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Lääketieteen ja biotieteiden tiedekuntaTampereen yliopisto BioMediTech

IBT julkaisut 2013

HUOMIO: Tämä luettelo ei ole ehdottoman täydellinen, koska se on koostettu automaattisesti PubMed-tietokannasta. Sama julkaisu voi esiintyä kahteen tai useampaan kertaan, koska aineisto koostetaan tutkimusryhmittäin. Luettelo voi myös sisältää artikkeita, jotka eivät ole IBT:n tutkijoiden kirjoittamia johtuen samannimisistä kirjoittajista.
Biotechnology
Vesa Hytönen - Protein Dynamics
Markku Kulomaa - Molecular Biotechnology
Näreoja T, Ebner A, Gruber HJ, Taskinen B, Kienberger F, Hänninen PE, Hytönen VP, Hinterdorfer P, Härmä H
Kinetics of bioconjugate nanoparticle label binding in a sandwich-type immunoassay.
Anal Bioanal Chem 2013 ;
PMID

Taskinen B, Zmurko J, Ojanen M, Kukkurainen S, Parthiban M, Määttä JA, Leppiniemi J, Jänis J, Parikka M, Turpeinen H, Rämet M, Pesu M, Johnson MS, Kulomaa MS, Airenne TT, Hytönen VP
Zebavidin - an avidin-like protein from zebrafish.
PLoS One 2013 ;8(10)e77207
PMID

Turpeinen H, Oksanen A, Kivinen V, Kukkurainen S, Uusimäki A, Rämet M, Parikka M, Hytönen VP, Nykter M, Pesu M
Proprotein Convertase Subtilisin/Kexin Type 7 (PCSK7) Is Essential for the Zebrafish Development and Bioavailability of Transforming Growth Factor β1a (TGFβ1a).
J Biol Chem 2013 ;288(51)36610-23
PMID

Pollheimer P, Taskinen B, Scherfler A, Gusenkov S, Creus M, Wiesauer P, Zauner D, Schöfberger W, Schwarzinger C, Ebner A, Tampé R, Stutz H, Hytönen VP, Gruber HJ
Reversible biofunctionalization of surfaces with a switchable mutant of avidin.
Bioconjug Chem 2013 ;24(10)1656-68
PMID

Leppiniemi J, Meir A, Kähkönen N, Kukkurainen S, Määttä JA, Ojanen M, Jänis J, Kulomaa MS, Livnah O, Hytönen VP
The highly dynamic oligomeric structure of bradavidin II is unique among avidin proteins.
Protein Sci 2013 ;22(7)980-94
PMID

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

Taskinen B, Zmurko J, Ojanen M, Kukkurainen S, Parthiban M, Määttä JA, Leppiniemi J, Jänis J, Parikka M, Turpeinen H, Rämet M, Pesu M, Johnson MS, Kulomaa MS, Airenne TT, Hytönen VP
Zebavidin - an avidin-like protein from zebrafish.
PLoS One 2013 ;8(10)e77207
PMID

Leppiniemi J, Meir A, Kähkönen N, Kukkurainen S, Määttä JA, Ojanen M, Jänis J, Kulomaa MS, Livnah O, Hytönen VP
The highly dynamic oligomeric structure of bradavidin II is unique among avidin proteins.
Protein Sci 2013 ;22(7)980-94
PMID

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
Laurila R, Parkkila S, Isola J, Kallioniemi A, Alarmo EL
The expression patterns of gremlin 1 and noggin in normal adult and tumor tissues.
Int J Clin Exp Pathol 2013 ;6(7)1400-8
PMID

Staff S, Kujala P, Karhu R, Rökman A, Ilvesaro J, Kares S, Isola J
Preservation of nucleic acids and tissue morphology in paraffin-embedded clinical samples: comparison of five molecular fixatives.
J Clin Pathol 2013 ;66(9)807-10
PMID

Laurila E, Vuorinen E, Savinainen K, Rauhala H, Kallioniemi A
KPNA7, a nuclear transport receptor, promotes malignant properties of pancreatic cancer cells in vitro.
Exp Cell Res 2013 ;
PMID

Ampuja M, Jokimäki R, Juuti-Uusitalo K, Rodriguez-Martinez A, Alarmo EL, Kallioniemi A
BMP4 inhibits the proliferation of breast cancer cells and induces an MMP-dependent migratory phenotype in MDA-MB-231 cells in 3D environment.
BMC Cancer 2013 ;13429
PMID

Laurila EM, Kallioniemi A
The diverse role of miR-31 in regulating cancer associated phenotypes.
Genes Chromosomes Cancer 2013 ;
PMID

Laurila R, Parkkila S, Isola J, Kallioniemi A, Alarmo EL
The expression patterns of gremlin 1 and noggin in normal adult and tumor tissues.
Int J Clin Exp Pathol 2013 ;6(7)1400-8
PMID

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

Leinonen KA, Saramäki OR, Furusato B, Kimura T, Takahashi H, Egawa S, Suzuki H, Keiger K, Ho Hahm S, Isaacs WB, Tolonen TT, Stenman UH, Tammela TL, Nykter M, Bova GS, Visakorpi T
Loss of PTEN Is Associated with Aggressive Behavior in ERG-Positive Prostate Cancer.
Cancer Epidemiol Biomarkers Prev 2013 ;22(12)2333-44
PMID

Khanna A, Kauko O, Böckelman C, Laine A, Schreck I, Partanen JI, Szwajda A, Bormann S, Bilgen T, Helenius M, Pokharel YR, Pimanda J, Russel MR, Haglund C, Cole KA, Klefström J, Aittokallio T, Weiss C, Ristimäki A, Visakorpi T, Westermarck J
Chk1 Targeting Reactivates PP2A Tumor Suppressor Activity in Cancer Cells.
Cancer Res 2013 ;73(22)6757-69
PMID

Haldrup C, Mundbjerg K, Vestergaard EM, Lamy P, Wild P, Schulz WA, Arsov C, Visakorpi T, Borre M, Høyer S, Orntoft TF, Sørensen KD
DNA methylation signatures for prediction of biochemical recurrence after radical prostatectomy of clinically localized prostate cancer.
J Clin Oncol 2013 ;31(26)3250-8
PMID

Barbieri CE, Bangma CH, Bjartell A, Catto JW, Culig Z, Grönberg H, Luo J, Visakorpi T, Rubin MA
The mutational landscape of prostate cancer.
Eur Urol 2013 ;64(4)567-76
PMID

Haddad BR, Gu L, Mirtti T, Dagvadorj A, Vogiatzi P, Hoang DT, Bajaj R, Leiby B, Ellsworth E, Blackmon S, Ruiz C, Curtis M, Fortina P, Ertel A, Liu C, Rui H, Visakorpi T, Bubendorf L, Lallas CD, Trabulsi EJ, McCue P, Gomella L, Nevalainen MT
STAT5A/B gene locus undergoes amplification during human prostate cancer progression.
Am J Pathol 2013 ;182(6)2264-75
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 FF, Nykter M, Zhang W
The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma.
J Clin Invest 2013 ;123(2)855-65
PMID

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

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

Sävblom C, Halldén C, Cronin AM, Säll T, Savage C, Vertosick EA, Klein RJ, Giwercman A, Lilja H
Genetic Variation in KLK2 and KLK3 Is Associated with Concentrations of hK2 and PSA in Serum and Seminal Plasma in Young Men.
Clin Chem 2013 ;
PMID

Lee S, Kim S, Malm J, Jeong OC, Lilja H, Laurell T
Improved porous silicon microarray based prostate specific antigen immunoassay by optimized surface density of the capture antibody.
Anal Chim Acta 2013 ;796108-14
PMID

Danila DC, Anand A, Schultz N, Heller G, Wan M, Sung CC, Dai C, Khanin R, Fleisher M, Lilja H, Scher HI
Analytic and Clinical Validation of a Prostate Cancer-Enhanced Messenger RNA Detection Assay in Whole Blood as a Prognostic Biomarker for Survival.
Eur Urol 2013 ;
PMID

Lindahl P, Säll T, Bjartell A, Johansson AM, Lilja H, Halldén C
Copy number variants in the kallikrein gene cluster.
PLoS One 2013 ;8(7)e69097
PMID

Végvári A, Sjödin K, Rezeli M, Malm J, Lilja H, Laurell T, Marko-Varga G
Identification of a novel proteoform of prostate specific antigen (SNP-L132I) in clinical samples by multiple reaction monitoring.
Mol Cell Proteomics 2013 ;12(10)2761-73
PMID

Burguillos MA, Magnusson C, Nordin M, Lenshof A, Augustsson P, Hansson MJ, Elmér E, Lilja H, Brundin P, Laurell T, Deierborg T
Microchannel acoustophoresis does not impact survival or function of microglia, leukocytes or tumor cells.
PLoS One 2013 ;8(5)e64233
PMID

Arsov C, Becker N, Hadaschik BA, Hohenfellner M, Herkommer K, Gschwend JE, Imkamp F, Kuczyk MA, Antoch G, Kristiansen G, Siener R, Semjonow A, Hamdy FC, Lilja H, Vickers AJ, Schröder FH, Albers P
Prospective randomized evaluation of risk-adapted prostate-specific antigen screening in young men: the PROBASE trial.
Eur Urol 2013 ;64(6)873-5
PMID

Larsen SB, Brasso K, Iversen P, Christensen J, Christiansen M, Carlsson S, Lilja H, Friis S, Tjønneland A, Dalton SO
Baseline prostate-specific antigen measurements and subsequent prostate cancer risk in the Danish Diet, Cancer and Health cohort.
Eur J Cancer 2013 ;49(14)3041-8
PMID

Carlsson S, Maschino A, Schröder F, Bangma C, Steyerberg EW, van der Kwast T, van Leenders G, Vickers A, Lilja H, Roobol MJ
Predictive value of four kallikrein markers for pathologically insignificant compared with aggressive prostate cancer in radical prostatectomy specimens: results from the European Randomized Study of Screening for Prostate Cancer section Rotterdam.
Eur Urol 2013 ;64(5)693-9
PMID

Vickers AJ, Ulmert D, Sjoberg DD, Bennette CJ, Björk T, Gerdtsson A, Manjer J, Nilsson PM, Dahlin A, Bjartell A, Scardino PT, Lilja H
Strategy for detection of prostate cancer based on relation between prostate specific antigen at age 40-55 and long term risk of metastasis: case-control study.
BMJ 2013 ;346f2023
PMID

Christensson A, Savage C, Sjoberg DD, Cronin AM, O'Brien MF, 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 ;133(6)1452-8
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 ;112(5)602-9
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 ;46(7-8)670-4
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

Chen J, Toghi Eshghi S, Bova GS, Li QK, Li X, Zhang H
Epithelium percentage estimation facilitates epithelial quantitative protein measurement in tissue specimens.
Clin Proteomics 2013 ;10(1)18
PMID

Leinonen KA, Saramäki OR, Furusato B, Kimura T, Takahashi H, Egawa S, Suzuki H, Keiger K, Ho Hahm S, Isaacs WB, Tolonen TT, Stenman UH, Tammela TL, Nykter M, Bova GS, Visakorpi T
Loss of PTEN Is Associated with Aggressive Behavior in ERG-Positive Prostate Cancer.
Cancer Epidemiol Biomarkers Prev 2013 ;22(12)2333-44
PMID

Chen J, Xi J, Tian Y, Bova GS, Zhang H
Identification, prioritization, and evaluation of glycoproteins for aggressive prostate cancer using quantitative glycoproteomics and antibody-based assays on tissue specimens.
Proteomics 2013 ;13(15)2268-77
PMID

Nickerson ML, Im KM, Misner KJ, Tan W, Lou H, Gold B, Wells DW, Bravo HC, Fredrikson KM, Harkins TT, Milos P, Zbar B, Linehan WM, Yeager M, Andresson T, Dean M, Bova GS
Somatic alterations contributing to metastasis of a castration-resistant prostate cancer.
Hum Mutat 2013 ;34(9)1231-41
PMID

Liu W, Xie CC, Thomas CY, Kim ST, Lindberg J, Egevad L, Wang Z, Zhang Z, Sun J, Sun J, Koty PP, Kader AK, Cramer SD, Bova GS, Zheng SL, Grönberg H, Isaacs WB, Xu J
Genetic markers associated with early cancer-specific mortality following prostatectomy.
Cancer 2013 ;119(13)2405-12
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
Ylipää A, Yli-Harja O, Zhang W, Nykter M
Characterization of aberrant pathways across human cancers.
BMC Syst Biol 2013 ;7 Suppl 1S1
PMID

Turpeinen H, Oksanen A, Kivinen V, Kukkurainen S, Uusimäki A, Rämet M, Parikka M, Hytönen VP, Nykter M, Pesu M
Proprotein Convertase Subtilisin/Kexin Type 7 (PCSK7) Is Essential for the Zebrafish Development and Bioavailability of Transforming Growth Factor β1a (TGFβ1a).
J Biol Chem 2013 ;288(51)36610-23
PMID

Leinonen KA, Saramäki OR, Furusato B, Kimura T, Takahashi H, Egawa S, Suzuki H, Keiger K, Ho Hahm S, Isaacs WB, Tolonen TT, Stenman UH, Tammela TL, Nykter M, Bova GS, Visakorpi T
Loss of PTEN Is Associated with Aggressive Behavior in ERG-Positive Prostate Cancer.
Cancer Epidemiol Biomarkers Prev 2013 ;22(12)2333-44
PMID

Manninen T, Huttunen H, Ruusuvuori P, Nykter M
Leukemia prediction using sparse logistic regression.
PLoS One 2013 ;8(8)e72932
PMID

Kong L, Aho KL, Granberg K, Lund R, Järvenpää L, Seppälä J, Gokhale P, Leinonen K, Hahne L, Mäkelä J, Laurila K, Pukkila H, Närvä E, Yli-Harja O, Andrews PW, Nykter M, Lahesmaa R, Roos C, Autio R
ESTOOLS Data@Hand: human stem cell gene expression resource.
Nat Methods 2013 ;10(9)814-5
PMID

Liuksiala T, Teittinen KJ, Granberg K, Heinäniemi M, Annala M, Mäki M, Nykter M, Lohi O
Overexpression of SNORD114-3 marks acute promyelocytic leukemia.
Leukemia 2013 ;
PMID

Lund RJ, Emani MR, Barbaric I, Kivinen V, Jones M, Baker D, Gokhale P, Nykter M, Lahesmaa R, Andrews PW
Karyotypically abnormal human ESCs are sensitive to HDAC inhibitors and show altered regulation of genes linked to cancers and neurological diseases.
Stem Cell Res 2013 ;11(3)1022-36
PMID

Marttila S, Jylhävä J, Nevalainen T, Nykter M, Jylhä M, Hervonen A, Tserel L, Peterson P, Hurme M
Transcriptional analysis reveals gender-specific changes in the aging of the human immune system.
PLoS One 2013 ;8(6)e66229
PMID

Zhang W, Nykter M, Chen K
Next generation sequencing applications in cancer research.
Cancer Lett 2013 ;340(2)149-50
PMID

Heinäniemi M, Nykter M, Kramer R, Wienecke-Baldacchino A, Sinkkonen L, Zhou JX, Kreisberg R, Kauffman SA, Huang S, Shmulevich I
Gene-pair expression signatures reveal lineage control.
Nat Methods 2013 ;10(6)577-83
PMID

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, , , 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 ;340(2)192-200
PMID

Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, , Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR
Evaluation of methods for modeling transcription factor sequence specificity.
Nat Biotechnol 2013 ;31(2)126-34
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 FF, Nykter M, Zhang W
The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma.
J Clin Invest 2013 ;123(2)855-65
PMID

Patel LR, Nykter M, Chen K, Zhang W
Cancer genome sequencing: Understanding malignancy as a disease of the genome, its conformation, and its evolution.
Cancer Lett 2013 ;340(2)152-60
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
Jõers P, Lewis SC, Fukuoh A, Parhiala M, Ellilä S, Holt IJ, Jacobs HT
Mitochondrial transcription terminator family members mTTF and mTerf5 have opposing roles in coordination of mtDNA synthesis.
PLoS Genet 2013 ;9(9)e1003800
PMID

Reyes A, Kazak L, Wood SR, Yasukawa T, Jacobs HT, Holt IJ
Mitochondrial DNA replication proceeds via a 'bootlace' mechanism involving the incorporation of processed transcripts.
Nucleic Acids Res 2013 ;41(11)5837-50
PMID

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

Fernández-Moreno MA, Hernández R, Adán C, Roberti M, Bruni F, Polosa PL, Cantatore P, Matsushima Y, Kaguni LS, Garesse R
Drosophila nuclear factor DREF regulates the expression of the mitochondrial DNA helicase and mitochondrial transcription factor B2 but not the mitochondrial translation factor B1.
Biochim Biophys Acta 2013 ;1829(10)1136-46
PMID

Martínez-Azorín F, Calleja M, Hernández-Sierra R, Farr CL, Kaguni LS, Garesse R
Muscle-specific overexpression of the catalytic subunit of DNA polymerase γ induces pupal lethality in Drosophila melanogaster.
Arch Insect Biochem Physiol 2013 ;83(3)127-37
PMID

Scialo F, Mallikarjun V, Stefanatos R, Sanz A
Regulation of lifespan by the mitochondrial electron transport chain: reactive oxygen species-dependent and reactive oxygen species-independent mechanisms.
Antioxid Redox Signal 2013 ;19(16)1953-69
PMID

Rajala N, Gerhold JM, Martinsson P, Klymov A, Spelbrink JN
Replication factors transiently associate with mtDNA at the mitochondrial inner membrane to facilitate replication.
Nucleic Acids Res 2013 ;
PMID

Hensen F, Cansiz S, Gerhold JM, Spelbrink JN
To be or not to be a nucleoid protein: A comparison of mass-spectrometry based approaches in the identification of potential mtDNA-nucleoid associated proteins.
Biochimie 2013 ;
PMID

Wessels HJ, Vogel RO, Lightowlers RN, Spelbrink JN, Rodenburg RJ, van den Heuvel LP, van Gool AJ, Gloerich J, Smeitink JA, Nijtmans LG
Analysis of 953 human proteins from a mitochondrial HEK293 fraction by complexome profiling.
PLoS One 2013 ;8(7)e68340
PMID

Molecular Immunology
Dan Hultmark - Genetic Immunology
Marko Pesu - Immunoregulation
Mika Rämet - Experimental Immunology
Olli Silvennoinen - Molecular Immunology
Taskinen B, Zmurko J, Ojanen M, Kukkurainen S, Parthiban M, Määttä JA, Leppiniemi J, Jänis J, Parikka M, Turpeinen H, Rämet M, Pesu M, Johnson MS, Kulomaa MS, Airenne TT, Hytönen VP
Zebavidin - an avidin-like protein from zebrafish.
PLoS One 2013 ;8(10)e77207
PMID

Turpeinen H, Oksanen A, Kivinen V, Kukkurainen S, Uusimäki A, Rämet M, Parikka M, Hytönen VP, Nykter M, Pesu M
Proprotein Convertase Subtilisin/Kexin Type 7 (PCSK7) Is Essential for the Zebrafish Development and Bioavailability of Transforming Growth Factor β1a (TGFβ1a).
J Biol Chem 2013 ;288(51)36610-23
PMID

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

Taskinen B, Zmurko J, Ojanen M, Kukkurainen S, Parthiban M, Määttä JA, Leppiniemi J, Jänis J, Parikka M, Turpeinen H, Rämet M, Pesu M, Johnson MS, Kulomaa MS, Airenne TT, Hytönen VP
Zebavidin - an avidin-like protein from zebrafish.
PLoS One 2013 ;8(10)e77207
PMID

Turpeinen H, Oksanen A, Kivinen V, Kukkurainen S, Uusimäki A, Rämet M, Parikka M, Hytönen VP, Nykter M, Pesu M
Proprotein Convertase Subtilisin/Kexin Type 7 (PCSK7) Is Essential for the Zebrafish Development and Bioavailability of Transforming Growth Factor β1a (TGFβ1a).
J Biol Chem 2013 ;288(51)36610-23
PMID

Oksanen KE, Halfpenny NJ, Sherwood E, Harjula SK, Hammarén MM, Ahava MJ, Pajula ET, Lahtinen MJ, Parikka M, Rämet M
An adult zebrafish model for preclinical tuberculosis vaccine development.
Vaccine 2013 ;31(45)5202-9
PMID

Junttila I, Meri S, Rämet M
[Inflammasome--essential regulator of the inflammatory reaction].
Duodecim 2013 ;129(7)705-11
PMID

Valanne S, Rämet M
Uracil debases pathogenic but not commensal bacteria.
Cell Host Microbe 2013 ;13(5)505-6
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

Niranjan Y, Ungureanu D, Hammarén H, Sanz-Sanz A, Westphal AH, Borst JW, Silvennoinen O, Hilhorst R
Analysis of steady-state Förster resonance energy transfer data by avoiding pitfalls: interaction of JAK2 tyrosine kinase with N-methylanthraniloyl nucleotides.
Anal Biochem 2013 ;442(2)213-22
PMID

Silvennoinen O, Ungureanu D, Niranjan Y, Hammaren H, Bandaranayake R, Hubbard SR
New insights into the structure and function of the pseudokinase domain in JAK2.
Biochem Soc Trans 2013 ;41(4)1002-7
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
Vuorenpää H, Ikonen L, Kujala K, Huttala O, Sarkanen JR, Ylikomi T, Aalto-Setälä K, Heinonen T
Novel in vitro cardiovascular constructs composed of vascular-like networks and cardiomyocytes.
In Vitro Cell Dev Biol Anim 2013 ;
PMID

Kreutzer J, Ikonen L, Hirvonen J, Pekkanen-Mattila M, Aalto-Setälä K, Kallio P
Pneumatic cell stretching system for cardiac differentiation and culture.
Med Eng Phys 2013 ;
PMID

Pradhapan P, Kuusela J, Viik J, Aalto-Setälä K, Hyttinen J
Cardiomyocyte MEA data analysis (CardioMDA)--a novel field potential data analysis software for pluripotent stem cell derived cardiomyocytes.
PLoS One 2013 ;8(9)e73637
PMID

Paci M, Hyttinen J, Aalto-Setälä K, Severi S
Computational models of ventricular- and atrial-like human induced pluripotent stem cell derived cardiomyocytes.
Ann Biomed Eng 2013 ;41(11)2334-48
PMID

Ikonen L, Kerkelä E, Metselaar G, Stuart MC, de Jong MR, Aalto-Setälä K
2D and 3D self-assembling nanofiber hydrogels for cardiomyocyte culture.
Biomed Res Int 2013 ;2013285678
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

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

Wolff J, Sándor GK, Miettinen A, Tuovinen VJ, Mannerström B, Patrikoski M, Miettinen S
GMP-level adipose stem cells combined with computer-aided manufacturing to reconstruct mandibular ameloblastoma resection defects: Experience with three cases.
Ann Maxillofac Surg 2013 ;3(2)114-25
PMID

Kyllönen L, Haimi S, Säkkinen J, Kuokkanen H, Mannerström B, Sándor GK, Miettinen S
Exogenously added BMP-6, BMP-7 and VEGF may not enhance the osteogenic differentiation of human adipose stem cells.
Growth Factors 2013 ;31(5)141-53
PMID

Peltoniemi HH, Salmi A, Miettinen S, Mannerström B, Saariniemi K, Mikkonen R, Kuokkanen H, Herold C
Stem cell enrichment does not warrant a higher graft survival in lipofilling of the breast: a prospective comparative study.
J Plast Reconstr Aesthet Surg 2013 ;66(11)1494-503
PMID

Ahtiainen K, Mauno J, Ellä V, Hagström J, Lindqvist C, Miettinen S, Ylikomi T, Kellomäki M, Seppänen R
Autologous adipose stem cells and polylactide discs in the replacement of the rabbit temporomandibular joint disc.
J R Soc Interface 2013 ;10(85)20130287
PMID

Pelto JM, Haimi SP, Siljander AS, Miettinen SS, Tappura KM, Higgins MJ, Wallace GG
Surface properties and interaction forces of biopolymer-doped conductive polypyrrole surfaces by atomic force microscopy.
Langmuir 2013 ;29(20)6099-108
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

Kyllönen L, Haimi S, Mannerström B, Huhtala H, Rajala KM, Skottman H, Sándor 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 ;71(5)938-50
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 ;9(5)6450-8
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

Kiiski H, Aänismaa R, Tenhunen J, Hagman S, Ylä-Outinen L, Aho A, Yli-Hankala A, Bendel S, Skottman H, Narkilahti S
Healthy human CSF promotes glial differentiation of hESC-derived neural cells while retaining spontaneous activity in existing neuronal networks.
Biol Open 2013 ;2(6)605-12
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

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 Suppl 2013 ;47(1)58-64
PMID

Sorkio A, Hongisto H, Kaarniranta K, Uusitalo H, Juuti-Uusitalo K, Skottman H
Structure and barrier properties of human embryonic stem cell derived retinal pigment epithelial cells are affected by extracellular matrix protein coating.
Tissue Eng Part A 2013 ;
PMID

Kiiski H, Aänismaa R, Tenhunen J, Hagman S, Ylä-Outinen L, Aho A, Yli-Hankala A, Bendel S, Skottman H, Narkilahti S
Healthy human CSF promotes glial differentiation of hESC-derived neural cells while retaining spontaneous activity in existing neuronal networks.
Biol Open 2013 ;2(6)605-12
PMID

Juuti-Uusitalo K, Delporte C, Grégoire F, Perret J, Huhtala H, Savolainen V, Nymark S, Hyttinen J, Uusitalo H, Willermain F, Skottman H
Aquaporin expression and function in human pluripotent stem cell-derived retinal pigmented epithelial cells.
Invest Ophthalmol Vis Sci 2013 ;54(5)3510-9
PMID

Kyllönen L, Haimi S, Mannerström B, Huhtala H, Rajala KM, Skottman H, Sándor 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

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

Ilmarinen T, Laine J, Juuti-Uusitalo K, Numminen J, Seppänen-Suuronen R, Uusitalo H, Skottman H
Towards a defined, serum- and feeder-free culture of stratified human oral mucosal epithelium for ocular surface reconstruction.
Acta Ophthalmol 2013 ;91(8)744-50
PMID

 
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