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Items: 46

1.

RNA modification landscape of the human mitochondrial tRNALys regulates protein synthesis.

Richter U, Evans ME, Clark WC, Marttinen P, Shoubridge EA, Suomalainen A, Wredenberg A, Wedell A, Pan T, Battersby BJ.

Nat Commun. 2018 Sep 27;9(1):3966. doi: 10.1038/s41467-018-06471-z.

2.

OXA1L mutations cause mitochondrial encephalopathy and a combined oxidative phosphorylation defect.

Thompson K, Mai N, Oláhová M, Scialó F, Formosa LE, Stroud DA, Garrett M, Lax NZ, Robertson FM, Jou C, Nascimento A, Ortez C, Jimenez-Mallebrera C, Hardy SA, He L, Brown GK, Marttinen P, McFarland R, Sanz A, Battersby BJ, Bonnen PE, Ryan MT, Chrzanowska-Lightowlers ZM, Lightowlers RN, Taylor RW.

EMBO Mol Med. 2018 Sep 10. pii: e9060. doi: 10.15252/emmm.201809060. [Epub ahead of print]

3.

Improving genomics-based predictions for precision medicine through active elicitation of expert knowledge.

Sundin I, Peltola T, Micallef L, Afrabandpey H, Soare M, Mamun Majumder M, Daee P, He C, Serim B, Havulinna A, Heckman C, Jacucci G, Marttinen P, Kaski S.

Bioinformatics. 2018 Jul 1;34(13):i395-i403. doi: 10.1093/bioinformatics/bty257.

4.

Bacmeta: simulator for genomic evolution in bacterial metapopulations.

Sipola A, Marttinen P, Corander J.

Bioinformatics. 2018 Jul 1;34(13):2308-2310. doi: 10.1093/bioinformatics/bty093.

PMID:
29474733
5.

Correction: Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila.

David S, Sánchez-Busó L, Harris SR, Marttinen P, Rusniok C, Buchrieser C, Harrison TG, Parkhill J.

PLoS Genet. 2017 Dec 1;13(12):e1007116. doi: 10.1371/journal.pgen.1007116. eCollection 2017 Dec.

6.

Speciation trajectories in recombining bacterial species.

Marttinen P, Hanage WP.

PLoS Comput Biol. 2017 Jul 3;13(7):e1005640. doi: 10.1371/journal.pcbi.1005640. eCollection 2017 Jul.

7.

Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila.

David S, Sánchez-Busó L, Harris SR, Marttinen P, Rusniok C, Buchrieser C, Harrison TG, Parkhill J.

PLoS Genet. 2017 Jun 26;13(6):e1006855. doi: 10.1371/journal.pgen.1006855. eCollection 2017 Jun. Erratum in: PLoS Genet. 2017 Dec 1;13(12 ):e1007116.

8.

A novel mitochondrial ATP6 frameshift mutation causing isolated complex V deficiency, ataxia and encephalomyopathy.

Jackson CB, Hahn D, Schröter B, Richter U, Battersby BJ, Schmitt-Mechelke T, Marttinen P, Nuoffer JM, Schaller A.

Eur J Med Genet. 2017 Jun;60(6):345-351. doi: 10.1016/j.ejmg.2017.04.006. Epub 2017 Apr 13.

PMID:
28412374
9.

biMM: efficient estimation of genetic variances and covariances for cohorts with high-dimensional phenotype measurements.

Pirinen M, Benner C, Marttinen P, Järvelin MR, Rivas MA, Ripatti S.

Bioinformatics. 2017 Aug 1;33(15):2405-2407. doi: 10.1093/bioinformatics/btx166.

10.

Cluster analysis to estimate the risk of preeclampsia in the high-risk Prediction and Prevention of Preeclampsia and Intrauterine Growth Restriction (PREDO) study.

Villa PM, Marttinen P, Gillberg J, Lokki AI, Majander K, Ordén MR, Taipale P, Pesonen A, Räikkönen K, Hämäläinen E, Kajantie E, Laivuori H.

PLoS One. 2017 Mar 28;12(3):e0174399. doi: 10.1371/journal.pone.0174399. eCollection 2017.

11.

Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations.

Mostowy R, Croucher NJ, Andam CP, Corander J, Hanage WP, Marttinen P.

Mol Biol Evol. 2017 May 1;34(5):1167-1182. doi: 10.1093/molbev/msx066.

12.

Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms.

Harms K, Lunnan A, Hülter N, Mourier T, Vinner L, Andam CP, Marttinen P, Fridholm H, Hansen AJ, Hanage WP, Nielsen KM, Willerslev E, Johnsen PJ.

Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):15066-15071. doi: 10.1073/pnas.1615819114. Epub 2016 Dec 12.

13.

Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

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 VS, 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 TW, 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.

Nat Commun. 2016 Oct 10;7:13205. doi: 10.1038/ncomms13205. No abstract available.

14.

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes.

Lees JA, Vehkala M, Välimäki N, Harris SR, Chewapreecha C, Croucher NJ, Marttinen P, Davies MR, Steer AC, Tong SY, Honkela A, Parkhill J, Bentley SD, Corander J.

Nat Commun. 2016 Sep 16;7:12797. doi: 10.1038/ncomms12797.

15.

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

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 VS, 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 TW, Kurreeman F, Allaart CF, Louis Bridges S Jr, Bridges SL, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM.

Nat Commun. 2016 Aug 23;7:12460. doi: 10.1038/ncomms12460. Erratum in: Nat Commun. 2016 Oct 10;7:13205.

16.

metaCCA: summary statistics-based multivariate meta-analysis of genome-wide association studies using canonical correlation analysis.

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.

Bioinformatics. 2016 Jul 1;32(13):1981-9. doi: 10.1093/bioinformatics/btw052. Epub 2016 Feb 19.

17.

The impact of host metapopulation structure on the population genetics of colonizing bacteria.

Numminen E, Gutmann M, Shubin M, Marttinen P, Méric G, van Schaik W, Coque TM, Baquero F, Willems RJ, Sheppard SK, Feil EJ, Hanage WP, Corander J.

J Theor Biol. 2016 May 7;396:53-62. doi: 10.1016/j.jtbi.2016.02.019. Epub 2016 Feb 23.

PMID:
26916623
18.

Tissue-specific modulation of mitochondrial DNA segregation by a defect in mitochondrial division.

Jokinen R, Marttinen P, Stewart JB, Neil Dear T, Battersby BJ.

Hum Mol Genet. 2016 Feb 15;25(4):706-14. doi: 10.1093/hmg/ddv508. Epub 2015 Dec 17.

PMID:
26681804
19.

Recombination produces coherent bacterial species clusters in both core and accessory genomes.

Marttinen P, Croucher NJ, Gutmann MU, Corander J, Hanage WP.

Microb Genom. 2015 Nov 5;1(5):e000038. doi: 10.1099/mgen.0.000038. eCollection 2015 Nov.

20.

Quality control of mitochondrial protein synthesis is required for membrane integrity and cell fitness.

Richter U, Lahtinen T, Marttinen P, Suomi F, Battersby BJ.

J Cell Biol. 2015 Oct 26;211(2):373-89. doi: 10.1083/jcb.201504062.

21.

Quantitative changes in Gimap3 and Gimap5 expression modify mitochondrial DNA segregation in mice.

Jokinen R, Lahtinen T, Marttinen P, Myöhänen M, Ruotsalainen P, Yeung N, Shvetsova A, Kastaniotis AJ, Hiltunen JK, Öhman T, Nyman TA, Weiler H, Battersby BJ.

Genetics. 2015 May;200(1):221-35. doi: 10.1534/genetics.115.175596. Epub 2015 Mar 25.

22.

Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes.

Chewapreecha C, Marttinen P, Croucher NJ, Salter SJ, Harris SR, Mather AE, Hanage WP, Goldblatt D, Nosten FH, Turner C, Turner P, Bentley SD, Parkhill J.

PLoS Genet. 2014 Aug 7;10(8):e1004547. doi: 10.1371/journal.pgen.1004547. eCollection 2014 Aug.

23.

Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus.

Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, Malmstrom RR, Stocker R, Follows MJ, Stepanauskas R, Chisholm SW.

Science. 2014 Apr 25;344(6182):416-20. doi: 10.1126/science.1248575.

24.

Cryptic ecology among host generalist Campylobacter jejuni in domestic animals.

Sheppard SK, Cheng L, Méric G, de Haan CP, Llarena AK, Marttinen P, Vidal A, Ridley A, Clifton-Hadley F, Connor TR, Strachan NJ, Forbes K, Colles FM, Jolley KA, Bentley SD, Maiden MC, Hänninen ML, Parkhill J, Hanage WP, Corander J.

Mol Ecol. 2014 May;23(10):2442-51. doi: 10.1111/mec.12742. Epub 2014 Apr 25.

25.

Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression.

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.

Bioinformatics. 2014 Jul 15;30(14):2026-34. doi: 10.1093/bioinformatics/btu140. Epub 2014 Mar 24.

26.

Dense genomic sampling identifies highways of pneumococcal recombination.

Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P, Cheng L, Pessia A, Aanensen DM, Mather AE, Page AJ, Salter SJ, Harris D, Nosten F, Goldblatt D, Corander J, Parkhill J, Turner P, Bentley SD.

Nat Genet. 2014 Mar;46(3):305-309. doi: 10.1038/ng.2895. Epub 2014 Feb 9.

27.

Plant sterol feeding induces tumor formation and alters sterol metabolism in the intestine of Apc(Min) mice.

Marttinen M, Pajari AM, Päivärinta E, Storvik M, Marttinen P, Nurmi T, Niku M, Piironen V, Mutanen M.

Nutr Cancer. 2014;66(2):259-69. doi: 10.1080/01635581.2014.865244. Epub 2014 Jan 10.

PMID:
24410462
28.

Genome-wide association studies with high-dimensional phenotypes.

Marttinen P, Gillberg J, Havulinna A, Corander J, Kaski S.

Stat Appl Genet Mol Biol. 2013 Aug;12(4):413-31. doi: 10.1515/sagmb-2012-0032.

PMID:
23759510
29.

A mitochondrial ribosomal and RNA decay pathway blocks cell proliferation.

Richter U, Lahtinen T, Marttinen P, Myöhänen M, Greco D, Cannino G, Jacobs HT, Lietzén N, Nyman TA, Battersby BJ.

Curr Biol. 2013 Mar 18;23(6):535-41. doi: 10.1016/j.cub.2013.02.019. Epub 2013 Feb 28.

30.

Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus.

Castillo-Ramírez S, Corander J, Marttinen P, Aldeljawi M, Hanage WP, Westh H, Boye K, Gulay Z, Bentley SD, Parkhill J, Holden MT, Feil EJ.

Genome Biol. 2012 Dec 27;13(12):R126. doi: 10.1186/gb-2012-13-12-r126.

31.

Finite adaptation and multistep moves in the metropolis-hastings algorithm for variable selection in genome-wide association analysis.

Peltola T, Marttinen P, Vehtari A.

PLoS One. 2012;7(11):e49445. doi: 10.1371/journal.pone.0049445. Epub 2012 Nov 15.

32.

Serum and CSF soluble CD26 and CD30 concentrations in healthy pediatric surgical outpatients.

Delezuch W, Marttinen P, Kokki H, Heikkinen M, Vanamo K, Pulkki K, Matinlauri I.

Tissue Antigens. 2012 Oct;80(4):368-75. doi: 10.1111/j.1399-0039.2012.01938.x. Epub 2012 Aug 3.

PMID:
22861386
33.

Bayesian variable selection in searching for additive and dominant effects in genome-wide data.

Peltola T, Marttinen P, Jula A, Salomaa V, Perola M, Vehtari A.

PLoS One. 2012;7(1):e29115. doi: 10.1371/journal.pone.0029115. Epub 2012 Jan 3.

34.

Detection of recombination events in bacterial genomes from large population samples.

Marttinen P, Hanage WP, Croucher NJ, Connor TR, Harris SR, Bentley SD, Corander J.

Nucleic Acids Res. 2012 Jan;40(1):e6. doi: 10.1093/nar/gkr928. Epub 2011 Nov 7.

35.

Gimap3 regulates tissue-specific mitochondrial DNA segregation.

Jokinen R, Marttinen P, Sandell HK, Manninen T, Teerenhovi H, Wai T, Teoli D, Loredo-Osti JC, Shoubridge EA, Battersby BJ.

PLoS Genet. 2010 Oct 14;6(10):e1001161. doi: 10.1371/journal.pgen.1001161.

36.

Reconstructing population histories from single nucleotide polymorphism data.

Sirén J, Marttinen P, Corander J.

Mol Biol Evol. 2011 Jan;28(1):673-83. doi: 10.1093/molbev/msq236. Epub 2010 Sep 6.

PMID:
20819907
37.

Efficient Bayesian approach for multilocus association mapping including gene-gene interactions.

Marttinen P, Corander J.

BMC Bioinformatics. 2010 Sep 2;11:443. doi: 10.1186/1471-2105-11-443.

38.

Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function.

Törönen P, Ojala PJ, Marttinen P, Holm L.

BMC Bioinformatics. 2009 Sep 23;10:307. doi: 10.1186/1471-2105-10-307.

39.

Bayesian clustering and feature selection for cancer tissue samples.

Marttinen P, Myllykangas S, Corander J.

BMC Bioinformatics. 2009 Mar 18;10:90. doi: 10.1186/1471-2105-10-90.

40.

Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations.

Corander J, Marttinen P, Sirén J, Tang J.

BMC Bioinformatics. 2008 Dec 16;9:539. doi: 10.1186/1471-2105-9-539.

41.

Bayesian clustering of fuzzy feature vectors using a quasi-likelihood approach.

Marttinen P, Tang J, De Baets B, Dawyndt P, Corander J.

IEEE Trans Pattern Anal Mach Intell. 2009 Jan;31(1):74-85. doi: 10.1109/TPAMI.2008.53.

PMID:
19029547
42.

Bayesian modeling of recombination events in bacterial populations.

Marttinen P, Baldwin A, Hanage WP, Dowson C, Mahenthiralingam E, Corander J.

BMC Bioinformatics. 2008 Oct 7;9:421. doi: 10.1186/1471-2105-9-421.

43.

Bayesian identification of admixture events using multilocus molecular markers.

Corander J, Marttinen P.

Mol Ecol. 2006 Sep;15(10):2833-43.

PMID:
16911204
44.

Changes in MMP-2 and -9 activity and MMP-8 reactivity after amphotericin B induced synovitis and treatment with bufexamac.

Marttinen PH, Raulo SM, Suominen MM, Tulamo RM.

J Vet Med A Physiol Pathol Clin Med. 2006 Aug;53(6):311-8.

PMID:
16901276
45.

Bayesian search of functionally divergent protein subgroups and their function specific residues.

Marttinen P, Corander J, Törönen P, Holm L.

Bioinformatics. 2006 Oct 15;22(20):2466-74. Epub 2006 Jul 26.

PMID:
16870932
46.

BAPS 2: enhanced possibilities for the analysis of genetic population structure.

Corander J, Waldmann P, Marttinen P, Sillanpää MJ.

Bioinformatics. 2004 Oct 12;20(15):2363-9. Epub 2004 Apr 8.

PMID:
15073024

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