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ArticlesPeer ReviewedFull Text
Plasma ctDNA is a tumor tissue surrogate and enables clinical-genomic stratification of metastatic bladder cancer
Author / Creator:Vandekerkhove, Gillian ; Lavoie, Jean-Michel ; Annala, Matti ; Murtha, Andrew J. ; Sundahl, Nora ; Walz, Simon ; Sano, Takeshi ; Taavitsainen, Sinja ; Ritch, Elie ; Fazli, Ladan ; Hurtado-Coll, Antonio ; Wang, Gang ; Nykter, Matti ; Black, Peter C. ; Todenhöfer, Tilman ; Ost, Piet ; Gibb, Ewan A. ; Chi, Kim N. ; Eigl, Bernhard J. ; Wyatt, Alexander W.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-01, Vol.12 (1), p.184-12, Article 184
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Optimal sequencing of enzalutamide and abiraterone acetate plus prednisone in metastatic castration-resistant prostate cancer: a multicentre, randomised, open-label, phase 2, crossover trial
Author / Creator:Khalaf, Daniel J, MD ; Annala, Matti, MSc ; Taavitsainen, Sinja, MSc ; Finch, Daygen L, MD ; Oja, Conrad, MD ; Vergidis, Joanna, MD ; Zulfiqar, Muhammad, MD ; Sunderland, Katherine, MPH ; Azad, Arun A, MD ; Kollmannsberger, Christian K, MD ; Eigl, Bernhard J, MD ; Noonan, Krista, MD ; Wadhwa, Deepa, MD ; Attwell, Andrew, MD ; Keith, Bruce, MD ; Ellard, Susan L, MD ; Le, Lyly, MD ; Gleave, Martin E, Prof ; Wyatt, Alexander W, DPhil ; Chi, Kim N, Prof
Publisher:England: Elsevier Ltd
Journal title:The lancet oncology, 2019-12, Vol.20 (12), p.1730-1739
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The evolutionary history of lethal metastatic prostate cancer
Author / Creator:Gundem, Gunes ; Van Loo, Peter ; Kremeyer, Barbara ; Alexandrov, Ludmil B. ; Tubio, Jose M. C. ; Papaemmanuil, Elli ; Brewer, Daniel S. ; Kallio, Heini M. L. ; Högnäs, Gunilla ; Annala, Matti ; Kivinummi, Kati ; Goody, Victoria ; Latimer, Calli ; O'Meara, Sarah ; Dawson, Kevin J. ; Isaacs, William ; Emmert-Buck, Michael R. ; Nykter, Matti ; Foster, Christopher ; Kote-Jarai, Zsofia ; Easton, Douglas ; Whitaker, Hayley C. ; Neal, David E. ; Cooper, Colin S. ; Eeles, Rosalind A. ; Visakorpi, Tapio ; Campbell, Peter J. ; McDermott, Ultan ; Wedge, David C. ; Bova, G. Steven
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2015-04, Vol.520 (7547), p.353-357
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Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression
Author / Creator:Latonen, Leena ; Afyounian, Ebrahim ; Jylhä, Antti ; Nättinen, Janika ; Aapola, Ulla ; Annala, Matti ; Kivinummi, Kati K. ; Tammela, Teuvo T. L. ; Beuerman, Roger W. ; Uusitalo, Hannu ; Nykter, Matti ; Visakorpi, Tapio
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2018-03, Vol.9 (1), p.1176-13, Article 1176
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Constitutively active androgen receptor splice variants AR-V3, AR-V7 and AR-V9 are co-expressed in castration-resistant prostate cancer metastases
Author / Creator:Kallio, Heini M. L. ; Hieta, Reija ; Latonen, Leena ; Brofeldt, Anniina ; Annala, Matti ; Kivinummi, Kati ; Tammela, Teuvo L. ; Nykter, Matti ; Isaacs, William B. ; Lilja, Hans G. ; Bova, G. Steven ; Visakorpi, Tapio
Publisher:London: Nature Publishing Group UK
Journal title:British journal of cancer, 2018-08, Vol.119 (3), p.347-356
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The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma
Author / Creator:Parker, Brittany C ; Annala, Matti J ; Cogdell, David E ; Granberg, Kirsi J ; Sun, Yan ; Ji, Ping ; Li, Xia ; Gumin, Joy ; Zheng, Hong ; Hu, Limei ; Yli-Harja, Olli ; Haapasalo, Hannu ; Visakorpi, Tapio ; Liu, Xiuping ; Liu, Chang-Gong ; Sawaya, Raymond ; Fuller, Gregory N ; Chen, Kexin ; Lang, Frederick F ; Nykter, Matti ; Zhang, Wei
Publisher:United States: American Society for Clinical Investigation
Journal title:The Journal of clinical investigation, 2013-02, Vol.123 (2), p.855-865
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A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding
Author / Creator:Huang, Qilai ; Whitington, Thomas ; Gao, Ping ; Lindberg, Johan F ; Yang, Yuehong ; Sun, Jielin ; Väisänen, Marja-Riitta ; Szulkin, Robert ; Annala, Matti ; Yan, Jian ; Egevad, Lars A ; Zhang, Kai ; Lin, Ruizhu ; Jolma, Arttu ; Nykter, Matti ; Manninen, Aki ; Wiklund, Fredrik ; Vaarala, Markku H ; Visakorpi, Tapio ; Xu, Jianfeng ; Taipale, Jussi ; Wei, Gong-Hong
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2014-02, Vol.46 (2), p.126-135
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ArticlesPeer ReviewedFull Text
Segmentum: a tool for copy number analysis of cancer genomes
Author / Creator:Afyounian, Ebrahim ; Annala, Matti ; Nykter, Matti
Publisher:England: BioMed Central
Journal title:BMC bioinformatics, 2017-04, Vol.18 (1), p.215-10, Article 215
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ArticlesPeer ReviewedFull Text
AR and ERG drive the expression of prostate cancer specific long noncoding RNAs
Author / Creator:Kohvakka, Annika ; Sattari, Mina ; Shcherban, Anastasia ; Annala, Matti ; Urbanucci, Alfonso ; Kesseli, Juha ; Tammela, Teuvo L. J. ; Kivinummi, Kati ; Latonen, Leena ; Nykter, Matti ; Visakorpi, Tapio
Publisher:London: Nature Publishing Group UK
Journal title:Oncogene, 2020-07, Vol.39 (30), p.5241-5251
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ArticlesPeer ReviewedFull Text
PTPRD and CNTNAP2 as markers of tumor aggressiveness in oligodendrogliomas
Author / Creator:Rautajoki, Kirsi J. ; Jaatinen, Serafiina ; Tiihonen, Aliisa M. ; Annala, Matti ; Vuorinen, Elisa M. ; Kivinen, Anni ; Rauhala, Minna J. ; Maass, Kendra K. ; Pajtler, Kristian W. ; Yli-Harja, Olli ; Helén, Pauli ; Haapasalo, Joonas ; Haapasalo, Hannu ; Zhang, Wei ; Nykter, Matti
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2022-08, Vol.12 (1), p.14083-14083, Article 14083
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ArticlesPeer ReviewedFull Text
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
Author / Creator:Holmes, Kristen M ; Annala, Matti ; Chua, Corrine Y. X ; Dunlap, Sarah M ; Liu, Yuexin ; Hugen, Niek ; Moore, Lynette M ; Cogdell, David ; Hu, Limei ; Nykter, Matti ; Hess, Kenneth ; Fuller, Gregory N ; Zhang, Wei
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2012-02, Vol.109 (9), p.3475-3480
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ArticlesPeer ReviewedFull Text
Microseminoprotein-Beta Expression in Different Stages of Prostate Cancer
Author / Creator:Sjöblom, Liisa ; Saramäki, Outi ; Annala, Matti ; Leinonen, Katri ; Nättinen, Janika ; Tolonen, Teemu ; Wahlfors, Tiina ; Nykter, Matti ; Bova, G Steven ; Schleutker, Johanna ; Tammela, Teuvo L J ; Lilja, Hans ; Visakorpi, Tapio
Publisher:United States: Public Library of Science
Journal title:PloS one, 2016-03, Vol.11 (3), p.e0150241-e0150241
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ArticlesPeer ReviewedFull Text
A linear model for transcription factor binding affinity prediction in protein binding microarrays
Author / Creator:Annala, Matti ; Laurila, Kirsti ; Lähdesmäki, Harri ; Nykter, Matti
Publisher:United States: Public Library of Science
Journal title:PloS one, 2011-05, Vol.6 (5), p.e20059-e20059
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ArticlesPeer ReviewedFull Text
Clinical association analysis of ependymomas and pilocytic astrocytomas reveals elevated FGFR3 and FGFR1 expression in aggressive ependymomas
Author / Creator:Lehtinen, Birgitta ; Raita, Annina ; Kesseli, Juha ; Annala, Matti ; Nordfors, Kristiina ; Yli-Harja, Olli ; Zhang, Wei ; Visakorpi, Tapio ; Nykter, Matti ; Haapasalo, Hannu ; Granberg, Kirsi J
Publisher:England: BioMed Central
Journal title:BMC cancer, 2017-05, Vol.17 (1), p.310-12, Article 310
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ArticlesPeer ReviewedFull Text
Frequent mutation of the FOXA1 untranslated region in prostate cancer
Author / Creator:Annala, Matti ; Taavitsainen, Sinja ; Vandekerkhove, Gillian ; Bacon, Jack V. W. ; Beja, Kevin ; Chi, Kim N. ; Nykter, Matti ; Wyatt, Alexander W.
Publisher:London: Nature Publishing Group UK
Journal title:Communications biology, 2018-08, Vol.1 (1), p.122-122, Article 122
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Genomic characterization of IDH-mutant astrocytoma progression to grade 4 in the treatment setting
Author / Creator:Rautajoki, Kirsi J ; Jaatinen, Serafiina ; Hartewig, Anja ; Tiihonen, Aliisa M ; Annala, Matti ; Salonen, Iida ; Valkonen, Masi ; Simola, Vili ; Vuorinen, Elisa M ; Kivinen, Anni ; Rauhala, Minna J ; Nurminen, Riikka ; Maass, Kendra K ; Lahtela, Sirpa-Liisa ; Jukkola, Arja ; Yli-Harja, Olli ; Helén, Pauli ; Pajtler, Kristian W ; Ruusuvuori, Pekka ; Haapasalo, Joonas ; Zhang, Wei ; Haapasalo, Hannu ; Nykter, Matti
Publisher:London: BioMed Central Ltd
Journal title:Acta neuropathologica communications, 2023-11, Vol.11 (1), p.1-176, Article 176
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ArticlesPeer ReviewedFull Text
DOT1L‐HES6 fusion drives androgen independent growth in prostate cancer
Author / Creator:Annala, Matti ; Kivinummi, Kati ; Leinonen, Katri ; Tuominen, Joonas ; Zhang, Wei ; Visakorpi, Tapio ; Nykter, Matti
Publisher:London: Nature Publishing Group UK
Journal title:EMBO molecular medicine, 2014-09, Vol.6 (9), p.1121-1123
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Newsletter articlesFull Text
Glioblastomas; Fusion gene contributes to glioblastoma progression
Publisher:Atlanta: NewsRx
Journal title:Obesity, Fitness & Wellness Week, 2013, p.626
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ArticlesPeer ReviewedFull Text
Deep whole-genome ctDNA chronology of treatment-resistant prostate cancer
Author / Creator:Herberts, Cameron ; Annala, Matti ; Sipola, Joonatan ; Ng, Sarah W. S. ; Chen, Xinyi E. ; Nurminen, Anssi ; Korhonen, Olga V. ; Munzur, Aslı D. ; Beja, Kevin ; Schönlau, Elena ; Bernales, Cecily Q. ; Ritch, Elie ; Bacon, Jack V. W. ; Lack, Nathan A. ; Nykter, Matti ; Aggarwal, Rahul ; Small, Eric J. ; Gleave, Martin E. ; Quigley, David A. ; Feng, Felix Y. ; Chi, Kim N. ; Wyatt, Alexander W.
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2022-08, Vol.608 (7921), p.199-208
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ArticlesPeer ReviewedFull Text
Evaluation of methods for modeling transcription factor sequence specificity
Author / Creator:Weirauch, Matthew T ; Cote, Atina ; Norel, Raquel ; Annala, Matti ; Zhao, Yue ; Riley, Todd R ; Saez-Rodriguez, Julio ; Cokelaer, Thomas ; Vedenko, Anastasia ; Talukder, Shaheynoor ; Bussemaker, Harmen J ; Morris, Quaid D ; Bulyk, Martha L ; Stolovitzky, Gustavo ; Hughes, Timothy R
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2013-02, Vol.31 (2), p.126-134
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Plasma ctDNA is a tumor tissue surrogate and enables clinical-genomic stratification of metastatic bladder cancer

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Optimal sequencing of enzalutamide and abiraterone acetate plus prednisone in metastatic castration-resistant prostate cancer: a multicentre, randomised, open-label, phase 2, crossover trial

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The evolutionary history of lethal metastatic prostate cancer

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

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

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

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

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Segmentum: a tool for copy number analysis of cancer genomes

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AR and ERG drive the expression of prostate cancer specific long noncoding RNAs

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PTPRD and CNTNAP2 as markers of tumor aggressiveness in oligodendrogliomas

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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

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Microseminoprotein-Beta Expression in Different Stages of Prostate Cancer

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

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

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Frequent mutation of the FOXA1 untranslated region in prostate cancer

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Genomic characterization of IDH-mutant astrocytoma progression to grade 4 in the treatment setting

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DOT1L‐HES6 fusion drives androgen independent growth in prostate cancer

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Glioblastomas; Fusion gene contributes to glioblastoma progression

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Deep whole-genome ctDNA chronology of treatment-resistant prostate cancer

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Evaluation of methods for modeling transcription factor sequence specificity

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