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IBT julkaisut 2006

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, Vihinen M
Immunome: a reference set of genes and proteins for systems biology of the human immune system.
Cell Immunol 2006 ;244(2)87-9
PMID

Ahola V, Aittokallio T, Vihinen M, Uusipaikka E
A statistical score for assessing the quality of multiple sequence alignments.
BMC Bioinformatics 2006 ;7484
PMID

Piirilä H, Väliaho J, Vihinen M
Immunodeficiency mutation databases (IDbases).
Hum Mutat 2006 ;27(12)1200-8
PMID

Thusberg J, Vihinen M
Bioinformatic analysis of protein structure-function relationships: case study of leukocyte elastase (ELA2) missense mutations.
Hum Mutat 2006 ;27(12)1230-43
PMID

Väliaho J, Smith CI, Vihinen M
BTKbase: the mutation database for X-linked agammaglobulinemia.
Hum Mutat 2006 ;27(12)1209-17
PMID

Salonen JM, Valmu L, Rönnholm G, Kalkkinen N, Vihinen M
Proteome analysis of B-cell maturation.
Proteomics 2006 ;6(19)5152-68
PMID

Mononen N, Seppälä EH, Duggal P, Autio V, Ikonen T, Ellonen P, Saharinen J, Saarela J, Vihinen M, Tammela TL, Kallioniemi O, Bailey-Wilson JE, Schleutker J
Profiling genetic variation along the androgen biosynthesis and metabolism pathways implicates several single nucleotide polymorphisms and their combinations as prostate cancer risk factors.
Cancer Res 2006 ;66(2)743-7
PMID

Biotechnology
Vesa Hytönen - Protein Dynamics
Markku Kulomaa - Molecular Biotechnology
Laitinen OH, Hytönen VP, Nordlund HR, Kulomaa MS
Genetically engineered avidins and streptavidins.
Cell Mol Life Sci 2006 ;63(24)2992-3017
PMID

Repo S, Paldanius TA, Hytönen VP, Nyholm TK, Halling KK, Huuskonen J, Pentikäinen OT, Rissanen K, Slotte JP, Airenne TT, Salminen TA, Kulomaa MS, Johnson MS
Binding properties of HABA-type azo derivatives to avidin and avidin-related protein 4.
Chem Biol 2006 ;13(10)1029-39
PMID

Tuukkanen S, Toppari JJ, Kuzyk A, Hirviniemi L, Hytönen VP, Ihalainen T, Törmä P
Carbon nanotubes as electrodes for dielectrophoresis of DNA.
Nano Lett 2006 ;6(7)1339-43
PMID

Hytönen VP, Hörhä J, Airenne TT, Niskanen EA, Helttunen KJ, Johnson MS, Salminen TA, Kulomaa MS, Nordlund HR
Controlling quaternary structure assembly: subunit interface engineering and crystal structure of dual chain avidin.
J Mol Biol 2006 ;359(5)1352-63
PMID

Prizant M, Eisenberg-Domovich Y, Hytönen VP, Kulomaa MS, Wilchek M, Bayer EA, Livnah O
Factors dictating the pseudocatalytic efficiency of avidins.
J Mol Biol 2006 ;358(3)754-63
PMID

Laitinen OH, Hytönen VP, Nordlund HR, Kulomaa MS
Genetically engineered avidins and streptavidins.
Cell Mol Life Sci 2006 ;63(24)2992-3017
PMID

Repo S, Paldanius TA, Hytönen VP, Nyholm TK, Halling KK, Huuskonen J, Pentikäinen OT, Rissanen K, Slotte JP, Airenne TT, Salminen TA, Kulomaa MS, Johnson MS
Binding properties of HABA-type azo derivatives to avidin and avidin-related protein 4.
Chem Biol 2006 ;13(10)1029-39
PMID

Hytönen VP, Hörhä J, Airenne TT, Niskanen EA, Helttunen KJ, Johnson MS, Salminen TA, Kulomaa MS, Nordlund HR
Controlling quaternary structure assembly: subunit interface engineering and crystal structure of dual chain avidin.
J Mol Biol 2006 ;359(5)1352-63
PMID

Prizant M, Eisenberg-Domovich Y, Hytönen VP, Kulomaa MS, Wilchek M, Bayer EA, Livnah O
Factors dictating the pseudocatalytic efficiency of avidins.
J Mol Biol 2006 ;358(3)754-63
PMID

Cancer Groups
Jorma Isola - Cancer Biology
Anne Kallioniemi - Cancer Genomics
Tapio Visakorpi - Molecular Biology of Prostate Cancer
Johanna Schleutker - Genetic Predisposition to Cancer
Puputti M, Tynninen O, Sihto H, Blom T, Mäenpää H, Isola J, Paetau A, Joensuu H, Nupponen NN
Amplification of KIT, PDGFRA, VEGFR2, and EGFR in gliomas.
Mol Cancer Res 2006 ;4(12)927-34
PMID

Lundin J, Lehtimäki T, Lundin M, Holli K, Elomaa L, Turpeenniemi-Hujanen T, Kataja V, Isola J, Joensuu H
Generalisability of survival estimates for patients with breast cancer--a comparison across two population-based series.
Eur J Cancer 2006 ;42(18)3228-35
PMID

Laakso M, Tanner M, Nilsson J, Wiklund T, Erikstein B, Kellokumpu-Lehtinen P, Malmström P, Wilking N, Bergh J, Isola J
Basoluminal carcinoma: a new biologically and prognostically distinct entity between basal and luminal breast cancer.
Clin Cancer Res 2006 ;12(14 Pt 1)4185-91
PMID

Sihto H, Franssila K, Tanner M, Vasama-Nolvi C, Sarlomo-Rikala M, Nupponen NN, Joensuu H, Isola J
Platelet-derived growth factor receptor family mutations in gastrointestinal stromal tumours.
Scand J Gastroenterol 2006 ;41(7)805-11
PMID

Korhonen K, Salminen T, Raitanen J, Auvinen A, Isola J, Haapasalo H
Female predominance in meningiomas can not be explained by differences in progesterone, estrogen, or androgen receptor expression.
J Neurooncol 2006 ;80(1)1-7
PMID

, Tanner M, Isola J, Wiklund T, Erikstein B, Kellokumpu-Lehtinen P, Malmström P, Wilking N, Nilsson J, Bergh J
Topoisomerase IIalpha gene amplification predicts favorable treatment response to tailored and dose-escalated anthracycline-based adjuvant chemotherapy in HER-2/neu-amplified breast cancer: Scandinavian Breast Group Trial 9401.
J Clin Oncol 2006 ;24(16)2428-36
PMID

Puputti M, Sihto H, Isola J, Butzow R, Joensuu H, Nupponen NN
Allelic imbalance of HER2 variant in sporadic breast and ovarian cancer.
Cancer Genet Cytogenet 2006 ;167(1)32-8
PMID

Lassus H, Sihto H, Leminen A, Joensuu H, Isola J, Nupponen NN, Butzow R
Gene amplification, mutation, and protein expression of EGFR and mutations of ERBB2 in serous ovarian carcinoma.
J Mol Med 2006 ;84(8)671-81
PMID

Joensuu H, Kellokumpu-Lehtinen PL, Bono P, Alanko T, Kataja V, Asola R, Utriainen T, Kokko R, Hemminki A, Tarkkanen M, Turpeenniemi-Hujanen T, Jyrkkiö S, Flander M, Helle L, Ingalsuo S, Johansson K, Jääskeläinen AS, Pajunen M, Rauhala M, Kaleva-Kerola J, Salminen T, Leinonen M, Elomaa I, Isola J,
Adjuvant docetaxel or vinorelbine with or without trastuzumab for breast cancer.
N Engl J Med 2006 ;354(8)809-20
PMID

Helin HO, Lundin ME, Laakso M, Lundin J, Helin HJ, Isola J
Virtual microscopy in prostate histopathology: simultaneous viewing of biopsies stained sequentially with hematoxylin and eosin, and alpha-methylacyl-coenzyme A racemase/p63 immunohistochemistry.
J Urol 2006 ;175(2)495-9
PMID

Zsebik B, Citri A, Isola J, Yarden Y, Szöllosi J, Vereb G
Hsp90 inhibitor 17-AAG reduces ErbB2 levels and inhibits proliferation of the trastuzumab resistant breast tumor cell line JIMT-1.
Immunol Lett 2006 ;104(1-2)146-55
PMID

Määttä JA, Sundvall M, Junttila TT, Peri L, Laine VJ, Isola J, Egeblad M, Elenius K
Proteolytic cleavage and phosphorylation of a tumor-associated ErbB4 isoform promote ligand-independent survival and cancer cell growth.
Mol Biol Cell 2006 ;17(1)67-79
PMID

Karhu R, Laurila E, Kallioniemi A, Syrjäkoski K
Large genomic BRCA2 rearrangements and male breast cancer.
Cancer Detect Prev 2006 ;30(6)530-4
PMID

Karhu R, Mahlamäki E, Kallioniemi A
Pancreatic adenocarcinoma -- genetic portrait from chromosomes to microarrays.
Genes Chromosomes Cancer 2006 ;45(8)721-30
PMID

Alarmo EL, Rauta J, Kauraniemi P, Karhu R, Kuukasjärvi T, Kallioniemi A
Bone morphogenetic protein 7 is widely overexpressed in primary breast cancer.
Genes Chromosomes Cancer 2006 ;45(4)411-9
PMID

Rauta J, Alarmo EL, Kauraniemi P, Karhu R, Kuukasjärvi T, Kallioniemi A
The serine-threonine protein phosphatase PPM1D is frequently activated through amplification in aggressive primary breast tumours.
Breast Cancer Res Treat 2006 ;95(3)257-63
PMID

Waltering KK, Wallén MJ, Tammela TL, Vessella RL, Visakorpi T
Mutation screening of the androgen receptor promoter and untranslated regions in prostate cancer.
Prostate 2006 ;66(15)1585-91
PMID

Mäki HE, Waltering KK, Wallén MJ, Martikainen PM, Tammela TL, van Weerden WM, Vessella RL, Visakorpi T
Screening of genetic and expression alterations of SRC1 gene in prostate cancer.
Prostate 2006 ;66(13)1391-8
PMID

Savinainen KJ, Helenius MA, Lehtonen HJ, Visakorpi T
Overexpression of EIF3S3 promotes cancer cell growth.
Prostate 2006 ;66(11)1144-50
PMID

Saramäki OR, Porkka KP, Vessella RL, Visakorpi T
Genetic aberrations in prostate cancer by microarray analysis.
Int J Cancer 2006 ;119(6)1322-9
PMID

Saramäki OR, Tammela TL, Martikainen PM, Vessella RL, Visakorpi T
The gene for polycomb group protein enhancer of zeste homolog 2 (EZH2) is amplified in late-stage prostate cancer.
Genes Chromosomes Cancer 2006 ;45(7)639-45
PMID

Helenius MA, Savinainen KJ, Bova GS, Visakorpi T
Amplification of the urokinase gene and the sensitivity of prostate cancer cells to urokinase inhibitors.
BJU Int 2006 ;97(2)404-9
PMID

Schaid DJ, McDonnell SK, Zarfas KE, Cunningham JM, Hebbring S, Thibodeau SN, Eeles RA, Easton DF, Foulkes WD, Simard J, Giles GG, Hopper JL, Mahle L, Moller P, Badzioch M, Bishop DT, Evans C, Edwards S, Meitz J, Bullock S, Hope Q, Guy M, Hsieh CL, Halpern J, Balise RR, Oakley-Girvan I, Whittemore AS, Xu J, Dimitrov L, Chang BL, Adams TS, Turner AR, Meyers DA, Friedrichsen DM, Deutsch K, Kolb S, Janer M, Hood L, Ostrander EA, Stanford JL, Ewing CM, Gielzak M, Isaacs SD, Walsh PC, Wiley KE, Isaacs WB, Lange EM, Ho LA, Beebe-Dimmer JL, Wood DP, Cooney KA, Seminara D, Ikonen T, Baffoe-Bonnie A, Fredriksson H, Matikainen MP, Tammela TL, Bailey-Wilson J, Schleutker J, Maier C, Herkommer K, Hoegel JJ, Vogel W, Paiss T, Wiklund F, Emanuelsson M, Stenman E, Jonsson BA, Grönberg H, Camp NJ, Farnham J, Cannon-Albright LA, Catalona WJ, Suarez BK, Roehl KA,
Pooled genome linkage scan of aggressive prostate cancer: results from the International Consortium for Prostate Cancer Genetics.
Hum Genet 2006 ;120(4)471-85
PMID

Kokko A, Laiho P, Lehtonen R, Korja S, Carvajal-Carmona LG, Järvinen H, Mecklin JP, Eng C, Schleutker J, Tomlinson IP, Vahteristo P, Aaltonen LA
EPHB2 germline variants in patients with colorectal cancer or hyperplastic polyposis.
BMC Cancer 2006 ;6145
PMID

Hebbring SJ, Fredriksson H, White KA, Maier C, Ewing C, McDonnell SK, Jacobsen SJ, Cerhan J, Schaid DJ, Ikonen T, Autio V, Tammela TL, Herkommer K, Paiss T, Vogel W, Gielzak M, Sauvageot J, Schleutker J, Cooney KA, Isaacs W, Thibodeau SN
Role of the Nijmegen breakage syndrome 1 gene in familial and sporadic prostate cancer.
Cancer Epidemiol Biomarkers Prev 2006 ;15(5)935-8
PMID

Mononen N, Seppälä EH, Duggal P, Autio V, Ikonen T, Ellonen P, Saharinen J, Saarela J, Vihinen M, Tammela TL, Kallioniemi O, Bailey-Wilson JE, Schleutker J
Profiling genetic variation along the androgen biosynthesis and metabolism pathways implicates several single nucleotide polymorphisms and their combinations as prostate cancer risk factors.
Cancer Res 2006 ;66(2)743-7
PMID

Chang BL, Lange EM, Dimitrov L, Valis CJ, Gillanders EM, Lange LA, Wiley KE, Isaacs SD, Wiklund F, Baffoe-Bonnie A, Langefeld CD, Zheng SL, Matikainen MP, Ikonen T, Fredriksson H, Tammela T, Walsh PC, Bailey-Wilson JE, Schleutker J, Gronberg H, Cooney KA, Isaacs WB, Suh E, Trent JM, Xu J
Two-locus genome-wide linkage scan for prostate cancer susceptibility genes with an interaction effect.
Hum Genet 2006 ;118(6)716-24
PMID

Syrjäkoski K, Fredriksson H, Ikonen T, Kuukasjärvi T, Autio V, Matikainen MP, Tammela TL, Koivisto PA, Schleutker J
Hemochromatosis gene mutations among Finnish male breast and prostate cancer patients.
Int J Cancer 2006 ;118(2)518-20
PMID

Cellular Biology
Ari-Pekka Huovila - Cell Interactions
Herma Renkema - Biochemistry of Cell Signaling
Bussink AP, van Eijk M, Renkema GH, Aerts JM, Boot RG
The biology of the Gaucher cell: the cradle of human chitinases.
Int Rev Cytol 2006 ;25271-128
PMID

Boot RG, Verhoek M, Langeveld M, Renkema GH, Hollak CE, Weening JJ, Donker-Koopman WE, Groener JE, Aerts JM
CCL18: a urinary marker of Gaucher cell burden in Gaucher patients.
J Inherit Metab Dis 2006 ;29(4)564-71
PMID

Kärkkäinen S, Hiipakka M, Wang JH, Kleino I, Vähä-Jaakkola M, Renkema GH, Liss M, Wagner R, Saksela K
Identification of preferred protein interactions by phage-display of the human Src homology-3 proteome.
EMBO Rep 2006 ;7(2)186-91
PMID

Mitochondrial Genetics
Howy Jacobs - Mitochondrial Gene Expression and Disease Group
Hans Spelbrink - Molecular Biology-Mitochondrial DNA maintenance
Yasukawa T, Reyes A, Cluett TJ, Yang MY, Bowmaker M, Jacobs HT, Holt IJ
Replication of vertebrate mitochondrial DNA entails transient ribonucleotide incorporation throughout the lagging strand.
EMBO J 2006 ;25(22)5358-71
PMID

Pohjoismäki JL, Wanrooij S, Hyvärinen AK, Goffart S, Holt IJ, Spelbrink JN, Jacobs HT
Alterations to the expression level of mitochondrial transcription factor A, TFAM, modify the mode of mitochondrial DNA replication in cultured human cells.
Nucleic Acids Res 2006 ;34(20)5815-28
PMID

Kirino Y, Yasukawa T, Marjavaara SK, Jacobs HT, Holt IJ, Watanabe K, Suzuki T
Acquisition of the wobble modification in mitochondrial tRNALeu(CUN) bearing the G12300A mutation suppresses the MELAS molecular defect.
Hum Mol Genet 2006 ;15(6)897-904
PMID

Smeitink JA, Zeviani M, Turnbull DM, Jacobs HT
Mitochondrial medicine: a metabolic perspective on the pathology of oxidative phosphorylation disorders.
Cell Metab 2006 ;3(1)9-13
PMID

Hakkaart GA, Dassa EP, Jacobs HT, Rustin P
Allotopic expression of a mitochondrial alternative oxidase confers cyanide resistance to human cell respiration.
EMBO Rep 2006 ;7(3)341-5
PMID

Pohjoismäki JL, Wanrooij S, Hyvärinen AK, Goffart S, Holt IJ, Spelbrink JN, Jacobs HT
Alterations to the expression level of mitochondrial transcription factor A, TFAM, modify the mode of mitochondrial DNA replication in cultured human cells.
Nucleic Acids Res 2006 ;34(20)5815-28
PMID

Lu B, Garrido N, Spelbrink JN, Suzuki CK
Tid1 isoforms are mitochondrial DnaJ-like chaperones with unique carboxyl termini that determine cytosolic fate.
J Biol Chem 2006 ;281(19)13150-8
PMID

Molecular Immunology
Mika Rämet - Experimental Immunology
Olli Silvennoinen - Molecular Immunology
Jukka Westermark - Cancer cell signaling
Ulvila J, Parikka M, Kleino A, Sormunen R, Ezekowitz RA, Kocks C, Rämet M
Double-stranded RNA is internalized by scavenger receptor-mediated endocytosis in Drosophila S2 cells.
J Biol Chem 2006 ;281(20)14370-5
PMID

Kurzer JH, Saharinen P, Silvennoinen O, Carter-Su C
Binding of SH2-B family members within a potential negative regulatory region maintains JAK2 in an active state.
Mol Cell Biol 2006 ;26(17)6381-94
PMID

Välineva T, Yang J, Silvennoinen O
Characterization of RNA helicase A as component of STAT6-dependent enhanceosome.
Nucleic Acids Res 2006 ;34(14)3938-46
PMID

Murumägi A, Silvennoinen O, Peterson P
Ets transcription factors regulate AIRE gene promoter.
Biochem Biophys Res Commun 2006 ;348(2)768-74
PMID

Koivusalo R, Mialon A, Pitkänen H, Westermarck J, Hietanen S
Activation of p53 in cervical cancer cells by human papillomavirus E6 RNA interference is transient, but can be sustained by inhibiting endogenous nuclear export-dependent p53 antagonists.
Cancer Res 2006 ;66(24)11817-24
PMID

Regenerative Medicine
Katriina Aalto-Setälä - Cardiology Group
Susanna Miettinen - Adult Stem Cell Group
Susanna Narkilahti - Neuro Group
Heli Skottman - Ophthalmology Group
Laitinen-Forsblom PJ, Mäkynen P, Mäkynen H, Yli-Mäyry S, Virtanen V, Kontula K, Aalto-Setälä K
SCN5A mutation associated with cardiac conduction defect and atrial arrhythmias.
J Cardiovasc Electrophysiol 2006 ;17(5)480-5
PMID

Kalueff A, Loseva E, Haapasalo H, Rantala I, Keranen J, Lou YR, Minasyan A, Keisala T, Miettinen S, Kuuslahti M, Tuchimaa P
Thalamic calcification in vitamin D receptor knockout mice.
Neuroreport 2006 ;17(7)717-21
PMID

Kalueff AV, Keisala T, Minasyan A, Kuuslahti M, Miettinen S, Tuohimaa P
Behavioural anomalies in mice evoked by "Tokyo" disruption of the Vitamin D receptor gene.
Neurosci Res 2006 ;54(4)254-60
PMID

Kalueff AV, Minasyan A, Keisala T, Kuuslahti M, Miettinen S, Tuohimaa P
Increased severity of chemically induced seizures in mice with partially deleted Vitamin D receptor gene.
Neurosci Lett 2006 ;394(1)69-73
PMID

Sarvilinna N, Eronen H, Miettinen S, Vienonen A, Ylikomi T
Steroid hormone receptors and coregulators in endocrine-resistant and estrogen-independent breast cancer cells.
Int J Cancer 2006 ;118(4)832-40
PMID

Nairismägi J, Pitkänen A, Narkilahti S, Huttunen J, Kauppinen RA, Gröhn OH
Manganese-enhanced magnetic resonance imaging of mossy fiber plasticity in vivo.
Neuroimage 2006 ;30(1)130-5
PMID

Grinnemo KH, Kumagai-Braesch M, Månsson-Broberg A, Skottman H, Hao X, Siddiqui A, Andersson A, Strömberg AM, Lahesmaa R, Hovatta O, Sylven C, Corbascio M, Dellgren G
Human embryonic stem cells are immunogenic in allogeneic and xenogeneic settings.
Reprod Biomed Online 2006 ;13(5)712-24
PMID

Skottman H, Hovatta O
Culture conditions for human embryonic stem cells.
Reproduction 2006 ;132(5)691-8
PMID

Aghajanova L, Skottman H, Strömberg AM, Inzunza J, Lahesmaa R, Hovatta O
Expression of leukemia inhibitory factor and its receptors is increased during differentiation of human embryonic stem cells.
Fertil Steril 2006 ;86(4 Suppl)1193-209
PMID

Skottman H, Dilber MS, Hovatta O
The derivation of clinical-grade human embryonic stem cell lines.
FEBS Lett 2006 ;580(12)2875-8
PMID

Skottman H, Strömberg AM, Matilainen E, Inzunza J, Hovatta O, Lahesmaa R
Unique gene expression signature by human embryonic stem cells cultured under serum-free conditions correlates with their enhanced and prolonged growth in an undifferentiated stage.
Stem Cells 2006 ;24(1)151-67
PMID

 
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