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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.
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

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

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

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

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

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

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

 
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