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IBT julkaisut 2007

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
Rannikko K, Ortutay C, Vihinen M
Immunity genes and their orthologs: a multi-species database.
Int Immunol 2007 ;19(12)1361-70
PMID

Khan S, Vihinen M
Spectrum of disease-causing mutations in protein secondary structures.
BMC Struct Biol 2007 ;756
PMID

Pajunen M, Turakainen H, Poussu E, Peränen J, Vihinen M, Savilahti H
High-precision mapping of protein protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform.
Nucleic Acids Res 2007 ;35(16)e103
PMID

Ollila J, Vihinen M
Immunological systems biology: gene expression analysis of B-cell development in Ramos B-cells.
Mol Immunol 2007 ;44(14)3537-51
PMID

Samarghitean C, Väliaho J, Vihinen M
IDR knowledge base for primary immunodeficiencies.
Immunome Res 2007 ;36
PMID

Ortutay C, Siermala M, Vihinen M
ImmTree: database of evolutionary relationships of genes and proteins in the human immune system.
Immunome Res 2007 ;34
PMID

Giardine B, Riemer C, Hefferon T, Thomas D, Hsu F, Zielenski J, Sang Y, Elnitski L, Cutting G, Trumbower H, Kern A, Kuhn R, Patrinos GP, Hughes J, Higgs D, Chui D, Scriver C, Phommarinh M, Patnaik SK, Blumenfeld O, Gottlieb B, Vihinen M, Väliaho J, Kent J, Miller W, Hardison RC
PhenCode: connecting ENCODE data with mutations and phenotype.
Hum Mutat 2007 ;28(6)554-62
PMID

Ortutay C, Siermala M, Vihinen M
Molecular characterization of the immune system: emergence of proteins, processes, and domains.
Immunogenetics 2007 ;59(5)333-48
PMID

Biotechnology
Vesa Hytönen - Protein Dynamics
Markku Kulomaa - Molecular Biotechnology
Laitinen OH, Nordlund HR, Hytönen VP, Kulomaa MS
Brave new (strept)avidins in biotechnology.
Trends Biotechnol 2007 ;25(6)269-77
PMID

Hytönen VP, Määttä JA, Niskanen EA, Huuskonen J, Helttunen KJ, Halling KK, Nordlund HR, Rissanen K, Johnson MS, Salminen TA, Kulomaa MS, Laitinen OH, Airenne TT
Structure and characterization of a novel chicken biotin-binding protein A (BBP-A).
BMC Struct Biol 2007 ;78
PMID

Rinne J, Albarran B, Jylhävä J, Ihalainen TO, Kankaanpää P, Hytönen VP, Stayton PS, Kulomaa MS, Vihinen-Ranta M
Internalization of novel non-viral vector TAT-streptavidin into human cells.
BMC Biotechnol 2007 ;71
PMID

Helppolainen SH, Nurminen KP, Määttä JA, Halling KK, Slotte JP, Huhtala T, Liimatainen T, Ylä-Herttuala S, Airenne KJ, Närvänen A, Jänis J, Vainiotalo P, Valjakka J, Kulomaa MS, Nordlund HR
Rhizavidin from Rhizobium etli: the first natural dimer in the avidin protein family.
Biochem J 2007 ;405(3)397-405
PMID

Laitinen OH, Nordlund HR, Hytönen VP, Kulomaa MS
Brave new (strept)avidins in biotechnology.
Trends Biotechnol 2007 ;25(6)269-77
PMID

Hytönen VP, Määttä JA, Niskanen EA, Huuskonen J, Helttunen KJ, Halling KK, Nordlund HR, Rissanen K, Johnson MS, Salminen TA, Kulomaa MS, Laitinen OH, Airenne TT
Structure and characterization of a novel chicken biotin-binding protein A (BBP-A).
BMC Struct Biol 2007 ;78
PMID

Kallistova AY, Kevbrina MV, Nekrasova VK, Shnyrev NA, Einola JK, Kulomaa MS, Rintala JA, Nozhevnikova AN
Enumeration of methanotrophic bacteria in the cover soil of an aged municipal landfill.
Microb Ecol 2007 ;54(4)637-45
PMID

Rinne J, Albarran B, Jylhävä J, Ihalainen TO, Kankaanpää P, Hytönen VP, Stayton PS, Kulomaa MS, Vihinen-Ranta M
Internalization of novel non-viral vector TAT-streptavidin into human cells.
BMC Biotechnol 2007 ;71
PMID

Cancer Groups
Jorma Isola - Cancer Biology
Anne Kallioniemi - Cancer Genomics
Tapio Visakorpi - Molecular Biology of Prostate Cancer
Johanna Schleutker - Genetic Predisposition to Cancer
Pályi-Krekk Z, Barok M, Isola J, Tammi M, Szöllosi J, Nagy P
Hyaluronan-induced masking of ErbB2 and CD44-enhanced trastuzumab internalisation in trastuzumab resistant breast cancer.
Eur J Cancer 2007 ;43(16)2423-33
PMID

Aqeilan RI, Donati V, Gaudio E, Nicoloso MS, Sundvall M, Korhonen A, Lundin J, Isola J, Sudol M, Joensuu H, Croce CM, Elenius K
Association of Wwox with ErbB4 in breast cancer.
Cancer Res 2007 ;67(19)9330-6
PMID

Barok M, Isola J, Pályi-Krekk Z, Nagy P, Juhász I, Vereb G, Kauraniemi P, Kapanen A, Tanner M, Vereb G, Szöllösi J
Trastuzumab causes antibody-dependent cellular cytotoxicity-mediated growth inhibition of submacroscopic JIMT-1 breast cancer xenografts despite intrinsic drug resistance.
Mol Cancer Ther 2007 ;6(7)2065-72
PMID

Sand J, Tani T, Laukkarinen J, Välikoski A, Isola J, Nordback I
Ultra thin needle histology may have impact in diagnosing chronic pancreatitis.
Scand J Gastroenterol 2007 ;42(4)508-12
PMID

Saal LH, Johansson P, Holm K, Gruvberger-Saal SK, She QB, Maurer M, Koujak S, Ferrando AA, Malmström P, Memeo L, Isola J, Bendahl PO, Rosen N, Hibshoosh H, Ringnér M, Borg A, Parsons R
Poor prognosis in carcinoma is associated with a gene expression signature of aberrant PTEN tumor suppressor pathway activity.
Proc Natl Acad Sci U S A 2007 ;104(18)7564-9
PMID

Laukkarinen JM, Sand JA, Chow P, Juuti H, Kellomäki M, Kärkkäinen P, Isola J, Yu S, Somanesan S, Kee I, Song IC, Ng TH, Nordback IH
A novel biodegradable biliary stent in the normal duct hepaticojejunal anastomosis: an 18-month follow-up in a large animal model.
J Gastrointest Surg 2007 ;11(6)750-7
PMID

Gruvberger-Saal SK, Bendahl PO, Saal LH, Laakso M, Hegardt C, Edén P, Peterson C, Malmström P, Isola J, Borg A, Fernö M
Estrogen receptor beta expression is associated with tamoxifen response in ERalpha-negative breast carcinoma.
Clin Cancer Res 2007 ;13(7)1987-94
PMID

Jumppanen M, Gruvberger-Saal S, Kauraniemi P, Tanner M, Bendahl PO, Lundin M, Krogh M, Kataja P, Borg A, Fernö M, Isola J
Basal-like phenotype is not associated with patient survival in estrogen-receptor-negative breast cancers.
Breast Cancer Res 2007 ;9(1)R16
PMID

Rennstam K, Jönsson G, Tanner M, Bendahl PO, Staaf J, Kapanen AI, Karhu R, Baldetorp B, Borg A, Isola J
Cytogenetic characterization and gene expression profiling of the trastuzumab-resistant breast cancer cell line JIMT-1.
Cancer Genet Cytogenet 2007 ;172(2)95-106
PMID

Kuuselo R, Savinainen K, Azorsa DO, Basu GD, Karhu R, Tuzmen S, Mousses S, Kallioniemi A
Intersex-like (IXL) is a cell survival regulator in pancreatic cancer with 19q13 amplification.
Cancer Res 2007 ;67(5)1943-9
PMID

Erkko H, Xia B, Nikkilä J, Schleutker J, Syrjäkoski K, Mannermaa A, Kallioniemi A, Pylkäs K, Karppinen SM, Rapakko K, Miron A, Sheng Q, Li G, Mattila H, Bell DW, Haber DA, Grip M, Reiman M, Jukkola-Vuorinen A, Mustonen A, Kere J, Aaltonen LA, Kosma VM, Kataja V, Soini Y, Drapkin RI, Livingston DM, Winqvist R
A recurrent mutation in PALB2 in Finnish cancer families.
Nature 2007 ;446(7133)316-9
PMID

Syrjäkoski K, Jäntti J, Kallioniemi A, Karhu R
Mutations in the BRCA2 interacting DSS1 are not a risk factor for male breast cancer.
Int J Cancer 2007 ;120(2)444-6
PMID

Alarmo EL, Kuukasjärvi T, Karhu R, Kallioniemi A
A comprehensive expression survey of bone morphogenetic proteins in breast cancer highlights the importance of BMP4 and BMP7.
Breast Cancer Res Treat 2007 ;103(2)239-46
PMID

Visakorpi T
[Not Available].
Duodecim 2007 ;123(11)1323-8
PMID

Porkka KP, Pfeiffer MJ, Waltering KK, Vessella RL, Tammela TL, Visakorpi T
MicroRNA expression profiling in prostate cancer.
Cancer Res 2007 ;67(13)6130-5
PMID

Saramaki O, Visakorpi T
Chromosomal aberrations in prostate cancer.
Front Biosci 2007 ;123287-301
PMID

Dagvadorj A, Collins S, Jomain JB, Abdulghani J, Karras J, Zellweger T, Li H, Nurmi M, Alanen K, Mirtti T, Visakorpi T, Bubendorf L, Goffin V, Nevalainen MT
Autocrine prolactin promotes prostate cancer cell growth via Janus kinase-2-signal transducer and activator of transcription-5a/b signaling pathway.
Endocrinology 2007 ;148(7)3089-101
PMID

Scott CL, Gil J, Hernando E, Teruya-Feldstein J, Narita M, Martínez D, Visakorpi T, Mu D, Cordon-Cardo C, Peters G, Beach D, Lowe SW
Role of the chromobox protein CBX7 in lymphomagenesis.
Proc Natl Acad Sci U S A 2007 ;104(13)5389-94
PMID

Laitinen S, Martikainen PM, Tammela TL, Visakorpi T
Cellular changes in prostate cancer cells induced by intermittent androgen suppression.
Eur Urol 2007 ;52(3)725-32
PMID

Torniainen S, Hedelin M, Autio V, Rasinperä H, Bälter KA, Klint A, Bellocco R, Wiklund F, Stattin P, Ikonen T, Tammela TL, Schleutker J, Grönberg H, Järvelä I
Lactase persistence, dietary intake of milk, and the risk for prostate cancer in Sweden and Finland.
Cancer Epidemiol Biomarkers Prev 2007 ;16(5)956-61
PMID

Camp NJ, Cannon-Albright LA, Farnham JM, Baffoe-Bonnie AB, George A, Powell I, Bailey-Wilson JE, Carpten JD, Giles GG, Hopper JL, Severi G, English DR, Foulkes WD, Maehle L, Moller P, Eeles R, Easton D, Badzioch MD, Whittemore AS, Oakley-Girvan I, Hsieh CL, Dimitrov L, Xu J, Stanford JL, Johanneson B, Deutsch K, McIntosh L, Ostrander EA, Wiley KE, Isaacs SD, Walsh PC, Thibodeau SN, McDonnell SK, Hebbring S, Schaid DJ, Lange EM, Cooney KA, Tammela TL, Schleutker J, Paiss T, Maier C, Grönberg H, Wiklund F, Emanuelsson M, Isaacs WB,
Compelling evidence for a prostate cancer gene at 22q12.3 by the International Consortium for Prostate Cancer Genetics.
Hum Mol Genet 2007 ;16(11)1271-8
PMID

Kouprina N, Noskov VN, Solomon G, Otstot J, Isaacs W, Xu J, Schleutker J, Larionov V
Mutational analysis of SPANX genes in families with X-linked prostate cancer.
Prostate 2007 ;67(8)820-8
PMID

Erkko H, Xia B, Nikkilä J, Schleutker J, Syrjäkoski K, Mannermaa A, Kallioniemi A, Pylkäs K, Karppinen SM, Rapakko K, Miron A, Sheng Q, Li G, Mattila H, Bell DW, Haber DA, Grip M, Reiman M, Jukkola-Vuorinen A, Mustonen A, Kere J, Aaltonen LA, Kosma VM, Kataja V, Soini Y, Drapkin RI, Livingston DM, Winqvist R
A recurrent mutation in PALB2 in Finnish cancer families.
Nature 2007 ;446(7133)316-9
PMID

Pakkanen S, Baffoe-Bonnie AB, Matikainen MP, Koivisto PA, Tammela TL, Deshmukh S, Ou L, Bailey-Wilson JE, Schleutker J
Segregation analysis of 1,546 prostate cancer families in Finland shows recessive inheritance.
Hum Genet 2007 ;121(2)257-67
PMID

Seppälä EH, Autio V, Duggal P, Ikonen T, Stenman UH, Auvinen A, Bailey-Wilson JE, Tammela TL, Schleutker J
KLF6 IVS1 -27G>A variant and the risk of prostate cancer in Finland.
Eur Urol 2007 ;52(4)1076-81
PMID

Cellular Biology
Ari-Pekka Huovila - Cell Interactions
Herma Renkema - Biochemistry of Cell Signaling
Kleino I, Ortiz RM, Huovila AP
ADAM15 gene structure and differential alternative exon use in human tissues.
BMC Mol Biol 2007 ;890
PMID

Machida K, Thompson CM, Dierck K, Jablonowski K, Kärkkäinen S, Liu B, Zhang H, Nash PD, Newman DK, Nollau P, Pawson T, Renkema GH, Saksela K, Schiller MR, Shin DG, Mayer BJ
High-throughput phosphotyrosine profiling using SH2 domains.
Mol Cell 2007 ;26(6)899-915
PMID

Mitochondrial Genetics
Howy Jacobs - Mitochondrial Gene Expression and Disease Group
Hans Spelbrink - Molecular Biology-Mitochondrial DNA maintenance
Hyvärinen AK, Pohjoismäki JL, Reyes A, Wanrooij S, Yasukawa T, Karhunen PJ, Spelbrink JN, Holt IJ, Jacobs HT
The mitochondrial transcription termination factor mTERF modulates replication pausing in human mitochondrial DNA.
Nucleic Acids Res 2007 ;35(19)6458-74
PMID

Toivonen JM, Walker GA, Martinez-Diaz P, Bjedov I, Driege Y, Jacobs HT, Gems D, Partridge L
No influence of Indy on lifespan in Drosophila after correction for genetic and cytoplasmic background effects.
PLoS Genet 2007 ;3(6)e95
PMID

Juhola M, Saarikoski J, Jacobs HT
On modeling of mutation probabilities.
Comput Biol Med 2007 ;37(12)1719-23
PMID

Zanotto E, Shah ZH, Jacobs HT
The bidirectional promoter of two genes for the mitochondrial translational apparatus in mouse is regulated by an array of CCAAT boxes interacting with the transcription factor NF-Y.
Nucleic Acids Res 2007 ;35(2)664-77
PMID

Goffart S, Martinsson P, Malka F, Rojo M, Spelbrink JN
The mitochondria of cultured mammalian cells: II. Expression and visualization of exogenous proteins in fixed and live cells.
Methods Mol Biol 2007 ;37217-32
PMID

Malka F, Auré K, Goffart S, Spelbrink JN, Rojo M
The mitochondria of cultured mammalian cells: I. Analysis by immunofluorescence microscopy, histochemistry, subcellular fractionation, and cell fusion.
Methods Mol Biol 2007 ;3723-16
PMID

Hyvärinen AK, Pohjoismäki JL, Reyes A, Wanrooij S, Yasukawa T, Karhunen PJ, Spelbrink JN, Holt IJ, Jacobs HT
The mitochondrial transcription termination factor mTERF modulates replication pausing in human mitochondrial DNA.
Nucleic Acids Res 2007 ;35(19)6458-74
PMID

Sarzi E, Goffart S, Serre V, Chrétien D, Slama A, Munnich A, Spelbrink JN, Rötig A
Twinkle helicase (PEO1) gene mutation causes mitochondrial DNA depletion.
Ann Neurol 2007 ;62(6)579-87
PMID

Holt IJ, He J, Mao CC, Boyd-Kirkup JD, Martinsson P, Sembongi H, Reyes A, Spelbrink JN
Mammalian mitochondrial nucleoids: organizing an independently minded genome.
Mitochondrion 2007 ;7(5)311-21
PMID

Wanrooij S, Goffart S, Pohjoismäki JL, Yasukawa T, Spelbrink JN
Expression of catalytic mutants of the mtDNA helicase Twinkle and polymerase POLG causes distinct replication stalling phenotypes.
Nucleic Acids Res 2007 ;35(10)3238-51
PMID

He J, Mao CC, Reyes A, Sembongi H, Di Re M, Granycome C, Clippingdale AB, Fearnley IM, Harbour M, Robinson AJ, Reichelt S, Spelbrink JN, Walker JE, Holt IJ
The AAA+ protein ATAD3 has displacement loop binding properties and is involved in mitochondrial nucleoid organization.
J Cell Biol 2007 ;176(2)141-6
PMID

Molecular Immunology
Mika Rämet - Experimental Immunology
Olli Silvennoinen - Molecular Immunology
Jukka Westermark - Cancer cell signaling
Valanne S, Kleino A, Myllymäki H, Vuoristo J, Rämet M
Iap2 is required for a sustained response in the Drosophila Imd pathway.
Dev Comp Immunol 2007 ;31(10)991-1001
PMID

Shaw N, Zhao M, Cheng C, Xu H, Saarikettu J, Li Y, Da Y, Yao Z, Silvennoinen O, Yang J, Liu ZJ, Wang BC, Rao Z
The multifunctional human p100 protein 'hooks' methylated ligands.
Nat Struct Mol Biol 2007 ;14(8)779-84
PMID

Yang J, Välineva T, Hong J, Bu T, Yao Z, Jensen ON, Frilander MJ, Silvennoinen O
Transcriptional co-activator protein p100 interacts with snRNP proteins and facilitates the assembly of the spliceosome.
Nucleic Acids Res 2007 ;35(13)4485-94
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
Hakkarainen T, Särkioja M, Lehenkari P, Miettinen S, Ylikomi T, Suuronen R, Desmond RA, Kanerva A, Hemminki A
Human mesenchymal stem cells lack tumor tropism but enhance the antitumor activity of oncolytic adenoviruses in orthotopic lung and breast tumors.
Hum Gene Ther 2007 ;18(7)627-41
PMID

Niemelä SM, Miettinen S, Konttinen Y, Waris T, Kellomäki M, Ashammakhi NA, Ylikomi T
Fat tissue: views on reconstruction and exploitation.
J Craniofac Surg 2007 ;18(2)325-35
PMID

Narkilahti S, Jutila L, Alafuzoff I, Karkola K, Paljärvi L, Immonen A, Vapalahti M, Mervaala E, Kälviäinen R, Pitkänen A
Increased expression of caspase 2 in experimental and human temporal lobe epilepsy.
Neuromolecular Med 2007 ;9(2)129-44
PMID

Skottman H, Narkilahti S, Hovatta O
Challenges and approaches to the culture of pluripotent human embryonic stem cells.
Regen Med 2007 ;2(3)265-73
PMID

Narkilahti S, Rajala K, Pihlajamäki H, Suuronen R, Hovatta O, Skottman H
Monitoring and analysis of dynamic growth of human embryonic stem cells: comparison of automated instrumentation and conventional culturing methods.
Biomed Eng Online 2007 ;611
PMID

Nat R, Nilbratt M, Narkilahti S, Winblad B, Hovatta O, Nordberg A
Neurogenic neuroepithelial and radial glial cells generated from six human embryonic stem cell lines in serum-free suspension and adherent cultures.
Glia 2007 ;55(4)385-99
PMID

Skottman H, Narkilahti S, Hovatta O
Challenges and approaches to the culture of pluripotent human embryonic stem cells.
Regen Med 2007 ;2(3)265-73
PMID

Narkilahti S, Rajala K, Pihlajamäki H, Suuronen R, Hovatta O, Skottman H
Monitoring and analysis of dynamic growth of human embryonic stem cells: comparison of automated instrumentation and conventional culturing methods.
Biomed Eng Online 2007 ;611
PMID

Rajala K, Hakala H, Panula S, Aivio S, Pihlajamäki H, Suuronen R, Hovatta O, Skottman H
Testing of nine different xeno-free culture media for human embryonic stem cell cultures.
Hum Reprod 2007 ;22(5)1231-8
PMID

Zhang P, Kerkelä E, Skottman H, Levkov L, Kivinen K, Lahesmaa R, Hovatta O, Kere J
Distinct sets of developmentally regulated genes that are expressed by human oocytes and human embryonic stem cells.
Fertil Steril 2007 ;87(3)677-90
PMID

Kerkelä E, Skottman H, Friden B, Bjuresten K, Kere J, Hovatta O
Exclusion of coding-region mutations in luteinizing hormone and follicle-stimulating hormone receptor genes as the cause of ovarian hyperstimulation syndrome.
Fertil Steril 2007 ;87(3)603-6
PMID

 
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