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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

Annala M, Vandekerkhove G, Khalaf D, Taavitsainen S, Beja K, Warner EW, Sunderland K, Kollmannsberger C, Eigl BJ, Finch D, Oja CD, Vergidis J, Zulfiqar M, Azad AA, Nykter M, Gleave ME, Wyatt AW, Chi KN
Circulating Tumor DNA Genomics Correlate with Resistance to Abiraterone and Enzalutamide in Prostate Cancer.
Cancer Discov ;2018

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 ;42(1)103-115, 2018

Haapasalo J, Nordfors K, Granberg KJ, Kivioja T, Nykter M, Haapasalo H, Soini Y
NRF2, DJ1 and SNRX1 and their prognostic impact in astrocytic gliomas.
Histol Histopathol ;2018

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 ;16(1)84-92, 2018

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

Zhang K, Myllymäki SM, Gao P, Devarajan R, Kytölä V, Nykter M, Wei GH, Manninen A
Oncogenic K-Ras upregulates ITGA6 expression via FOSL1 to induce anoikis resistance and synergizes with αV-Class integrins to promote EMT.
Oncogene ;36(41)5681-5694, 2017

Kivinummi K, Urbanucci A, Leinonen K, Tammela TLJ, Annala M, Isaacs WB, Bova GS, Nykter M, Visakorpi T
The expression of AURKA is androgen regulated in castration-resistant prostate cancer.
Sci Rep ;7(1)17978, 2017

Wyatt AW, Annala M, Aggarwal R, Beja K, Feng F, Youngren J, Foye A, Lloyd P, Nykter M, Beer TM, Alumkal JJ, Thomas GV, Reiter RE, Rettig MB, Evans CP, Gao AC, Chi KN, Small EJ, Gleave ME
Concordance of Circulating Tumor DNA and Matched Metastatic Tissue Biopsy in Prostate Cancer.
J Natl Cancer Inst ;2017

Karvonen H, Chiron D, Niininen W, Ek S, Jerkeman M, Moradi E, Nykter M, Heckman CA, Kallioniemi O, Murumägi A, Ungureanu D
Crosstalk between ROR1 and BCR pathways defines novel treatment strategies in mantle cell lymphoma.
Blood Adv ;1(24)2257-2268, 2017

Vandekerkhove G, Todenhöfer T, Annala M, Struss WJ, Wong A, Beja K, Ritch E, Brahmbhatt S, Volik SV, 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 ;23(21)6487-6497, 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

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

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

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
+and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells.
Stem Cell Reports ;8(5)1442-1454, 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

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

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

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

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

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

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

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

Ampuja M, Rantapero T, Rodriguez-Martinez A, Palmroth M, Alarmo EL, Nykter M, Kallioniemi A
Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer.
BMC Genomics ;18(1)68, 2017

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