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Items: 41

1.

Biallelic tumor suppressor loss and DNA repair defects in de novo small cell prostate cancer.

Chedgy EC, Vandekerkhove G, Herberts C, Annala M, Donoghue AJ, Sigouros M, Ritch E, Struss W, Konomura S, Liew J, Parimi S, Vergidis J, Hurtado-Coll A, Sboner A, Fazli L, Beltran H, Chi KN, Wyatt AW.

J Pathol. 2018 Jul 17. doi: 10.1002/path.5137. [Epub ahead of print]

PMID:
30015382
2.

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
3.

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.

4.

Isolation and genome sequencing of individual circulating tumor cells using hydrogel encapsulation and laser capture microdissection.

Park ES, Yan JP, Ang RA, Lee JH, Deng X, Duffy SP, Beja K, Annala M, Black PC, Chi KN, Wyatt AW, Ma H.

Lab Chip. 2018 Jun 12;18(12):1736-1749. doi: 10.1039/c8lc00184g.

PMID:
29762619
5.

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):.

6.

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.

7.

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
8.

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.

9.

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
10.

Impact of Therapy on Genomics and Transcriptomics in High-Risk Prostate Cancer Treated with Neoadjuvant Docetaxel and Androgen Deprivation Therapy.

Beltran H, Wyatt AW, Chedgy EC, Donoghue A, Annala M, Warner EW, Beja K, Sigouros M, Mo F, Fazli L, Collins CC, Eastham J, Morris M, Taplin ME, Sboner A, Halabi S, Gleave ME.

Clin Cancer Res. 2017 Nov 15;23(22):6802-6811. doi: 10.1158/1078-0432.CCR-17-1034. Epub 2017 Aug 25.

PMID:
28842510
11.

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
12.

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.

13.

Analysis of Circulating Cell-Free DNA Identifies Multiclonal Heterogeneity of BRCA2 Reversion Mutations Associated with Resistance to PARP Inhibitors.

Quigley D, Alumkal JJ, Wyatt AW, Kothari V, Foye A, Lloyd P, Aggarwal R, Kim W, Lu E, Schwartzman J, Beja K, Annala M, Das R, Diolaiti M, Pritchard C, Thomas G, Tomlins S, Knudsen K, Lord CJ, Ryan C, Youngren J, Beer TM, Ashworth A, Small EJ, Feng FY.

Cancer Discov. 2017 Sep;7(9):999-1005. doi: 10.1158/2159-8290.CD-17-0146. Epub 2017 Apr 27.

14.

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.

15.

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.

16.

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
17.

Molecular Dissection of Complete Response to Receptor Tyrosine Kinase Inhibition in Type II Papillary Renal Cell Carcinoma.

Annala M, Nappi L, Azad AA, Mo F, Fazli L, Chi KN, Wyatt AW.

Clin Genitourin Cancer. 2017 Feb;15(1):e145-e150. doi: 10.1016/j.clgc.2016.05.019. Epub 2016 May 27. No abstract available.

PMID:
27324055
18.

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.

19.

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.

20.

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.

21.

Moving Toward Personalized Care: Liquid Biopsy Predicts Response to Cisplatin in an Unusual Case of BRCA2-Null Neuroendocrine Prostate Cancer.

Chedgy EC, Annala M, Beja K, Warner EW, Gleave ME, Chi KN, Wyatt AW.

Clin Genitourin Cancer. 2016 Apr;14(2):e233-6. doi: 10.1016/j.clgc.2015.12.023. Epub 2015 Dec 24. No abstract available.

PMID:
26797585
22.

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.

23.

Multi-stressor impacts on fungal diversity and ecosystem functions in streams: natural vs. anthropogenic stress.

Tolkkinen M, Mykrä H, Annala M, Markkola AM, Vuori KM, Muotka T.

Ecology. 2015 Mar;96(3):672-83.

PMID:
26236864
24.

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.

25.

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.

26.

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.

27.

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.

28.

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
29.

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.

30.

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.

31.

Emergence of FGFR family gene fusions as therapeutic targets in a wide spectrum of solid tumours.

Parker BC, Engels M, Annala M, Zhang W.

J Pathol. 2014 Jan;232(1):4-15. Review.

PMID:
24588013
32.

A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding.

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.

Nat Genet. 2014 Feb;46(2):126-35. doi: 10.1038/ng.2862. Epub 2014 Jan 5.

PMID:
24390282
33.

Are biological communities in naturally unproductive streams resistant to additional anthropogenic stressors?

Annala M, Mykrä H, Tolkkinen M, Kauppila T, Muotka T.

Ecol Appl. 2014;24(8):1887-97.

PMID:
29185660
34.

Overexpression of SNORD114-3 marks acute promyelocytic leukemia.

Liuksiala T, Teittinen KJ, Granberg K, Heinäniemi M, Annala M, Mäki M, Nykter M, Lohi O.

Leukemia. 2014 Jan;28(1):233-6. doi: 10.1038/leu.2013.250. Epub 2013 Aug 27. No abstract available.

PMID:
23979522
35.

Fusion genes and their discovery using high throughput sequencing.

Annala MJ, Parker BC, Zhang W, Nykter M.

Cancer Lett. 2013 Nov 1;340(2):192-200. doi: 10.1016/j.canlet.2013.01.011. Epub 2013 Jan 29. Review.

36.

Evaluation of methods for modeling transcription factor sequence specificity.

Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S; DREAM5 Consortium, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR.

Nat Biotechnol. 2013 Feb;31(2):126-34. doi: 10.1038/nbt.2486. Epub 2013 Jan 27.

37.

The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma.

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.

J Clin Invest. 2013 Feb;123(2):855-65. doi: 10.1172/JCI67144. Epub 2013 Jan 9.

38.

Transcriptome and small RNA deep sequencing reveals deregulation of miRNA biogenesis in human glioma.

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.

J Pathol. 2013 Feb;229(3):449-59. doi: 10.1002/path.4109.

39.

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.

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.

Proc Natl Acad Sci U S A. 2012 Feb 28;109(9):3475-80. doi: 10.1073/pnas.1120375109. Epub 2012 Feb 15.

40.

A linear model for transcription factor binding affinity prediction in protein binding microarrays.

Annala M, Laurila K, Lähdesmäki H, Nykter M.

PLoS One. 2011;6(5):e20059. doi: 10.1371/journal.pone.0020059. Epub 2011 May 26.

41.

Investigations on the humidity-induced transformations of salbutamol sulphate particles coated with L-leucine.

Raula J, Thielmann F, Kansikas J, Hietala S, Annala M, Seppälä J, Lähde A, Kauppinen EI.

Pharm Res. 2008 Oct;25(10):2250-61. doi: 10.1007/s11095-008-9613-4. Epub 2008 Jun 27.

PMID:
18584311

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