university of tampere: institute of biomedical technology:

IBT Publications 2013

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 IBT or 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.

Biotechnology
Vesa Hytönen - Protein Dynamics
Markku Kulomaa - Molecular Biotechnology

Tossavainen H, Helppolainen SH, Määttä JA, Pihlajamaa T, Hytönen VP, Kulomaa MS, Permi P
Resonance assignments of the 56 kDa chimeric avidin in the biotin-bound and free forms.
Biomol NMR Assign 2013 ;7(1)35-8
PMID

Cancer Groups
Jorma Isola - Cancer Biology
Anne Kallioniemi - Cancer Genomics
Tapio Visakorpi - Molecular Biology of Prostate Cancer
Hans Lilja - Prostate Cancer Biomarkers
G Steven Bova - PELICAN-personalized cancer medicine

Laitinen VH, Wahlfors T, Saaristo L, Rantapero T, Pelttari LM, Kilpivaara O, Laasanen SL, Kallioniemi A, Nevanlinna H, Aaltonen L, Vessella RL, Auvinen A, Visakorpi T, Tammela TL, Schleutker J
HOXB13 G84E Mutation in Finland: Population-Based Analysis of Prostate, Breast, and Colorectal Cancer Risk.
Cancer Epidemiol Biomarkers Prev 2013 ;22(3)452-60
PMID

Rauhala HE, Teppo S, Niemelä S, Kallioniemi A
Silencing of the ARP2/3 complex disturbs pancreatic cancer cell migration.
Anticancer Res 2013 ;33(1)45-52
PMID

Alarmo EL, Huhtala H, Korhonen T, Pylkkänen L, Holli K, Kuukasjärvi T, Parkkila S, Kallioniemi A
Bone morphogenetic protein 4 expression in multiple normal and tumor tissues reveals its importance beyond development.
Mod Pathol 2013 ;26(1)10-21
PMID

Bruchmann A, Roller C, Walther TV, Schäfer G, Lehmusvaara S, Visakorpi T, Klocker H, Cato AC, Maddalo D
Bcl-2 associated athanogene 5 (Bag5) is overexpressed in prostate cancer and inhibits ER-stress induced apoptosis.
BMC Cancer 2013 ;1396
PMID

Parker BC, Annala MJ, Cogdell DE, Granberg KJ, Sun Y, Ji P, Li X, Gumin J, Zheng H, Hu L, Yli-Harja O, Haapasalo H, Visakorpi T, Liu X, Liu CG, Sawaya R, Fuller GN, Chen K, Lang FL, Nykter M, Zhang W
The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma.
J Clin Invest 2013 ;
PMID

Augello MA, Burd CJ, Birbe R, McNair C, Ertel A, Magee MS, Frigo DE, Wilder-Romans K, Shilkrut M, Han S, Jernigan DL, Dean JL, Fatatis A, McDonnell DP, Visakorpi T, Feng FY, Knudsen KE
Convergence of oncogenic and hormone receptor pathways promotes metastatic phenotypes.
J Clin Invest 2013 ;123(1)493-508
PMID

Lehmusvaara S, Erkkilä T, Urbanucci A, Jalava S, Seppälä J, Kaipia A, Kujala P, Lähdesmäki H, Tammela TL, Visakorpi T
Goserelin and bicalutamide treatments alter the expression of microRNAs in the prostate.
Prostate 2013 ;73(1)101-12
PMID

Christensson A, Savage C, Sjoberg DD, Cronin AM, Frank O'Brien M, Lowrance W, Nilsson PM, Vickers AJ, Russo P, Lilja H
Association of cancer with moderately impaired renal function at baseline in a large, representative, population-based cohort followed for up to 30 years.
Int J Cancer 2013 ;
PMID

Carlsson SV, Peltola MT, Sjoberg D, Schröder FH, Hugosson J, Pettersson K, Scardino PT, Vickers AJ, Lilja H, Roobol MJ
Can one blood draw replace transrectal ultrasonography-estimated prostate volume to predict prostate cancer risk?
BJU Int 2013 ;
PMID

Väänänen RM, Lilja H, Cronin A, Kauko L, Rissanen M, Kauko O, Kekki H, Vidbäck S, Nurmi M, Alanen K, Pettersson K
Association of transcript levels of 10 established or candidate-biomarker gene targets with cancerous versus non-cancerous prostate tissue from radical prostatectomy specimens.
Clin Biochem 2013 ;
PMID

Jin G, Zheng SL, Lilja H, Kim ST, Tao S, Gao Z, Young T, Wiklund F, Feng J, Isaacs WB, Rittmaster RS, Gronberg H, Condreay LD, Sun J, Xu J
Genome-wide association study identifies loci at ATF7IP and KLK2 associated with percentage of circulating free PSA.
Neoplasia 2013 ;15(1)95-101
PMID

Vucetic Z, Dnistrian A, Nilsson O, Lilja HG, Plebani M
Suitability of quality control materials for prostate-specific antigen (PSA) measurement: inter-method variability of common tumor marker control materials.
Clin Chem Lab Med 2013 ;51(4)873-80
PMID

Nilsson CL, Berven F, Selheim F, Liu H, Moskal JR, Kroes RA, Sulman EP, Conrad CA, Lang FF, Andrén PE, Nilsson A, Carlsohn E, Lilja H, Malm J, Fenyö D, Subramaniyam D, Wang X, Gonzales-Gonzales M, Dasilva N, Diez P, Fuentes M, Végvári Á, Sjödin K, Welinder C, Laurell T, Fehniger TE, Lindberg H, Rezeli M, Edula G, Hober S, Marko-Varga G
Chromosome 19 annotations with disease speciation: a first report from the Global Research Consortium.
J Proteome Res 2013 ;12(1)135-50
PMID

Haiman CA, Stram DO, Vickers AJ, Wilkens LR, Braun K, Valtonen-André C, Peltola M, Pettersson K, Waters KM, Marchand LL, Kolonel LN, Henderson BE, Lilja H
Levels of beta-microseminoprotein in blood and risk of prostate cancer in multiple populations.
J Natl Cancer Inst 2013 ;105(3)237-43
PMID

Rodriguez-Canales J, Hanson JC, Hipp JD, Balis UJ, Tangrea MA, Emmert-Buck MR, Bova GS
Optimal molecular profiling of tissue and tissue components: defining the best processing and microdissection methods for biomedical applications.
Methods Mol Biol 2013 ;98061-120
PMID

Aryee MJ, Liu W, Engelmann JC, Nuhn P, Gurel M, Haffner MC, Esopi D, Irizarry RA, Getzenberg RH, Nelson WG, Luo J, Xu J, Isaacs WB, Bova GS, Yegnasubramanian S
DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases.
Sci Transl Med 2013 ;5(169)169ra10
PMID

Computational Biology
Matti Nykter - Computational Biology

Sadot A, Sarbu S, Kesseli J, Amir-Kroll H, Zhang W, Nykter M, Shmulevich I
Information-theoretic analysis of the dynamics of an executable biological model.
PLoS One 2013 ;8(3)e59303
PMID

Mäki-Marttunen T, Kesseli J, Nykter M
Balance between Noise and Information Flow Maximizes Set Complexity of Network Dynamics.
PLoS One 2013 ;8(3)e56523
PMID

Yang D, Sun Y, Hu L, Zheng H, Ji P, Pecot CV, Zhao Y, Reynolds S, Cheng H, Rupaimoole R, Cogdell D, Nykter M, Broaddus R, Rodriguez-Aguayo C, Lopez-Berestein G, Liu J, Shmulevich I, Sood AK, Chen K, Zhang W
Integrated analyses identify a master microRNA regulatory network for the mesenchymal subtype in serous ovarian cancer.
Cancer Cell 2013 ;23(2)186-99
PMID

Aghaeepour N, Finak G, , Dougall D, Khodabakhshi AH, Mah P, Obermoser G, Spidlen J, Taylor I, Wuensch SA, Bramson J, Eaves C, Weng AP, Iii ES, Ho K, Kollmann T, Rogers W, De Rosa S, Dalal B, Azad A, Pothen A, Brandes A, Bretschneider H, Bruggner R, Finck R, Jia R, Zimmerman N, Linderman M, Dill D, Nolan G, Chan C, Khettabi FE, O'Neill K, Chikina M, Ge Y, Sealfon S, Sugár I, Gupta A, Shooshtari P, Zare H, De Jager PL, Jiang M, Keilwagen J, Maisog JM, Luta G, Barbo AA, Májek P, Vilček J, Manninen T, Huttunen H, Ruusuvuori P, Nykter M, McLachlan GJ, Wang K, Naim I, Sharma G, Nikolic R, Pyne S, Qian Y, Qiu P, Quinn J, Roth A, , Meyer P, Stolovitzky G, Saez-Rodriguez J, Norel R, Bhattacharjee M, Biehl M, Bucher P, Bunte K, Di Camillo B, Sambo F, Sanavia T, Trifoglio E, Toffolo G, Dimitrieva S, Dreos R, Ambrosini G, Grau J, Grosse I, Posch S, Guex N, Keilwagen J, Kursa M, Rudnicki W, Liu B, Maienschein-Cline M, Manninen T, Huttunen H, Ruusuvuori P, Nykter M, Schneider P, Seifert M, Strickert M, Vilar JM, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH
Critical assessment of automated flow cytometry data analysis techniques.
Nat Methods 2013 ;10(3)228-38
PMID

Annala MJ, Parker BC, Zhang W, Nykter M
Fusion genes and their discovery using high throughput sequencing.
Cancer Lett 2013 ;
PMID

Moore LM, Kivinen V, Liu Y, Annala M, Cogdell D, Liu X, Liu CG, Sawaya R, Yli-Harja O, Shmulevich I, Fuller GN, Zhang W, Nykter M
Transcriptome and small RNA deep sequencing reveals deregulation of miRNA biogenesis in human glioma.
J Pathol 2013 ;229(3)449-59
PMID

Mitochondrial Genetics
Howy Jacobs - Mitochondrial Gene Expression and Disease Group
Laurie Kaguni - Mitochondrial Biogenesis in Health and Disease
Alberto Sanz - Mitochondrial Gerontology and Age-related Diseases
Hans Spelbrink - Molecular Biology-Mitochondrial DNA maintenance

Richter U, Lahtinen T, Marttinen P, Myöhänen M, Greco D, Cannino G, Jacobs HT, Lietzén N, Nyman TA, Battersby BJ
A mitochondrial ribosomal and RNA decay pathway blocks cell proliferation.
Curr Biol 2013 ;23(6)535-41
PMID

Jõers P, Jacobs HT
Analysis of replication intermediates indicates that Drosophila melanogaster mitochondrial DNA replicates by a strand-coupled theta mechanism.
PLoS One 2013 ;8(1)e53249
PMID

El-Khoury R, Dufour E, Rak M, Ramanantsoa N, Grandchamp N, Csaba Z, Duvillié B, Bénit P, Gallego J, Gressens P, Sarkis C, Jacobs HT, Rustin P
Alternative oxidase expression in the mouse enables bypassing cytochrome c oxidase blockade and limits mitochondrial ROS overproduction.
PLoS Genet 2013 ;9(1)e1003182
PMID

Molecular Immunology
Dan Hultmark - Genetic Immunology
Marko Pesu - Immunoregulation
Mika Rämet - Experimental Immunology
Olli Silvennoinen - Molecular Immunology

Taverniti V, Stuknyte M, Minuzzo M, Arioli S, De Noni I, Scabiosi C, Cordova ZM, Junttila I, Hämäläinen S, Turpeinen H, Mora D, Karp M, Pesu M, Guglielmetti S
S-layer protein mediates the stimulatory effect of Lactobacillus helveticus MIMLh5 on innate immunity.
Appl Environ Microbiol 2013 ;79(4)1221-31
PMID

Aspatwar A, Tolvanen ME, Jokitalo E, Parikka M, Ortutay C, Harjula SK, Rämet M, Vihinen M, Parkkila S
Abnormal cerebellar development and ataxia in CARP VIII morphant zebrafish.
Hum Mol Genet 2013 ;22(3)417-32
PMID

Lohi O, Parikka M, Rämet M
The zebrafish as a model for paediatric diseases.
Acta Paediatr 2013 ;102(2)104-10
PMID

Toivonen S, Ojala M, Hyysalo A, Ilmarinen T, Rajala K, Pekkanen-Mattila M, Äänismaa R, Lundin K, Palgi J, Weltner J, Trokovic R, Silvennoinen O, Skottman H, Narkilahti S, Aalto-Setälä K, Otonkoski T
Comparative analysis of targeted differentiation of human induced pluripotent stem cells (hiPSCs) and human embryonic stem cells reveals variability associated with incomplete transgene silencing in retrovirally derived hiPSC lines.
Stem Cells Transl Med 2013 ;2(2)83-93
PMID

Fashe T, Saarikettu J, Isomäki P, Yang J, Silvennoinen O
Expression analysis of Tudor-SN protein in mouse tissues.
Tissue Cell 2013 ;45(1)21-31
PMID

Regenerative Medicine
Katriina Aalto-Setälä - Cardiology Group
Susanna Miettinen - Adult Stem Cell Group
Susanna Narkilahti - Neuro Group
Heli Skottman - Ophthalmology Group

Jääskeläinen P, Heliö T, Aalto-Setälä K, Kaartinen M, Ilveskoski E, Hämäläinen L, Melin J, Nieminen MS, Laakso M, Kuusisto J, , Kervinen H, Mustonen J, Juvonen J, Niemi M, Uusimaa P, Huttunen M, Kotila M, Pietilä M
Two founder mutations in the alpha-tropomyosin and the cardiac myosin-binding protein C genes are common causes of hypertrophic cardiomyopathy in the Finnish population.
Ann Med 2013 ;45(1)85-90
PMID

Patrikoski M, Juntunen M, Boucher S, Campbell A, Vemuri MC, Mannerström B, Miettinen S
Development of fully defined xeno-free culture system for the preparation and propagation of cell therapy compliant human adipose stem cells.
Stem Cell Res Ther 2013 ;4(2)27
PMID

Kyllonen L, Haimi S, Mannerstrom B, Huhtala H, Rajala KM, Skottman H, Sandor GK, Miettinen S
Effects of different serum conditions on osteogenic differentiation of human adipose stem cells in vitro.
Stem Cell Res Ther 2013 ;4(1)17
PMID

Sándor GK, Tuovinen VJ, Wolff J, Patrikoski M, Jokinen J, Nieminen E, Mannerström B, Lappalainen OP, Seppänen R, Miettinen S
Adipose Stem Cell Tissue-Engineered Construct Used to Treat Large Anterior Mandibular Defect: A Case Report and Review of the Clinical Application of Good Manufacturing Practice-Level Adipose Stem Cells for Bone Regeneration.
J Oral Maxillofac Surg 2013 ;
PMID

Diban N, Haimi S, Bolhuis-Versteeg L, Teixeira S, Miettinen S, Poot A, Grijpma D, Stamatialis D
Hollow fibers of poly(lactide-co-glycolide) and poly(ε-caprolactone) blends for vascular tissue engineering applications.
Acta Biomater 2013 ;
PMID

Pelto J, Björninen M, Pälli A, Talvitie E, Hyttinen J, Mannerström B, Suuronen Seppanen R, Kellomäki M, Miettinen S, Haimi S
Novel polypyrrole-coated polylactide scaffolds enhance adipose stem cell proliferation and early osteogenic differentiation.
Tissue Eng Part A 2013 ;19(7-8)882-92
PMID

Mennander AA, Vuohelainen V, Aanismaa RS, Narkilahti S, Paavonen T, Tarkka M
Sildenafil after cardiac arrest and infarction; an experimental rat model.
Scand Cardiovasc J 2013 ;47(1)58-64
PMID

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Last update: 8.2.2013 14.01