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IBT julkaisut 2003

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
Vihinen M
Signal transduction-related bioinformatics services.
Brief Bioinform 2003 ;4(4)325-31
PMID

Ahola V, Aittokallio T, Uusipaikka E, Vihinen M
Efficient estimation of emission probabilities in profile hidden Markov models.
Bioinformatics 2003 ;19(18)2359-68
PMID

Shen B, Vihinen M
RankViaContact: ranking and visualization of amino acid contacts.
Bioinformatics 2003 ;19(16)2161-2
PMID

Casas S, Ollila J, Aventín A, Vihinen M, Sierra J, Knuutila S
Changes in apoptosis-related pathways in acute myelocytic leukemia.
Cancer Genet Cytogenet 2003 ;146(2)89-101
PMID

Saharinen P, Vihinen M, Silvennoinen O
Autoinhibition of Jak2 tyrosine kinase is dependent on specific regions in its pseudokinase domain.
Mol Biol Cell 2003 ;14(4)1448-59
PMID

Biotechnology
Vesa Hytönen - Protein Dynamics
Markku Kulomaa - Molecular Biotechnology
Nordlund HR, Hytönen VP, Laitinen OH, Uotila ST, Niskanen EA, Savolainen J, Porkka E, Kulomaa MS
Introduction of histidine residues into avidin subunit interfaces allows pH-dependent regulation of quaternary structure and biotin binding.
FEBS Lett 2003 ;555(3)449-54
PMID

Airenne KJ, Peltomaa E, Hytönen VP, Laitinen OH, Ylä-Herttuala S
Improved generation of recombinant baculovirus genomes in Escherichia coli.
Nucleic Acids Res 2003 ;31(17)e101
PMID

Hytönen VP, Laitinen OH, Grapputo A, Kettunen A, Savolainen J, Kalkkinen N, Marttila AT, Nordlund HR, Nyholm TK, Paganelli G, Kulomaa MS
Characterization of poultry egg-white avidins and their potential as a tool in pretargeting cancer treatment.
Biochem J 2003 ;372(Pt 1)219-25
PMID

Laitinen OH, Nordlund HR, Hytönen VP, Uotila ST, Marttila AT, Savolainen J, Airenne KJ, Livnah O, Bayer EA, Wilchek M, Kulomaa MS
Rational design of an active avidin monomer.
J Biol Chem 2003 ;278(6)4010-4
PMID

Nordlund HR, Laitinen OH, Uotila ST, Nyholm T, Hytönen VP, Slotte JP, Kulomaa MS
Enhancing the thermal stability of avidin. Introduction of disulfide bridges between subunit interfaces.
J Biol Chem 2003 ;278(4)2479-83
PMID

Marttila AT, Hytönen VP, Laitinen OH, Bayer EA, Wilchek M, Kulomaa MS
Mutation of the important Tyr-33 residue of chicken avidin: functional and structural consequences.
Biochem J 2003 ;369(Pt 2)249-54
PMID

Nordlund HR, Hytönen VP, Laitinen OH, Uotila ST, Niskanen EA, Savolainen J, Porkka E, Kulomaa MS
Introduction of histidine residues into avidin subunit interfaces allows pH-dependent regulation of quaternary structure and biotin binding.
FEBS Lett 2003 ;555(3)449-54
PMID

Kukkonen SP, Airenne KJ, Marjomäki V, Laitinen OH, Lehtolainen P, Kankaanpää P, Mähönen AJ, Räty JK, Nordlund HR, Oker-Blom C, Kulomaa MS, Ylä-Herttuala S
Baculovirus capsid display: a novel tool for transduction imaging.
Mol Ther 2003 ;8(5)853-62
PMID

Lehtolainen P, Wirth T, Taskinen AK, Lehenkari P, Leppänen O, Lappalainen M, Pulkkanen K, Marttila A, Marjomäki V, Airenne KJ, Horton M, Kulomaa MS, Ylä-Herttuala S
Targeting of biotinylated compounds to its target tissue using a low-density lipoprotein receptor-avidin fusion protein.
Gene Ther 2003 ;10(25)2090-7
PMID

Pazy Y, Eisenberg-Domovich Y, Laitinen OH, Kulomaa MS, Bayer EA, Wilchek M, Livnah O
Dimer-tetramer transition between solution and crystalline states of streptavidin and avidin mutants.
J Bacteriol 2003 ;185(14)4050-6
PMID

Tiirola MA, Suvilampi JE, Kulomaa MS, Rintala JA
Microbial diversity in a thermophilic aerobic biofilm process: analysis by length heterogeneity PCR (LH-PCR).
Water Res 2003 ;37(10)2259-68
PMID

Hytönen VP, Laitinen OH, Grapputo A, Kettunen A, Savolainen J, Kalkkinen N, Marttila AT, Nordlund HR, Nyholm TK, Paganelli G, Kulomaa MS
Characterization of poultry egg-white avidins and their potential as a tool in pretargeting cancer treatment.
Biochem J 2003 ;372(Pt 1)219-25
PMID

Laitinen OH, Nordlund HR, Hytönen VP, Uotila ST, Marttila AT, Savolainen J, Airenne KJ, Livnah O, Bayer EA, Wilchek M, Kulomaa MS
Rational design of an active avidin monomer.
J Biol Chem 2003 ;278(6)4010-4
PMID

Nordlund HR, Laitinen OH, Uotila ST, Nyholm T, Hytönen VP, Slotte JP, Kulomaa MS
Enhancing the thermal stability of avidin. Introduction of disulfide bridges between subunit interfaces.
J Biol Chem 2003 ;278(4)2479-83
PMID

Marttila AT, Hytönen VP, Laitinen OH, Bayer EA, Wilchek M, Kulomaa MS
Mutation of the important Tyr-33 residue of chicken avidin: functional and structural consequences.
Biochem J 2003 ;369(Pt 2)249-54
PMID

Cancer Groups
Jorma Isola - Cancer Biology
Anne Kallioniemi - Cancer Genomics
Tapio Visakorpi - Molecular Biology of Prostate Cancer
Johanna Schleutker - Genetic Predisposition to Cancer
Rennstam K, Ahlstedt-Soini M, Baldetorp B, Bendahl PO, Borg A, Karhu R, Tanner M, Tirkkonen M, Isola J
Patterns of chromosomal imbalances defines subgroups of breast cancer with distinct clinical features and prognosis. A study of 305 tumors by comparative genomic hybridization.
Cancer Res 2003 ;63(24)8861-8
PMID

Lundin J, Lundin M, Isola J, Joensuu H
Evaluation of a web-based system for survival estimation in breast cancer.
Stud Health Technol Inform 2003 ;95788-93
PMID

Junttila TT, Laato M, Vahlberg T, Söderström KO, Visakorpi T, Isola J, Elenius K
Identification of patients with transitional cell carcinoma of the bladder overexpressing ErbB2, ErbB3, or specific ErbB4 isoforms: real-time reverse transcription-PCR analysis in estimation of ErbB receptor status from cancer patients.
Clin Cancer Res 2003 ;9(14)5346-57
PMID

Di Leo A, Isola J
Topoisomerase II alpha as a marker predicting the efficacy of anthracyclines in breast cancer: are we at the end of the beginning?
Clin Breast Cancer 2003 ;4(3)179-86
PMID

Zhang F, Lundin M, Ristimäki A, Heikkilä P, Lundin J, Isola J, Joensuu H, Laiho M
Ski-related novel protein N (SnoN), a negative controller of transforming growth factor-beta signaling, is a prognostic marker in estrogen receptor-positive breast carcinomas.
Cancer Res 2003 ;63(16)5005-10
PMID

Staff S, Isola J, Tanner M
Haplo-insufficiency of BRCA1 in sporadic breast cancer.
Cancer Res 2003 ;63(16)4978-83
PMID

Sallinen SL, Sallinen P, Ahlstedt-Soini M, Haapasalo H, Helin H, Isola J, Karhu R
Arm-specific multicolor fluorescence in situ hybridization reveals widespread chromosomal instability in glioma cell lines.
Cancer Genet Cytogenet 2003 ;144(1)52-60
PMID

Linja MJ, Savinainen KJ, Tammela TL, Isola JJ, Visakorpi T
Expression of ERalpha and ERbeta in prostate cancer.
Prostate 2003 ;55(3)180-6
PMID

Johannsson OT, Staff S, Vallon-Christersson J, Kytöla S, Gudjonsson T, Rennstam K, Hedenfalk IA, Adeyinka A, Kjellén E, Wennerberg J, Baldetorp B, Petersen OW, Olsson H, Oredsson S, Isola J, Borg A
Characterization of a novel breast carcinoma xenograft and cell line derived from a BRCA1 germ-line mutation carrier.
Lab Invest 2003 ;83(3)387-96
PMID

Joensuu H, Isola J, Lundin M, Salminen T, Holli K, Kataja V, Pylkkänen L, Turpeenniemi-Hujanen T, von Smitten K, Lundin J
Amplification of erbB2 and erbB2 expression are superior to estrogen receptor status as risk factors for distant recurrence in pT1N0M0 breast cancer: a nationwide population-based study.
Clin Cancer Res 2003 ;9(3)923-30
PMID

Bilous M, Dowsett M, Hanna W, Isola J, Lebeau A, Moreno A, Penault-Llorca F, Rüschoff J, Tomasic G, van de Vijver M
Current perspectives on HER2 testing: a review of national testing guidelines.
Mod Pathol 2003 ;16(2)173-82
PMID

Lundin J, Lundin M, Isola J, Joensuu H
A web-based system for individualised survival estimation in breast cancer.
BMJ 2003 ;326(7379)29
PMID

Autio R, Hautaniemi S, Kauraniemi P, Yli-Harja O, Astola J, Wolf M, Kallioniemi A
CGH-Plotter: MATLAB toolbox for CGH-data analysis.
Bioinformatics 2003 ;19(13)1714-5
PMID

Skotheim RI, Kallioniemi A, Bjerkhagen B, Mertens F, Brekke HR, Monni O, Mousses S, Mandahl N, Soeter G, Nesland JM, Smeland S, Kallioniemi OP, Lothe RA
Topoisomerase-II alpha is upregulated in malignant peripheral nerve sheath tumors and associated with clinical outcome.
J Clin Oncol 2003 ;21(24)4586-91
PMID

Kauraniemi P, Kuukasjärvi T, Sauter G, Kallioniemi A
Amplification of a 280-kilobase core region at the ERBB2 locus leads to activation of two hypothetical proteins in breast cancer.
Am J Pathol 2003 ;163(5)1979-84
PMID

Kallioniemi A
[Gene expression profile as a crystal ball].
Duodecim 2003 ;119(12)1101-2
PMID

Junttila TT, Laato M, Vahlberg T, Söderström KO, Visakorpi T, Isola J, Elenius K
Identification of patients with transitional cell carcinoma of the bladder overexpressing ErbB2, ErbB3, or specific ErbB4 isoforms: real-time reverse transcription-PCR analysis in estimation of ErbB receptor status from cancer patients.
Clin Cancer Res 2003 ;9(14)5346-57
PMID

Visakorpi T
The molecular genetics of prostate cancer.
Urology 2003 ;62(5 Suppl 1)3-10
PMID

Porkka KP, Nupponen NN, Tammela TL, Vessella RL, Visakorpi T
Human pHyde is not a classical tumor suppressor gene in prostate cancer.
Int J Cancer 2003 ;106(5)729-35
PMID

Linja MJ, Savinainen KJ, Tammela TL, Isola JJ, Visakorpi T
Expression of ERalpha and ERbeta in prostate cancer.
Prostate 2003 ;55(3)180-6
PMID

Seppälä EH, Ikonen T, Autio V, Rökman A, Mononen N, Matikainen MP, Tammela TL, Schleutker J
Germ-line alterations in MSR1 gene and prostate cancer risk.
Clin Cancer Res 2003 ;9(14)5252-6
PMID

Schleutker J, Baffoe-Bonnie AB, Gillanders E, Kainu T, Jones MP, Freas-Lutz D, Markey C, Gildea D, Riedesel E, Albertus J, Gibbs KD, Matikainen M, Koivisto PA, Tammela T, Bailey-Wilson JE, Trent JM, Kallioniemi OP
Genome-wide scan for linkage in finnish hereditary prostate cancer (HPC) families identifies novel susceptibility loci at 11q14 and 3p25-26.
Prostate 2003 ;57(4)280-9
PMID

Marchesani M, Hakkarainen A, Tuomainen TP, Kaikkonen J, Pukkala E, Uimari P, Seppälä E, Matikainen M, Kallioniemi OP, Schleutker J, Lehtimäki T, Salonen JT
New paraoxonase 1 polymorphism I102V and the risk of prostate cancer in Finnish men.
J Natl Cancer Inst 2003 ;95(11)812-8
PMID

Cellular Biology
Ari-Pekka Huovila - Cell Interactions
Herma Renkema - Biochemistry of Cell Signaling
Aguilera B, Ghauharali-van der Vlugt K, Helmond MT, Out JM, Donker-Koopman WE, Groener JE, Boot RG, Renkema GH, van der Marel GA, van Boom JH, Overkleeft HS, Aerts JM
Transglycosidase activity of chitotriosidase: improved enzymatic assay for the human macrophage chitinase.
J Biol Chem 2003 ;278(42)40911-6
PMID

Mitochondrial Genetics
Howy Jacobs - Mitochondrial Gene Expression and Disease Group
Hans Spelbrink - Molecular Biology-Mitochondrial DNA maintenance
Toivonen JM, Manjiry S, Touraille S, Alziari S, O'Dell KM, Jacobs HT
Gene dosage and selective expression modify phenotype in a Drosophila model of human mitochondrial disease.
Mitochondrion 2003 ;3(2)83-96
PMID

Bowmaker M, Yang MY, Yasukawa T, Reyes A, Jacobs HT, Huberman JA, Holt IJ
Mammalian mitochondrial DNA replicates bidirectionally from an initiation zone.
J Biol Chem 2003 ;278(51)50961-9
PMID

Jacobs HT
Rebuttal to Pak et al.: new data, chestnuts.
Aging Cell 2003 ;2(1)19-20
PMID

Jacobs HT
Disorders of mitochondrial protein synthesis.
Hum Mol Genet 2003 ;12 Spec No 2R293-301
PMID

Jacobs HT
The mitochondrial theory of aging: dead or alive?
Aging Cell 2003 ;2(1)11-7
PMID

Holt IJ, Jacobs HT
Response: The mitochondrial DNA replication bubble has not burst.
Trends Biochem Sci 2003 ;28(7)355-6
PMID

Garrido N, Griparic L, Jokitalo E, Wartiovaara J, van der Bliek AM, Spelbrink JN
Composition and dynamics of human mitochondrial nucleoids.
Mol Biol Cell 2003 ;14(4)1583-96
PMID

Okamaoto M, Ohsato T, Nakada K, Isobe K, Spelbrink JN, Hayashi J, Hamasaki N, Kang D
Ditercalinium chloride, a pro-anticancer drug, intimately associates with mammalian mitochondrial DNA and inhibits its replication.
Curr Genet 2003 ;43(5)364-70
PMID

Molecular Immunology
Mika Rämet - Experimental Immunology
Olli Silvennoinen - Molecular Immunology
Marttila R, Haataja R, Rämet M, Pokela ML, Tammela O, Hallman M
Surfactant protein A gene locus and respiratory distress syndrome in Finnish premature twin pairs.
Ann Med 2003 ;35(5)344-52
PMID

Pearson AM, Baksa K, Rämet M, Protas M, McKee M, Brown D, Ezekowitz RA
Identification of cytoskeletal regulatory proteins required for efficient phagocytosis in Drosophila.
Microbes Infect 2003 ;5(10)815-24
PMID

Rämet ME, Rämet M, Lu Q, Nickerson M, Savolainen MJ, Malzone A, Karas RH
High-density lipoprotein increases the abundance of eNOS protein in human vascular endothelial cells by increasing its half-life.
J Am Coll Cardiol 2003 ;41(12)2288-97
PMID

Marttila R, Haataja R, Rämet M, Löfgren J, Hallman M
Surfactant protein B polymorphism and respiratory distress syndrome in premature twins.
Hum Genet 2003 ;112(1)18-23
PMID

Ungureanu D, Vanhatupa S, Kotaja N, Yang J, Aittomaki S, Jänne OA, Palvimo JJ, Silvennoinen O
PIAS proteins promote SUMO-1 conjugation to STAT1.
Blood 2003 ;102(9)3311-3
PMID

Paukku K, Yang J, Silvennoinen O
Tudor and nuclease-like domains containing protein p100 function as coactivators for signal transducer and activator of transcription 5.
Mol Endocrinol 2003 ;17(9)1805-14
PMID

Silvennoinen O, Hurme M
[New knowledge about cytokines].
Duodecim 2003 ;119(8)773-9
PMID

Pesu M, Aittomäki S, Välineva T, Silvennoinen O
PU.1 is required for transcriptional activation of the Stat6 response element in the Igepsilon promoter.
Eur J Immunol 2003 ;33(6)1727-35
PMID

Saharinen P, Vihinen M, Silvennoinen O
Autoinhibition of Jak2 tyrosine kinase is dependent on specific regions in its pseudokinase domain.
Mol Biol Cell 2003 ;14(4)1448-59
PMID

Junttila I, Bourette RP, Rohrschneider LR, Silvennoinen O
M-CSF induced differentiation of myeloid precursor cells involves activation of PKC-delta and expression of Pkare.
J Leukoc Biol 2003 ;73(2)281-8
PMID

 
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