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Items: 49

1.

Donor Simvastatin Treatment in Heart Transplantation.

Nykänen AI, Holmström EJ, Tuuminen R, Krebs R, Dhaygude K, Kankainen M, Jokinen JJ, Lommi J, Helanterä I, Räisänen-Sokolowski A, Syrjälä SO, Lemström KB.

Circulation. 2019 Aug 20;140(8):627-640. doi: 10.1161/CIRCULATIONAHA.119.039932. Epub 2019 Jul 29.

PMID:
31352795
2.

Network pharmacology modeling identifies synergistic Aurora B and ZAK interaction in triple-negative breast cancer.

Tang J, Gautam P, Gupta A, He L, Timonen S, Akimov Y, Wang W, Szwajda A, Jaiswal A, Turei D, Yadav B, Kankainen M, Saarela J, Saez-Rodriguez J, Wennerberg K, Aittokallio T.

NPJ Syst Biol Appl. 2019 Jul 8;5:20. doi: 10.1038/s41540-019-0098-z. eCollection 2019.

3.

Hierarchical clustering in evaluating inflammatory upper airway phenotypes; increased symptoms in adults with allergic multimorbidity.

Hanif T, Laulajainen-Hongisto A, Luukkainen A, Numminen J, Kääriäinen J, Myller J, Kalogjera L, Huhtala H, Kankainen M, Renkonen R, Toppila-Salmi S.

Asian Pac J Allergy Immunol. 2019 Jun 4. doi: 10.12932/AP-170818-0395. [Epub ahead of print]

4.

Birch pollen allergen immunotherapy reprograms nasal epithelial transcriptome and recovers microbial diversity.

Hanif T, Dhaygude K, Kankainen M, Renkonen J, Mattila P, Ojala T, Joenväärä S, Mäkelä M, Pelkonen A, Kauppi P, Haahtela T, Renkonen R, Toppila-Salmi S.

J Allergy Clin Immunol. 2019 Jun;143(6):2293-2296.e11. doi: 10.1016/j.jaci.2019.02.002. Epub 2019 Feb 12. No abstract available.

5.

Association of tamoxifen resistance and lipid reprogramming in breast cancer.

Hultsch S, Kankainen M, Paavolainen L, Kovanen RM, Ikonen E, Kangaspeska S, Pietiäinen V, Kallioniemi O.

BMC Cancer. 2018 Aug 24;18(1):850. doi: 10.1186/s12885-018-4757-z.

6.

Characterizing the Key Metabolic Pathways of the Neonatal Mouse Heart Using a Quantitative Combinatorial Omics Approach.

Lalowski MM, Björk S, Finckenberg P, Soliymani R, Tarkia M, Calza G, Blokhina D, Tulokas S, Kankainen M, Lakkisto P, Baumann M, Kankuri E, Mervaala E.

Front Physiol. 2018 Apr 11;9:365. doi: 10.3389/fphys.2018.00365. eCollection 2018.

7.

Aggressive natural killer-cell leukemia mutational landscape and drug profiling highlight JAK-STAT signaling as therapeutic target.

Dufva O, Kankainen M, Kelkka T, Sekiguchi N, Awad SA, Eldfors S, Yadav B, Kuusanmäki H, Malani D, Andersson EI, Pietarinen P, Saikko L, Kovanen PE, Ojala T, Lee DA, Loughran TP Jr, Nakazawa H, Suzumiya J, Suzuki R, Ko YH, Kim WS, Chuang SS, Aittokallio T, Chan WC, Ohshima K, Ishida F, Mustjoki S.

Nat Commun. 2018 Apr 19;9(1):1567. doi: 10.1038/s41467-018-03987-2.

8.

Interleukin 8 activity influences the efficacy of adenoviral oncolytic immunotherapy in cancer patients.

Taipale K, Tähtinen S, Havunen R, Koski A, Liikanen I, Pakarinen P, Koivisto-Korander R, Kankainen M, Joensuu T, Kanerva A, Hemminki A.

Oncotarget. 2018 Jan 5;9(5):6320-6335. doi: 10.18632/oncotarget.23967. eCollection 2018 Jan 19.

9.

The impact of RNA sequence library construction protocols on transcriptomic profiling of leukemia.

Kumar A, Kankainen M, Parsons A, Kallioniemi O, Mattila P, Heckman CA.

BMC Genomics. 2017 Aug 17;18(1):629. doi: 10.1186/s12864-017-4039-1.

10.

Systematic drug sensitivity testing reveals synergistic growth inhibition by dasatinib or mTOR inhibitors with paclitaxel in ovarian granulosa cell tumor cells.

Haltia UM, Andersson N, Yadav B, Färkkilä A, Kulesskiy E, Kankainen M, Tang J, Bützow R, Riska A, Leminen A, Heikinheimo M, Kallioniemi O, Unkila-Kallio L, Wennerberg K, Aittokallio T, Anttonen M.

Gynecol Oncol. 2017 Mar;144(3):621-630. doi: 10.1016/j.ygyno.2016.12.016. Epub 2017 Jan 16.

PMID:
28104295
11.

Functional genomics provides insights into the role of Propionibacterium freudenreichii ssp. shermanii JS in cheese ripening.

Ojala T, Laine PKS, Ahlroos T, Tanskanen J, Pitkänen S, Salusjärvi T, Kankainen M, Tynkkynen S, Paulin L, Auvinen P.

Int J Food Microbiol. 2017 Jan 16;241:39-48. doi: 10.1016/j.ijfoodmicro.2016.09.022. Epub 2016 Sep 26.

PMID:
27744211
12.

Pseudoexons provide a mechanism for allele-specific expression of APC in familial adenomatous polyposis.

Nieminen TT, Pavicic W, Porkka N, Kankainen M, Järvinen HJ, Lepistö A, Peltomäki P.

Oncotarget. 2016 Oct 25;7(43):70685-70698. doi: 10.18632/oncotarget.12206.

13.

Fusarium mycotoxin enniatin B: Cytotoxic effects and changes in gene expression profile.

Jonsson M, Jestoi M, Anthoni M, Welling A, Loivamaa I, Hallikainen V, Kankainen M, Lysøe E, Koivisto P, Peltonen K.

Toxicol In Vitro. 2016 Aug;34:309-320. doi: 10.1016/j.tiv.2016.04.017. Epub 2016 May 6.

PMID:
27163883
14.

Phase I study with ONCOS-102 for the treatment of solid tumors - an evaluation of clinical response and exploratory analyses of immune markers.

Ranki T, Pesonen S, Hemminki A, Partanen K, Kairemo K, Alanko T, Lundin J, Linder N, Turkki R, Ristimäki A, Jäger E, Karbach J, Wahle C, Kankainen M, Backman C, von Euler M, Haavisto E, Hakonen T, Heiskanen R, Jaderberg M, Juhila J, Priha P, Suoranta L, Vassilev L, Vuolanto A, Joensuu T.

J Immunother Cancer. 2016 Mar 15;4:17. doi: 10.1186/s40425-016-0121-5. eCollection 2016.

15.

Genome-Wide Analysis of Evolutionary Markers of Human Influenza A(H1N1)pdm09 and A(H3N2) Viruses May Guide Selection of Vaccine Strain Candidates.

Belanov SS, Bychkov D, Benner C, Ripatti S, Ojala T, Kankainen M, Kai Lee H, Wei-Tze Tang J, Kainov DE.

Genome Biol Evol. 2015 Nov 27;7(12):3472-83. doi: 10.1093/gbe/evv240.

16.

Chronic Activation of Innate Immunity Correlates With Poor Prognosis in Cancer Patients Treated With Oncolytic Adenovirus.

Taipale K, Liikanen I, Juhila J, Turkki R, Tähtinen S, Kankainen M, Vassilev L, Ristimäki A, Koski A, Kanerva A, Diaconu I, Cerullo V, Vähä-Koskela M, Oksanen M, Linder N, Joensuu T, Lundin J, Hemminki A.

Mol Ther. 2016 Feb;24(1):175-83. doi: 10.1038/mt.2015.143. Epub 2015 Aug 27.

17.

Comparative Analysis of Whole-Genome Sequences of Influenza A(H1N1)pdm09 Viruses Isolated from Hospitalized and Nonhospitalized Patients Identifies Missense Mutations That Might Be Associated with Patient Hospital Admissions in Finland during 2009 to 2014.

Mishel P, Ojala T, Benner C, Lakspere T, Bychkov D, Jalovaara P, Kakkola L, Kallio-Kokko H, Kantele A, Kankainen M, Ikonen N, Ripatti S, Julkunen I, Kainov DE.

Genome Announc. 2015 Jul 30;3(4). pii: e00676-15. doi: 10.1128/genomeA.00676-15.

18.

Repeated intratumoral administration of ONCOS-102 leads to systemic antitumor CD8+ T-cell response and robust cellular and transcriptional immune activation at tumor site in a patient with ovarian cancer.

Vassilev L, Ranki T, Joensuu T, Jäger E, Karbach J, Wahle C, Partanen K, Kairemo K, Alanko T, Turkki R, Linder N, Lundin J, Ristimäki A, Kankainen M, Hemminki A, Backman C, Dienel K, von Euler M, Haavisto E, Hakonen T, Juhila J, Jäderberg M, Priha P, Vuolanto A, Pesonen S.

Oncoimmunology. 2015 Apr 1;4(7):e1017702. eCollection 2015 Jul.

19.

Local treatment of a pleural mesothelioma tumor with ONCOS-102 induces a systemic antitumor CD8+ T-cell response, prominent infiltration of CD8+ lymphocytes and Th1 type polarization.

Ranki T, Joensuu T, Jäger E, Karbach J, Wahle C, Kairemo K, Alanko T, Partanen K, Turkki R, Linder N, Lundin J, Ristimäki A, Kankainen M, Hemminki A, Backman C, Dienel K, von Euler M, Haavisto E, Hakonen T, Juhila J, Jaderberg M, Priha P, Vassilev L, Vuolanto A, Pesonen S.

Oncoimmunology. 2014 Dec 15;3(10):e958937. eCollection 2014 Nov.

20.

Immunological data from cancer patients treated with Ad5/3-E2F-Δ24-GMCSF suggests utility for tumor immunotherapy.

Hemminki O, Parviainen S, Juhila J, Turkki R, Linder N, Lundin J, Kankainen M, Ristimäki A, Koski A, Liikanen I, Oksanen M, Nettelbeck DM, Kairemo K, Partanen K, Joensuu T, Kanerva A, Hemminki A.

Oncotarget. 2015 Feb 28;6(6):4467-81.

21.

Comparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis.

Ojala T, Kankainen M, Castro J, Cerca N, Edelman S, Westerlund-Wikström B, Paulin L, Holm L, Auvinen P.

BMC Genomics. 2014 Dec 5;15:1070. doi: 10.1186/1471-2164-15-1070.

22.

Loss of Rad51c accelerates tumourigenesis in sebaceous glands of Trp53-mutant mice.

Tumiati M, Hemmes A, Uusivirta S, Koopal S, Kankainen M, Lehtonen E, Kuznetsov SG.

J Pathol. 2015 Jan;235(1):136-46. doi: 10.1002/path.4455.

PMID:
25270124
23.

Genomics and Proteomics Provide New Insight into the Commensal and Pathogenic Lifestyles of Bovine- and Human-Associated Staphylococcus epidermidis Strains.

Savijoki K, Iivanainen A, Siljamäki P, Laine PK, Paulin L, Karonen T, Pyörälä S, Kankainen M, Nyman TA, Salomäki T, Koskinen P, Holm L, Simojoki H, Taponen S, Sukura A, Kalkkinen N, Auvinen P, Varmanen P.

J Proteome Res. 2014 Aug 1;13(8):3748-3762. doi: 10.1021/pr500322d. Epub 2014 Jul 18.

PMID:
25014494
24.

Comparative proteome profiling of bovine and human Staphylococcus epidermidis strains for screening specifically expressed virulence and adaptation proteins.

Siljamäki P, Varmanen P, Kankainen M, Pyörälä S, Karonen T, Iivanainen A, Auvinen P, Paulin L, Laine PK, Taponen S, Simojoki H, Sukura A, Nyman TA, Savijoki K.

Proteomics. 2014 Aug;14(16):1890-4. doi: 10.1002/pmic.201300275. Epub 2014 Jul 10.

PMID:
24909406
25.

Comparative exoprotein profiling of different Staphylococcus epidermidis strains reveals potential link between nonclassical protein export and virulence.

Siljamäki P, Varmanen P, Kankainen M, Sukura A, Savijoki K, Nyman TA.

J Proteome Res. 2014 Jul 3;13(7):3249-61. doi: 10.1021/pr500075j. Epub 2014 Jun 2.

PMID:
24840314
26.

Effects of ellagitannin-rich berries on blood lipids, gut microbiota, and urolithin production in human subjects with symptoms of metabolic syndrome.

Puupponen-Pimiä R, Seppänen-Laakso T, Kankainen M, Maukonen J, Törrönen R, Kolehmainen M, Leppänen T, Moilanen E, Nohynek L, Aura AM, Poutanen K, Tómas-Barberán FA, Espín JC, Oksman-Caldentey KM.

Mol Nutr Food Res. 2013 Dec;57(12):2258-63. doi: 10.1002/mnfr.201300280. Epub 2013 Aug 12.

PMID:
23934737
27.

Systems-level analysis of clinically different phenotypes of juvenile nasopharyngeal angiofibromas.

Renkonen S, Kankainen M, Hagström J, Haglund C, Monni O, Mäkitie AA.

Laryngoscope. 2012 Dec;122(12):2728-35. doi: 10.1002/lary.23592. Epub 2012 Sep 10.

PMID:
22965421
28.

Nonpathogenic Lactobacillus rhamnosus activates the inflammasome and antiviral responses in human macrophages.

Miettinen M, Pietilä TE, Kekkonen RA, Kankainen M, Latvala S, Pirhonen J, Österlund P, Korpela R, Julkunen I.

Gut Microbes. 2012 Nov-Dec;3(6):510-22. doi: 10.4161/gmic.21736. Epub 2012 Aug 16.

29.

BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins.

Kankainen M, Ojala T, Holm L.

BMC Bioinformatics. 2012 Feb 15;13:33. doi: 10.1186/1471-2105-13-33.

30.

Effect of acid stress on protein expression and phosphorylation in Lactobacillus rhamnosus GG.

Koponen J, Laakso K, Koskenniemi K, Kankainen M, Savijoki K, Nyman TA, de Vos WM, Tynkkynen S, Kalkkinen N, Varmanen P.

J Proteomics. 2012 Feb 2;75(4):1357-74. doi: 10.1016/j.jprot.2011.11.009. Epub 2011 Nov 16.

PMID:
22119544
31.

Growth phase-associated changes in the proteome and transcriptome of Lactobacillus rhamnosus GG in industrial-type whey medium.

Laakso K, Koskenniemi K, Koponen J, Kankainen M, Surakka A, Salusjärvi T, Auvinen P, Savijoki K, Nyman TA, Kalkkinen N, Tynkkynen S, Varmanen P.

Microb Biotechnol. 2011 Nov;4(6):746-66. doi: 10.1111/j.1751-7915.2011.00275.x. Epub 2011 Sep 1.

32.

Identification of regulatory elements in the AGT1 promoter of ale and lager strains of brewer's yeast.

Vidgren V, Kankainen M, Londesborough J, Ruohonen L.

Yeast. 2011 Aug;28(8):579-94. doi: 10.1002/yea.1888. Epub 2011 Jul 13.

33.

Adhesive polypeptides of Staphylococcus aureus identified using a novel secretion library technique in Escherichia coli.

Kylväjä R, Kankainen M, Holm L, Westerlund-Wikström B.

BMC Microbiol. 2011 May 27;11:117. doi: 10.1186/1471-2180-11-117.

34.

Comparative proteome cataloging of Lactobacillus rhamnosus strains GG and Lc705.

Savijoki K, Lietzén N, Kankainen M, Alatossava T, Koskenniemi K, Varmanen P, Nyman TA.

J Proteome Res. 2011 Aug 5;10(8):3460-73. doi: 10.1021/pr2000896. Epub 2011 Jun 17.

PMID:
21615180
35.

MPEA--metabolite pathway enrichment analysis.

Kankainen M, Gopalacharyulu P, Holm L, Oresic M.

Bioinformatics. 2011 Jul 1;27(13):1878-9. doi: 10.1093/bioinformatics/btr278. Epub 2011 May 5.

PMID:
21551139
36.

Probiotic Lactobacillus rhamnosus downregulates FCER1 and HRH4 expression in human mast cells.

Oksaharju A, Kankainen M, Kekkonen RA, Lindstedt KA, Kovanen PT, Korpela R, Miettinen M.

World J Gastroenterol. 2011 Feb 14;17(6):750-9. doi: 10.3748/wjg.v17.i6.750.

37.

Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG.

Koskenniemi K, Laakso K, Koponen J, Kankainen M, Greco D, Auvinen P, Savijoki K, Nyman TA, Surakka A, Salusjärvi T, de Vos WM, Tynkkynen S, Kalkkinen N, Varmanen P.

Mol Cell Proteomics. 2011 Feb;10(2):M110.002741. doi: 10.1074/mcp.M110.002741. Epub 2010 Nov 15.

38.

Genome sequence of Lactobacillus crispatus ST1.

Ojala T, Kuparinen V, Koskinen JP, Alatalo E, Holm L, Auvinen P, Edelman S, Westerlund-Wikström B, Korhonen TK, Paulin L, Kankainen M.

J Bacteriol. 2010 Jul;192(13):3547-8. doi: 10.1128/JB.00399-10. Epub 2010 Apr 30.

39.

Mucosal adhesion properties of the probiotic Lactobacillus rhamnosus GG SpaCBA and SpaFED pilin subunits.

von Ossowski I, Reunanen J, Satokari R, Vesterlund S, Kankainen M, Huhtinen H, Tynkkynen S, Salminen S, de Vos WM, Palva A.

Appl Environ Microbiol. 2010 Apr;76(7):2049-57. doi: 10.1128/AEM.01958-09. Epub 2010 Jan 29.

40.

Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein.

Kankainen M, Paulin L, Tynkkynen S, von Ossowski I, Reunanen J, Partanen P, Satokari R, Vesterlund S, Hendrickx AP, Lebeer S, De Keersmaecker SC, Vanderleyden J, Hämäläinen T, Laukkanen S, Salovuori N, Ritari J, Alatalo E, Korpela R, Mattila-Sandholm T, Lassig A, Hatakka K, Kinnunen KT, Karjalainen H, Saxelin M, Laakso K, Surakka A, Palva A, Salusjärvi T, Auvinen P, de Vos WM.

Proc Natl Acad Sci U S A. 2009 Oct 6;106(40):17193-8. doi: 10.1073/pnas.0908876106. Epub 2009 Sep 17.

41.

Proteome analysis of Lactobacillus rhamnosus GG using 2-D DIGE and mass spectrometry shows differential protein production in laboratory and industrial-type growth media.

Koskenniemi K, Koponen J, Kankainen M, Savijoki K, Tynkkynen S, de Vos WM, Kalkkinen N, Varmanen P.

J Proteome Res. 2009 Nov;8(11):4993-5007. doi: 10.1021/pr9003823.

PMID:
19780546
42.

LOCP--locating pilus operons in gram-positive bacteria.

Plyusnin I, Holm L, Kankainen M.

Bioinformatics. 2009 May 1;25(9):1187-8. doi: 10.1093/bioinformatics/btp127. Epub 2009 Mar 4.

PMID:
19261721
43.

Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae.

Salusjärvi L, Kankainen M, Soliymani R, Pitkänen JP, Penttilä M, Ruohonen L.

Microb Cell Fact. 2008 Jun 4;7:18. doi: 10.1186/1475-2859-7-18.

44.

MATLIGN: a motif clustering, comparison and matching tool.

Kankainen M, Löytynoja A.

BMC Bioinformatics. 2007 Jun 8;8:189.

45.

Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana.

Kankainen M, Brader G, Törönen P, Palva ET, Holm L.

Nucleic Acids Res. 2006;34(18):e124. Epub 2006 Sep 26.

46.

POXO: a web-enabled tool series to discover transcription factor binding sites.

Kankainen M, Pehkonen P, Rosenstöm P, Törönen P, Wong G, Holm L.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W534-40.

47.

POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets.

Kankainen M, Holm L.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W427-31.

48.

POBO, transcription factor binding site verification with bootstrapping.

Kankainen M, Holm L.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W222-9.

49.

DANCER: a program for digital anatomical reconstruction of gene expression data.

Kankainen M, Wong G.

Nucleic Acids Res. 2003 Nov 1;31(21):e132.

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