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university of tampere: faculty of medicine and life sciences: research: matti nykter - computational biology:
Lääketieteen ja biotieteiden tiedekuntaUniversity of TampereLääketieteen ja biotieteiden tiedekunta
Matti Nykter - Computational biology

Previous publications

Ulman V, Svoboda D, Nykter M, Kozubek M, Ruusuvuori P
Virtual cell imaging: A review on simulation methods employed in image cytometry.
Cytometry A ;89(12)1057-1072, 2016
PMID

Wyatt AW, Azad AA, Volik SV, Annala M, Beja K, McConeghy B, Haegert A, Warner EW, Mo F, Brahmbhatt S, Shukin R, Le Bihan S, Gleave ME, Nykter M, Collins CC, Chi KN
Genomic Alterations in Cell-Free DNA and Enzalutamide Resistance in Castration-Resistant Prostate Cancer.
JAMA Oncol ;2(12)1598-1606, 2016
PMID

Teppo S, Laukkanen S, Liuksiala T, Nordlund J, Oittinen M, Teittinen K, Grönroos T, St-Onge P, Sinnett D, Syvänen AC, Nykter M, Viiri K, Heinäniemi M, Lohi O
Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemia.
Genome Res ;26(11)1468-1477, 2016
PMID

Cordova ZM, Grönholm A, Kytölä V, Taverniti V, Hämäläinen S, Aittomäki S, Niininen W, Junttila I, Ylipää A, Nykter M, Pesu M
Myeloid cell expressed proprotein convertase FURIN attenuates inflammation.
Oncotarget ;7(34)54392-54404, 2016
PMID

Nurminen R, Rantapero T, Wong SC, Fischer D, Lehtonen R, Tammela TL, Nykter M, Visakorpi T, Wahlfors T, Schleutker J
Expressional profiling of prostate cancer risk SNPs at 11q13.5 identifies DGAT2 as a new target gene.
Genes Chromosomes Cancer ;55(8)661-73, 2016
PMID

Bova GS, Kallio HM, Annala M, Kivinummi K, Högnäs G, Häyrynen S, Rantapero T, Kivinen V, Isaacs WB, Tolonen T, Nykter M, Visakorpi T
Integrated clinical, whole-genome, and transcriptome analysis of multisampled lethal metastatic prostate cancer.
Cold Spring Harb Mol Case Stud ;2(3)a000752, 2016
PMID

Sjöblom L, Saramäki O, Annala M, Leinonen K, Nättinen J, Tolonen T, Wahlfors T, Nykter M, Bova GS, Schleutker J, Tammela TL, Lilja H, Visakorpi T
Microseminoprotein-Beta Expression in Different Stages of Prostate Cancer.
PLoS One ;11(3)e0150241, 2016
PMID

Alarmo EL, Havunen R, Häyrynen S, Penkki S, Ketolainen J, Nykter M, Kallioniemi A
Bone morphogenetic protein 4 regulates microRNA expression in breast cancer cell lines in diverse fashion.
Genes Chromosomes Cancer ;55(3)227-36, 2016
PMID

Määttä K, Rantapero T, Lindström A, Nykter M, Kankuri-Tammilehto M, Laasanen SL, Schleutker J
Whole-exome sequencing of Finnish hereditary breast cancer families.
Eur J Hum Genet ;25(1)85-93, 2016
PMID

Ruusuvuori P, Valkonen M, Nykter M, Visakorpi T, Latonen L
Feature-based analysis of mouse prostatic intraepithelial neoplasia in histological tissue sections.
J Pathol Inform ;2016
PMID

The Cancer Genome Atlas Research Network
The Molecular Taxonomy of Primary Prostate Cancer.
Cell 2015 ;163(4)1011-25
PMID

Ylipää A, Kivinummi K, Kohvakka A, Annala M, Latonen L, Scaravilli M, Kartasalo K, Leppänen SP, Karakurt S, Seppälä J, Yli-Harja O, Tammela TL, Zhang W, Visakorpi T, Nykter M
Transcriptome Sequencing Reveals PCAT5 as a Novel ERG-Regulated Long Noncoding RNA in Prostate Cancer.
Cancer Res 2015 ;75(19)4026-31
PMID

Rane JK, Ylipää A, Adamson R, Mann VM, Simms MS, Collins AT, Visakorpi T, Nykter M, Maitland NJ
Construction of therapeutically relevant human prostate epithelial fate map by utilising miRNA and mRNA microarray expression data.
Br J Cancer 2015 ;113(4)611-5
PMID

Nordfors K, Haapasalo J, Mäkelä K, Granberg KJ, Nykter M, Korja M, Paavonen T, Haapasalo H, Soini Y
Twist predicts poor outcome of patients with astrocytic glioma.
J Clin Pathol 2015 ;68(11)905-12
PMID

Kaukoniemi KM, Rauhala HE, Scaravilli M, Latonen L, Annala M, Vessella RL, Nykter M, Tammela TL, Visakorpi T
Epigenetically altered miR-193b targets cyclin D1 in prostate cancer.
Cancer Med 2015 ;4(9)1417-25
PMID

Marttila S, Kananen L, Häyrynen S, Jylhävä J, Nevalainen T, Hervonen A, Jylhä M, Nykter M, Hurme M
Ageing-associated changes in the human DNA methylome: genomic locations and effects on gene expression.
BMC Genomics 2015 ;16179
PMID

Gundem G, Van Loo P, Kremeyer B, Alexandrov LB, Tubio JM, Papaemmanuil E, Brewer DS, Kallio HM, Högnäs G, Annala M, Kivinummi K, Goody V, Latimer C, O'Meara S, Dawson KJ, Isaacs W, Emmert-Buck MR, Nykter M, Foster C, Kote-Jarai Z, Easton D, Whitaker HC, , Neal DE, Cooper CS, Eeles RA, Visakorpi T, Campbell PJ, McDermott U, Wedge DC, Bova GS
The evolutionary history of lethal metastatic prostate cancer.
Nature 2015 ;520(7547)353-7
PMID

Annala M, Kivinummi K, Tuominen J, Karakurt S, Granberg K, Latonen L, Ylipää A, Sjöblom L, Ruusuvuori P, Saramäki O, Kaukoniemi KM, Yli-Harja O, Vessella RL, Tammela TL, Zhang W, Visakorpi T, Nykter M
Recurrent SKIL-activating rearrangements in ETS-negative prostate cancer.
Oncotarget 2015 ;6(8)6235-50
PMID

Turner KM, Sun Y, Ji P, Granberg KJ, Bernard B, Hu L, Cogdell DE, Zhou X, Yli-Harja O, Nykter M, Shmulevich I, Yung WK, Fuller GN, Zhang W
Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression.
Proc Natl Acad Sci U S A 2015 ;112(11)3421-6
PMID

Scaravilli M, Porkka KP, Brofeldt A, Annala M, Tammela TL, Jenster GW, Nykter M, Visakorpi T
MiR-1247-5p is overexpressed in castration resistant prostate cancer and targets MYCBP2.
Prostate 2015 ;75(8)798-805
PMID

Veskimäe K, Staff S, Tabaro F, Nykter M, Isola J, Mäenpää J
Microarray analysis of differentially expressed genes in ovarian and fallopian tube epithelium from risk-reducing salpingo-oophorectomies.
Genes Chromosomes Cancer 2015 ;54(5)276-87
PMID

Rane JK, Scaravilli M, Ylipää A, Pellacani D, Mann VM, Simms MS, Nykter M, Collins AT, Visakorpi T, Maitland NJ
MicroRNA expression profile of primary prostate cancer stem cells as a source of biomarkers and therapeutic targets.
Eur Urol 2015 ;67(1)7-10
PMID

Li X, Liu Y, Granberg KJ, Wang Q, Moore LM, Ji P, Gumin J, Sulman EP, Calin GA, Haapasalo H, Nykter M, Shmulevich I, Fuller GN, Lang FF, Zhang W
Two mature products of MIR-491 coordinate to suppress key cancer hallmarks in glioblastoma.
Oncogene 2015 ;34(13)1619-28
PMID

Yang J, Annala M, Ji P, Wang G, Zheng H, Codgell D, Du X, Fang Z, Sun B, Nykter M, Chen K, Zhang W
Recurrent LRP1-SNRNP25 and KCNMB4-CCND3 fusion genes promote tumor cell motility in human osteosarcoma.
J Hematol Oncol 2014 ;7(1)76
PMID

Annala M, Kivinummi K, Leinonen K, Tuominen J, Zhang W, Visakorpi T, Nykter M
DOT1L-HES6 fusion drives androgen independent growth in prostate cancer.
EMBO Mol Med 2014 ;6(9)1121-3
PMID

Li X, Liu Y, Granberg KJ, Wang Q, Moore LM, Ji P, Gumin J, Sulman EP, Calin GA, Haapasalo H, Nykter M, Shmulevich I, Fuller GN, Lang FF, Zhang W
Two mature products of MIR-491 coordinate to suppress key cancer hallmarks in glioblastoma.
Oncogene 2014 ;
PMID

Ruusuvuori P, Lin J, Scott AC, Tan Z, Sorsa S, Kallio A, Nykter M, Yli-Harja O, Shmulevich I, Dudley AM
Quantitative analysis of colony morphology in yeast.
Biotechniques 2014 ;56(1)18-27
PMID

Huang Q, Whitington T, Gao P, Lindberg JF, Yang Y, Sun J, Väisänen MR, Szulkin R, Annala M, Yan J, Egevad LA, Zhang K, Lin R, Jolma A, Nykter M, Manninen A, Wiklund F, Vaarala MH, Visakorpi T, Xu J, Taipale J, Wei GH
A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding.
Nat Genet 2014 ;46(2)126-35
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 2014 ;28(1)233-6
PMID

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

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 2012 ;
PMID

Holmes KM, Annala M, Chua CY, Dunlap SM, Liu Y, Hugen N, Moore LM, Cogdell D, Hu L, Nykter M, Hess K, Fuller GN, Zhang W
Insulin-like growth factor-binding protein 2-driven glioma progression is prevented by blocking a clinically significant integrin, integrin-linked kinase, and NF-κB network.
Proc Natl Acad Sci U S A 2012 ;109(9)3475-80
PMID

Yang J, Ylipää A, Sun Y, Zheng H, Chen K, Nykter M, Trent J, Ratner N, Lev DC, Zhang W
Genomic and molecular characterization of malignant peripheral nerve sheath tumor identifies the IGF1R pathway as a primary target for treatment.
Clin Cancer Res 2011 ;17(24)7563-73
PMID

Mäki-Marttunen T, Aćimović J, Nykter M, Kesseli J, Ruohonen K, Yli-Harja O, Linne ML
Information diversity in structure and dynamics of simulated neuronal networks.
Front Comput Neurosci 2011 ;526
PMID

Annala M, Laurila K, Lähdesmäki H, Nykter M
A linear model for transcription factor binding affinity prediction in protein binding microarrays.
PLoS One 2011 ;6(5)e20059
PMID

Cheng H, Zhang L, Cogdell DE, Zheng H, Schetter AJ, Nykter M, Harris CC, Chen K, Hamilton SR, Zhang W
Circulating plasma MiR-141 is a novel biomarker for metastatic colon cancer and predicts poor prognosis.
PLoS One 2011 ;6(3)e17745
PMID

Yli-Harja O, Ylipää A, Nykter M, Zhang W
Cancer systems biology: signal processing for cancer research.
Chin J Cancer 2011 ;30(4)221-5
PMID

Ylipää A, Yli-Harja O, Zhang W, Nykter M
A systems biological approach to identify key transcription factors and their genomic neighborhoods in human sarcomas.
Chin J Cancer 2011 ;30(1)27-40
PMID

Ylipää A, Hunt KK, Yang J, Lazar AJ, Torres KE, Lev DC, Nykter M, Pollock RE, Trent J, Zhang W
Integrative genomic characterization and a genomic staging system for gastrointestinal stromal tumors.
Cancer 2011 ;117(2)380-9
PMID

Yang D, Ylipaa A, Yang J, Hunt K, Pollock R, Trent J, Yli-Harja O, Shmulevich I, Nykter M, Zhang W
An integrated study of aberrant gene copy number and gene expression in GIST and LMS.
Technol Cancer Res Treat 2010 ;9(2)171-8
PMID

Nykter M, Lähdesmäki H, Rust A, Thorsson V, Shmulevich I
A data integration framework for prediction of transcription factor targets.
Ann N Y Acad Sci 2009 ;1158205-14
PMID

Litvak V, Ramsey SA, Rust AG, Zak DE, Kennedy KA, Lampano AE, Nykter M, Shmulevich I, Aderem A
Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals.
Nat Immunol 2009 ;10(4)437-43
PMID

Nykter M, Price ND, Larjo A, Aho T, Kauffman SA, Yli-Harja O, Shmulevich I
Critical networks exhibit maximal information diversity in structure-dynamics relationships.
Phys Rev Lett 2008 ;100(5)058702
PMID

Nykter M, Price ND, Aldana M, Ramsey SA, Kauffman SA, Hood LE, Yli-Harja O, Shmulevich I
Gene expression dynamics in the macrophage exhibit criticality.
Proc Natl Acad Sci U S A 2008 ;105(6)1897-900
PMID

Niemistö A, Nykter M, Aho T, Jalovaara H, Marjanen K, Ahdesmäki M, Ruusuvuori P, Tiainen M, Linne ML, Yli-Harja O
Computational methods for estimation of cell cycle phase distributions of yeast cells.
EURASIP J Bioinform Syst Biol 2007 ;46150
PMID

Ruusuvuori P, Nykter M, Mäkiraatikka E, Lehmussola A, Korpelainen T, Erkkilä T, Yli-Harja O
Microarray simulator as educational tool.
Conf Proc IEEE Eng Med Biol Soc 2007 ;20075920-3
PMID

Harjunpää A, Taskinen M, Nykter M, Karjalainen-Lindsberg ML, Nyman H, Monni O, Hemmer S, Yli-Harja O, Hautaniemi S, Meri S, Leppä S
Differential gene expression in non-malignant tumour microenvironment is associated with outcome in follicular lymphoma patients treated with rituximab and CHOP.
Br J Haematol 2006 ;135(1)33-42
PMID

Nykter M, Aho T, Ahdesmäki M, Ruusuvuori P, Lehmussola A, Yli-Harja O
Simulation of microarray data with realistic characteristics.
BMC Bioinformatics 2006 ;7349
PMID

Nykter M, Hunt KK, Pollock RE, El-Naggar AK, Taylor E, Shmulevich I, Yli-Harja O, Zhang W
Unsupervised analysis uncovers changes in histopathologic diagnosis in supervised genomic studies.
Technol Cancer Res Treat 2006 ;5(2)177-82
PMID

 
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