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Items: 1 to 50 of 99

1.

Constitutively active androgen receptor splice variants AR-V3, AR-V7 and AR-V9 are co-expressed in castration-resistant prostate cancer metastases.

Kallio HML, Hieta R, Latonen L, Brofeldt A, Annala M, Kivinummi K, Tammela TL, Nykter M, Isaacs WB, Lilja HG, Bova GS, Visakorpi T.

Br J Cancer. 2018 Jul 10. doi: 10.1038/s41416-018-0172-0. [Epub ahead of print]

PMID:
29988112
2.

Interleukin 10 mutant zebrafish have an enhanced interferon gamma response and improved survival against a Mycobacterium marinum infection.

Harjula SE, Ojanen MJT, Taavitsainen S, Nykter M, Rämet M.

Sci Rep. 2018 Jul 9;8(1):10360. doi: 10.1038/s41598-018-28511-w.

3.

Essential physiological differences characterise short- and long-lived strains of Drosophila melanogaster.

Gubina N, Naudi A, Stefanatos R, Jove M, Scialo F, Fernandez-Ayala DJ, Rantapero T, Yurkevych I, Portero-Otin M, Nykter M, Lushchak O, Navas P, Pamplona R, Sanz A.

J Gerontol A Biol Sci Med Sci. 2018 Jun 26. doi: 10.1093/gerona/gly143. [Epub ahead of print]

PMID:
29945183
4.

Computational characterization of suppressive immune microenvironments in glioblastoma.

Luoto S, Hermelo I, Vuorinen EM, Hannus P, Kesseli J, Nykter M, Granberg KJ.

Cancer Res. 2018 Jun 19. pii: canres.3714.2017. doi: 10.1158/0008-5472.CAN-17-3714. [Epub ahead of print]

PMID:
29921698
5.

Erratum: Whole-exome sequencing identifies germline mutation in TP53 and ATRX in a child with genomically aberrant AT/RT and her mother with anaplastic astrocytoma.

Nordfors K, Haapasalo J, Afyounian E, Tuominen J, Annala M, Häyrynen S, Karhu R, Helén P, Lohi O, Nykter M, Haapasalo H, Granberg KJ.

Cold Spring Harb Mol Case Stud. 2018 Jun 1;4(3). pii: a003129. doi: 10.1101/mcs.a003129. Print 2018 Jun. No abstract available.

6.

Comparative Analysis of Tissue Reconstruction Algorithms for 3D Histology.

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

Bioinformatics. 2018 Apr 19. doi: 10.1093/bioinformatics/bty210. [Epub ahead of print]

PMID:
29684099
7.

Chromatin accessibility is associated with CRISPR-Cas9 efficiency in the zebrafish (Danio rerio).

Uusi-Mäkelä MIE, Barker HR, Bäuerlein CA, Häkkinen T, Nykter M, Rämet M.

PLoS One. 2018 Apr 23;13(4):e0196238. doi: 10.1371/journal.pone.0196238. eCollection 2018.

8.

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gao Q, Liang WW, Foltz SM, Mutharasu G, Jayasinghe RG, Cao S, Liao WW, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ; Fusion Analysis Working Group; Cancer Genome Atlas Research Network, Chen K, Lazar AJ, Fields RC, Wendl MC, Van Tine BA, Vij R, Chen F, Nykter M, Shmulevich I, Ding L.

Cell Rep. 2018 Apr 3;23(1):227-238.e3. doi: 10.1016/j.celrep.2018.03.050.

9.

Whole-exome sequencing identifies germline mutation in TP53 and ATRX in a child with genomically aberrant AT/RT and her mother with anaplastic astrocytoma.

Nordfors K, Haapasalo J, Afyounian E, Tuominen J, Annala M, Häyrynen S, Karhu R, Helén P, Lohi O, Nykter M, Haapasalo H, Granberg KJ.

Cold Spring Harb Mol Case Stud. 2018 Apr 2;4(2). pii: a002246. doi: 10.1101/mcs.a002246. Print 2018 Apr. Erratum in: Cold Spring Harb Mol Case Stud. 2018 Jun 1;4(3):.

10.

Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression.

Latonen L, Afyounian E, Jylhä A, Nättinen J, Aapola U, Annala M, Kivinummi KK, Tammela TTL, Beuerman RW, Uusitalo H, Nykter M, Visakorpi T.

Nat Commun. 2018 Mar 21;9(1):1176. doi: 10.1038/s41467-018-03573-6.

11.

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
12.

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 Apr;8(4):444-457. doi: 10.1158/2159-8290.CD-17-0937. Epub 2018 Jan 24.

PMID:
29367197
13.

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.

14.

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.

15.

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
16.

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
17.

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.

18.

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.

19.

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.

20.

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
21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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
33.

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.

34.

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
35.

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.

36.

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.

37.

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.

38.

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
39.

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.

40.

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.

41.

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.

42.

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
43.

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.

44.

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.

45.

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
46.

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.

47.

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.

48.

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
49.

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.

50.

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.

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