IBT julkaisut 2008
NOTE: This list is not exhaustive because it has been collected by an automatic procedure from PubMed. It may also contain publications not related to IMT or Regea authors (authors having the same name). The same publication may also appear more than once in case several research groups have participated in the writing. |
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Bioinformatics Mauno Vihinen - Bioinformatics Group |
| Ortutay C, Nore BF, Vihinen M, Smith CI Phylogeny of Tec family kinases identification of a premetazoan origin of Btk, Bmx, Itk, Tec, Txk, and the Btk regulator SH3BP5. Adv Genet 2008 ;6451-80 PMID |
| Fan YM, Karhunen PJ, Levula M, Ilveskoski E, Mikkelsson J, Kajander OA, Järvinen O, Oksala N, Thusberg J, Vihinen M, Salenius JP, Kytömäki L, Soini JT, Laaksonen R, Lehtimäki T Expression of sterol regulatory element-binding transcription factor (SREBF) 2 and SREBF cleavage-activating protein (SCAP) in human atheroma and the association of their allelic variants with sudden cardiac death. Thromb J 2008 ;617 PMID |
| Ahola V, Aittokallio T, Vihinen M, Uusipaikka E Model-based prediction of sequence alignment quality. Bioinformatics 2008 ;24(19)2165-71 PMID |
| Ortutay C, Vihinen M PseudoGeneQuest - service for identification of different pseudogene types in the human genome. BMC Bioinformatics 2008 ;9299 PMID |
| Ortutay C, Vihinen M Efficiency of the immunome protein interaction network increases during evolution. Immunome Res 2008 ;44 PMID |
| Lappalainen I, Thusberg J, Shen B, Vihinen M Genome wide analysis of pathogenic SH2 domain mutations. Proteins 2008 ;72(2)779-92 PMID |
| Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL, Björling E, Blagoev B, Bose R, Brahmachari SK, Burlingame AS, Bustelo XR, Cagney G, Cantin GT, Cardasis HL, Celis JE, Chaerkady R, Chu F, Cole PA, Costello CE, Cotter RJ, Crockett D, DeLany JP, De Marzo AM, DeSouza LV, Deutsch EW, Dransfield E, Drewes G, Droit A, Dunn MJ, Elenitoba-Johnson K, Ewing RM, Van Eyk J, Faca V, Falkner J, Fang X, Fenselau C, Figeys D, Gagné P, Gelfi C, Gevaert K, Gimble JM, Gnad F, Goel R, Gromov P, Hanash SM, Hancock WS, Harsha HC, Hart G, Hays F, He F, Hebbar P, Helsens K, Hermeking H, Hide W, Hjernø K, Hochstrasser DF, Hofmann O, Horn DM, Hruban RH, Ibarrola N, James P, Jensen ON, Jensen PH, Jung P, Kandasamy K, Kheterpal I, Kikuno RF, Korf U, Körner R, Kuster B, Kwon MS, Lee HJ, Lee YJ, Lefevre M, Lehvaslaiho M, Lescuyer P, Levander F, Lim MS, Löbke C, Loo JA, Mann M, Martens L, Martinez-Heredia J, McComb M, McRedmond J, Mehrle A, Menon R, Miller CA, Mischak H, Mohan SS, Mohmood R, Molina H, Moran MF, Morgan JD, Moritz R, Morzel M, Muddiman DC, Nalli A, Navarro JD, Neubert TA, Ohara O, Oliva R, Omenn GS, Oyama M, Paik YK, Pennington K, Pepperkok R, Periaswamy B, Petricoin EF, Poirier GG, Prasad TS, Purvine SO, Rahiman BA, Ramachandran P, Ramachandra YL, Rice RH, Rick J, Ronnholm RH, Salonen J, Sanchez JC, Sayd T, Seshi B, Shankari K, Sheng SJ, Shetty V, Shivakumar K, Simpson RJ, Sirdeshmukh R, Siu KW, Smith JC, Smith RD, States DJ, Sugano S, Sullivan M, Superti-Furga G, Takatalo M, Thongboonkerd V, Trinidad JC, Uhlen M, Vandekerckhove J, Vasilescu J, Veenstra TD, Vidal-Taboada JM, Vihinen M, Wait R, Wang X, Wiemann S, Wu B, Xu T, Yates JR, Zhong J, Zhou M, Zhu Y, Zurbig P, Pandey A Human Proteinpedia enables sharing of human protein data. Nat Biotechnol 2008 ;26(2)164-7 PMID |
| Kivioja T, Tiirikka T, Siermala M, Vihinen M Dynamic covariation between gene expression and genome characteristics. Gene 2008 ;410(1)53-66 PMID |
| Shen B, Bai J, Vihinen M Physicochemical feature-based classification of amino acid mutations. Protein Eng Des Sel 2008 ;21(1)37-44 PMID |
| Pärssinen J, Alarmo EL, Khan S, Karhu R, Vihinen M, Kallioniemi A Identification of differentially expressed genes after PPM1D silencing in breast cancer. Cancer Lett 2008 ;259(1)61-70 PMID |
| Wehr C, Kivioja T, Schmitt C, Ferry B, Witte T, Eren E, Vlkova M, Hernandez M, Detkova D, Bos PR, Poerksen G, von Bernuth H, Baumann U, Goldacker S, Gutenberger S, Schlesier M, Bergeron-van der Cruyssen F, Le Garff M, Debré P, Jacobs R, Jones J, Bateman E, Litzman J, van Hagen PM, Plebani A, Schmidt RE, Thon V, Quinti I, Espanol T, Webster AD, Chapel H, Vihinen M, Oksenhendler E, Peter HH, Warnatz K The EUROclass trial: defining subgroups in common variable immunodeficiency. Blood 2008 ;111(1)77-85 PMID |
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Biotechnology Vesa Hytönen - Protein Dynamics Markku Kulomaa - Molecular Biotechnology |
| Määttä JA, Airenne TT, Nordlund HR, Jänis J, Paldanius TA, Vainiotalo P, Johnson MS, Kulomaa MS, Hytönen VP Rational modification of ligand-binding preference of avidin by circular permutation and mutagenesis. Chembiochem 2008 ;9(7)1124-35 PMID |
| Hayouka R, Eisenberg-Domovich Y, Hytönen VP, Määttä JA, Nordlund HR, Kulomaa MS, Wilchek M, Bayer EA, Livnah O Critical importance of loop conformation to avidin-enhanced hydrolysis of an active biotin ester. Acta Crystallogr D Biol Crystallogr 2008 ;64(Pt 3)302-8 PMID |
| Hytönen VP, Vogel V How force might activate talin's vinculin binding sites: SMD reveals a structural mechanism. PLoS Comput Biol 2008 ;4(2)e24 PMID |
| Hilvo M, Baranauskiene L, Salzano AM, Scaloni A, Matulis D, Innocenti A, Scozzafava A, Monti SM, Di Fiore A, De Simone G, Lindfors M, Jänis J, Valjakka J, Pastoreková S, Pastorek J, Kulomaa MS, Nordlund HR, Supuran CT, Parkkila S Biochemical characterization of CA IX, one of the most active carbonic anhydrase isozymes. J Biol Chem 2008 ;283(41)27799-809 PMID |
| Määttä JA, Airenne TT, Nordlund HR, Jänis J, Paldanius TA, Vainiotalo P, Johnson MS, Kulomaa MS, Hytönen VP Rational modification of ligand-binding preference of avidin by circular permutation and mutagenesis. Chembiochem 2008 ;9(7)1124-35 PMID |
| Hayouka R, Eisenberg-Domovich Y, Hytönen VP, Määttä JA, Nordlund HR, Kulomaa MS, Wilchek M, Bayer EA, Livnah O Critical importance of loop conformation to avidin-enhanced hydrolysis of an active biotin ester. Acta Crystallogr D Biol Crystallogr 2008 ;64(Pt 3)302-8 PMID |
| Innocenti A, Hilvo M, Scozzafava A, Lindfors M, Nordlund HR, Kulomaa MS, Parkkila S, Supuran CT Carbonic anhydrase inhibitors: the very weak inhibitors dithiothreitol, beta-mercaptoethanol, tris(carboxyethyl)phosphine and threitol interfere with the binding of sulfonamides to isozymes II and IX. Bioorg Med Chem Lett 2008 ;18(6)1898-903 PMID |
| Laakkonen JP, Kaikkonen MU, Ronkainen PH, Ihalainen TO, Niskanen EA, Häkkinen M, Salminen M, Kulomaa MS, Ylä-Herttuala S, Airenne KJ, Vihinen-Ranta M Baculovirus-mediated immediate-early gene expression and nuclear reorganization in human cells. Cell Microbiol 2008 ;10(3)667-81 PMID |
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Cancer Groups Jorma Isola - Cancer Biology Anne Kallioniemi - Cancer Genomics Tapio Visakorpi - Molecular Biology of Prostate Cancer Johanna Schleutker - Genetic Predisposition to Cancer |
| Linder E, Lundin M, Thors C, Lebbad M, Winiecka-Krusnell J, Helin H, Leiva B, Isola J, Lundin J Web-based virtual microscopy for parasitology: a novel tool for education and quality assurance. PLoS Negl Trop Dis 2008 ;2(10)e315 PMID |
| Sihto H, Lundin J, Lehtimäki T, Sarlomo-Rikala M, Bützow R, Holli K, Sailas L, Kataja V, Lundin M, Turpeenniemi-Hujanen T, Isola J, Heikkilä P, Joensuu H Molecular subtypes of breast cancers detected in mammography screening and outside of screening. Clin Cancer Res 2008 ;14(13)4103-10 PMID |
| Parkkila S, Pan PW, Ward A, Gibadulinova A, Oveckova I, Pastorekova S, Pastorek J, Martinez AR, Helin HO, Isola J The calcium-binding protein S100P in normal and malignant human tissues. BMC Clin Pathol 2008 ;82 PMID |
| Barok M, Balázs M, Nagy P, Rákosy Z, Treszl A, Tóth E, Juhász I, Park JW, Isola J, Vereb G, Szöllosi J Trastuzumab decreases the number of circulating and disseminated tumor cells despite trastuzumab resistance of the primary tumor. Cancer Lett 2008 ;260(1-2)198-208 PMID |
| Saal LH, Gruvberger-Saal SK, Persson C, Lövgren K, Jumppanen M, Staaf J, Jönsson G, Pires MM, Maurer M, Holm K, Koujak S, Subramaniyam S, Vallon-Christersson J, Olsson H, Su T, Memeo L, Ludwig T, Ethier SP, Krogh M, Szabolcs M, Murty VV, Isola J, Hibshoosh H, Parsons R, Borg A Recurrent gross mutations of the PTEN tumor suppressor gene in breast cancers with deficient DSB repair. Nat Genet 2008 ;40(1)102-7 PMID |
| Laitinen S, Martikainen PM, Tolonen T, Isola J, Tammela TL, Visakorpi T EZH2, Ki-67 and MCM7 are prognostic markers in prostatectomy treated patients. Int J Cancer 2008 ;122(3)595-602 PMID |
| Dihge L, Bendahl PO, Grabau D, Isola J, Lövgren K, Rydén L, Fernö M Epidermal growth factor receptor (EGFR) and the estrogen receptor modulator amplified in breast cancer (AIB1) for predicting clinical outcome after adjuvant tamoxifen in breast cancer. Breast Cancer Res Treat 2008 ;109(2)255-62 PMID |
| Heinonen H, Nieminen A, Saarela M, Kallioniemi A, Klefström J, Hautaniemi S, Monni O Deciphering downstream gene targets of PI3K/mTOR/p70S6K pathway in breast cancer. BMC Genomics 2008 ;9348 PMID |
| Erkko H, Dowty JG, Nikkilä J, Syrjäkoski K, Mannermaa A, Pylkäs K, Southey MC, Holli K, Kallioniemi A, Jukkola-Vuorinen A, Kataja V, Kosma VM, Xia B, Livingston DM, Winqvist R, Hopper JL Penetrance analysis of the PALB2 c.1592delT founder mutation. Clin Cancer Res 2008 ;14(14)4667-71 PMID |
| Fagerholm R, Hofstetter B, Tommiska J, Aaltonen K, Vrtel R, Syrjäkoski K, Kallioniemi A, Kilpivaara O, Mannermaa A, Kosma VM, Uusitupa M, Eskelinen M, Kataja V, Aittomäki K, von Smitten K, Heikkilä P, Lukas J, Holli K, Bartkova J, Blomqvist C, Bartek J, Nevanlinna H NAD(P)H:quinone oxidoreductase 1 NQO1*2 genotype (P187S) is a strong prognostic and predictive factor in breast cancer. Nat Genet 2008 ;40(7)844-53 PMID |
| Lind GE, Ahlquist T, Kolberg M, Berg M, Eknaes M, Alonso MA, Kallioniemi A, Meling GI, Skotheim RI, Rognum TO, Thiis-Evensen E, Lothe RA Hypermethylated MAL gene - a silent marker of early colon tumorigenesis. J Transl Med 2008 ;613 PMID |
| Pärssinen J, Alarmo EL, Karhu R, Kallioniemi A PPM1D silencing by RNA interference inhibits proliferation and induces apoptosis in breast cancer cell lines with wild-type p53. Cancer Genet Cytogenet 2008 ;182(1)33-9 PMID |
| Kallioniemi A CGH microarrays and cancer. Curr Opin Biotechnol 2008 ;19(1)36-40 PMID |
| Pärssinen J, Alarmo EL, Khan S, Karhu R, Vihinen M, Kallioniemi A Identification of differentially expressed genes after PPM1D silencing in breast cancer. Cancer Lett 2008 ;259(1)61-70 PMID |
| Ylösmäki E, Hakkarainen T, Hemminki A, Visakorpi T, Andino R, Saksela K Generation of a conditionally replicating adenovirus based on targeted destruction of E1A mRNA by a cell type-specific MicroRNA. J Virol 2008 ;82(22)11009-15 PMID |
| Alhopuro P, Karhu A, Winqvist R, Waltering K, Visakorpi T, Aaltonen LA Somatic mutation analysis of MYH11 in breast and prostate cancer. BMC Cancer 2008 ;8263 PMID |
| Urbanucci A, Waltering KK, Suikki HE, Helenius MA, Visakorpi T Androgen regulation of the androgen receptor coregulators. BMC Cancer 2008 ;8219 PMID |
| Rauhala HE, Porkka KP, Saramäki OR, Tammela TL, Visakorpi T Clusterin is epigenetically regulated in prostate cancer. Int J Cancer 2008 ;123(7)1601-9 PMID |
| Murtola TJ, Visakorpi T, Lahtela J, Syvälä H, Tammela TLj Statins and prostate cancer prevention: where we are now, and future directions. Nat Clin Pract Urol 2008 ;5(7)376-87 PMID |
| Saramäki OR, Harjula AE, Martikainen PM, Vessella RL, Tammela TL, Visakorpi T TMPRSS2:ERG fusion identifies a subgroup of prostate cancers with a favorable prognosis. Clin Cancer Res 2008 ;14(11)3395-400 PMID |
| Abdulghani J, Gu L, Dagvadorj A, Lutz J, Leiby B, Bonuccelli G, Lisanti MP, Zellweger T, Alanen K, Mirtti T, Visakorpi T, Bubendorf L, Nevalainen MT Stat3 promotes metastatic progression of prostate cancer. Am J Pathol 2008 ;172(6)1717-28 PMID |
| Tan SH, Dagvadorj A, Shen F, Gu L, Liao Z, Abdulghani J, Zhang Y, Gelmann EP, Zellweger T, Culig Z, Visakorpi T, Bubendorf L, Kirken RA, Karras J, Nevalainen MT Transcription factor Stat5 synergizes with androgen receptor in prostate cancer cells. Cancer Res 2008 ;68(1)236-48 PMID |
| Laitinen S, Martikainen PM, Tolonen T, Isola J, Tammela TL, Visakorpi T EZH2, Ki-67 and MCM7 are prognostic markers in prostatectomy treated patients. Int J Cancer 2008 ;122(3)595-602 PMID |
| Kote-Jarai Z, Easton DF, Stanford JL, Ostrander EA, Schleutker J, Ingles SA, Schaid D, Thibodeau S, Dörk T, Neal D, Donovan J, Hamdy F, Cox A, Maier C, Vogel W, Guy M, Muir K, Lophatananon A, Kedda MA, Spurdle A, Steginga S, John EM, Giles G, Hopper J, Chappuis PO, Hutter P, Foulkes WD, Hamel N, Salinas CA, Koopmeiners JS, Karyadi DM, Johanneson B, Wahlfors T, Tammela TL, Stern MC, Corral R, McDonnell SK, Schürmann P, Meyer A, Kuefer R, Leongamornlert DA, Tymrakiewicz M, Liu JF, O'Mara T, Gardiner RA, Aitken J, Joshi AD, Severi G, English DR, Southey M, Edwards SM, Al Olama AA, , Eeles RA Multiple novel prostate cancer predisposition loci confirmed by an international study: the PRACTICAL Consortium. Cancer Epidemiol Biomarkers Prev 2008 ;17(8)2052-61 PMID |
| Siltanen S, Syrjäkoski K, Fagerholm R, Ikonen T, Lipman P, Mallott J, Holli K, Tammela TL, Järvinen HJ, Mecklin JP, Aittomäki K, Blomqvist C, Bailey-Wilson JE, Nevanlinna H, Aaltonen LA, Schleutker J, Vahteristo P ARLTS1 germline variants and the risk for breast, prostate, and colorectal cancer. Eur J Hum Genet 2008 ;16(8)983-91 PMID |
| Vaarala MH, Mattila H, Ohtonen P, Tammela TL, Paavonen TK, Schleutker J The interaction of CYP3A5 polymorphisms along the androgen metabolism pathway in prostate cancer. Int J Cancer 2008 ;122(11)2511-6 PMID |
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Cellular Biology Ari-Pekka Huovila - Cell Interactions Herma Renkema - Biochemistry of Cell Signaling |
| Karjalainen M, Kakkonen E, Upla P, Paloranta H, Kankaanpää P, Liberali P, Renkema GH, Hyypiä T, Heino J, Marjomäki V A Raft-derived, Pak1-regulated entry participates in alpha2beta1 integrin-dependent sorting to caveosomes. Mol Biol Cell 2008 ;19(7)2857-69 PMID |
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Mitochondrial Genetics Howy Jacobs - Mitochondrial Gene Expression and Disease Group Hans Spelbrink - Molecular Biology-Mitochondrial DNA maintenance |
| Zanotto E, Lehtonen V, Jacobs HT Modulation of Mrps12/Sarsm promoter activity in response to mitochondrial stress. Biochim Biophys Acta 2008 ;1783(12)2352-62 PMID |
| Lindsay HA, Baines R, ffrench-Constant R, Lilley K, Jacobs HT, O'Dell KM The dominant cold-sensitive Out-cold mutants of Drosophila melanogaster have novel missense mutations in the voltage-gated sodium channel gene paralytic. Genetics 2008 ;180(2)873-84 PMID |
| Hakonen AH, Goffart S, Marjavaara S, Paetau A, Cooper H, Mattila K, Lampinen M, Sajantila A, Lönnqvist T, Spelbrink JN, Suomalainen A Infantile-onset spinocerebellar ataxia and mitochondrial recessive ataxia syndrome are associated with neuronal complex I defect and mtDNA depletion. Hum Mol Genet 2008 ;17(23)3822-35 PMID |
| Krishnan KJ, Reeve AK, Samuels DC, Chinnery PF, Blackwood JK, Taylor RW, Wanrooij S, Spelbrink JN, Lightowlers RN, Turnbull DM What causes mitochondrial DNA deletions in human cells? Nat Genet 2008 ;40(3)275-9 PMID |
| Cooper HM, Spelbrink JN The human SIRT3 protein deacetylase is exclusively mitochondrial. Biochem J 2008 ;411(2)279-85 PMID |
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Molecular Immunology Mika Rämet - Experimental Immunology Olli Silvennoinen - Molecular Immunology Jukka Westermark - Cancer cell signaling |
| Kleino A, Myllymäki H, Kallio J, Vanha-aho LM, Oksanen K, Ulvila J, Hultmark D, Valanne S, Rämet M Pirk is a negative regulator of the Drosophila Imd pathway. J Immunol 2008 ;180(8)5413-22 PMID |
| Paukku K, Kalkkinen N, Silvennoinen O, Kontula KK, Lehtonen JY p100 increases AT1R expression through interaction with AT1R 3'-UTR. Nucleic Acids Res 2008 ;36(13)4474-87 PMID |
| Vanhatupa S, Ungureanu D, Paakkunainen M, Silvennoinen O MAPK-induced Ser727 phosphorylation promotes SUMOylation of STAT1. Biochem J 2008 ;409(1)179-85 PMID |
| Junttila MR, Puustinen P, Niemelä M, Ahola R, Arnold H, Böttzauw T, Ala-aho R, Nielsen C, Ivaska J, Taya Y, Lu SL, Lin S, Chan EK, Wang XJ, Grènman R, Kast J, Kallunki T, Sears R, Kähäri VM, Westermarck J CIP2A inhibits PP2A in human malignancies. Cell 2007 ;130(1)51-62 PMID |
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Regenerative Medicine Katriina Aalto-Setälä - Cardiology Group Susanna Miettinen - Adult Stem Cell Group Susanna Narkilahti - Neuro Group Heli Skottman - Ophthalmology Group |
| Lindroos B, Mäenpää K, Ylikomi T, Oja H, Suuronen R, Miettinen S Characterisation of human dental stem cells and buccal mucosa fibroblasts. Biochem Biophys Res Commun 2008 ;368(2)329-35 PMID |
| Lappalainen RS, Narkilahti S, Huhtala T, Liimatainen T, Suuronen T, Närvänen A, Suuronen R, Hovatta O, Jolkkonen J The SPECT imaging shows the accumulation of neural progenitor cells into internal organs after systemic administration in middle cerebral artery occlusion rats. Neurosci Lett 2008 ;440(3)246-50 PMID |
| Unger C, Skottman H, Blomberg P, Dilber MS, Hovatta O Good manufacturing practice and clinical-grade human embryonic stem cell lines. Hum Mol Genet 2008 ;17(R1)R48-53 PMID |
Biolääketieteellisen teknologian yksikkö
Biokatu 8
33520 Tampere, Finland
Biokatu 8
33520 Tampere, Finland
