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Items: 1 to 50 of 89

1.

NRF2, DJ1 and SNRX1 and their prognostic impact in astrocytic gliomas.

Haapasalo J, Nordfors K, Granberg KJ, Kivioja T, Nykter M, Haapasalo H, Soini Y.

Histol Histopathol. 2018 Feb 14:11973. doi: 10.14670/HH-11-973. [Epub ahead of print]

PMID:
29441509
2.

Circulating tumor DNA genomics correlate with resistance to abiraterone and enzalutamide in prostate cancer.

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.

Cancer Discov. 2018 Jan 24. pii: CD-17-0937. doi: 10.1158/2159-8290.CD-17-0937. [Epub ahead of print]

PMID:
29367197
3.

Crosstalk between ROR1 and BCR pathways defines novel treatment strategies in mantle cell lymphoma.

Karvonen H, Chiron D, Niininen W, Ek S, Jerkeman M, Moradi E, Nykter M, Heckman CA, Kallioniemi O, Murumägi A, Ungureanu D.

Blood Adv. 2017 Nov 9;1(24):2257-2268. doi: 10.1182/bloodadvances.2017010215. eCollection 2017 Nov 14.

4.

The expression of AURKA is androgen regulated in castration-resistant prostate cancer.

Kivinummi K, Urbanucci A, Leinonen K, Tammela TLJ, Annala M, Isaacs WB, Bova GS, Nykter M, Visakorpi T.

Sci Rep. 2017 Dec 21;7(1):17978. doi: 10.1038/s41598-017-18210-3.

5.

Concordance of Circulating Tumor DNA and Matched Metastatic Tissue Biopsy in Prostate Cancer.

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.

J Natl Cancer Inst. 2017 Dec 1;109(12). doi: 10.1093/jnci/djx118.

PMID:
29206995
6.

Feasibility of Prostate PAXgene Fixation for Molecular Research and Diagnostic Surgical Pathology: Comparison of Matched Fresh Frozen, FFPE, and PFPE Tissues.

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.

Am J Surg Pathol. 2018 Jan;42(1):103-115. doi: 10.1097/PAS.0000000000000961.

PMID:
28984675
7.

Laminin α5 substrates promote survival, network formation and functional development of human pluripotent stem cell-derived neurons in vitro.

Hyysalo A, Ristola M, Mäkinen ME, Häyrynen S, Nykter M, Narkilahti S.

Stem Cell Res. 2017 Oct;24:118-127. doi: 10.1016/j.scr.2017.09.002. Epub 2017 Sep 12.

8.

Topical fluorometholone treatment and desiccating stress change inflammatory protein expression in tears.

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.

Ocul Surf. 2018 Jan;16(1):84-92. doi: 10.1016/j.jtos.2017.09.003. Epub 2017 Sep 14.

9.

Mutational Landscapes of Smoking-Related Cancers in Caucasians and African Americans: Precision Oncology Perspectives at Wake Forest Baptist Comprehensive Cancer Center.

Kytola V, Topaloglu U, Miller LD, Bitting RL, Goodman MM, D Agostino RB Jr, 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.

Theranostics. 2017 Jul 12;7(11):2914-2923. doi: 10.7150/thno.20355. eCollection 2017.

10.

Circulating Tumor DNA Reveals Clinically Actionable Somatic Genome of Metastatic Bladder Cancer.

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.

Clin Cancer Res. 2017 Nov 1;23(21):6487-6497. doi: 10.1158/1078-0432.CCR-17-1140. Epub 2017 Jul 31.

PMID:
28760909
11.

Oncogenic K-Ras upregulates ITGA6 expression via FOSL1 to induce anoikis resistance and synergizes with αV-Class integrins to promote EMT.

Zhang K, Myllymäki SM, Gao P, Devarajan R, Kytölä V, Nykter M, Wei GH, Manninen A.

Oncogene. 2017 Oct 12;36(41):5681-5694. doi: 10.1038/onc.2017.177. Epub 2017 Jun 12.

12.

Androgen Receptor Deregulation Drives Bromodomain-Mediated Chromatin Alterations in Prostate Cancer.

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.

Cell Rep. 2017 Jun 6;19(10):2045-2059. doi: 10.1016/j.celrep.2017.05.049.

13.

Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples.

Lin J, Kramna L, Autio R, Hyöty H, Nykter M, Cinek O.

BMC Genomics. 2017 May 15;18(1):378. doi: 10.1186/s12864-017-3721-7.

14.

Comparative analysis of osteoblast gene expression profiles and Runx2 genomic occupancy of mouse and human osteoblasts in vitro.

Tarkkonen K, Hieta R, Kytölä V, Nykter M, Kiviranta R.

Gene. 2017 Aug 30;626:119-131. doi: 10.1016/j.gene.2017.05.028. Epub 2017 May 11.

15.

RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA+ and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells.

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.

Stem Cell Reports. 2017 May 9;8(5):1442-1454. doi: 10.1016/j.stemcr.2017.04.016.

16.

Circulating mutational portrait of cancer: manifestation of aggressive clonal events in both early and late stages.

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 Jr, Petro RM, Blackstock W, Powell BL, Abraham E, Pasche B, Zhang W.

J Hematol Oncol. 2017 May 4;10(1):100. doi: 10.1186/s13045-017-0468-1.

17.

Clinical association analysis of ependymomas and pilocytic astrocytomas reveals elevated FGFR3 and FGFR1 expression in aggressive ependymomas.

Lehtinen B, Raita A, Kesseli J, Annala M, Nordfors K, Yli-Harja O, Zhang W, Visakorpi T, Nykter M, Haapasalo H, Granberg KJ.

BMC Cancer. 2017 May 3;17(1):310. doi: 10.1186/s12885-017-3274-9.

18.

Metastasis detection from whole slide images using local features and random forests.

Valkonen M, Kartasalo K, Liimatainen K, Nykter M, Latonen L, Ruusuvuori P.

Cytometry A. 2017 Jun;91(6):555-565. doi: 10.1002/cyto.a.23089. Epub 2017 Apr 20.

PMID:
28426134
19.

Segmentum: a tool for copy number analysis of cancer genomes.

Afyounian E, Annala M, Nykter M.

BMC Bioinformatics. 2017 Apr 13;18(1):215. doi: 10.1186/s12859-017-1626-8.

20.

Strong FGFR3 staining is a marker for FGFR3 fusions in diffuse gliomas.

Granberg KJ, Annala M, Lehtinen B, Kesseli J, Haapasalo J, Ruusuvuori P, Yli-Harja O, Visakorpi T, Haapasalo H, Nykter M, Zhang W.

Neuro Oncol. 2017 Sep 1;19(9):1206-1216. doi: 10.1093/neuonc/nox028.

21.

Analysis of spatial heterogeneity in normal epithelium and preneoplastic alterations in mouse prostate tumor models.

Valkonen M, Ruusuvuori P, Kartasalo K, Nykter M, Visakorpi T, Latonen L.

Sci Rep. 2017 Mar 20;7:44831. doi: 10.1038/srep44831.

22.

Treatment Outcomes and Tumor Loss of Heterozygosity in Germline DNA Repair-deficient Prostate Cancer.

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.

Eur Urol. 2017 Jul;72(1):34-42. doi: 10.1016/j.eururo.2017.02.023. Epub 2017 Mar 1.

PMID:
28259476
23.

Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer.

Ampuja M, Rantapero T, Rodriguez-Martinez A, Palmroth M, Alarmo EL, Nykter M, Kallioniemi A.

BMC Genomics. 2017 Jan 11;18(1):68. doi: 10.1186/s12864-016-3428-1.

24.

Overexpression of PTP4A3 in ETV6-RUNX1 acute lymphoblastic leukemia.

Grönroos T, Teppo S, Mehtonen J, Laukkanen S, Liuksiala T, Nykter M, Heinäniemi M, Lohi O.

Leuk Res. 2017 Mar;54:1-6. doi: 10.1016/j.leukres.2016.12.005. Epub 2016 Dec 26.

PMID:
28063378
25.

Virtual cell imaging: A review on simulation methods employed in image cytometry.

Ulman V, Svoboda D, Nykter M, Kozubek M, Ruusuvuori P.

Cytometry A. 2016 Dec;89(12):1057-1072. doi: 10.1002/cyto.a.23031. Epub 2016 Dec 6. Review.

26.

Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemia.

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 Res. 2016 Nov;26(11):1468-1477. Epub 2016 Sep 12.

27.

Whole-exome sequencing of Finnish hereditary breast cancer families.

Määttä K, Rantapero T, Lindström A, Nykter M, Kankuri-Tammilehto M, Laasanen SL, Schleutker J.

Eur J Hum Genet. 2016 Jan;25(1):85-93. doi: 10.1038/ejhg.2016.141. Epub 2016 Oct 26.

28.

Assessment of PARP protein expression in epithelial ovarian cancer by ELISA pharmacodynamic assay and immunohistochemistry.

Veskimäe K, Staff S, Grönholm A, Pesu M, Laaksonen M, Nykter M, Isola J, Mäenpää J.

Tumour Biol. 2016 Sep;37(9):11991-11999. Epub 2016 May 7.

PMID:
27155850
29.

Myeloid cell expressed proprotein convertase FURIN attenuates inflammation.

Cordova ZM, Grönholm A, Kytölä V, Taverniti V, Hämäläinen S, Aittomäki S, Niininen W, Junttila I, Ylipää A, Nykter M, Pesu M.

Oncotarget. 2016 Aug 23;7(34):54392-54404. doi: 10.18632/oncotarget.11106.

30.

Genomic Alterations in Cell-Free DNA and Enzalutamide Resistance in Castration-Resistant Prostate Cancer.

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.

JAMA Oncol. 2016 Dec 1;2(12):1598-1606. doi: 10.1001/jamaoncol.2016.0494.

31.

Integrated clinical, whole-genome, and transcriptome analysis of multisampled lethal metastatic prostate cancer.

Bova GS, Kallio HM, Annala M, Kivinummi K, Högnäs G, Häyrynen S, Rantapero T, Kivinen V, Isaacs WB, Tolonen T, Nykter M, Visakorpi T.

Cold Spring Harb Mol Case Stud. 2016 May;2(3):a000752. doi: 10.1101/mcs.a000752.

32.

Expressional profiling of prostate cancer risk SNPs at 11q13.5 identifies DGAT2 as a new target gene.

Nurminen R, Rantapero T, Wong SC, Fischer D, Lehtonen R, Tammela TL, Nykter M, Visakorpi T, Wahlfors T, Schleutker J.

Genes Chromosomes Cancer. 2016 Aug;55(8):661-73. doi: 10.1002/gcc.22368. Epub 2016 May 24.

PMID:
27113481
33.

Feature-based analysis of mouse prostatic intraepithelial neoplasia in histological tissue sections.

Ruusuvuori P, Valkonen M, Nykter M, Visakorpi T, Latonen L.

J Pathol Inform. 2016 Jan 29;7:5. doi: 10.4103/2153-3539.175378. eCollection 2016.

34.

Microseminoprotein-Beta Expression in Different Stages of Prostate Cancer.

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.

PLoS One. 2016 Mar 3;11(3):e0150241. doi: 10.1371/journal.pone.0150241. eCollection 2016. Erratum in: PLoS One. 2016;11(4):e0153732.

35.

Bone morphogenetic protein 4 regulates microRNA expression in breast cancer cell lines in diverse fashion.

Alarmo EL, Havunen R, Häyrynen S, Penkki S, Ketolainen J, Nykter M, Kallioniemi A.

Genes Chromosomes Cancer. 2016 Mar;55(3):227-36. doi: 10.1002/gcc.22324. Epub 2015 Dec 18.

PMID:
26684238
36.

Transcriptome Sequencing Reveals PCAT5 as a Novel ERG-Regulated Long Noncoding RNA in Prostate Cancer.

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.

Cancer Res. 2015 Oct 1;75(19):4026-31. doi: 10.1158/0008-5472.CAN-15-0217. Epub 2015 Aug 17.

37.

Construction of therapeutically relevant human prostate epithelial fate map by utilising miRNA and mRNA microarray expression data.

Rane JK, Ylipää A, Adamson R, Mann VM, Simms MS, Collins AT, Visakorpi T, Nykter M, Maitland NJ.

Br J Cancer. 2015 Aug 11;113(4):611-5. doi: 10.1038/bjc.2015.262. Epub 2015 Jul 23.

38.

Twist predicts poor outcome of patients with astrocytic glioma.

Nordfors K, Haapasalo J, Mäkelä K, Granberg KJ, Nykter M, Korja M, Paavonen T, Haapasalo H, Soini Y.

J Clin Pathol. 2015 Nov;68(11):905-12. doi: 10.1136/jclinpath-2015-202868. Epub 2015 Jul 10.

PMID:
26163539
39.

Epigenetically altered miR-193b targets cyclin D1 in prostate cancer.

Kaukoniemi KM, Rauhala HE, Scaravilli M, Latonen L, Annala M, Vessella RL, Nykter M, Tammela TL, Visakorpi T.

Cancer Med. 2015 Sep;4(9):1417-25. doi: 10.1002/cam4.486. Epub 2015 Jul 1.

40.

IGFBP2 potentiates nuclear EGFR-STAT3 signaling.

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.

Oncogene. 2016 Feb 11;35(6):738-47. doi: 10.1038/onc.2015.131. Epub 2015 Apr 20.

41.

Ageing-associated changes in the human DNA methylome: genomic locations and effects on gene expression.

Marttila S, Kananen L, Häyrynen S, Jylhävä J, Nevalainen T, Hervonen A, Jylhä M, Nykter M, Hurme M.

BMC Genomics. 2015 Mar 14;16:179. doi: 10.1186/s12864-015-1381-z.

42.

The evolutionary history of lethal metastatic prostate cancer.

Gundem G, Van Loo P, Kremeyer B, Alexandrov LB, Tubio JMC, Papaemmanuil E, Brewer DS, Kallio HML, 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; ICGC Prostate Group, Neal DE, Cooper CS, Eeles RA, Visakorpi T, Campbell PJ, McDermott U, Wedge DC, Bova GS.

Nature. 2015 Apr 16;520(7547):353-357. doi: 10.1038/nature14347. Epub 2015 Apr 1.

43.

Recurrent SKIL-activating rearrangements in ETS-negative prostate cancer.

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.

Oncotarget. 2015 Mar 20;6(8):6235-50.

44.

Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression.

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.

Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):3421-6. doi: 10.1073/pnas.1414573112. Epub 2015 Mar 3.

45.

MiR-1247-5p is overexpressed in castration resistant prostate cancer and targets MYCBP2.

Scaravilli M, Porkka KP, Brofeldt A, Annala M, Tammela TL, Jenster GW, Nykter M, Visakorpi T.

Prostate. 2015 Jun;75(8):798-805. doi: 10.1002/pros.22961. Epub 2015 Mar 1.

PMID:
25731699
46.

Microarray analysis of differentially expressed genes in ovarian and fallopian tube epithelium from risk-reducing salpingo-oophorectomies.

Veskimäe K, Staff S, Tabaro F, Nykter M, Isola J, Mäenpää J.

Genes Chromosomes Cancer. 2015 May;54(5):276-87. doi: 10.1002/gcc.22241. Epub 2015 Feb 23.

PMID:
25706666
47.

Recurrent LRP1-SNRNP25 and KCNMB4-CCND3 fusion genes promote tumor cell motility in human osteosarcoma.

Yang J, Annala M, Ji P, Wang G, Zheng H, Codgell D, Du X, Fang Z, Sun B, Nykter M, Chen K, Zhang W.

J Hematol Oncol. 2014 Oct 10;7:76. doi: 10.1186/s13045-014-0076-2.

48.

MicroRNA expression profile of primary prostate cancer stem cells as a source of biomarkers and therapeutic targets.

Rane JK, Scaravilli M, Ylipää A, Pellacani D, Mann VM, Simms MS, Nykter M, Collins AT, Visakorpi T, Maitland NJ.

Eur Urol. 2015 Jan;67(1):7-10. doi: 10.1016/j.eururo.2014.09.005. Epub 2014 Sep 16.

PMID:
25234358
49.

DOT1L-HES6 fusion drives androgen independent growth in prostate cancer.

Annala M, Kivinummi K, Leinonen K, Tuominen J, Zhang W, Visakorpi T, Nykter M.

EMBO Mol Med. 2014 Sep;6(9):1121-3. doi: 10.15252/emmm.201404210. No abstract available.

50.

Two mature products of MIR-491 coordinate to suppress key cancer hallmarks in glioblastoma.

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.

Oncogene. 2015 Mar 26;34(13):1619-1628. doi: 10.1038/onc.2014.98. Epub 2014 Apr 21.

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