewski KJ, Kerminen S, Kurki MI, Sarin AP, Artomov M, Eriksson JG, Esko T, Genovese G, Havulinna AS, Kaprio J, Konradi A, Korányi L, Kostareva A, Männikkö M, Metspalu A, Perola M, Prasad RB, Raitakari O, Rotar O, Salomaa V, Groop L, Palotie A, Neale BM, Ripatti S, Pirinen M, Daly MJ.
    Haplotype Sharing Provides Insights into Fine-Scale Population History and Disease in Finland.
    Am J Hum Genet. 2018 May 3;102(5):760-775. DOI:10.1016/j.ajhg.2018.03.003, PMID:29706349, PMCID:PMC5986696.

  66. Rivas MA, Avila BE, Koskela J, Huang H, Stevens C, Pirinen M, Haritunians T, Neale BM, Kurki M, Ganna A, Graham D, Glaser B, Peter I, Atzmon G, Barzilai N, Levine AP, Schiff E, Pontikos N, Weisburd B, Lek M, Karczewski KJ, Bloom J, Minikel EV, Petersen BS, Beaugerie L, Seksik P, Cosnes J, Schreiber S, Bokemeyer B, Bethge J; International IBD Genetics Consortium; NIDDK IBD Genetics Consortium; T2D-GENES Consortium; Heap G, Ahmad T, Plagnol V, Segal AW, Targan S, Turner D, Saavalainen P, Farkkila M, Kontula K, Palotie A, Brant SR, Duerr RH, Silverberg MS, Rioux JD, Weersma RK, Franke A, Jostins L, Anderson CA, Barrett JC, MacArthur DG, Jalas C, Sokol H, Xavier RJ, Pulver A, Cho JH, McGovern DPB, Daly MJ.
    Insights into the genetic epidemiology of Crohn’s and rare diseases in the Ashkenazi Jewish population.
    PLoS Genet. 2018 May 24;14(5):e1007329. DOI:10.1371/journal.pgen.1007329, PMID:29795570, PMCID:PMC5967709.

  67. Chheda H, Palta P, Pirinen M, McCarthy S, Walter K, Koskinen S, Salomaa V, Daly M, Durbin R, Palotie A, Aittokallio T, Ripatti S.
    Whole-genome view of the consequences of a population bottleneck using 2926 genome sequences from Finland and United Kingdom.
    Eur J Hum Genet. 2017 Apr;25(4):477-484. DOI:10.1038/ejhg.2016.205, PMID:28145424, PMCID:PMC5346294.

  68. Wang L, Ko ER, Gilchrist JJ, Pittman KJ, Rautanen A, Pirinen M, Thompson JW, Dubois LG, Langley RJ, Jaslow SL, Salinas RE, Rouse DC, Moseley MA, Mwarumba S, Njuguna P, Mturi N; Wellcome Trust Case Control Consortium 2; Kenyan Bacteraemia Study Group; Williams TN, Scott JA, Hill AV, Woods CW, Ginsburg GS, Tsalik EL, Ko DC.
    Human genetic and metabolite variation reveals that methylthioadenosine is a prognostic biomarker and an inflammatory regulator in sepsis.
    Sci Adv. 2017 Mar 8;3(3):e1602096. DOI:10.1126/sciadv.1602096, PMID:28345042, PMCID:PMC5342653.

  69. Pirinen M, Benner C, Marttinen P, Järvelin MR, Rivas MA, Ripatti S.
    biMM: efficient estimation of genetic variances and covariances for cohorts with high-dimensional phenotype measurements.
    Bioinformatics. 2017 Aug 1;33(15):2405-2407. DOI:10.1093/bioinformatics/btx166, PMID:28369165, PMCID:PMC5860115.

  70. Benner C, Havulinna AS, Järvelin MR, Salomaa V, Ripatti S, Pirinen M.
    Prospects of Fine-Mapping Trait-Associated Genomic Regions by Using Summary Statistics from Genome-wide Association Studies.
    Am J Hum Genet. 2017 Oct 5;101(4):539-551. DOI:10.1016/j.ajhg.2017.08.012, PMID:28942963, PMCID:PMC5630179.

  71. Kerminen S, Havulinna AS, Hellenthal G, Martin AR, Sarin AP, Perola M, Palotie A, Salomaa V, Daly MJ, Ripatti S, Pirinen M.
    Fine-Scale Genetic Structure in Finland.
    G3 (Bethesda). 2017 Oct 5;7(10):3459-3468. DOI:10.1534/g3.117.300217, PMID:28983069, PMCID:PMC5633394.

  72. Benner C, Spencer CC, Havulinna AS, Salomaa V, Ripatti S, Pirinen M.
    FINEMAP: efficient variable selection using summary data from genome-wide association studies.
    Bioinformatics. 2016 May 15;32(10):1493-501. DOI:10.1093/bioinformatics/btw018, PMID:26773131, PMCID:PMC4866522.

  73. Kettunen J, Demirkan A, Würtz P, Draisma HH, Haller T, Rawal R, Vaarhorst A, Kangas AJ, Lyytikäinen LP, Pirinen M, Pool R, Sarin AP, Soininen P, Tukiainen T, Wang Q, Tiainen M, Tynkkynen T, Amin N, Zeller T, Beekman M, Deelen J, van Dijk KW, Esko T, Hottenga JJ, van Leeuwen EM, Lehtimäki T, Mihailov E, Rose RJ, de Craen AJ, Gieger C, Kähönen M, Perola M, Blankenberg S, Savolainen MJ, Verhoeven A, Viikari J, Willemsen G, Boomsma DI, van Duijn CM, Eriksson J, Jula A, Järvelin MR, Kaprio J, Metspalu A, Raitakari O, Salomaa V, Slagboom PE, Waldenberger M, Ripatti S, Ala-Korpela M.
    Genome-wide study for circulating metabolites identifies 62 loci and reveals novel systemic effects of LPA.
    Nat Commun. 2016 Mar 23;7:11122. DOI:10.1038/ncomms11122, PMID:27005778, PMCID:PMC4814583.

  74. Cichonska A, Rousu J, Marttinen P, Kangas AJ, Soininen P, Lehtimäki T, Raitakari OT, Järvelin MR, Salomaa V, Ala-Korpela M, Ripatti S, Pirinen M.
    metaCCA: summary statistics-based multivariate meta-analysis of genome-wide association studies using canonical correlation analysis.
    Bioinformatics. 2016 Jul 1;32(13):1981-9. DOI:10.1093/bioinformatics/btw052, PMID:27153689, PMCID:PMC4920109.

  75. Ripatti P, Rämö JT, Söderlund S, Surakka I, Matikainen N, Pirinen M, Pajukanta P, Sarin AP, Service SK, Laurila PP, Ehnholm C, Salomaa V, Wilson RK, Palotie A, Freimer NB, Taskinen MR, Ripatti S.
    The Contribution of GWAS Loci in Familial Dyslipidemias.
    PLoS Genet. 2016 May 26;12(5):e1006078. DOI:10.1371/journal.pgen.1006078, PMID:27227539, PMCID:PMC4882070.

  76. Kenyan Bacteraemia Study Group; Wellcome Trust Case Control Consortium 2 (WTCCC2); Rautanen A, Pirinen M, Mills TC, Rockett KA, Strange A, Ndungu AW, Naranbhai V, Gilchrist JJ, Bellenguez C, Freeman C, Band G, Bumpstead SJ, Edkins S, Giannoulatou E, Gray E, Dronov S, Hunt SE, Langford C, Pearson RD, Su Z, Vukcevic D, Macharia AW, Uyoga S, Ndila C, Mturi N, Njuguna P, Mohammed S, Berkley JA, Mwangi I, Mwarumba S, Kitsao BS, Lowe BS, Morpeth SC, Khandwalla I; Kilifi Bacteraemia Surveillance Group; Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski J, Markus HS, Mathew CG, Palmer CNA, Plomin R, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Deloukas P, Peltonen L, Williams TN, Scott JAG, Chapman SJ, Donnelly P, Hill AVS, Spencer CCA.
    Polymorphism in a lincRNA Associates with a Doubled Risk of Pneumococcal Bacteremia in Kenyan Children.
    Am J Hum Genet. 2016 Jun 2;98(6):1092-1100. DOI:10.1016/j.ajhg.2016.03.025, PMID:27236921, PMCID:PMC4908194.

  77. Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VSK, Dillenberger D, Neto EC, Norman T, Aittokallio T, Ammad-Ud-Din M, Azencott CA, Bellón V, Boeva V, Bunte K, Chheda H, Cheng L, Corander J, Dumontier M, Goldenberg A, Gopalacharyulu P, Hajiloo M, Hidru D, Jaiswal A, Kaski S, Khalfaoui B, Khan SA, Kramer ER, Marttinen P, Mezlini AM, Molparia B, Pirinen M, Saarela J, Samwald M, Stoven V, Tang H, Tang J, Torkamani A, Vert JP, Wang B, Wang T, Wennerberg K, Wineinger NE, Xiao G, Xie Y, Yeung R, Zhan X, Zhao C; Members of the Rheumatoid Arthritis Challenge Consortium; Greenberg J, Kremer J, Michaud K, Barton A, Coenen M, Mariette X, Miceli C, Shadick N, Weinblatt M, de Vries N, Tak PP, Gerlag D, Huizinga TWJ, Kurreeman F, Allaart CF, Louis Bridges S Jr, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM.
    Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.
    Nat Commun. 2016 Aug 23;7:12460. DOI:10.1038/ncomms12460, PMID:27549343, PMCID:PMC4996969.

  78. Tikkanen E, Pirinen M, Sarin AP, Havulinna AS, Männistö S, Saltevo J, Lokki ML, Sinisalo J, Lundqvist A, Jula A, Salomaa V, Ripatti S.
    Genetic support for the causal role of insulin in coronary heart disease.
    Diabetologia. 2016 Nov;59(11):2369-2377. DOI:10.1007/s00125-016-4081-6, PMID:27561896, PMCID: none.

  79. Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VSK, Dillenberger D, Neto EC, Norman T, Aittokallio T, Ammad-Ud-Din M, Azencott CA, Bellón V, Boeva V, Bunte K, Chheda H, Cheng L, Corander J, Dumontier M, Goldenberg A, Gopalacharyulu P, Hajiloo M, Hidru D, Jaiswal A, Kaski S, Khalfaoui B, Khan SA, Kramer ER, Marttinen P, Mezlini AM, Molparia B, Pirinen M, Saarela J, Samwald M, Stoven V, Tang H, Tang J, Torkamani A, Vert JP, Wang B, Wang T, Wennerberg K, Wineinger NE, Xiao G, Xie Y, Yeung R, Zhan X, Zhao C; Members of the Rheumatoid Arthritis Challenge Consortium; Greenberg J, Kremer J, Michaud K, Barton A, Coenen M, Mariette X, Miceli C, Shadick N, Weinblatt M, de Vries N, Tak PP, Gerlag D, Huizinga TWJ, Kurreeman F, Allaart CF, Bridges SL Jr, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM.
    Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.
    Nat Commun. 2016 Oct 10;7:13205. DOI:10.1038/ncomms13205, PMID:27721464, PMCID:PMC5062501.

  80. Gillberg J, Marttinen P, Pirinen M, Kangas AJ, Soininen P, Ali M, Havulinna AS, Järvelin MR, Ala-Korpela M, Kaski S.
    Multiple output regression with latent noise.
    Journal of Machine Learning Research. 2016 17: 4170-4204. DOI:none, PMID: none, PMCID: none.

  81. Leslie S, Winney B, Hellenthal G, Davison D, Boumertit A, Day T, Hutnik K, Royrvik EC, Cunliffe B; Wellcome Trust Case Control Consortium 2; International Multiple Sclerosis Genetics Consortium; Lawson DJ, Falush D, Freeman C, Pirinen M, Myers S, Robinson M, Donnelly P, Bodmer W.
    The fine-scale genetic structure of the British population.
    Nature. 2015 Mar 19;519(7543):309-314. DOI:10.1038/nature14230, PMID:25788095, PMCID:PMC4632200.

  82. Pirinen M, Lappalainen T, Zaitlen NA; GTEx Consortium; Dermitzakis ET, Donnelly P, McCarthy MI, Rivas MA.
    Assessing allele-specific expression across multiple tissues from RNA-seq read data.
    Bioinformatics. 2015 Aug 1;31(15):2497-504. DOI:10.1093/bioinformatics/btv074, PMID:25819081, PMCID:PMC4514921.

  83. Baran Y, Subramaniam M, Biton A, Tukiainen T, Tsang EK, Rivas MA, Pirinen M, Gutierrez-Arcelus M, Smith KS, Kukurba KR, Zhang R, Eng C, Torgerson DG, Urbanek C; GTEx Consortium; Li JB, Rodriguez-Santana JR, Burchard EG, Seibold MA, MacArthur DG, Montgomery SB, Zaitlen NA, Lappalainen T.
    The landscape of genomic imprinting across diverse adult human tissues.
    Genome Res. 2015 Jul;25(7):927-36. DOI:10.1101/gr.192278.115, PMID:25953952, PMCID:PMC4484390.

  84. Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J; GTEx Consortium; Geuvadis Consortium; Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG.
    Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.
    Science. 2015 May 8;348(6235):666-9. DOI:10.1126/science.1261877, PMID:25954003, PMCID:PMC4537935.

  85. Surakka I, Horikoshi M, Mägi R, Sarin AP, Mahajan A, Lagou V, Marullo L, Ferreira T, Miraglio B, Timonen S, Kettunen J, Pirinen M, Karjalainen J, Thorleifsson G, Hägg S, Hottenga JJ, Isaacs A, Ladenvall C, Beekman M, Esko T, Ried JS, Nelson CP, Willenborg C, Gustafsson S, Westra HJ, Blades M, de Craen AJ, de Geus EJ, Deelen J, Grallert H, Hamsten A, Havulinna AS, Hengstenberg C, Houwing-Duistermaat JJ, Hyppönen E, Karssen LC, Lehtimäki T, Lyssenko V, Magnusson PK, Mihailov E, Müller-Nurasyid M, Mpindi JP, Pedersen NL, Penninx BW, Perola M, Pers TH, Peters A, Rung J, Smit JH, Steinthorsdottir V, Tobin MD, Tsernikova N, van Leeuwen EM, Viikari JS, Willems SM, Willemsen G, Schunkert H, Erdmann J, Samani NJ, Kaprio J, Lind L, Gieger C, Metspalu A, Slagboom PE, Groop L, van Duijn CM, Eriksson JG, Jula A, Salomaa V, Boomsma DI, Power C, Raitakari OT, Ingelsson E, Järvelin MR, Thorsteinsdottir U, Franke L, Ikonen E, Kallioniemi O, Pietiäinen V, Lindgren CM, Stefansson K, Palotie A, McCarthy MI, Morris AP, Prokopenko I, Ripatti S; ENGAGE Consortium.
    The impact of low-frequency and rare variants on lipid levels.
    Nat Genet. 2015 Jun;47(6):589-97. DOI:10.1038/ng.3300, PMID:25961943, PMCID:PMC4757735.

  86. Salo PP, Vaara S, Kettunen J, Pirinen M, Sarin AP, Huikuri H, Karhunen PJ, Eskola M, Nikus K, Lokki ML, Ripatti S, Havulinna AS, Salomaa V, Palotie A, Nieminen MS, Sinisalo J, Perola M.
    Genetic Variants on Chromosome 1p13.3 Are Associated with Non-ST Elevation Myocardial Infarction and the Expression of DRAM2 in the Finnish Population.
    PLoS One. 2015 Oct 28;10(10):e0140576. DOI:10.1371/journal.pone.0140576, PMID:26509668, PMCID:PMC4625034.

  87. Psychosis Endophenotypes International Consortium; Wellcome Trust Case-Control Consortium 2; Bramon E, Pirinen M, Strange A, Lin K, Freeman C, Bellenguez C, Su Z, Band G, Pearson R, Vukcevic D, Langford C, Deloukas P, Hunt S, Gray E, Dronov S, Potter SC, Tashakkori-Ghanbaria A, Edkins S, Bumpstead SJ, Arranz MJ, Bakker S, Bender S, Bruggeman R, Cahn W, Chandler D, Collier DA, Crespo-Facorro B, Dazzan P, de Haan L, Di Forti M, Dragović M, Giegling I, Hall J, Iyegbe C, Jablensky A, Kahn RS, Kalaydjieva L, Kravariti E, Lawrie S, Linszen DH, Mata I, McDonald C, McIntosh A, Myin-Germeys I, Ophoff RA, Pariante CM, Paunio T, Picchioni M; Psychiatric Genomics Consortium; Ripke S, Rujescu D, Sauer H, Shaikh M, Sussmann J, Suvisaari J, Tosato S, Toulopoulou T, Van Os J, Walshe M, Weisbrod M, Whalley H, Wiersma D, Blackwell JM, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski JA, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Wood NW, Barroso I, Peltonen L, Lewis CM, Murray RM, Donnelly P, Powell J, Spencer CC.
    A genome-wide association analysis of a broad psychosis phenotype identifies three loci for further investigation.
    Biol Psychiatry. 2014 Mar 1;75(5):386-97. DOI:10.1016/j.biopsych.2013.03.033, PMID:23871474, PMCID:PMC3923972.

  88. Morris DW, Pearson RD, Cormican P, Kenny EM, O’Dushlaine CT, Perreault LP, Giannoulatou E, Tropea D, Maher BS, Wormley B, Kelleher E, Fahey C, Molinos I, Bellini S, Pirinen M, Strange A, Freeman C, Thiselton DL, Elves RL, Regan R, Ennis S, Dinan TG, McDonald C, Murphy KC, O’Callaghan E, Waddington JL, Walsh D, O’Donovan M, Grozeva D, Craddock N, Stone J, Scolnick E, Purcell S, Sklar P, Coe B, Eichler EE, Ophoff R, Buizer J, Szatkiewicz J, Hultman C, Sullivan P, Gurling H, Mcquillin A, St Clair D, Rees E, Kirov G, Walters J, Blackwood D, Johnstone M, Donohoe G; International Schizophrenia Consortium, SGENE+ Consortium; O’Neill FA; Wellcome Trust Case Control Consortium 2; Kendler KS, Gill M, Riley BP, Spencer CC, Corvin A.
    An inherited duplication at the gene p21 Protein-Activated Kinase 7 (PAK7) is a risk factor for psychosis.
    Hum Mol Genet. 2014 Jun 15;23(12):3316-26. DOI:10.1093/hmg/ddu025, PMID:24474471, PMCID:PMC4030770.

  89. Tukiainen T, Pirinen M, Sarin AP, Ladenvall C, Kettunen J, Lehtimäki T, Lokki ML, Perola M, Sinisalo J, Vlachopoulou E, Eriksson JG, Groop L, Jula A, Järvelin MR, Raitakari OT, Salomaa V, Ripatti S.
    Chromosome X-wide association study identifies Loci for fasting insulin and height and evidence for incomplete dosage compensation.
    PLoS Genet. 2014 Feb 6;10(2):e1004127. DOI:10.1371/journal.pgen.1004127, PMID:24516404, PMCID:PMC3916240.

  90. Marttinen P, Pirinen M, Sarin AP, Gillberg J, Kettunen J, Surakka I, Kangas AJ, Soininen P, O’Reilly P, Kaakinen M, Kähönen M, Lehtimäki T, Ala-Korpela M, Raitakari OT, Salomaa V, Järvelin MR, Ripatti S, Kaski S.
    Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression.
    Bioinformatics. 2014 Jul 15;30(14):2026-34. DOI:10.1093/bioinformatics/btu140, PMID:24665129, PMCID:PMC4080737.

  91. Davis OS, Band G, Pirinen M, Haworth CM, Meaburn EL, Kovas Y, Harlaar N, Docherty SJ, Hanscombe KB, Trzaskowski M, Curtis CJ, Strange A, Freeman C, Bellenguez C, Su Z, Pearson R, Vukcevic D, Langford C, Deloukas P, Hunt S, Gray E, Dronov S, Potter SC, Tashakkori-Ghanbaria A, Edkins S, Bumpstead SJ, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski JA, Markus HS, Mathew CG, Palmer CN, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Barroso I, Peltonen L, Dale PS, Petrill SA, Schalkwyk LS, Craig IW, Lewis CM, Price TS; Wellcome Trust Case Control Consortium 2; Donnelly P, Plomin R, Spencer CC.
    The correlation between reading and mathematics ability at age twelve has a substantial genetic component.
    Nat Commun. 2014 Jul 8;5:4204. DOI:10.1038/ncomms5204, PMID:25003214, PMCID:PMC4102107.

  92. LeishGEN Consortium; Wellcome Trust Case Control Consortium 2; Fakiola M, Strange A, Cordell HJ, Miller EN, Pirinen M, Su Z, Mishra A, Mehrotra S, Monteiro GR, Band G, Bellenguez C, Dronov S, Edkins S, Freeman C, Giannoulatou E, Gray E, Hunt SE, Lacerda HG, Langford C, Pearson R, Pontes NN, Rai M, Singh SP, Smith L, Sousa O, Vukcevic D, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski J, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Wilson ME, Deloukas P, Peltonen L, Christiansen F, Witt C, Jeronimo SM, Sundar S, Spencer CC, Blackwell JM, Donnelly P.
    Common variants in the HLA-DRB1-HLA-DQA1 HLA class II region are associated with susceptibility to visceral leishmaniasis.
    Nat Genet. 2013 Feb;45(2):208-13. DOI:10.1038/ng.2518, PMID:23291585, PMCID:PMC3664012.

  93. Band G, Le QS, Jostins L, Pirinen M, Kivinen K, Jallow M, Sisay-Joof F, Bojang K, Pinder M, Sirugo G, Conway DJ, Nyirongo V, Kachala D, Molyneux M, Taylor T, Ndila C, Peshu N, Marsh K, Williams TN, Alcock D, Andrews R, Edkins S, Gray E, Hubbart C, Jeffreys A, Rowlands K, Schuldt K, Clark TG, Small KS, Teo YY, Kwiatkowski DP, Rockett KA, Barrett JC, Spencer CC; Malaria Genomic Epidemiology Network.
    Imputation-based meta-analysis of severe malaria in three African populations.
    PLoS Genet. 2013 May;9(5):e1003509. DOI:10.1371/journal.pgen.1003509, PMID:23717212, PMCID:PMC3662650.

  94. Rivas MA, Pirinen M, Neville MJ, Gaulton KJ, Moutsianas L; GoT2D Consortium; Lindgren CM, Karpe F, McCarthy MI, Donnelly P.
    Assessing association between protein truncating variants and quantitative traits.
    Bioinformatics. 2013 Oct 1;29(19):2419-26. DOI:10.1093/bioinformatics/btt409, PMID:23860716, PMCID:PMC3777107.

  95. Ripke S, O’Dushlaine C, Chambert K, Moran JL, Kähler AK, Akterin S, Bergen SE, Collins AL, Crowley JJ, Fromer M, Kim Y, Lee SH, Magnusson PK, Sanchez N, Stahl EA, Williams S, Wray NR, Xia K, Bettella F, Borglum AD, Bulik-Sullivan BK, Cormican P, Craddock N, de Leeuw C, Durmishi N, Gill M, Golimbet V, Hamshere ML, Holmans P, Hougaard DM, Kendler KS, Lin K, Morris DW, Mors O, Mortensen PB, Neale BM, O’Neill FA, Owen MJ, Milovancevic MP, Posthuma D, Powell J, Richards AL, Riley BP, Ruderfer D, Rujescu D, Sigurdsson E, Silagadze T, Smit AB, Stefansson H, Steinberg S, Suvisaari J, Tosato S, Verhage M, Walters JT; Multicenter Genetic Studies of Schizophrenia Consortium; Levinson DF, Gejman PV, Kendler KS, Laurent C, Mowry BJ, O’Donovan MC, Owen MJ, Pulver AE, Riley BP, Schwab SG, Wildenauer DB, Dudbridge F, Holmans P, Shi J, Albus M, Alexander M, Campion D, Cohen D, Dikeos D, Duan J, Eichhammer P, Godard S, Hansen M, Lerer FB, Liang KY, Maier W, Mallet J, Nertney DA, Nestadt G, Norton N, O’Neill FA, Papadimitriou GN, Ribble R, Sanders AR, Silverman JM, Walsh D, Williams NM, Wormley B; Psychosis Endophenotypes International Consortium; Arranz MJ, Bakker S, Bender S, Bramon E, Collier D, Crespo-Facorro B, et al.
    Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
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  96. Lappalainen T, Sammeth M, Friedländer MR, ’t Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HP, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM; Geuvadis Consortium; Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, Häsler R, Syvänen AC, van Ommen GJ, Brazma A, Meitinger T, Rosenstiel P, Guigó R, Gut IG, Estivill X, Dermitzakis ET.
    Transcriptome and genome sequencing uncovers functional variation in humans.
    Nature. 2013 Sep 26;501(7468):506-11. DOI:10.1038/nature12531, PMID:24037378, PMCID:PMC3918453.

  97. International Multiple Sclerosis Genetics Consortium (IMSGC); Beecham AH, Patsopoulos NA, Xifara DK, Davis MF, Kemppinen A, Cotsapas C, Shah TS, Spencer C, Booth D, Goris A, Oturai A, Saarela J, Fontaine B, Hemmer B, Martin C, Zipp F, D’Alfonso S, Martinelli-Boneschi F, Taylor B, Harbo HF, Kockum I, Hillert J, Olsson T, Ban M, Oksenberg JR, Hintzen R, Barcellos LF; Wellcome Trust Case Control Consortium 2 (WTCCC2); International IBD Genetics Consortium (IIBDGC); Agliardi C, Alfredsson L, Alizadeh M, Anderson C, Andrews R, Søndergaard HB, Baker A, Band G, Baranzini SE, Barizzone N, Barrett J, Bellenguez C, Bergamaschi L, Bernardinelli L, Berthele A, Biberacher V, Binder TM, Blackburn H, Bomfim IL, Brambilla P, Broadley S, Brochet B, Brundin L, Buck D, Butzkueven H, Caillier SJ, Camu W, Carpentier W, Cavalla P, Celius EG, Coman I, Comi G, Corrado L, Cosemans L, Cournu-Rebeix I, Cree BA, Cusi D, Damotte V, Defer G, Delgado SR, Deloukas P, di Sapio A, Dilthey AT, Donnelly P, Dubois B, Duddy M, Edkins S, Elovaara I, Esposito F, Evangelou N, Fiddes B, Field J, Franke A, Freeman C, Frohlich IY, Galimberti D, Gieger C, Gourraud PA, Graetz C, Graham A, Grummel V, Guaschino C, Hadjixenofontos A, Hakonarson H, Halfpenny C, Hall G, Hall P, Hamsten A, Harley J, Harrower T, et al.
    Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis.
    Nat Genet. 2013 Nov;45(11):1353-60. DOI:10.1038/ng.2770, PMID:24076602, PMCID:PMC3832895.

  98. Pirinen M, Donnelly P, and Spencer C.
    Efficient computation with a linear mixed model on large-scale data sets with applications to genetic studies.
    Ann. Appl. Stat. 7(1): 369-390 (March 2013). DOI:10.1214/12-AOAS586, PMID: none, PMCID: none.

  99. International Stroke Genetics Consortium (ISGC); Wellcome Trust Case Control Consortium 2 (WTCCC2); Bellenguez C, Bevan S, Gschwendtner A, Spencer CC, Burgess AI, Pirinen M, Jackson CA, Traylor M, Strange A, Su Z, Band G, Syme PD, Malik R, Pera J, Norrving B, Lemmens R, Freeman C, Schanz R, James T, Poole D, Murphy L, Segal H, Cortellini L, Cheng YC, Woo D, Nalls MA, Müller-Myhsok B, Meisinger C, Seedorf U, Ross-Adams H, Boonen S, Wloch-Kopec D, Valant V, Slark J, Furie K, Delavaran H, Langford C, Deloukas P, Edkins S, Hunt S, Gray E, Dronov S, Peltonen L, Gretarsdottir S, Thorleifsson G, Thorsteinsdottir U, Stefansson K, Boncoraglio GB, Parati EA, Attia J, Holliday E, Levi C, Franzosi MG, Goel A, Helgadottir A, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski J, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Worrall BB, Kittner SJ, Mitchell BD, Kissela B, Meschia JF, Thijs V, Lindgren A, Macleod MJ, Slowik A, Walters M, Rosand J, Sharma P, Farrall M, Sudlow CL, Rothwell PM, Dichgans M, Donnelly P, Markus HS.
    Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke.
    Nat Genet. 2012 Feb 5;44(3):328-33. DOI:10.1038/ng.1081, PMID:22306652, PMCID:PMC3303115.

  100. Pirinen M, Donnelly P, Spencer CC.
    Including known covariates can reduce power to detect genetic effects in case-control studies.
    Nat Genet. 2012 Jul 22;44(8):848-51. DOI:10.1038/ng.2346, PMID:22820511, PMCID: none.

  101. Su Z, Gay LJ, Strange A, Palles C, Band G, Whiteman DC, Lescai F, Langford C, Nanji M, Edkins S, van der Winkel A, Levine D, Sasieni P, Bellenguez C, Howarth K, Freeman C, Trudgill N, Tucker AT, Pirinen M, Peppelenbosch MP, van der Laan LJ, Kuipers EJ, Drenth JP, Peters WH, Reynolds JV, Kelleher DP, McManus R, Grabsch H, Prenen H, Bisschops R, Krishnadath K, Siersema PD, van Baal JW, Middleton M, Petty R, Gillies R, Burch N, Bhandari P, Paterson S, Edwards C, Penman I, Vaidya K, Ang Y, Murray I, Patel P, Ye W, Mullins P, Wu AH, Bird NC, Dallal H, Shaheen NJ, Murray LJ, Koss K, Bernstein L, Romero Y, Hardie LJ, Zhang R, Winter H, Corley DA, Panter S, Risch HA, Reid BJ, Sargeant I, Gammon MD, Smart H, Dhar A, McMurtry H, Ali H, Liu G, Casson AG, Chow WH, Rutter M, Tawil A, Morris D, Nwokolo C, Isaacs P, Rodgers C, Ragunath K, MacDonald C, Haigh C, Monk D, Davies G, Wajed S, Johnston D, Gibbons M, Cullen S, Church N, Langley R, Griffin M, Alderson D, Deloukas P, Hunt SE, Gray E, Dronov S, Potter SC, Tashakkori-Ghanbaria A, Anderson M, Brooks C, Blackwell JM, Bramon E, et al.
    Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett’s esophagus.
    Nat Genet. 2012 Oct;44(10):1131-6. DOI:10.1038/ng.2408, PMID:22961001, PMCID:PMC3459818.

  102. Wellcome Trust Case Control Consortium; Maller JB, McVean G, Byrnes J, Vukcevic D, Palin K, Su Z, Howson JM, Auton A, Myers S, Morris A, Pirinen M, Brown MA, Burton PR, Caulfield MJ, Compston A, Farrall M, Hall AS, Hattersley AT, Hill AV, Mathew CG, Pembrey M, Satsangi J, Stratton MR, Worthington J, Craddock N, Hurles M, Ouwehand W, Parkes M, Rahman N, Duncanson A, Todd JA, Kwiatkowski DP, Samani NJ, Gough SC, McCarthy MI, Deloukas P, Donnelly P.
    Bayesian refinement of association signals for 14 loci in 3 common diseases.
    Nat Genet. 2012 Dec;44(12):1294-301. DOI:10.1038/ng.2435, PMID:23104008, PMCID:PMC3791416.

  103. UK Parkinson’s Disease Consortium; Wellcome Trust Case Control Consortium 2; Spencer CC, Plagnol V, Strange A, Gardner M, Paisan-Ruiz C, Band G, Barker RA, Bellenguez C, Bhatia K, Blackburn H, Blackwell JM, Bramon E, Brown MA, Brown MA, Burn D, Casas JP, Chinnery PF, Clarke CE, Corvin A, Craddock N, Deloukas P, Edkins S, Evans J, Freeman C, Gray E, Hardy J, Hudson G, Hunt S, Jankowski J, Langford C, Lees AJ, Markus HS, Mathew CG, McCarthy MI, Morrison KE, Palmer CN, Pearson JP, Peltonen L, Pirinen M, Plomin R, Potter S, Rautanen A, Sawcer SJ, Su Z, Trembath RC, Viswanathan AC, Williams NW, Morris HR, Donnelly P, Wood NW.
    Dissection of the genetics of Parkinson’s disease identifies an additional association 5’ of SNCA and multiple associated haplotypes at 17q21.
    Hum Mol Genet. 2011 Jan 15;20(2):345-53. DOI:10.1093/hmg/ddq469, PMID:21044948, PMCID:PMC3005904.

  104. Gasbarra D, Kulathinal S, Pirinen M, Sillanpää MJ.
    Estimating haplotype frequencies by combining data from large DNA pools with database information.
    IEEE/ACM Trans Comput Biol Bioinform. 2011 Jan-Mar;8(1):36-44. DOI:10.1109/TCBB.2009.71, PMID:21071795, PMCID: none.

  105. Evans DM, Spencer CC, Pointon JJ, Su Z, Harvey D, Kochan G, Oppermann U, Dilthey A, Pirinen M, Stone MA, Appleton L, Moutsianas L, Leslie S, Wordsworth T, Kenna TJ, Karaderi T, Thomas GP, Ward MM, Weisman MH, Farrar C, Bradbury LA, Danoy P, Inman RD, Maksymowych W, Gladman D, Rahman P; Spondyloarthritis Research Consortium of Canada (SPARCC); Morgan A, Marzo-Ortega H, Bowness P, Gaffney K, Gaston JS, Smith M, Bruges-Armas J, Couto AR, Sorrentino R, Paladini F, Ferreira MA, Xu H, Liu Y, Jiang L, Lopez-Larrea C, Díaz-Peña R, López-Vázquez A, Zayats T, Band G, Bellenguez C, Blackburn H, Blackwell JM, Bramon E, Bumpstead SJ, Casas JP, Corvin A, Craddock N, Deloukas P, Dronov S, Duncanson A, Edkins S, Freeman C, Gillman M, Gray E, Gwilliam R, Hammond N, Hunt SE, Jankowski J, Jayakumar A, Langford C, Liddle J, Markus HS, Mathew CG, McCann OT, McCarthy MI, Palmer CN, Peltonen L, Plomin R, Potter SC, Rautanen A, Ravindrarajah R, Ricketts M, Samani N, Sawcer SJ, Strange A, Trembath RC, Viswanathan AC, Waller M, Weston P, Whittaker P, Widaa S, Wood NW, McVean G, Reveille JD, Wordsworth BP, Brown MA, Donnelly P; Australo-Anglo-American Spondyloarthritis Consortium (TASC); Wellcome Trust Case Control Consortium 2 (WTCCC2).
    Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility.
    Nat Genet. 2011 Jul 10;43(8):761-7. DOI:10.1038/ng.873, PMID:21743469, PMCID:PMC3640413.

  106. International Multiple Sclerosis Genetics Consortium; Wellcome Trust Case Control Consortium 2; Sawcer S, Hellenthal G, Pirinen M, Spencer CC, Patsopoulos NA, Moutsianas L, Dilthey A, Su Z, Freeman C, Hunt SE, Edkins S, Gray E, Booth DR, Potter SC, Goris A, Band G, Oturai AB, Strange A, Saarela J, Bellenguez C, Fontaine B, Gillman M, Hemmer B, Gwilliam R, Zipp F, Jayakumar A, Martin R, Leslie S, Hawkins S, Giannoulatou E, D’alfonso S, Blackburn H, Martinelli Boneschi F, Liddle J, Harbo HF, Perez ML, Spurkland A, Waller MJ, Mycko MP, Ricketts M, Comabella M, Hammond N, Kockum I, McCann OT, Ban M, Whittaker P, Kemppinen A, Weston P, Hawkins C, Widaa S, Zajicek J, Dronov S, Robertson N, Bumpstead SJ, Barcellos LF, Ravindrarajah R, Abraham R, Alfredsson L, Ardlie K, Aubin C, Baker A, Baker K, Baranzini SE, Bergamaschi L, Bergamaschi R, Bernstein A, Berthele A, Boggild M, Bradfield JP, Brassat D, Broadley SA, Buck D, Butzkueven H, Capra R, Carroll WM, Cavalla P, Celius EG, Cepok S, Chiavacci R, Clerget-Darpoux F, Clysters K, Comi G, Cossburn M, Cournu-Rebeix I, Cox MB, Cozen W, Cree BA, Cross AH, Cusi D, Daly MJ, Davis E, de Bakker PI, Debouverie M, D’hooghe MB, Dixon K, Dobosi R, Dubois B, Ellinghaus D, et al.
    Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
    Nature. 2011 Aug 10;476(7359):214-9. DOI:10.1038/nature10251, PMID:21833088, PMCID:PMC3182531.

  107. Genetic Analysis of Psoriasis Consortium & the Wellcome Trust Case Control Consortium 2; Strange A, Capon F, Spencer CC, Knight J, Weale ME, Allen MH, Barton A, Band G, Bellenguez C, Bergboer JG, Blackwell JM, Bramon E, Bumpstead SJ, Casas JP, Cork MJ, Corvin A, Deloukas P, Dilthey A, Duncanson A, Edkins S, Estivill X, Fitzgerald O, Freeman C, Giardina E, Gray E, Hofer A, Hüffmeier U, Hunt SE, Irvine AD, Jankowski J, Kirby B, Langford C, Lascorz J, Leman J, Leslie S, Mallbris L, Markus HS, Mathew CG, McLean WH, McManus R, Mössner R, Moutsianas L, Naluai AT, Nestle FO, Novelli G, Onoufriadis A, Palmer CN, Perricone C, Pirinen M, Plomin R, Potter SC, Pujol RM, Rautanen A, Riveira-Munoz E, Ryan AW, Salmhofer W, Samuelsson L, Sawcer SJ, Schalkwijk J, Smith CH, Ståhle M, Su Z, Tazi-Ahnini R, Traupe H, Viswanathan AC, Warren RB, Weger W, Wolk K, Wood N, Worthington J, Young HS, Zeeuwen PL, Hayday A, Burden AD, Griffiths CE, Kere J, Reis A, McVean G, Evans DM, Brown MA, Barker JN, Peltonen L, Donnelly P, Trembath RC.
    A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1.
    Nat Genet. 2010 Nov;42(11):985-90. DOI:10.1038/ng.694, PMID:20953190, PMCID:PMC3749730.

  108. Gasbarra D, Pirinen M, Sillanpää MJ, Arjas E.
    Bayesian quantitative trait locus mapping based on reconstruction of recent genetic histories.
    Genetics. 2009 Oct;183(2):709-21. DOI:10.1534/genetics.109.104190, PMID:19620396, PMCID:PMC2766329.

  109. Pirinen M.
    Estimating population haplotype frequencies from pooled SNP data using incomplete database information.
    Bioinformatics. 2009 Dec 15;25(24):3296-302. DOI:10.1093/bioinformatics/btp584, PMID:19861356, PMCID: none.

  110. Pirinen M, Kulathinal S, Gasbarra D, Sillanpää MJ.
    Estimating population haplotype frequencies from pooled DNA samples using PHASE algorithm.
    Genet Res (Camb). 2008 Dec;90(6):509-24. DOI:10.1017/S0016672308009877, PMID:19123969, PMCID: none.

  111. Gasbarra D, Pirinen M, Sillanpää MJ, Salmela E, Arjas E.
    Estimating genealogies from unlinked marker data: a Bayesian approach.
    Theor Popul Biol. 2007 Nov;72(3):305-22. DOI:10.1016/j.tpb.2007.06.004, PMID:17681576, PMCID: none.

  112. Gasbarra D, Pirinen M, Sillanpää MJ, Arjas E.
    Estimating genealogies from linked marker data: a Bayesian approach.
    BMC Bioinformatics. 2007 Oct 25;8:411. DOI:10.1186/1471-2105-8-411, PMID:17961219, PMCID:PMC2233650.

  113. Pirinen M, Gasbarra D.
    Finding consistent gene transmission patterns on large and complex pedigrees.
    IEEE/ACM Trans Comput Biol Bioinform. 2006 Jul-Sep;3(3):252-62. DOI:10.1109/TCBB.2006.36, PMID:17048463, PMCID: none.