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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

Latest publications

Högnäs G, Kivinummi K, Kallio HML, Hieta R, Ruusuvuori P, Koskenalho A, Kesseli J, Tammela TLJ, Riikonen J, Ilvesaro J, Kares S, Hirvikoski PP, Laurila M, Mirtti T, Nykter M, Kujala PM, Visakorpi T, Tolonen T, Bova GS
Feasibility of Prostate PAXgene Fixation for Molecular Research and Diagnostic Surgical Pathology: Comparison of Matched Fresh Frozen, FFPE, and PFPE Tissues.
Am J Surg Pathol ;2017

Nättinen J, Jylhä A, Aapola U, Enríquez-de-Salamanca A, Pinto-Fraga J, López-Miguel A, González-García MJ, Stern ME, Calonge M, Zhou L, Nykter M, Uusitalo H, Beuerman R
Topical fluorometholone treatment and desiccating stress change inflammatory protein expression in tears.
Ocul Surf ;2017

Hyysalo A, Ristola M, Mäkinen ME, Häyrynen S, Nykter M, Narkilahti S
Laminin α5 substrates promote survival, network formation and functional development of human pluripotent stem cell-derived neurons in vitro.
Stem Cell Res ;2017

Granberg KJ, Annala M, Lehtinen B, Kesseli J, Haapasalo J, Ruusuvuori P, Yli-Harja O, Visakorpi T, Haapasalo H, Nykter M, Zhang W
Strong FGFR3 staining is a marker for FGFR3 fusions in diffuse gliomas.
Neuro Oncol ;19(9)1206-1216, 2017

Kytola V, Topaloglu U, Miller LD, Bitting RL, Goodman MM, D Agostino RB, Desnoyers RJ, Albright C, Yacoub G, Qasem SA, DeYoung B, Thorsson V, Shmulevich I, Yang M, Shcherban A, Pagni M, Liu L, Nykter M, Chen K, Hawkins GA, Grant SC, Petty WJ, Alistar AT, Levine EA, Staren ED, Langefeld CD, Miller V, Singal G, Petro RM, Robinson M, Blackstock W, Powell BL, Wagner LI, Foley KL, Abraham E, Pasche B, Zhang W
Mutational Landscapes of Smoking-Related Cancers in Caucasians and African Americans: Precision Oncology Perspectives at Wake Forest Baptist Comprehensive Cancer Center.
Theranostics ;7(11)2914-2923, 2017

Vandekerkhove GR, Todenhöfer T, Annala M, Struss WJ, Wong A, Beja K, Ritch E, Brahmbhatt S, Volik S, Hennenlotter J, Nykter M, Chi KN, North S, Stenzl A, Collins CC, Eigl BJ, Black PC, Wyatt AW
Circulating tumor DNA reveals clinically-actionable somatic genome of metastatic bladder cancer.
Clin Cancer Res ;2017

Annala M, Struss WJ, Warner EW, Beja K, Vandekerkhove G, Wong A, Khalaf D, Seppälä IL, So A, Lo G, Aggarwal R, Small EJ, Nykter M, Gleave ME, Chi KN, Wyatt AW
Treatment Outcomes and Tumor Loss of Heterozygosity in Germline DNA Repair-deficient Prostate Cancer.
Eur Urol ;72(1)34-42, 2017

Tarkkonen K, Hieta R, Kytölä V, Nykter M, Kiviranta R
Comparative analysis of osteoblast gene expression profiles and Runx2 genomic occupancy of mouse and human osteoblasts in vitro.
Gene ;2017

Valkonen M, Kartasalo K, Liimatainen K, Nykter M, Latonen L, Ruusuvuori P
Metastasis detection from whole slide images using local features and random forests.
Cytometry A ;91(6)555-565, 2017

Lund RJ, Rahkonen N, Malonzo M, Kauko L, Emani MR, Kivinen V, Närvä E, Kemppainen E, Laiho A, Skottman H, Hovatta O, Rasool O, Nykter M, Lähdesmäki H, Lahesmaa R
RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA(+) and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells.
Stem Cell Reports ;8(5)1442-1454, 2017

Lehtinen B, Raita A, Kesseli J, Annala M, Nordfors K, Yli-Harja O, Zhang W, Visakorpi T, Nykter M, Haapasalo H, Granberg KJ
Clinical association analysis of ependymomas and pilocytic astrocytomas reveals elevated FGFR3 and FGFR1 expression in aggressive ependymomas.
BMC Cancer ;17(1)310, 2017

Urbanucci A, Barfeld SJ, Kytölä V, Itkonen HM, Coleman IM, Vodák D, Sjöblom L, Sheng X, Tolonen T, Minner S, Burdelski C, Kivinummi KK, Kohvakka A, Kregel S, Takhar M, Alshalalfa M, Davicioni E, Erho N, Lloyd P, Karnes RJ, Ross AE, Schaeffer EM, Vander Griend DJ, Knapp S, Corey E, Feng FY, Nelson PS, Saatcioglu F, Knudsen KE, Tammela TLJ, Sauter G, Schlomm T, Nykter M, Visakorpi T, Mills IG
Androgen Receptor Deregulation Drives Bromodomain-Mediated Chromatin Alterations in Prostate Cancer.
Cell Rep ;19(10)2045-2059, 2017

Lin J, Kramna L, Autio R, Hyöty H, Nykter M, Cinek O
Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples.
BMC Genomics ;18(1)378, 2017

Yang M, Topaloglu U, Petty WJ, Pagni M, Foley KL, Grant SC, Robinson M, Bitting RL, Thomas A, Alistar AT, Desnoyers RJ, Goodman M, Albright C, Porosnicu M, Vatca M, Qasem SA, DeYoung B, Kytola V, Nykter M, Chen K, Levine EA, Staren ED, D'Agostino RB, Petro RM, Blackstock W, Powell BL, Abraham E, Pasche B, Zhang W
Circulating mutational portrait of cancer: manifestation of aggressive clonal events in both early and late stages.
J Hematol Oncol ;10(1)100, 2017

Valkonen M, Ruusuvuori P, Kartasalo K, Nykter M, Visakorpi T, Latonen L
Analysis of spatial heterogeneity in normal epithelium and preneoplastic alterations in mouse prostate tumor models.
Sci Rep ;2017

Grönroos T, Teppo S, Mehtonen J, Laukkanen S, Liuksiala T, Nykter M, Heinäniemi M, Lohi O
Overexpression of PTP4A3 in ETV6-RUNX1 acute lymphoblastic leukemia.
Leuk Res ;2017

Afyounian E, Annala M, Nykter M
Segmentum: a tool for copy number analysis of cancer genomes.
BMC Bioinformatics ;18(1)215, 2017

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

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

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

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

Veskimäe K, Staff S, Grönholm A, Pesu M, Laaksonen M, Nykter M, Isola J, Mäenpää J
Assessment of PARP protein expression in epithelial ovarian cancer by ELISA pharmacodynamic assay and immunohistochemistry.
Tumour Biol ;37(9)11991-11999, 2016

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

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

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

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

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

Chua CY, Liu Y, Granberg KJ, Hu L, Haapasalo H, Annala MJ, Cogdell DE, Verploegen M, Moore LM, Fuller GN, Nykter M, Cavenee WK, Zhang W
IGFBP2 potentiates nuclear EGFR-STAT3 signaling.
Oncogene ;35(6)738-47, 2016

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

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