Scientific references

Our team members have published across the fields of bioinformatics, biology and biomedicine. This list is generated from our Goole Scholar profile

Link to Genevia Technologies' Google Scholar profile

Authors Title Publication Volume Number Pages Year Publisher
Valkonen, Mira; Kartasalo, Kimmo; Liimatainen, Kaisa; Nykter, Matti; Latonen, Leena; Ruusuvuori, Pekka; Dual structured convolutional neural network with feature augmentation for quantitative characterization of tissue histology Proceedings of the IEEE International Conference on Computer Vision Workshops 27-35 2017
Siltanen, Sanna; Fischer, Daniel; Rantapero, Tommi; Laitinen, Virpi; Mpindi, John Patrick; Kallioniemi, Olli; Wahlfors, Tiina; Schleutker, Johanna; ARLTS1 and prostate cancer risk-analysis of expression and regulation PLoS One 8 8 e72040 2013 Public Library of Science
Vainio, Paula; Mpindi, John-Patrick; Kohonen, Pekka; Fey, Vidal; Mirtti, Tuomas; Alanen, Kalle A; Perälä, Merja; Kallioniemi, Olli; Iljin, Kristiina; High-throughput transcriptomic and RNAi analysis identifies AIM1, ERGIC1, TMED3 and TPX2 as potential drug targets in prostate cancer PloS one 7 6 e39801 2012 Public Library of Science
Waterhouse, Robert M; Seppey, Mathieu; Simão, Felipe A; Manni, Mosè; Ioannidis, Panagiotis; Klioutchnikov, Guennadi; Kriventseva, Evgenia V; Zdobnov, Evgeny M; BUSCO applications from quality assessments to gene prediction and phylogenomics Molecular biology and evolution 35 3 543-548 2018 Oxford University Press
Kivinummi, Kati; Urbanucci, Alfonso; Leinonen, Katri; Tammela, Teuvo LJ; Annala, Matti; Isaacs, William B; Bova, G Steven; Nykter, Matti; Visakorpi, Tapio; The expression of AURKA is androgen regulated in castration-resistant prostate cancer Scientific reports 7 1 1-11 2017 Nature Publishing Group
Yli-Hietanen, Jari; Ylipää, Antti; Yli-Harja, Olli; Cancer research in the era of next-generation sequencing and big data calls for intelligent modeling 2015 BioMed Central
Taavitsainen, Sinja; Annala, Matti; Ledet, Elisa; Beja, Kevin; Miller, Patrick J; Moses, Marcus; Nykter, Matti; Chi, Kim N; Sartor, Oliver; Wyatt, Alexander W; Evaluation of commercial circulating tumor DNA test in metastatic prostate cancer JCO Precision Oncology 3 1-9 2019 American Society of Clinical Oncology
Nykter, Matti; Aho, Tommi; Ahdesmäki, Miika; Ruusuvuori, Pekka; Lehmussola, Antti; Yli-Harja, Olli; Simulation of microarray data with realistic characteristics BMC bioinformatics 7 1 349 2006 Springer
Moore, Lynette M; Kivinen, Virpi; Liu, Yuexin; Annala, Matti; Cogdell, David; Liu, Xiuping; Liu, Chang-Gong; Sawaya, Raymond; Yli-Harja, Olli; Shmulevich, Ilya; Transcriptome and Small RNA Deep Sequencing Reveals Deregulation of
Zhang, Wei; Parker, Brittany C; Annala, Matti J; Cogdell, David; Granberg, Kirsi; Sun, Yan; Ji, Ping; Li, Xia; Gumin, Joy; Zheng, Hong; The tumorigenic fusion FGFR3-TACC3 escapes miR-99a regulation in glioblastoma. 2013 AACR
Granberg, Kirsi J; Raita, Annina; Lehtinen, Birgitta; Tiihonen, Aliisa M; Kesseli, Juha; Annala, Matti; Rodriguez-Martinez, Alejandra; Nordfors, Kristiina; Zhang, Wei; Visakorpi, Tapio; Moderate-to-strong expression of FGFR3 and TP53 alterations in a subpopulation of choroid plexus tumors. Histology and Histopathology 18180-18180 2019
Lehtinen, Birgitta; Raita, Annina; Kesseli, Juha; Annala, Matti; Nordfors, Kristiina; Yli-Harja, Olli; Zhang, Wei; Visakorpi, Tapio; Nykter, Matti; Haapasalo, Hannu; Clinical association analysis of ependymomas and pilocytic astrocytomas reveals elevated FGFR3 and FGFR1 expression in aggressive ependymomas BMC cancer 17 1 310 2017 Springer
Ylipää, Antti; Yli-Harja, Olli; Zhang, Wei; Nykter, Matti; Characterization of aberrant pathways across human cancers BMC systems biology 7 S1 S1 2013 Springer
Yang, Da; Sun, Yan; Hu, Limei; Zheng, Hong; Ji, Ping; Pecot, Chad V; Zhao, Yanrui; Reynolds, Sheila; Cheng, Hanyin; Rupaimoole, Rajesha; Integrated analyses identify a master microRNA regulatory network for the mesenchymal subtype in serous ovarian cancer Cancer cell 23 2 186-199 2013 Elsevier
Alarmo, Emma‐Leena; Havunen, Riikka; Häyrynen, Sergei; Penkki, Sanna; Ketolainen, Johanna; Nykter, Matti; Kallioniemi, Anne; Bone morphogenetic protein 4 regulates micro RNA expression in breast cancer cell lines in diverse fashion Genes, Chromosomes and Cancer 55 3 227-236 2016 Wiley Online Library
Yang, Jilong; Ylipää, Antti; Sun, Yan; Zheng, Hong; Chen, Kexin; Nykter, Matti; Trent, Jonathan; Ratner, Nancy; Lev, Dina C; Zhang, Wei; Genomic and molecular characterization of malignant peripheral nerve sheath tumor identifies the IGF1R pathway as a primary target for treatment Clinical cancer research 17 24 7563-7573 2011 AACR
Ruusuvuori, Pekka; Valkonen, Mira; Kartasalo, Kimmo; Visakorpi, Tapio; Latonen, Leena; Nykter, Matti; Histological modeling of prostate cancer Androgens 2016 42 2016 BioScientifica
Hieta, Reija; Studying androgen receptor gene aberrations in prostate cancer using targeted DNA and RNA sequencing panels 2018
Luoto, Suvi; Hermelo, Ismaïl; Vuorinen, Elisa; Hannus, Paavo; Kesseli, Juha; Nykter, Matti; Granberg, Kirsi; TMIC-30. COMPUTATIONAL CHARACTERIZATION OF SUPPRESSIVE IMMUNE MICROENVIRONMENTS IN GLIOBLASTOMA Neuro-oncology 20 Suppl 6 vi262 2018 Oxford University Press
Gundem, Gunes; Van Loo, Peter; Kremeyer, Barbara; Alexandrov, Ludmil B; Tubio, Jose MC; Papaemmanuil, Elli; Brewer, Daniel S; Kallio, Heini ML; Högnäs, Gunilla; Annala, Matti; The evolutionary history of lethal metastatic prostate cancer Nature 520 7547 353-357 2015 Nature Publishing Group
Uusi-Mäkelä, Meri IE; Barker, Harlan R; Bäuerlein, Carina A; Häkkinen, Tomi; Nykter, Matti; Rämet, Mika; Chromatin accessibility is associated with CRISPR-Cas9 efficiency in the zebrafish (Danio rerio) PloS one 13 4 e0196238 2018 Public Library of Science San Francisco, CA USA
Annala, MJ; Parker, BC; Zhang, W; Nykter, M; Fusion genes and their discovery using high throughput sequencing Cancer letters 340 2 192-200 2013 Elsevier
Scaravilli, Mauro; Afyounian, Ebrahim; Nykter, Matti; Visakorpi, Tapio; Latonen, Leena; Integrative proteomics of prostate cancer Current Opinion in Endocrine and Metabolic Research 2020 Elsevier
Bova, G Steven; Kallio, Heini ML; Annala, Matti; Kivinummi, Kati; Högnäs, Gunilla; Häyrynen, Sergei; Rantapero, Tommi; Kivinen, Virpi; Isaacs, William B; Tolonen, Teemu; Integrated clinical, whole-genome, and transcriptome analysis of multisampled lethal metastatic prostate cancer Molecular Case Studies 2 3 a000752 2016 Cold Spring Harbor Laboratory Press
Urbanucci, Alfonso; Barfeld, Stefan J; Kytölä, Ville; Itkonen, Harri M; Coleman, Ilsa M; Vodák, Daniel; Sjöblom, Liisa; Sheng, Xia; Tolonen, Teemu; Minner, Sarah; Androgen receptor deregulation drives bromodomain-mediated chromatin alterations in prostate cancer Cell reports 19 10 2045-2059 2017 Elsevier
Valkonen, Mira; Kartasalo, Kimmo; Liimatainen, Kaisa; Nykter, Matti; Latonen, Leena; Ruusuvuori, Pekka; Metastasis detection from whole slide images using local features and random forests Cytometry Part A 91 6 555-565 2017 Wiley Online Library
Yang, Jilong; Ylipää, Antti; Sun, Yan; Zheng, Hong; Chen, Kexin; Nykter, Matti; Trent, Jonathan; Ratner, Nancy; Lev, Dina C; Zhang, Wei; Editor's Note: Genomic and Molecular Characterization of Malignant Peripheral Nerve Sheath Tumor Identifies the IGF1R Pathway as a Primary Target for Treatment Clinical Cancer Research 25 10 3195-3195 2019 AACR
Hieta, Reija; Prolyl 4-hydroxylase: Structural and Functional Characterization of the Peptide-substrate-binding Domain of the Human Enzyme, and Cloning and Characterization of a Plant Enzyme with Unique Properties 2003 Oulun yliopisto
Kivinen, Virpi; Nykter, Matti; Yli-Harja, Olli; Shmulevich, Ilya; CLASSIFIER DESIGN WITH PATHWAY BASED FEATURE SELECTION Seventh International Workshop on Computational Systems Biology, WCSB 2010, June 16–18, 2010, Luxembourg
Scaravilli, Mauro; Porkka, Kati P; Brofeldt, Anniina; Annala, Matti; Tammela, Teuvo LJ; Jenster, Guido W; Nykter, Matti; Visakorpi, Tapio; MiR‐1247‐5p is overexpressed in castration resistant prostate cancer and targets MYCBP2 The Prostate 75 8 798-805 2015 Wiley Online Library
Veskimäe, Kristina; Staff, Synnöve; Tabaro, Francesco; Nykter, Matti; Isola, Jorma; Mäenpää, Johanna; Microarray analysis of differentially expressed genes in ovarian and fallopian tube epithelium from risk‐reducing salpingo‐oophorectomies Genes, Chromosomes and Cancer 54 5 276-287 2015 Wiley Online Library
Laajala, Teemu D; Jumppanen, Mikael; Huhtaniemi, Riikka; Fey, Vidal; Kaur, Amanpreet; Knuuttila, Matias; Aho, Eija; Oksala, Riikka; Westermarck, Jukka; Mäkelä, Sari; Optimized design and analysis of preclinical intervention studies in vivo Scientific reports 6 1 1-13 2016 Nature Publishing Group
Aherto, Hannareetta; Alahuhta, Janne; Eloranta, Juho; Eloranta, Sami; Hakala, Niina; Halonen, Ville; Heikkilä, Jussi; Hurjanen, Jukka; Koivulampi, Elina; Koivumäki, Lassi; Lausekielinen ohjelmointi 2009: ryhmä 1 (ma klo 14-16), harjoitus _
Granberg, Kirsi J; Annala, Matti; Lehtinen, Birgitta; Kesseli, Juha; Haapasalo, Joonas; Yli-Harja, Olli; Visakorpi, Tapio; Haapasalo, Hannu; Nykter, Matti; Zhang, Wei; Strong FGFR3 staining is a marker for FGFR3 fusions and poor prognosis in diffuse gliomas 2016 AACR
Turner, Kristen M; Sun, Youting; Ji, Ping; Granberg, Kirsi J; Bernard, Brady; Hu, Limei; Cogdell, David E; Zhou, Xinhui; Yli-Harja, Olli; Nykter, Matti; Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression Proceedings of the National Academy of Sciences 112 11 3421-3426 2015 National Acad Sciences
Kangas, Reeta; Törmäkangas, Timo; Fey, Vidal; Pursiheimo, Juha; Miinalainen, Ilkka; Alen, Markku; Kaprio, Jaakko; Sipilä, Sarianna; Säämänen, Anna-Marja; Kovanen, Vuokko; Aging and serum exomiR content in women-effects of estrogenic hormone replacement therapy Scientific Reports 7 42702 2017 Nature Publishing Group
Turpeinen, Hannu; Oksanen, Anna; Kivinen, Virpi; Kukkurainen, Sampo; Uusimäki, Annemari; Rämet, Mika; Parikka, Mataleena; Hytönen, Vesa P; Nykter, Matti; Pesu, Marko; Proprotein convertase subtilisin/kexin type 7 (PCSK7) is essential for the zebrafish development and bioavailability of transforming growth factor β1a (TGFβ1a) Journal of Biological Chemistry 288 51 36610-36623 2013 ASBMB
Cordova, Zuzet Martinez; Grönholm, Anna; Kytölä, Ville; Taverniti, Valentina; Hämäläinen, Sanna; Aittomäki, Saara; Niininen, Wilhelmiina; Junttila, Ilkka; Ylipää, Antti; Nykter, Matti; Myeloid cell expressed proprotein convertase FURIN attenuates inflammation Oncotarget 7 34 54392 2016 Impact Journals, LLC
Nykter, Matti; Feature selection for Lymphoma outcome prediction Proceedings of the 2nd TICSP workshop on computational systems biology. WCSB 51-52 2004
YLIPÄÄ, ANTTI; SARJALLISET MONTE CARLO-MENETELMÄT STOKAS-TISEN HODGKIN–HUXLEY-MALLIN PARAMETRIEN ESTI-MOINNISSA
Marttila, Saara; Jylhävä, Juulia; Nevalainen, Tapio; Nykter, Matti; Jylhä, Marja; Hervonen, Antti; Tserel, Liina; Peterson, Pärt; Hurme, Mikko; Transcriptional analysis reveals gender-specific changes in the aging of the human immune system PloS one 8 6 e66229 2013 Public Library of Science
Yang, Jilong; Du, Xiaoling; Chen, Kexin; Ylipää, Antti; Lazar, Alexander JF; Trent, Jonathan; Lev, Dina; Pollock, Raphael; Hao, Xishan; Hunt, Kelly; Genetic aberrations in soft tissue leiomyosarcoma Cancer letters 275 1 1-8 2009 Elsevier
Haapasalo, Joonas; Nordfors, Kristiina; Granberg, Kirsi J; Kivioja, Tomi; Nykter, Matti; Haapasalo, Hannu; Soini, Ylermi; From Cell Biology to Tissue Engineering
Valkonen, Mira; Nykter, Matti; Visakorpi, Tapio; Latonen, Leena; Health figures: an open source JavaScript library for health data visualization./Ledesma, Andres; Al-Musawi, Mohammed; Nieminen, Hannu. In: BMC Medical Informatics and Decision Making, Vol. 16, No. 1, 38, 22.03. 2016. Research output: Scientific-peer-review› Article BMC Medical Informatics and Decision Making 16 1 38 2016
Simão, Felipe A; Waterhouse, Robert M; Seppey, Mathieu; Ioannidis, Panagiotis; Kriventseva, Evgenia V; Zdobnov, Evgeny M; Genomic Utilities of BUSCO v3 Plant and Animal Genome XXVI Conference (January 13-17, 2018) PAG
Lund, Riikka J; Rahkonen, Nelly; Malonzo, Maia; Kauko, Leni; Emani, Maheswara Reddy; Kivinen, Virpi; Närvä, Elisa; Kemppainen, Esko; Laiho, Asta; Skottman, Heli; RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA+ and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells Stem cell reports 8 5 1442-1454 2017 Elsevier
Nykter, Matti; Signal processing methods and information approach to systems biology 2006 Tampere University of Technology
Laitinen, Virpi H; Wahlfors, Tiina; Saaristo, Leena; Rantapero, Tommi; Pelttari, Liisa M; Kilpivaara, Outi; Laasanen, Satu-Leena; Kallioniemi, Anne; Nevanlinna, Heli; Aaltonen, Lauri; HOXB13 G84E mutation in Finland: population-based analysis of prostate, breast, and colorectal cancer risk Cancer Epidemiology and Prevention Biomarkers 22 3 452-460 2013 AACR
Harjunpää, Antti; Nykter, Matti; Monni, Outi; Karjalainen-Lindsberg, Marja-Liisa; Hemmer, Samuli; Yli-Harja, Olli; Meri, Seppo; Leppä, Sirpa; The Use of Gene-Expression Profiling to Predict Outcome of Follicular Lymphoma Patients Treated with Rituximab and Chemotherapy. 2004 American Society of Hematology
Dufva, Olli; Pölönen, Petri; Keränen, Mikko A; Liuksiala, Thomas; Lin, Jake; Mehtonen, Juha; Häyrynen, Sergei; Granberg, Kirsi; Nykter, Matti; Lohi, Olli; Pan-Hematopoietic Cancer Gene Expression Analysis Identifies Immunologically Active Acute Myeloid Leukemia Subtypes 2016 American Society of Hematology Washington, DC
Hieta, Reija; Kukkola, Liisa; Permi, Perttu; Pirila, Paivi; Kivirikko, Kari I; Kilpelainen, Ilkka; Myllyharju, Johanna; PROTEIN STRUCTURE AND FOLDING-The Peptide-Substrate-binding Domain of Human Collagen Prolyl 4-Hydroxylases. BACKBONE ASSIGNMENTS, SECONDARY STRUCTURE, AND BINDING OF PROLINE-RICH PEPTIDES. Journal of Biological Chemistry 278 37 34966-34974 2003 Baltimore [etc.]
Annala, Matti; Taavitsainen, Sinja; Vandekerkhove, Gillian; Bacon, Jack VW; Beja, Kevin; Chi, Kim N; Nykter, Matti; Wyatt, Alexander W; Frequent mutation of the FOXA1 untranslated region in prostate cancer Communications biology 1 1 1-8 2018 Nature Publishing Group
Tarkkonen, Kati; Hieta, Reija; Kytölä, Ville; Nykter, Matti; Kiviranta, Riku; Comparative analysis of osteoblast gene expression profiles and Runx2 genomic occupancy of mouse and human osteoblasts in vitro Gene 626 119-131 2017 Elsevier
Ketola, Kirsi; Vainio, Paula; Halonen, Pasi; Kohonen, Pekka; Fey, Vidal; Grafström, Roland; Perälä, Merja; Kallioniemi, Olli; Iljin, Kristiina; Known drugs, disulfiram, monensin and salinomycin, induce oxidative stress in prostate cancer cells Stem Cells, Cancer and Metastasis (C4): Keystone Symposium 2011
Ylipää, Antti; Kivinummi, Kati; Annala, Matti; Kohvakka, Annika; Latonen, Leena; Scaravilli, Mauro; Kartasalo, Kimmo; Leppänen, Simo-Pekka; Karakurt, Serdar; Seppälä, Janne; Transcriptome sequencing reveals PCAT5-new ERG-regulated non-coding transcript in prostate cancer 2015 AACR
Jylhä, Antti; Aapola, Ulla; Nättinen, Janika; Nykter, Matti; Beuerman, Roger W; Uusitalo, Hannu MT; Tear proteome reveals predictive biomarkers for clinical improvement in glaucoma patients switching from preserved to preservative free medication Investigative Ophthalmology & Visual Science 56 7 3674-3674 2015 The Association for Research in Vision and Ophthalmology
Granberg, Kirsi J; Annala, Matti; Lehtinen, Birgitta; Kesseli, Juha; Haapasalo, Joonas; Ruusuvuori, Pekka; Yli-Harja, Olli; Visakorpi, Tapio; Haapasalo, Hannu; Nykter, Matti; Strong FGFR3 staining is a marker for FGFR3 fusions in diffuse gliomas Neuro-oncology 19 9 1206-1216 2017 Oxford University Press US
Pettinen, A; Mäkiraatikka, E; Manninen, T; Smolander, O; Ylipää, A; Hituri, K; Linne, M; Evaluation of deterministic and stochastic simulation tools for cellular signaling Front. Neuroinform. Conference Abstract: Neuroinformatics 2008
Haapasalo, Joonas; Nordfors, Kristiina; Granberg, Kirsi J; Kivioja, Tomi; Nykter, Matti; Haapasalo, Hannu; Soini, Ylermi; NRF2, DJ1 and SNRX1 and their prognostic impact in astrocytic gliomas 2018
Hieta, Reija; Kukkola, Liisa; Permi, Perttu; Pirilä, Päivi; Kivirikko, Kari I; Kilpeläinen, Ilkka; Myllyharju, Johanna; The Peptide-Substrate-binding Domain of Human Collagen Prolyl 4-Hydroxylases BACKBONE ASSIGNMENTS, SECONDARY STRUCTURE, AND BINDING OF PROLINE-RICH PEPTIDES Journal of Biological Chemistry 278 37 34966-34974 2003 ASBMB
Scaravilli, Mauro; Kohvakka, Annika; Ruusuvuori, Pekka; Afyounian, Ebrahim; Nykter, Matti; Visakorpi, Tapio; Latonen, Leena; Integrative proteomic analysis of prostate cancer reveals distinct regulation of RNA binding proteins during disease progression 2019 AACR
Lehtipuro, Suvi; Nykter, Matti; Granberg, Kirsi J; Modes of immunosuppression in glioblastoma microenvironment Oncotarget 10 9 920 2019 Impact Journals, LLC
Rantapero, Tommi; Wahlfors, Tiina; Kähler, Anna; Hultman, Christina; Lindberg, Johan; Tammela, Teuvo LJ; Nykter, Matti; Schleutker, Johanna; Wiklund, Fredrik; Inherited DNA Repair Gene Mutations in Men with Lethal Prostate Cancer Genes 11 3 314 2020 Multidisciplinary Digital Publishing Institute
Koski, MK; Hieta, R; Böllner, K; Bergmann, U; Kivirikko, KI; Myllyharju, J; Wierenga, RK; STRUCTURAL STUDIES OF HUMAN AND Chlamydomonas Reinhardtii PROLYL 4–HYDROXYLASES (P4Hs)
He, Tao; Surdez, Didier; Rantala, Juha K; Haapa-Paananen, Saija; Ban, Jozef; Kauer, Maximilian; Tomazou, Eleni; Fey, Vidal; Alonso, Javier; Kovar, Heinrich; High-throughput RNAi screen in Ewing sarcoma cells identifies leucine rich repeats and WD repeat domain containing 1 (LRWD1) as a regulator of EWS-FLI1 driven cell viability Gene 596 137-146 2017 Elsevier
Annala, Matti J; Waltering, Kati K; Ylipää, Antti; Kartasalo, Kimmo; Tuppurainen, Kirsi; Karakurt, Serdar; Latonen, Leena; Saramäki, Outi; Leppänen, Simo-Pekka; Seppälä, Janne; Integrative sequencing reveals novel alterations in untreated and castration resistant prostate cancer. 2013 AACR
Pölönen, Petri; Mehtonen, Juha; Lin, Jake; Liuksiala, Thomas; Häyrynen, Sergei; Teppo, Susanna; Mäkinen, Artturi; Kumar, Ashwini; Malani, Disha; Pohjolainen, Virva; Hemap: An interactive online resource for characterizing molecular phenotypes across hematologic malignancies Cancer research 79 10 2466-2479 2019 AACR
Kallio, Heini ML; Annala, Matti; Kivinummi, Kati; Högnäs, Gunilla; Gundem, Gunes; Wedge, David C; Van Loo, Peter; Heyn, Holger; Emmert-Buck, Michael R; Isaacs, William B; Clonal evolution of a lethal prostate cancer: Integrated whole genome analysis case study 2015 AACR
Laitinen, Virpi H; Rantapero, Tommi; Fischer, Daniel; Vuorinen, Elisa M; Tammela, Teuvo LJ; Practical Consortium; Wahlfors, Tiina; Schleutker, Johanna; Fine‐mapping the 2q37 and 17q11. 2‐q22 loci for novel genes and sequence variants associated with a genetic predisposition to prostate cancer International journal of cancer 136 10 2316-2327 2015 Wiley Online Library
Heinäniemi, Merja; Vuorenmaa, Tapio; Teppo, Susanna; Kaikkonen, Minna U; Bouvy-Liivrand, Maria; Mehtonen, Juha; Niskanen, Henri; Zachariadis, Vasilios; Laukkanen, Saara; Liuksiala, Thomas; Transcription-coupled genetic instability marks acute lymphoblastic leukemia structural variation hotspots Elife 5 e13087 2016 eLife Sciences Publications Limited
Nordfors, Kristiina; Haapasalo, Joonas; Mäkelä, Katri; Granberg, Kirsi J; Nykter, Matti; Korja, Miikka; Paavonen, Timo; Haapasalo, Hannu; Soini, Ylermi; Twist predicts poor outcome of patients with astrocytic glioma Journal of clinical pathology 68 11 905-912 2015 BMJ Publishing Group
Kesseli, Juha; Hahne, Lauri; Yli-Harja, Olli; Shmulevich, Ilya; Nykter, Matti; Structure-Dynamics Relationships in Biological Networks Information Processing and Biological Systems 153-178 2011 Springer
Lund, Riikka J; Emani, Maheswara Reddy; Barbaric, Ivana; Kivinen, Virpi; Jones, Mark; Baker, Duncan; Gokhale, Paul; Nykter, Matti; Lahesmaa, Riitta; Andrews, Peter W; Karyotypically abnormal human ESCs are sensitive to HDAC inhibitors and show altered regulation of genes linked to cancers and neurological diseases Stem Cell Research 11 3 1022-1036 2013 Elsevier
Erkkilä, Timo; Nykter, Matti; Lähdesmäki, Harri; Ahdesmäki, Miika; Yli-Harja, Olli; Testing for differential expression in simulated and real cdna microarray data using frequentist and bayesian methods Fifth International Workshop on Computational Systems Biology (WCSB08) 2008
Heinäniemi, Merja; Nykter, Matti; Kramer, Roger; Wienecke-Baldacchino, Anke; Sinkkonen, Lasse; Zhou, Joseph Xu; Kreisberg, Richard; Kauffman, Stuart A; Huang, Sui; Shmulevich, Ilya; Gene-pair expression signatures reveal lineage control Nature methods 10 6 577-583 2013 Nature Publishing Group
Kaukoniemi, Kirsi M; Rauhala, Hanna E; Scaravilli, Mauro; Latonen, Leena; Annala, Matti; Vessella, Robert L; Nykter, Matti; Tammela, Teuvo LJ; Visakorpi, Tapio; Epigenetically altered miR‐193b targets cyclin D1 in prostate cancer Cancer medicine 4 9 1417-1425 2015 Wiley Online Library
Ketola, Kirsi; Vainio, Paula; Fey, V; Kohonen, Pekka; Kallioniemi, O; Iljin, K; 234 Drugs with known pharmacological profiles, such as monensin, disulfiram and salinomycin, show cancer-selective inhibition of prostate cancer cell growth by increasing oxidative stress ejc supplements 5 8 61-62 2010
PS, Bujanda L; Prieto, J; Medina, JF; LaRusso, NF; Rupaimoole, R; Cogdell, D; Nykter, M; Broaddus, R; Rodriguez-Aguayo, C; Lopez-Berestein, G; PMC1347474. Tumour Biol 36 9 6823-31 2015
Kallio, Heini ML; Annala, Matti; Brofeldt, Anniina; Hieta, Reija; Kivinummi, Kati; Tammela, Teuvo; Nykter, Matti; Lilja, Hans G; Bova, G Steven; Visakorpi, Tapio; Next generation sequencing panels to predict response to hormonal therapy in prostate cancer Androgens 2016 42 2016 BioScientifica
Ruusuvuori, P; Nykter, M; Latonen, L; 712 Processing of stacked histological tissue sections in digital pathology European Journal of Cancer 51 S131 2015 Elsevier
Hieta, Reija; Myllyharju, Johanna; ENZYME CATALYSIS AND REGULATION-Cloning and characterization of a low molecular weight prolyl 4-hydroxylase from Arabidopsis thaliana. Effective hydroxylation of proline-rich, collagen-like, and Journal of Biological Chemistry 277 26 23965-23971 2002 Baltimore [etc.]
Ylipää, Antti; Hunt, Kelly K; Yang, Jilong; Lazar, Alexander JF; Torres, Keila E; Lev, Dina C; Nykter, Matti; Pollock, Raphael E; Trent, Jonathan; Zhang, Wei; Integrative genomic characterization and a genomic staging system for gastrointestinal stromal tumors Cancer 117 2 380-389 2011 Wiley Online Library
Litvak, Vladimir; Ramsey, Stephen A; Rust, Alistair G; Zak, Daniel E; Kennedy, Kathleen A; Lampano, Aaron E; Nykter, Matti; Shmulevich, Ilya; Aderem, Alan; Role of the transcription factor C/EBPδ in a regulatory circuit that discriminates between transient and persistent Toll-like receptor 4-induced signals Nature immunology 10 4 437 2009 NIH Public Access
Nurminen, Riikka; Rantapero, Tommi; Wong, Swee C; Fischer, Daniel; Lehtonen, Rainer; Tammela, Teuvo LJ; Nykter, Matti; Visakorpi, Tapio; Wahlfors, Tiina; Schleutker, Johanna; Expressional profiling of prostate cancer risk SNPs at 11q13. 5 identifies DGAT2 as a new target gene Genes, Chromosomes and Cancer 55 8 661-673 2016 Wiley Online Library
Mäntylä, S; Haapasalo, J; Ilvesaro, J; Nordfors, K; Isola, J; Haapasalo, H; Nykter, M; Granberg, K; P04. 78 Ultrarapid FGFR3 immunostaining for diagnosis of gliomas harboring FGFR3 gene fusions Neuro-oncology 20 Suppl 3 iii298 2018 Oxford University Press
Huvila, Jutta; Brandt, Annika; Rojas, Clarissa Rios; Pasanen, Salla; Talve, Lauri; HirsimÄKi, Pirkko; Fey, Vidal; KytÖMÄK, Leena; Saukko, Pekka; CarpÉN, Olli; Gene expression profiling of endometrial adenocarcinomas reveals increased apolipoprotein E expression in poorly differentiated tumors International Journal of Gynecologic Cancer 19 7 2009 BMJ Specialist Journals
Tuominen, Joonas; Häkkinen, Tomi; Annala, Matti; Kivinummi, Kati; Tammela, Teuvo; Latonen, Leena; Granberg, Kirsi; Visakorpi, Tapio; Nykter, Matti; Abstract A077: Chromatin state alterations in human prostate cancer progression 2018 AACR
Huang, Qilai; Whitington, Thomas; Gao, Ping; Lindberg, Johan F; Yang, Yuehong; Sun, Jielin; Väisänen, Marja-Riitta; Szulkin, Robert; Annala, Matti; Yan, Jian; A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding Nature genetics 46 2 126-135 2014 Nature Publishing Group
Kohvakka, Annika; Kivinummi, Kati; Kytola, Ville; Ylipaa, Antti; Annala, Matti; Urbanucci, Alfonso; Nykter, Matti; Visakorpi, Tapio; Expression of a novel androgen-regulated long noncoding RNA correlates with progression-free survival in prostate cancer patients Androgens 2016 42 2016 BioScientifica
Nordfors, Kristiina; Haapasalo, Joonas; Afyounian, Ebrahim; Tuominen, Joonas; Annala, Matti; Häyrynen, Sergei; Karhu, Ritva; Helén, Pauli; Lohi, Olli; Nykter, Matti; Whole-exome sequencing identifies germline mutation in TP53 and ATRX in a child with genomically aberrant AT/RT and her mother with anaplastic astrocytoma Molecular Case Studies 4 2 a002246 2018 Cold Spring Harbor Laboratory Press
Härmä, Harri; Rozwandowicz-Jansen, Anita; Martikkala, Eija; Frang, Heini; Hemmilä, Ilkka; Sahlberg, Niko; Fey, Vidal; Perälä, Merja; Hänninen, Pekka; A new simple cell-based homogeneous time-resolved fluorescence QRET technique for receptor-ligand interaction screening Journal of biomolecular screening 14 8 936-943 2009 Sage Publications Sage CA: Los Angeles, CA
Ylipää, Antti; Nykter, Matti; Trent, Jonathan; Zhang, Wei; Yli-Harja, Olli; A GENE COPY NUMBER BASED CLASSIFIER FOR GASTROINTESTINAL STROMAL TUMORS AND LEIOMYOSARCOMAS Sixth International Workshop on Computational Systems Biology, WCSB 2009, June 10-12, 2009, Aarhus, Denmark 21
Vainio, Paula; Gupta, Santosh; Ketola, Kirsi; Mirtti, Tuomas; Mpindi, John-Patrick; Kohonen, Pekka; Fey, Vidal; Perälä, Merja; Smit, Frank; Verhaegh, Gerald; Arachidonic acid pathway members PLA2G7, HPGD, EPHX2, and CYP4F8 identified as putative novel therapeutic targets in prostate cancer The American journal of pathology 178 2 525-536 2011 Elsevier
Valkonen, Mira; Ruusuvuori, Pekka; Kartasalo, Kimmo; Nykter, Matti; Visakorpi, Tapio; Latonen, Leena; Analysis of spatial heterogeneity in normal epithelium and preneoplastic alterations in mouse prostate tumor models Scientific reports 7 44831 2017 Nature Publishing Group
Moradi, Elaheh; Marttinen, Mikael; Häkkinen, Tomi; Hiltunen, Mikko; Nykter, Matti; Supervised pathway analysis of blood gene expression profiles in Alzheimer's disease Neurobiology of aging 84 98-108 2019 Elsevier
Laukkanen, Saara; Liuksiala, Thomas; Nykter, Matti; Heinäniemi, Merja; Lohi, Olli; Identification of Novel Drug Targets in T-Cell Acute Lymphoblastic Leukemia 2015 American Society of Hematology Washington, DC
Kohvakka, Annika; Shcherban, Anastasia; Kivinummi, Kati K; Annala, Matti; Urbanucci, Alfonso; Nykter, Matti; Visakorpi, Tapio; Discovery of an androgen-responsive long noncoding RNA that associates with progression of ERG-overexpressing prostate cancers 2018 AACR
Kartasalo, Kimmo; Latonen, Leena; Visakorpi, Tapio; Nykter, Matti; Ruusuvuori, Pekka; Benchmarking of algorithms for 3D tissue reconstruction 2016 IEEE International Conference on Image Processing (ICIP) 2360-2364 2016 IEEE
Pöllänen, Eija; Fey, Vidal; Törmäkangas, Timo; Ronkainen, Paula HA; Taaffe, Dennis R; Takala, Timo; Koskinen, Satu; Cheng, Sulin; Puolakka, Jukka; Kujala, Urho M; Power training and postmenopausal hormone therapy affect transcriptional control of specific co-regulated gene clusters in skeletal muscle Age 32 3 347-363 2010 Springer
Annala, M; Laurila, K; Lähdesmäki, H; Nykter, M; A Linear Model for Transcription Factor Binding Affinity Prediction in Protein Binding 2011
Högnäs, Gunilla; Kivinummi, Kati; Kallio, Heini ML; Hieta, Reija; Ruusuvuori, Pekka; Koskenalho, Antti; Kesseli, Juha; Tammela, Teuvo LJ; Riikonen, Jarno; Ilvesaro, Joanna; Feasibility of Prostate PAXgene Fixation for Molecular Research and Diagnostic Surgical Pathology The American Journal of Surgical Pathology 42 1 103-115 2018 Wolters Kluwer
Moore, Lynette M; Kivinen, Virpi; Liu, Yuexin; Annala, Matti; Cogdell, David; Liu, Xiuping; Liu, Chang‐Gong; Sawaya, Raymond; Yli‐Harja, Olli; Shmulevich, Ilya; Transcriptome and small RNA deep sequencing reveals deregulation of miRNA biogenesis in human glioma The Journal of pathology 229 3 449-459 2013 Wiley Online Library
Ylipää, Antti; Kivinummi, Kati; Kohvakka, Annika; Annala, Matti; Latonen, Leena; Scaravilli, Mauro; Kartasalo, Kimmo; Leppänen, Simo-Pekka; Karakurt, Serdar; Seppälä, Janne; Transcriptome sequencing reveals PCAT5 as a novel ERG-regulated long noncoding RNA in prostate cancer Cancer research 75 19 4026-4031 2015 AACR
Gubina, Nina; Naudi, Alba; Stefanatos, Rhoda; Jove, Mariona; Scialo, Filippo; Fernandez-Ayala, Daniel J; Rantapero, Tommi; Yurkevych, Ihor; Portero-Otin, Manuel; Nykter, Matti; Essential physiological differences characterize short-and long-lived strains of Drosophila melanogaster The Journals of Gerontology: Series A 74 12 1835-1843 2019 Oxford University Press US
Fey, Vidal; Wagner, Raik; Braütigam, Katharina; Wirtz, Markus; Hell, Rüdiger; Dietzmann, Angela; Leister, Dario; Oelmüller, Ralf; Pfannschmidt, Thomas; Retrograde plastid redox signals in the expression of nuclear genes for chloroplast proteins of Arabidopsis thaliana. Vol. 280 (2005) 5318–5328 Journal of Biological Chemistry 280 17 17572-17572 2005 ASBMB
Vainio, Paula; Lehtinen, Laura; Hilvo, Mika; Mirtti, T; Mpindi, John; Kohonen, Pekka; Fey, Vidal; Ketola, Kirsi; Alanen, K; Perälä, Merja; High-throughput screening for novel prostate cancer drug targets identifies PLA2G7 as a putative target for ERG oncogene positive cancers Metabolomics 2010: Breakthroughs in plant, microbial and human biology, clinical and nutritional research, and biomarker discovery 135 2010
Sarbu, Septimia; Shmulevich, Ilya; Yli-Harja, Olli; Nykter, Matti; Kesseli, Juha; Mapping dynamical states to structural classes for Boolean networks using a classification algorithm 2015 23rd European Signal Processing Conference (EUSIPCO) 160-164 2015 IEEE
Annala, Matti; Vandekerkhove, Gillian; Khalaf, Daniel; Taavitsainen, Sinja; Beja, Kevin; Warner, Evan W; Sunderland, Katherine; Kollmannsberger, Christian; Eigl, Bernhard J; Finch, Daygen; Circulating tumor DNA genomics correlate with resistance to abiraterone and enzalutamide in prostate cancer Cancer discovery 8 4 444-457 2018 AACR
Ruusuvuori, Pekka; Kartasalo, Kimmo; Valkonen, Mira; Valkonen, Masi; Visakorpi, Tapio; Nykter, Matti; Latonen, Leena; 3D reconstruction and quantitative analysis of histology for prostate cancer 2019 AACR
Johnson, DH; Galas, DJ; Nykter, M; Carter, GW; Price, ND; Shmulevich, I; Battail, G; Vikalo, H; Hassibi, B; Hassibi, A; O. Milenkovic Introduction to the Special Issue on Information Theory in Molecular Biology and Neuroscience 649
Yang, Da; Ylipää, Antti; Yang, Jilong; Hunt, Kelly; Pollock, Raphael; Trent, Jonathan; Yli-Harja, Olli; Shmulevich, Ilya; Nykter, Matti; Zhang, Wei; An integrated study of aberrant gene copy number and gene expression in GIST and LMS Technology in cancer research & treatment 9 2 171-177 2010 SAGE Publications Sage CA: Los Angeles, CA
Cordova, Zuzet; Grönholm, Anna; Kytölä, Ville; Taverniti, Valentina; Hämäläinen, Sanna; Niininen, Wilhelmiina; Junttila, Ilkka; Ylipää, Antti; Nykter, Matti; Pesu, Marko; Myeloid cell expressed proprotein convertase FURIN attenuates inflammation: P406 Scandinavian Journal of Immunology 83 5 2016
Nordfors, Kristiina; Haapasalo, Joonas; Afyounian, Ebrahim; Tuominen, Joonas; Annala, Matti; Häyrynen, Sergei; Karhu, Ritva; Helén, Pauli; Lohi, Olli; Nykter, Matti; 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 Cold Spring Harbor molecular case studies 4 3 2018 Cold Spring Harbor Laboratory Press
Sadot, Avital; Sarbu, Septimia; Kesseli, Juha; Amir-Kroll, Hila; Zhang, Wei; Nykter, Matti; Shmulevich, Ilya; Information-theoretic analysis of the dynamics of an executable biological model PloS one 8 3 e59303 2013 Public Library of Science
Häyrynen, Sergei; Nykter, Matti; Pan-cancer analysis of alternative splicing patterns and association to genomic aberrations 2016 AACR
Pekkala, Mira; Hieta, Reija; Kursula, Petri; Kivirikko, Kari I; Wierenga, Rik K; Myllyharju, Johanna; Crystallization of the proline-rich-peptide binding domain of human type I collagen prolyl 4-hydroxylase Acta Crystallographica Section D: Biological Crystallography 59 5 940-942 2003 International Union of Crystallography
Vainio, Paula; Ketola, Kirsi; Mpindi, John; Kilpinen, Sami; Kohonen, Pekka; Fey, Vidal; Björkman, Mari; Perälä, Merja; Kallioniemi, Olli; Iljin, Kristiina; High-throughput screening for novel prostate cancer drug targets 19th Annual BioCity Symposium Tumor Microenvironment in Cancer Progression 2009
Mäkiraatikka, Eeva; Manninen, Tiina; Saarinen, Antti; Ylipää, Antti; Teppola, Heidi; Hituri, Katri; Pettinen, Antti; Yli-Harja, Olli; Linne, Marja-Leena; Stochastic simulation tools for cellular signaling: survey, evaluation, and quantitative analysis Proceedings of the 2nd Conference on Foundations of Systems Biology in Engineering (FOSBE 2007), eds F. Allgöwer and M. Reuss (Stuttgart) 171-176 2007
Pollari, S; Leivonen, SK; Perälä, M; Fey, V; Käkönen, SM; Identification of MicroRNAs Inhibiting TGF-b-Induced IL-11 Production in Bone 2012
Ruusuvuori, Pekka; Valkonen, Mira; Kartasalo, Kimmo; Visakorpi, Tapio; Nykter, Matti; Latonen, Leena; Abstract B077: 3D reconstruction and machine learning-based analysis of prostate cancer from histologic images 2018 AACR
Lim, Kean Jin; Junttila, Sini; Fey, Vidal; Rudd, Stephen; Genomeless genomics in crop improvement Genomics-Assisted Crop Improvement 151-176 2007 Springer
Cangiano, M; Leung, H; Janssen, B; Nykter, M; Jenster, G; A transcription factor activity profile as a prognostic signature for androgen deprivation therapy resistance predisposition in prostate cancer patients European Urology Supplements 18 8 e3048-e3049 2019 Elsevier
Kong, Lingjia; Aho, Kaisa-Leena; Granberg, Kirsi; Lund, Riikka; Järvenpää, Laura; Seppälä, Janne; Gokhale, Paul; Leinonen, Kalle; Hahne, Lauri; Mäkelä, Jarno; ESTOOLS Data@ Hand: human stem cell gene expression resource nature methods 10 9 814-815 2013 Nature Publishing Group
Urbanucci, Alfonso; Barfeld, Stefan; Kytola, Ville; Vodak, Daniel; Sjoblom, Liisa; Tolonen, Teemu; Minner, Sarah; Burdelski, Christoph; Kivinummi, Kati K; Kregel, Steven; Chromatin relaxation is a feature of advanced prostate cancer Androgens 2016 42 2016 BioScientifica
Harjunpää, Antti; Taskinen, Minna; Nykter, Matti; Karjalainen‐Lindsberg, Marja‐Liisa; Nyman, Heidi; Monni, Outi; Hemmer, Samuli; Yli‐Harja, Olli; Hautaniemi, Sampsa; Meri, Seppo; Differential gene expression in non‐malignant tumour microenvironment is associated with outcome in follicular lymphoma patients treated with rituximab and CHOP British journal of haematology 135 1 33-42 2006 Wiley Online Library
Hongisto, Vesa; Jernström, Sandra; Fey, Vidal; Mpindi, John-Patrick; Sahlberg, Kristine Kleivi; Kallioniemi, Olli; Perälä, Merja; High-throughput 3D screening reveals differences in drug sensitivities between culture models of JIMT1 breast cancer cells PloS one 8 10 e77232 2013 Public Library of Science
Oeyen, Jan Philip; Baa-Puyoulet, Patrice; Benoit, Joshua B; Beukeboom, Leo W; Bornberg-Bauer, Erich; Buttstedt, Anja; Calevro, Federica; Cash, Elizabeth I; Chao, Hsu; Charles, Hubert; Sawfly genomes reveal evolutionary acquisitions that fostered the mega-radiation of parasitoid and eusocial Hymenoptera Genome Biology and Evolution 2020 Oxford Univ. Press
Simão, Felipe A; Waterhouse, Robert M; Ioannidis, Panagiotis; Kriventseva, Evgenia V; Zdobnov, Evgeny M; BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Bioinformatics 31 19 3210-3212 2015 Oxford University Press
Manninen, Tiina; Makiraatikka, Eeva; Ylipaa, Antti; Pettinen, Antti; Leinonen, Kalle; Linne, Marja-Leena; Discrete stochastic simulation of cell signaling: comparison of computational tools 2006 International Conference of the IEEE Engineering in Medicine and Biology Society 2013-2016 2006 IEEE
Soininen, Tero; Nykter, Matti; Kesseli, Juha; PERTURBATION PROPAGATION IN BOOLEAN NETWORKS WITH LOCAL STRUCTURES The 10th International Workshop on Computational Systems Biology, WCSB 2013, June 10-12, Tampere, Finland 92
Steiner, Sebastian; Dietzel, Lars; Schröter, Yvonne; Fey, Vidal; Wagner, Raik; Pfannschmidt, Thomas; The role of phosphorylation in redox regulation of photosynthesis genes psaA and psbA during photosynthetic acclimation of mustard Molecular plant 2 3 416-429 2009 Elsevier
Latonen, Leena; Afyounian, Ebrahim; Jylhä, Antti; Nättinen, Janika; Aapola, Ulla; Annala, Matti; Kivinummi, Kati; Tammela, Teuvo; Beuerman, Roger W; Uusitalo, Hannu; Abstract A020: Integrative analysis of the proteome in primary and advanced prostate cancer 2018 AACR
Larjo, Antti; Pettinen, Antti; Kong, Lingjia; Yaroslavsky, Leonid; Äijö, Tarmo; Kim, Harold D; O'Shea, Erin K; Chowdhury, Sharif; Lia, Kang; Millera, Eric D; Journal Club is held in room TB219 (19.01.-29.06. 2010) about once a week on Tuesdays at 14.15. Changes are possible. Order and exact date after next 2 forthcoming presentation are temporary and for reference only. Credits policy: 70% attendance of one semaster+ 2 presentation (in total) could gain 3 credits, 70% attendance of one semaster+ 1 presentation (in total) could gain 2 credits BMC Systems Biology 3 100 2009
Leppä, Sirpa; Taskinen, Minna; Sommarhem, Antti; Elonen, Erkki; Nykter, Matti; Monni, Outi; Timonen, Tuomo; Hautaniemi, Sampsa; Karjalainen-Lindsberg, Marja-Liisa; Meri, Seppo; STAT5 Signaling Is Associated with the Outcome of Follicular and Mantle Cell Lymphoma Patients Treated with Immunochemotherapy. 2007 American Society of Hematology
DeAmbrogio, Enzo; Doerge, Rebecca W; Ejeta, Gebisa; Ersoz, Elhan S; Feuillet, Catherine; Fey, Vidal; Foolad, Majid R; Friedt, Wolfgang; Ganal, Martin W; Gardiner, Susan; IA 50131-0552, USA Genomics-Assisted Crop Improvement 495 Springer
Duffy, David J; Krstic, Aleksandar; Halasz, Melinda; Schwarzl, Thomas; Fey, Dirk; Iljin, Kristiina; Mehta, Jai Prakash; Killick, Kate; Whilde, Jenny; Turriziani, Benedetta; Integrative omics reveals MYCN as a global suppressor of cellular signalling and enables network-based therapeutic target discovery in neuroblastoma Oncotarget 6 41 43182 2015 Impact Journals, LLC
Patel, Lalit R; Nykter, Matti; Chen, Kexin; Zhang, Wei; Cancer genome sequencing: understanding malignancy as a disease of the genome, its conformation, and its evolution Cancer letters 340 2 152-160 2013 Elsevier
Havunen, Riikka; Santos, João M; Sorsa, Suvi; Rantapero, Tommi; Lumen, Dave; Siurala, Mikko; Airaksinen, Anu J; Cervera-Carrascon, Victor; Tähtinen, Siri; Kanerva, Anna; Abscopal effect in non-injected tumors achieved with cytokine-armed oncolytic adenovirus Molecular Therapy-Oncolytics 11 109-121 2018 Elsevier
Lin, Jake; Kreisberg, Richard; Kallio, Aleksi; Dudley, Aimée M; Nykter, Matti; Shmulevich, Ilya; May, Patrick; Autio, Reija; POMO-Plotting Omics analysis results for Multiple Organisms BMC genomics 14 1 1-10 2013 BioMed Central
Uusitalo, Hannu MT; Jylhä, Antti; Nättinen, Janika; Vaajanen, Anu; Härkönen, Miihkali; Nykter, Matti; Zhou, Lei; Beuerman, Roger W; Conjunctival tissue proteome demonstrates abnormal expression of wound response proteins in glaucoma patients Investigative Ophthalmology & Visual Science 57 12 2924-2924 2016 The Association for Research in Vision and Ophthalmology
Saarinen, A; Ylipää, A; Yli-Harja, O; Linne, M; Computational methods for stochastic modeling and parameter fitting of models based on Hodgkin-Huxley formalism Front. Neuroinform. Conference Abstract: Neuroinformatics 2008
Yli-Harja, Olli; Ylipää, Antti; Nykter, Matti; Zhang, Wei; Cancer systems biology: signal processing for cancer research Chinese journal of cancer 30 4 221 2011 BioMed Central
Afyounian, Ebrahim; Annala, Matti; Nykter, Matti; Segmentum: a tool for copy number analysis of cancer genomes BMC bioinformatics 18 1 215 2017 Springer
Zdobnov, Evgeny M; Tegenfeldt, Fredrik; Kuznetsov, Dmitry; Waterhouse, Robert M; Simao, Felipe A; Ioannidis, Panagiotis; Seppey, Mathieu; Loetscher, Alexis; Kriventseva, Evgenia V; OrthoDB v9. 1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs Nucleic acids research 45 D1 D744-D749 2017 Oxford University Press
Abeshouse, Adam; Ahn, Jaeil; Akbani, Rehan; Ally, Adrian; Amin, Samirkumar; Andry, Christopher D; Annala, Matti; Aprikian, Armen; Armenia, Joshua; Arora, Arshi; The molecular taxonomy of primary prostate cancer Cell 163 4 1011-1025 2015 Elsevier
Huvila, J; Brandt, A; Fey, V; Junni, P; Talve, L; Soini, J; Rudd, S; Carpen, O; Saukko, P; Grenman, S; 0713: Gene Expression Profiling of Well and Poorly Differentiated Endometrial Adenocarcinoma International Journal of Gynecologic Cancer 16 Suppl 3 800-800 2006 BMJ Specialist Journals
Nykter, Matti; Yli-Harja, Olli; Shmulevich, Ilya; Normalized compression distance for gene expression analysis Workshop on Genomic Signal Processing and Statistics (GENSIPS)(May 2005) 2005
Keskiaho, Katriina; Hieta, Reija; Sormunen, Raija; Myllyharju, Johanna; Chlamydomonas reinhardtii has multiple prolyl 4-hydroxylases, one of which is essential for proper cell wall assembly The Plant Cell 19 1 256-269 2007 Am Soc Plant Biol
Simão, Felipe A; Machida, Ryuichiro; Misof, Bernhard; Niehuis, Oliver; Zdobnov, Evgeny M; Sequencing of an Extremophilic Ice Crawler: Galloisiana yuasai Plant and Animal Genome XXVI Conference (January 13-17, 2018) PAG
Granberg, Kirsi Johanna; Annala, Matti; Jaatinen, Serafiina; Haapasalo, Joonas; Yli-Harja, Olli; Haapasalo, Hannu; Zhang, Wei; Nykter, Matti; Gatekeeper inactivation drives glioma progression into secondary glioblastoma 2018 AACR
Manni, Mosè; Simao, Felipe A; Robertson, Hugh M; Gabaglio, Marco A; Waterhouse, Robert M; Misof, Bernhard; Niehuis, Oliver; Szucsich, Nikolaus U; Zdobnov, Evgeny M; The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea augens: A Key Reference Hexapod for Studying the Emergence of Insect Innovations Genome biology and evolution 12 1 3534-3549 2020 Oxford University Press
Liuksiala, Thomas; Granberg, Kirsi; Häyrynen, Sergei; Mehtonen, Juha; Pölönen, Petri; Teppo, Susanna; Lin, Jake; Laukkanen, Saara; May, Patrick; Nykter, Matti; Mapping the Gene Expression Diversity Across Hematological and Lymphoid Malignancies 2015 American Society of Hematology Washington, DC
Latonen, Leena; Afyounian, Ebrahim; Jylha, Antti; Nattinen, Janika; Aapola, Ulla; Annala, Matti; Kivinummi, Kati; Tammela, Teuvo; Beuerman, Roger W; Uusitalo, Hannu; Integrative analysis of the proteome in primary and advanced prostate cancer. CANCER RESEARCH 78 16 34-34 2018 AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA …
Nykter, M; Bioinformatics in tear proteome Acta Ophthalmologica 93 2015 Wiley Online Library
Luoto, Suvi; Hermelo, Ismaïl; Vuorinen, Elisa M; Hannus, Paavo; Kesseli, Juha; Nykter, Matti; Granberg, Kirsi J; Computational characterization of suppressive immune microenvironments in glioblastoma Cancer research 78 19 5574-5585 2018 AACR
Chen, Kexin; Cheng, Hanyin; Zhang, Lina; Cogdell, David E; Zheng, Hong; Schetter, Aaron J; Nykter, Matti; Harris, Curtis C; Hamilton, Stanley R; Zhang, Wei; Circulating plasma MiR-141 is a novel biomarker for metastatic colon cancer and predicts poor prognosis 2011 AACR
Viiri, Leena E; Rantapero, Tommi; Kiamehr, Mostafa; Alexanova, Anna; Oittinen, Mikko; Viiri, Keijo; Niskanen, Henri; Nykter, Matti; Kaikkonen, Minna U; Aalto-Setälä, Katriina; Extensive reprogramming of the nascent transcriptome during iPSC to hepatocyte differentiation Scientific reports 9 1 1-12 2019 Nature Publishing Group
Manninen, Tapio; Huttunen, Heikki; Ruusuvuori, Pekka; Nykter, Matti; Leukemia prediction using sparse logistic regression PloS one 8 8 e72932 2013 Public Library of Science
Fey, Vidal; Wagner, Raik; Braütigam, Katharina; Wirtz, Markus; Hell, Rüdiger; Dietzmann, Angela; Leister, Dario; Oelmüller, Ralf; Pfannschmidt, Thomas; Retrograde plastid redox signals in the expression of nuclear genes for chloroplast proteins of Arabidopsis thaliana Journal of Biological Chemistry 280 7 5318-5328 2005 ASBMB
Portero-Otin, Manuel; Nykter, Matti; Lushchak, Oleh; Navas, Placido; Pamplona, Reinald; Sanz, Alberto; Essential physiological differences characterise short-and long-lived strains of Drosophila melanogaster 2018
Lin, Jake; Kramna, Lenka; Autio, Reija; Hyöty, Heikki; Nykter, Matti; Cinek, Ondrej; Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples BMC genomics 18 1 378 2017 Springer
Veskimäe, K; Staff, S; Grönholm, A; Pesu, M; Laaksonen, M; Nykter, M; Isola, J; Mäenpää, J; Assessment of PARP protein expression in epithelial ovarian cancer by ELISA pharmacodynamic assay and immunohistochemistry Tumor Biology 37 9 11991-11999 2016 Springer
Kriventseva, Evgenia V; Tegenfeldt, Fredrik; Petty, Tom J; Waterhouse, Robert M; Simao, Felipe A; Pozdnyakov, Igor A; Ioannidis, Panagiotis; Zdobnov, Evgeny M; OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software Nucleic acids research 43 D1 D250-D256 2015 Oxford University Press
Annala, Matti; Kivinummi, Kati; Tuominen, Joonas; Karakurt, Serdar; Granberg, Kirsi; Latonen, Leena; Ylipää, Antti; Sjöblom, Liisa; Ruusuvuori, Pekka; Saramäki, Outi; Recurrent SKIL-activating rearrangements in ETS-negative prostate cancer Oncotarget 6 8 6235 2015 Impact Journals, LLC
Cheng, Hanyin; Zhang, Lina; Cogdell, David E; Zheng, Hong; Schetter, Aaron J; Nykter, Matti; Harris, Curtis C; Chen, Kexin; Hamilton, Stanley R; Zhang, Wei; Circulating plasma MiR-141 is a novel biomarker for metastatic colon cancer and predicts poor prognosis PloS one 6 3 e17745 2011 Public Library of Science
Vandekerkhove, Gillian; Todenhöfer, Tilman; Annala, Matti; Struss, Werner J; Wong, Amanda; Beja, Kevin; Ritch, Elie; Brahmbhatt, Sonal; Volik, Stanislav V; Hennenlotter, Jörg; Circulating tumor DNA reveals clinically actionable somatic genome of metastatic bladder cancer Clinical cancer research 23 21 6487-6497 2017 AACR
Ylipaa, Antti; Nykter, Matti; Shmulevich, Ilya; Zhang, Wei; An investigation of the regulation of cellular processes in glioblastoma multiforme via integrated analysis of paired microRNA and gene expression profiles 2010 AACR
Chua, Corrine Yingxuan; Liu, Yuexin; Granberg, Kirsi J; Hu, Limei; Haapasalo, Hannu; Annala, Matti J; Cogdell, David E; Verploegen, Maartje; Moore, Lynette M; Fuller, Gregory N; IGFBP2 potentiates nuclear EGFR–STAT3 signaling Oncogene 35 6 738-747 2016 Nature Publishing Group
Simão, Felipe A; Utilities of OrthoDB and BUSCO Plant and Animal Genome XXVI Conference (January 13-17, 2018) PAG
Sarbu, Septimia; Kesseli, Juha; Nykter, Matti; Quantifying the relationship between the structure and the dynamics of random Boolean networks from time series data Ninth International Workshop on Computational Systems Biology, WCSB 2012, June 4-6, Ulm, Germany 75 2012
Niemistö, Antti; Nykter, Matti; Aho, Tommi; Jalovaara, Henna; Marjanen, Kalle; Ahdesmäki, Miika; Ruusuvuori, Pekka; Tiainen, Mikko; Linne, Marja-Leena; Yli-Harja, Olli; Computational methods for estimation of cell cycle phase distributions of yeast cells EURASIP Journal on Bioinformatics and Systems Biology 2007 1-9 2007 Springer
Valkonen, Mira; Ruusuvuori, Pekka; Kartasalo, Kimmo; Nykter, Matti; Visakorpi, Tapio; Latonen, Leena; Analysis of spatial heterogeneity in normal epithelium and preneoplastic alterations in mouse prostate tumor models–Supplementary material
Ketola, Kirsi; Vainio, P; Halonen, P; Kohonen, P; Fey, V; Grafström, R; Perälä, M; Kallioniemi, O; Iljin, K; FOCUSED CONFERENCE GROUP: PW04-ANTIOXIDANTS AS THERAPEUTIC TARGETS DRUGS WITH KNOWN PHARMACOLOGICAL PROFILES, SUCH AS MONENSIN, DISULFIRAM AND SALINOMYCIN, SHOW CANCER-SELECTIVE INHIBITION OF PROSTATE CANCER CELL GROWTH BY INCREASING OXIDATIVE STRESS: Paper No.: 2361 Basic & Clinical Pharmacology & Toxicology 107 2010
Gao, Qingsong; Liang, Wen-Wei; Foltz, Steven M; Mutharasu, Gnanavel; Jayasinghe, Reyka G; Cao, Song; Liao, Wen-Wei; Reynolds, Sheila M; Wyczalkowski, Matthew A; Yao, Lijun; Driver fusions and their implications in the development and treatment of human cancers Cell reports 23 1 227-238. e3 2018 Elsevier
Iljin, Kristiina; Ketola, Kirsi; Vainio, Paula; Halonen, Pasi; Kohonen, Pekka; Fey, Vidal; Grafström, Roland C; Perälä, Merja; Kallioniemi, Olli; High-throughput cell-based screening of 4910 known drugs and drug-like small molecules identifies disulfiram as an inhibitor of prostate cancer cell growth Clinical Cancer Research 15 19 6070-6078 2009 AACR
Annala, Matti; Laurila, Kirsti; Lähdesmäki, Harri; Nykter, Matti; A linear model for transcription factor binding affinity prediction in protein binding microarrays PloS one 6 5 e20059 2011 Public Library of Science
Ylipää, A; Kivinummi, KK; Annala, MJ; Kartasalo, K; Latonen, L; Leppänen, SP; Scaravilli, M; Zhang, W; Tammela, TLJ; Visakorpi, T; 299 Novel prostate cancer specific transcripts identified using RNA-seq European Urology Supplements 13 1 e299 2014 Elsevier
Nykter, Matti; Ruusuvuori, Pekka; Carlberg, Carsten; Yli-Harja, Olli; Seventh International Workshop on Computational Systems Biology, WCSB 2010, June 16–18, 2010, Luxembourg
Mäki-Marttunen, Tuomo; Acimovic, Jugoslava; Nykter, Matti; Kesseli, Juha; Ruohonen, Keijo; Yli-Harja, Olli; Linne, Marja-Leena; Information diversity in structure and dynamics of simulated neuronal networks Frontiers in Computational Neuroscience 5 26 2011 Frontiers
Li, Xia; Liu, Yuexin; Granberg, Kirsi J; Wang, Qinhao; Moore, Lynette M; Ji, Ping; Gumin, Joy; Sulman, Erik P; Calin, George A; Haapasalo, Hannu; Two mature products of MIR-491 coordinate to suppress key cancer hallmarks in glioblastoma Oncogene 34 13 1619-1628 2015 Nature Publishing Group
Veskimäe, K; Scaravilli, M; Niininen, W; Karvonen, H; Jaatinen, S; Nykter, M; Visakorpi, T; Mäenpää, J; Ungureanu, D; Staff, S; Expression analysis of platinum sensitive and resistant epithelial ovarian cancer patient samples reveals new candidates for targeted therapies Translational oncology 11 5 1160-1170 2018 Elsevier
Kivinen, Virpi; Nykter, Matti; Ylipää, Antti; Hu, Limei; Cogdell, David; Hunt, Kelly; Zhang, Wei; Yli-Harja, Olli; RELATIONSHIPS BETWEEN GENETIC ABERRATIONS AND GENE EXPRESSION LEVELS IN GASTROINTESTINAL TRACT TUMORS
Saralahti, Anni; Harjula, Sanna-Kaisa; Partanen, Essi; Rantapero, Tommi; Granberg, Kirsi; Lohi, Olli; Nykter, Matti; Rounioja, Samuli; Parikka, Mataleena; Ramet, Mika; A forward genetic screen for zebrafish genes involved in pneumococcal infection Scandinavian Journal of Immunology 83 5 384-384 2016 WILEY-BLACKWELL 111 RIVER ST, HOBOKEN 07030-5774, NJ USA
Hieta, Reija; Myllyharju, Johanna; Cloning and characterization of a low molecular weight prolyl 4-hydroxylase from Arabidopsis thaliana effective hydroxylation of proline-rich, collagen-like, and hypoxia-inducible transcription factor α-like peptides Journal of Biological Chemistry 277 26 23965-23971 2002 ASBMB
Mehtonen, Juha; Pölönen, Petri; Häyrynen, Sergei; Dufva, Olli; Lin, Jake; Liuksiala, Thomas; Granberg, Kirsi; Lohi, Olli; Hautamäki, Ville; Nykter, Matti; Data-driven characterization of molecular phenotypes across heterogeneous sample collections Nucleic acids research 47 13 e76-e76 2019 Oxford University Press
Zhang, W; Nykter, M; Kexin, C; Featuring the Guest Editor Special issue Genome Sequencing. 2013
Kaikkonen, Elina; Rantapero, Tommi; Zhang, Qin; Taimen, Pekka; Laitinen, Virpi; Kallajoki, Markku; Jambulingam, Dhanaprakash; Ettala, Otto; Knaapila, Juha; Boström, Peter J; ANO7 is associated with aggressive prostate cancer International journal of cancer 143 10 2479-2487 2018 Wiley Online Library
Zhang, Wei; Nykter, Matti; Chen, Kexin; Next generation sequencing applications in cancer research. Cancer letters 340 2 149 2013
Galas, David J; Nykter, Matti; Carter, Gregory W; Price, Nathan D; Shmulevich, Ilya; Set-based complexity and biological information arXiv preprint arXiv:0801.4024 2008
Wyatt, Alexander W; Azad, Arun A; Volik, Stanislav V; Annala, Matti; Beja, Kevin; McConeghy, Brian; Haegert, Anne; Warner, Evan W; Mo, Fan; Brahmbhatt, Sonal; Genomic alterations in cell-free DNA and enzalutamide resistance in castration-resistant prostate cancer JAMA oncology 2 12 1598-1606 2016 American Medical Association
Valkonen, Mira; Isola, Jorma; Ylinen, Onni; Muhonen, Ville; Saxlin, Anna; Tolonen, Teemu; Nykter, Matti; Ruusuvuori, Pekka; Cytokeratin-Supervised Deep Learning for Automatic Recognition of Epithelial Cells in Breast Cancers Stained for ER, PR, and Ki-67 IEEE Transactions on Medical Imaging 39 2 534-542 2019 IEEE
Luoto, Suvi; Kesseli, Juha; Nykter, Matti; Granberg, Kirsi J; Different immune cell responses are associated with glioblastoma subclassification and typical genetic alterations 2016 AACR
Heinäniemi, Merja; Nykter, Matti; Kramer, Roger; Wienecke-Baldacchino, Anke; Sinkkonen, Lasse; Zhou, Joseph Xu; Kreisberg, Richard; Kauffman, Stuart A; Huang, Sui; Shmulevich, Ilya; Gene pair signatures in cell type transcriptomes reveal lineage control
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 Springer
Pfannschmidt, Thomas; Schütze, Katia; Fey, Vidal; Sherameti, Irena; Oelmüller, Ralf; Chloroplast redox control of nuclear gene expression—a new class of plastid signals in interorganellar communication Antioxidants and Redox Signaling 5 1 95-101 2003 Mary Ann Liebert, Inc.
Niemistö, Antti; Nykter, Matti; Aho, Tommi; Jalovaara, Henna; Marjanen, Kalle; Ahdesmäki, Miika; Ruusuvuori, Pekka; Tiainen, Mikko; Linne, Marja-Leena; Yli-Harja, Olli; Distribution estimation of synchronized budding yeast population Proceedings of the winter international synposium on Information and communication technologies 1-6 2004
Nykter, Matti; Price, Nathan D; Larjo, Antti; Aho, Tommi; Kauffman, Stuart A; Yli-Harja, Olli; Shmulevich, Ilya; Critical networks exhibit maximal information diversity in structure-dynamics relationships Physical review letters 100 5 058702 2008 APS
Fey, Vidal; Allahverdiyeva, Yagut; Aro, Eva-Mari; Pfannschmidt, Thomas; Photosynthetic redox control during light-quality acclimation in Sinapis alba has spe Mediation of Photosynthetic Redox Signals in the Regulation of Plant Gene Expression 18 2961-2969 2001
Ruusuvuori, Pekka; Lin, Jake; Scott, Adrian C; Tan, Zhihao; Sorsa, Saija; Kallio, Aleksi; Nykter, Matti; Yli-Harja, Olli; Shmulevich, Ilya; Dudley, Aimée M; Quantitative analysis of colony morphology in yeast BioTechniques 56 1 18-27 2014 Future Science
Ruusuvuori, Pekka; Valkonen, Mira; Nykter, Matti; Visakorpi, Tapio; Latonen, Leena; Feature-based analysis of mouse prostatic intraepithelial neoplasia in histological tissue sections Journal of pathology informatics 7 2016 Wolters Kluwer--Medknow Publications
Tuominen, Joonas I; Afyounian, Ebrahim; Tabaro, Francesco; Häkkinen, Tomi; Shcherban, Anastasia; Annala, Matti; Kivinummi, Kati; Tammela, Teuvo; Kesseli, Juha; Latonen, Leena; Abstract LB-096: Chromatin alterations in human prostate cancer 2019 AACR
Koski, M Kristian; Hieta, Reija; Hirsilä, Maija; Rönkä, Anna; Myllyharju, Johanna; Wierenga, Rik K; The crystal structure of an algal prolyl 4-hydroxylase complexed with a proline-rich peptide reveals a novel buried tripeptide binding motif Journal of Biological Chemistry 284 37 25290-25301 2009 ASBMB
Teppo, Susanna; Laukkanen, Saara; Liuksiala, Thomas; Nordlund, Jessica; Oittinen, Mikko; Teittinen, Kaisa; Grönroos, Toni; St-Onge, Pascal; Sinnett, Daniel; Syvänen, Ann-Christine; Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemia Genome research 26 11 1468-1477 2016 Cold Spring Harbor Lab
Anantharajan, Jothi; Koski, M Kristian; Kursula, Petri; Hieta, Reija; Bergmann, Ulrich; Myllyharju, Johanna; Wierenga, Rik K; The structural motifs for substrate binding and dimerization of the α subunit of collagen prolyl 4-hydroxylase Structure 21 12 2107-2118 2013 Elsevier
Ylipää, Antti; Yli-Harja, Olli; Zhang, Wei; Nykter, Matti; FROM GENETIC MARKERS TO CHARACTERISTIC REGULATORS IN SOFT-TISSUE SARCOMAS Seventh International Workshop on Computational Systems Biology, WCSB 2010, June 16–18, 2010, Luxembourg
Sattari, M; Kohvakka, A; Urhonen, H; Moradi, E; Rauhala, H; Nykter, M; Latonen, L; Bova, GS; Kesseli, J; Visakorpi, T; Identification of novel long non-coding RNA based biomarkers in prostate cancer European Urology Supplements 18 8 e3078 2019 Elsevier
Rane, Jayant K; Ylipää, Antti; Adamson, Rachel; Mann, Vincent M; Simms, Matthew S; Collins, Anne T; Visakorpi, Tapio; Nykter, Matti; Maitland, Norman J; Construction of therapeutically relevant human prostate epithelial fate map by utilising miRNA and mRNA microarray expression data British journal of cancer 113 4 611-615 2015 Nature Publishing Group
Latonen, Leena; Nykter, Matti; Visakorpi, Tapio; Proteomics of prostate cancer–revealing how cancer cells master their messy genomes Oncoscience 5 7-8 216 2018 Impact Journals, LLC
Pekkala, Mira; Hieta, Reija; Bergmann, Ulrich; Kivirikko, Kari I; Wierenga, Rik K; Myllyharju, Johanna; The peptide-substrate-binding domain of collagen prolyl 4-hydroxylases is a tetratricopeptide repeat domain with functional aromatic residues Journal of Biological Chemistry 279 50 52255-52261 2004 ASBMB
Ruusuvuori, Pekka; Valkonen, Mira; Kartasalo, Kimmo; Visakorpi, Tapio; Nykter, Matti; Latonen, Leena; 3D reconstruction and machine learning-based analysis of prostate cancer from histologic images. CANCER RESEARCH 78 16 120-121 2018 AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA …
Simão, Felipe A; Seppey, Mathieu; Waterhouse, Robert M; Manni, Mose; Ioannidis, Panagiotis; Klioutchnikov, Guennadi; Sierro, Nicolas; Ivanov, Nikolai V; Kriventseva, Evgenia V; Zdobnov, Evgeny M; BUSCO v3: Expanded Plant Coverage and Utilities Beyond Benchmarking. Plant and Animal Genome XXVI Conference (January 13-17, 2018) 2018 PAG
Rane, Jayant K; Scaravilli, Mauro; Ylipää, Antti; Pellacani, Davide; Mann, Vincent M; Simms, Matthew S; Nykter, Matti; Collins, Anne T; Visakorpi, Tapio; Maitland, Norman J; MicroRNA expression profile of primary prostate cancer stem cells as a source of biomarkers and therapeutic targets European urology 67 1 7-10 2015 Elsevier
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 Nature Publishing Group
Herberts, Cameron; Murtha, Andrew J; Fu, Simon; Wang, Gang; Schönlau, Elena; Xue, Hui; Lin, Dong; Gleave, Anna; Yip, Steven; Angeles, Arkhjamil; Activating AKT1 and PIK3CA Mutations in Metastatic Castration-Resistant Prostate Cancer European Urology 2020 Elsevier
Kangas, Reeta; Fey, Vidal; Pursiheimo, Juha; Alen, Markku; Kaprio, Jaakko; Sipilä, Sarianna; Säämänen, Anna-Marja; Kovanen, Vuokko; Pöllänen, Eija; Hormonal Status As Determinant Of Serum Exosomal MicroRNA Content In Pre-And Postmenopausal Women: 2278 Board# 3 June 2, 315 PM-515 PM Medicine & Science in Sports & Exercise 48 5S 634 2016 LWW
Nykter, Matti; Lähdesmäki, Harri; Lahesmaa, Riitta; Riikka J. Lund,* Nelly Rahkonen, Maia Malonzo, 2, 5 Leni Kauko, Maheswara Reddy Emani, Virpi Kivinen, 3 Elisa Närvä, Esko Kemppainen, Asta Laiho, Heli Skottman, 3 Outi Hovatta, 4 Omid Rasool
Campbell, Sharon E; Stone, William; Zhang, Wei; Taylor, Ellen; Nykter, Matti; Lippman, Scott; Krishnan, Koyamangalath; Alpha-and gamma-tocopherol regulate different sets of genes in the human colon cancer cell line, HCT-116. 2006 AACR
Polonen, P; Mehtonen, J; Lin, J; Liuksiala, T; Hayrinen, S; Teppo, S; May, P; Hautamaki, V; Granberg, K; Lohi, O; MOLECULAR CLASSIFICATION AND COMPARATIVE ANALYSIS OF ACUTE MYELOID LEUKEMIA MULTI-OMICS DATA USING THE INTERACTIVE HEMAP RESOURCE HAEMATOLOGICA 101 205-205 2016 FERRATA STORTI FOUNDATION VIA GIUSEPPE BELLI 4, 27100 PAVIA, ITALY
He, Tao; Haapa-Paananen, Saija; Kaminskyy, VO; Kohonen, P; Fey, Vidal; Zhivotovsky, B; Kallioniemi, Olli; Perälä, Merja; Inhibition of the mitochondrial pyrimidine biosynthesis enzyme dihydroorotate dehydrogenase by doxorubicin and brequinar sensitizes cancer cells to TRAIL-induced apoptosis Oncogene 33 27 3538-3549 2014 Nature Publishing Group
Parker, Brittany C; Annala, Matti J; Cogdell, David E; Granberg, Kirsi J; Sun, Yan; Ji, Ping; Li, Xia; Gumin, Joy; Zheng, Hong; Hu, Limei; The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma The Journal of clinical investigation 123 2 2013 Am Soc Clin Investig
Waterhouse, Robert M; Seppey, Mathieu; Simão, Felipe A; Zdobnov, Evgeny M; Using BUSCO to assess insect genomic resources Insect Genomics 59-74 2019 Springer
Kohvakka, Annika; Sattari, Mina; Shcherban, Anastasia; Annala, Matti; Urbanucci, Alfonso; Kesseli, Juha; Tammela, Teuvo LJ; Kivinummi, Kati; Latonen, Leena; Nykter, Matti; AR and ERG drive the expression of prostate cancer specific long noncoding RNAs Oncogene 1-11 2020 Nature Publishing Group
Gronroos, T; Teppo, S; Mehtonen, J; Laukkanen, S; Liuksiala, T; Nykter, M; Heinaniemi, M; Lohi, O; OVEREXPRESSION OF PTP4A3 IN ETV6-RUNX1 ACUTE LEUKEMIA HAEMATOLOGICA 101 347-347 2016 FERRATA STORTI FOUNDATION VIA GIUSEPPE BELLI 4, 27100 PAVIA, ITALY
Kartasalo, Kimmo; Latonen, Leena; Vihinen, Jorma; Visakorpi, Tapio; Nykter, Matti; Ruusuvuori, Pekka; Comparative analysis of tissue reconstruction algorithms for 3D histology Bioinformatics 34 17 3013-3021 2018 Oxford University Press
Nykter, Matti; Kesseli, Juha; Shmulevich, Ilya; Yli-Harja, Olli; Analyzing Boolean network dynamics using attractor basin structure 4th TICSP WORKSHOP ON COMPUTATIONAL SYSTEMS BIOLOGY, WCSB 2006 69 2006 Citeseer
Karvonen, Hanna; Chiron, David; Niininen, Wilhelmiina; Ek, Sara; Jerkeman, Mats; Moradi, Elaheh; Nykter, Matti; Heckman, Caroline A; Kallioniemi, Olli; Murumägi, Astrid; Crosstalk between ROR1 and BCR pathways defines novel treatment strategies in mantle cell lymphoma Blood advances 1 24 2257-2268 2017 American Society of Hematology
Laitinen, Virpi H; Akinrinade, Oyediran; Rantapero, Tommi; Tammela, Teuvo LJ; Wahlfors, Tiina; Schleutker, Johanna; Germline copy number variation analysis in Finnish families with hereditary prostate cancer The Prostate 76 3 316-324 2016 Wiley Online Library
Warner, Evan; Yip, Steven; Annala, Matti; Wang, Gang; Angeles, Arkhjamil; Beigi, Arshia; Schönlau, Elena; Wong, Amanda; Taavitsainen, Sinja; Vandekerkhove, Gillian; Abstract PR09: Frequency and etiology of ctDNA-positive metastatic prostate cancer with BRCA2, ATM, or CDK12 mutations 2020 AACR
Marttila, Saara; Kananen, Laura; Häyrynen, Sergei; Jylhävä, Juulia; Nevalainen, Tapio; Hervonen, Antti; Jylhä, Marja; Nykter, Matti; Hurme, Mikko; Ageing-associated changes in the human DNA methylome: genomic locations and effects on gene expression BMC genomics 16 1 179 2015 Springer
Waterhouse, Robert; Tenan, Mirna; Simão, Felipe A; Ioannidis, Panagiotis; Kriventseva, Evgenia V; Zdobnov, Evgeny M; Large-scale gene functional inference through orthology F1000Research 5 2016
Rane, Jayant K; Pellacani, Davide; Droop, Alastair P; Ylipää, Antti; Stower, Michael J; Simms, Matthew S; Mann, Vincet M; Visakorpi, Tapio; Collins, Anne T; Maitland, Norman J; Elucidation of dynamic prostate epithelial hierarchy: Insights into transcriptional and epigenetic regulatory mechanisms 2012 AACR
Åkerfelt, Malin; Björk, Johanna; Mirtti, Tuomas; Fey, Vidal; Sistonen, Lea; Nees, Matthias; Abstract A46: Opposing effects of heat shock factors 1 and 2 on prostate cancer invasion 2013 AACR
Pollari, Sirkku; Leivonen, Suvi-Katri; Perälä, Merja; Fey, Vidal; Käkönen, Sanna-Maria; Kallioniemi, Olli; Identification of microRNAs inhibiting TGF-β-induced IL-11 production in bone metastatic breast cancer cells PloS one 7 5 e37361 2012 Public Library of Science
Manninen, Tiina; Saarinen, Antti; Ylipää, Antti; Linne, Marja-Leena; Yli-Harja, Olli; Ruohonen, Keijo; Sequential Monte Carlo based maximum likelihood estimation for calcium binding reactions Proc. of the 2nd Conference on Foundations of Systems Biology in Engineering (FOSBE 2007) 189-194 2007
Rotenberg, Dorith; Baumann, Aaron A; Ben-Mahmoud, Sulley; Christiaens, Olivier; Dermauw, Wannes; Ioannidis, Panagiotis; Jacobs, Chris GC; Jentzsch, Iris M Vargas; Oliver, Jonathan E; Poelchau, Monica F; Genome-enabled insights into the biology of thrips as crop pests bioRxiv 2020 Cold Spring Harbor Laboratory
Bucher, Elmar; Kohonen, Pekka; Fey, Vidal; Mpindi, John; Sara, Henri; Pisto, Tommi; Edgren, Henrik; Kilpinen, Sami; Ojala, Kalle; Tiikkainen, Pekka; A link between multiple high throughput technology datasets 9th International Conference on Systems Biology, ICSB2008 186 2008
Lin, Jake; Kimura, Bryn Y; Oikarinen, Sami; Nykter, Matti; Bioinformatics Assembling and Assessment of Novel Coxsackievirus B1 Genome The Human Virome 261-272 2018 Springer
Leppae, Sirpa; Taskinen, Minna; Sommarhem, Antti; Elonen, Erkki; Nykter, Matti; Monni, Outi; Timonen, Tuomo; Hautaniemi, Sampsa; Karjalainen-Lindsberg, Marja-Liisa; Meri, Seppo; STAT5 signaling is associated with the outcome of follicular and mantle cell lymphoma patients treated with immunochemotherapy. BLOOD 110 11 773A-773A 2007 AMER SOC HEMATOLOGY 1900 M STREET. NW SUITE 200, WASHINGTON, DC 20036 USA
Neafsey, Daniel E; Waterhouse, Robert M; Abai, Mohammad R; Aganezov, Sergey S; Alekseyev, Max A; Allen, James E; Amon, James; Arcà, Bruno; Arensburger, Peter; Artemov, Gleb; Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes Science 347 6217 2015 American Association for the Advancement of Science
Harjula, Sanna-Kaisa E; Saralahti, Anni K; Ojanen, Markus JT; Rantapero, Tommi; Uusi-Mäkelä, Meri IE; Nykter, Matti; Lohi, Olli; Parikka, Mataleena; Rämet, Mika; Characterization of immune response against Mycobacterium marinum infection in the main hematopoietic organ of adult zebrafish (Danio rerio) Developmental & Comparative Immunology 103 103523 2020 Elsevier
Holmes, Kristen M; Annala, Matti; Chua, Corrine YX; Dunlap, Sarah M; Liu, Yuexin; Hugen, Niek; Moore, Lynette M; Cogdell, David; Hu, Limei; Nykter, Matti; 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 Proceedings of the National Academy of Sciences 109 9 3475-3480 2012 National Acad Sciences
Litvak, Vladimir; Ramsey, Stephen A; Rust, Alistair G; Zak, Daniel E; Kennedy, Kathleen A; Lampano, Aaron E; Nykter, Matti; Shmulevich, Ilya; Aderem, Alan; Function of C/EBPδ in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals Nature immunology 10 4 437-443 2009 Nature Publishing Group
Martínez, Alejandra Rodríguez; Vuorinen, Elisa M; Shcherban, Anastasia; Rajala, Nina K; Nykter, Matti; Kallioniemi, Anne; ZNF414 as a functionally relevant transcription factor in pancreatic and breast cancer cells 2018 AACR
Sjöblom, Liisa; Saramäki, Outi; Annala, Matti; Leinonen, Katri; Nättinen, Janika; Tolonen, Teemu; Wahlfors, Tiina; Nykter, Matti; Bova, G Steven; Schleutker, Johanna; Microseminoprotein-beta expression in different stages of prostate cancer PloS one 11 3 e0150241 2016 Public Library of Science San Francisco, CA USA
Tsafou, Kalliopi; Katschnig, Anna Maria; Radic-Sarikas, Branka; Mutz, Cornelia Noëlle; Iljin, Kristiina; Schwentner, Raphaela; Kauer, Maximilian O; Mühlbacher, Karin; Aryee, Dave NT; Westergaard, David; Identifying the druggable interactome of EWS-FLI1 reveals MCL-1 dependent differential sensitivities of Ewing sarcoma cells to apoptosis inducers Oncotarget 9 57 31018 2018 Impact Journals, LLC
Hautamäki, V; Nykter, M; Heinäniemi, M; Nykter, Matti; Data-driven characterization of molecular phenotypes across heterogenous sample collections
Ketola, Kirsi; Vainio, Paula; Fey, Vidal; Kallioniemi, Olli; Iljin, Kristiina; Monensin is a potent inducer of oxidative stress and inhibitor of androgen signaling leading to apoptosis in prostate cancer cells Molecular cancer therapeutics 9 12 3175-3185 2010 AACR
Leinonen, Katri A; Saramäki, Outi R; Furusato, Bungo; Kimura, Takahiro; Takahashi, Hiroyuki; Egawa, Shin; Suzuki, Hiroyoshi; Keiger, Kerri; Hahm, Sung Ho; Isaacs, William B; Loss of PTEN is associated with aggressive behavior in ERG-positive prostate cancer Cancer Epidemiology and Prevention Biomarkers 22 12 2333-2344 2013 AACR
Nättinen, Janika; Jylhä, Antti; Aapola, Ulla; Enríquez-de-Salamanca, Amalia; Pinto-Fraga, José; López-Miguel, Alberto; González-García, María J; Stern, Michael E; Calonge, Margarita; Zhou, Lei; Topical fluorometholone treatment and desiccating stress change inflammatory protein expression in tears The ocular surface 16 1 84-92 2018 Elsevier
Du, Xiaoling; Yang, Jilong; Ylipää, Antti; Zhu, Ze; Genomic amplification and high expression of EGFR are key targetable oncogenic events in malignant peripheral nerve sheath tumor Journal of hematology & oncology 6 1 1-12 2013 BioMed Central
Wyatt, AW; Annala, M; Beja, K; Parimi, S; Vandekerkhove, G; Warner, E; Zulfiqar, M; Finch, D; Oja, C; Vergidis, J; Genomic alterations in circulating tumor DNA (ctDNA) are associated with clinical outcomes in treatment-naive metastatic castration-resistant prostate cancer (mCRPC) patients commencing androgen receptor (AR)-targeted therapy Annals of Oncology 27 suppl_6 2016 Oxford University Press
Iljin, Kristiina; Vainio, Paula; Ketola, Kirsi; Björkman, M; Kohonen, Pekka; Mpindi, John; Fey, Vidal; Mirtti, T; Alanen, K; Perälä, Merja; High-throughput compound and siRNA screening to identify novel treatment options for ERG oncogene positive prostate cancers BIT’s 8th Annual Congress of International Drug Discovery Science and Technology, IDDST 2010 2010
Hytonen, Vesa P; Nykter, Matti; Uusimaki, Marko; Ramet, Mika; Parikka, Mataleena; Hannu Turpeinen, Anna Oksanen, Virpi 2013
Ylipaa, Antti; Nykter, Matti; Kivinen, Virpi; Hu, Limei; Cogdell, David; Hunt, Kelly; Zhang, Wei; Yli-Harja, Olli; Finding common aberrations in array CGH data 2008 3rd International Symposium on Communications, Control and Signal Processing 1199-1204 2008 IEEE
Liuksiala, Thomas Edward; Blood Cancer Lineage Identification: A Machine Learning Approach 2015
Dottorini, Tania; Neafsey, Daniel E; Waterhouse, Robert M; Abai, Mohammad R; Aganezov, Sergey S; Alekseyev, Max A; Allen, James E; Amon, James; Arcà, Bruno; Arensburger, Peter; Highly evolvable malaria vectors: the genomes of 16 anopheles mosquitoes Science 347 6217 2015
Jylhä, Antti; Nattinen, Janika; Aapola, Ulla; Nykter, Matti; Beuerman, Roger W; Uusitalo, Hannu MT; Tear proteome provides basis for patient stratification after switching to a unpreserved glaucoma medication Investigative Ophthalmology & Visual Science 58 8 2115-2115 2017 The Association for Research in Vision and Ophthalmology
Sjöblom, L; Saramäki, O; Annala, M; Leinonen, K; Nättinen, J; Tolonen, T; Wahlfors, T; Nykter, M; Bova, G; Schleutker, J; 1074 Microseminoprotein-beta expression in different stages of prostate cancer European Urology Supplements 15 3 e1074 2016 Elsevier
Hoy, Marjorie A; Waterhouse, Robert M; Wu, Ke; Estep, Alden S; Ioannidis, Panagiotis; Palmer, William J; Pomerantz, Aaron F; Simao, Felipe A; Thomas, Jainy; Jiggins, Francis M; Genome sequencing of the phytoseiid predatory mite Metaseiulus occidentalis reveals completely atomized Hox genes and superdynamic intron evolution Genome biology and evolution 8 6 1762-1775 2016 Oxford University Press
Boström, P; Fey, V; Kaikkonen, E; Lamminen, T; Laitinen, A; Mirtti, T; Koskinen, I; Salminen, A; Taimen, P; Schleutker, J; Utilization of next-generation sequencing techniques to investigate markers for chemosensitivity in bladder cancer patients treated with neoadjuvant chemotherapy prior to radical cystectomy European Urology Supplements 16 3 e909-e910 2017 Elsevier
Yang, Meng; Topaloglu, Umit; Petty, W Jeffrey; Pagni, Matthew; Foley, Kristie L; Grant, Stefan C; Robinson, Mac; Bitting, Rhonda L; Thomas, Alexandra; Alistar, Angela T; Circulating mutational portrait of cancer: manifestation of aggressive clonal events in both early and late stages Journal of hematology & oncology 10 1 1-13 2017 BioMed Central
Zhang; Nykter, Matti; Kexin, Chen; Featuring the guest editor special issue genome sequencing 2013 ELSEVIER IRELAND LTD ELSEVIER HOUSE, BROOKVALE PLAZA, EAST PARK SHANNON, CO …
Ketola, Kirsi; Viitala, Miro; Kohonen, Pekka; Fey, Vidal; Culig, Zoran; Kallioniemi, Olli; Iljin, Kristiina; High-throughput cell-based compound screen identifies pinosylvin methyl ether and tanshinone IIA as inhibitors of castration-resistant prostate cancer Journal of molecular biochemistry 5 1 12 2016 Europe PMC Funders
Nykter, Matti; Hunt, Kelly K; Pollock, Raphael E; El-Naggar, Adel K; Taylor, Ellen; Shmulevich, Ilya; Yli-Harja, Olli; Zhang, Wei; Unsupervised analysis uncovers changes in histopathologic diagnosis in supervised genomic studies Technology in cancer research & treatment 5 2 177-182 2006 SAGE Publications Sage CA: Los Angeles, CA
Kriventseva, Evgenia V; Kuznetsov, Dmitry; Tegenfeldt, Fredrik; Manni, Mosè; Dias, Renata; Simão, Felipe A; Zdobnov, Evgeny M; OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs Nucleic acids research 47 D1 D807-D811 2019 Oxford University Press
Fey, Vidal; Wagner, Raik; Bräutigam, Katharina; Pfannschmidt, Thomas; Photosynthetic redox control of nuclear gene expression Journal of Experimental Botany 56 416 1491-1498 2005 Oxford University Press
Vainio, Paula; Ketola, K; Mpindi, JP; Kilpinen, S; Kohonen, P; Fey, V; Gupta, S; Perälä, M; Kallioniemi, O; Iljin, K; FOCUSED CONFERENCE GROUP: P19-GENERAL SESSION-ONCOLOGY HIGH-THROUGHPUT SCREENING FOR NOVEL PROSTATE CANCER DRUG TARGETS: Paper No.: 2744 Basic & Clinical Pharmacology & Toxicology 107 2010
Kallio, Heini ML; Hieta, Reija; Latonen, Leena; Brofeldt, Anniina; Annala, Matti; Kivinummi, Kati; Tammela, Teuvo L; Nykter, Matti; Isaacs, William B; Lilja, Hans G; Constitutively active androgen receptor splice variants AR-V3, AR-V7 and AR-V9 are co-expressed in castration-resistant prostate cancer metastases British journal of cancer 119 3 347-356 2018 Nature Publishing Group
Warner, Evan; Yip, Steven; Annala, Matti; Wang, Gang; Angeles, Arkhjamil; Beigi, Arshia; Schonlau, Elena; Wong, Amanda; Taavitsainen, Sinja; Vandekerkhove, Gillian; Frequency and etiology of ctDNA-positive metastatic prostate cancer with BRCA2, ATM, or CDK12 mutations CLINICAL CANCER RESEARCH 26 11 30-30 2020 AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA …
Jylhä, Antti; Nättinen, Janika; Aapola, Ulla; Mikhailova, Alexandra; Nykter, Matti; Zhou, Lei; Beuerman, Roger; Uusitalo, Hannu; Comparison of iTRAQ and SWATH in a clinical study with multiple time points Clinical proteomics 15 1 24 2018 BioMed Central
Galas, David J; Nykter, Matti; Carter, Gregory W; Price, Nathan D; Shmulevich, Ilya; Biological information as set-based complexity IEEE Transactions on Information Theory 56 2 667-677 2010 IEEE
Liuksiala, Thomas; Teittinen, Kaisa; Granberg, Kirsi; Heinäniemi, Merja; Annala, Matti; Ylipää, Antti; Mäki, Markku; Nykter, Matti; Lohi, Olli; Large scale gene expression analysis identifies key oncogenic pathways across hematological malignancies 2014 AACR
Fey, Vidal; Mediation of Photosynthetic Redox Signals in the Regulation of Plant Gene Expression 2005 Citeseer
Kytola, Ville; Topaloglu, Umit; Miller, Lance D; Bitting, Rhonda L; Goodman, Michael M; DAgostino Jr, Ralph B; Desnoyers, Rodwige J; Albright, Carol; Yacoub, George; Qasem, Shadi A; 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 2017 Ivyspring International Publisher
Annala, Matti; Struss, Werner J; Warner, Evan W; Beja, Kevin; Vandekerkhove, Gillian; Wong, Amanda; Khalaf, Daniel; Seppälä, Irma-Liisa; So, Alan; Lo, Gregory; Treatment outcomes and tumor loss of heterozygosity in germline DNA repair–deficient prostate cancer European urology 72 1 34-42 2017 Elsevier
Harjula, Sanna-Kaisa; Saralahti, Anni; Ojanen, Markus; Mathie, Heather; Halfpenny, Nicholas; Rantapero, Tommi; Granberg, Kirsi; Nykter, Matti; Lohi, Olli; Parikka, Mataleena; Genes affecting mycobacterial infection in zebrafish: P802 Scandinavian Journal of Immunology 83 5 2016
Kesseli, Juha; Ribeiro, Andre S; Nykter, Matti; Measuring Information Propagation and Processing in Biological Systems Open Information Management: Applications of Interconnectivity and Collaboration 190-226 2009 IGI Global
Annala, Matti; Kivinummi, Kati; Leinonen, Katri; Tuominen, Joonas; Zhang, Wei; Visakorpi, Tapio; Nykter, Matti; DOT1L‐HES6 fusion drives androgen independent growth in prostate cancer EMBO molecular medicine 6 9 1121-1123 2014
Manni, Mosè; Simao, Felipe A; Robertson, Hugh M; Gabaglio, Marco A; Waterhouse, Robert M; Misof, Bernhard; Niehuis, Oliver; Szucsich, Nikolaus U; Zdobnov, Evgeny M; Supplementary Materials for The genome of the blind soil-dwelling and ancestrally wingless dipluran Campodea augens, a key reference hexapod for studying the emergence of insect innovations
Hyysalo, Anu; Ristola, Mervi; Mäkinen, Meeri E-L; Häyrynen, Sergei; Nykter, Matti; Narkilahti, Susanna; Laminin α5 substrates promote survival, network formation and functional development of human pluripotent stem cell-derived neurons in vitro Stem cell research 24 118-127 2017 Elsevier
Hermelo, I; Haapasalo, J; Nordfors, K; Haapasalo, H; Nykter, M; Granberg, K; P01. 143 Unravelling the immune response components landscape in diffuse gliomas using immunophenotyping approach Neuro-oncology 20 Suppl 3 iii265 2018 Oxford University Press
Zhu, Lingyu; Kesseli, Juha; Nykter, Matti; Huttunen, Heikki; Predicting Gene Expression Levels from Histone Modification Signals with Convolutional Recurrent Neural Networks EMBEC & NBC 2017 555-558 2017 Springer
Mäki-Marttunen, Tuomo; Kesseli, Juha; Kauffman, Stuart; Yli-Harja, Olli; Nykter, Matti; Of the complexity of Boolean network state trajectories Proceedings of the Eighth International Workshop on Computational Systems Biology, WCSB 6-8 2011
Ulman, Vladimír; Svoboda, David; Nykter, Matti; Kozubek, Michal; Ruusuvuori, Pekka; Virtual cell imaging: A review on simulation methods employed in image cytometry Cytometry Part A 89 12 1057-1072 2016 Wiley Online Library
Tammela, T; Kallio, H; Annala, M; Brofeldt, A; Hieta, R; Kivinummi, K; Nykter, M; Lilja, H; Bova, G; Visakorpi, T; Neoadjuvant hormonal therapies induce the expression of AR transcript variants European Urology Supplements 16 3 e255-e256 2017 Elsevier
Lindfors, Katri; Lin, Jake; Lee, Hye-Seung; Hyöty, Heikki; Nykter, Matti; Kurppa, Kalle; Liu, Edwin; Koletzko, Sibylle; Rewers, Marian; Hagopian, William; Metagenomics of the faecal virome indicate a cumulative effect of enterovirus and gluten amount on the risk of coeliac disease autoimmunity in genetically at risk children: the TEDDY study Gut 2019 BMJ Publishing Group
Dufva, Olli; Pölönen, Petri; Brück, Oscar; Keränen, Mikko A; Mehtonen, Juha; Siitonen, Sanna M; Leivonen, Suvi-Katri; Meriranta, Leo; Leppa, Sirpa; Nykter, Matti; Immunogenomic landscape of hematological malignancies Blood 132 Supplement 1 2596-2596 2018 American Society of Hematology
Grönroos, Toni; Teppo, Susanna; Mehtonen, Juha; Laukkanen, Saara; Liuksiala, Thomas; Nykter, Matti; Heinäniemi, Merja; Lohi, Olli; Overexpression of PTP4A3 in ETV6-RUNX1 acute lymphoblastic leukemia Leukemia research 54 1-6 2017 Elsevier
Wyatt, Alexander W; Annala, Matti; Aggarwal, Rahul; Beja, Kevin; Feng, Felix; Youngren, Jack; Foye, Adam; Lloyd, Paul; Nykter, Matti; Beer, Tomasz M; Concordance of circulating tumor DNA and matched metastatic tissue biopsy in prostate cancer JNCI: Journal of the National Cancer Institute 109 12 2017 Oxford University Press
Nykter, Matti; Kesseli, Juha; Shmulevich, Ilya; Dynamical systems analysis of stack filters arXiv preprint arXiv:0907.4551 2009
Ylipää, Antti; Yli-Harja, Olli; Zhang, Wei; Nykter, Matti; A systems biological approach to identify key transcription factors and their genomic neighborhoods in human sarcomas Chinese journal of cancer 30 1 27 2011 BioMed Central
Ylipää, Antti; Zhang, Wei; Nykter, Matti; A characterization of pathway aberrations across human cancers 2012 AACR
Veskimae, K; Staff, S; Tabaro, F; Nykter, M; Isola, J; Maenpaa, J; MICROARRAY ANALYSIS OF DIFFERENTIALLY EXPRESSED GENES IN OVARIAN AND FALLOPIAN TUBE EPITHELIUM FROM RISK-REDUCING SALPINGO-OOPHORECTOMIES PUBLISHED: GENES CHROMOSOMES CANCER. 2015 FEB 23 INTERNATIONAL JOURNAL OF GYNECOLOGICAL CANCER 25 9 576-576 2015 LIPPINCOTT WILLIAMS & WILKINS TWO COMMERCE SQ, 2001 MARKET ST, PHILADELPHIA …
Yang, Jilong; Annala, Matti; Ji, Ping; Wang, Guowen; Zheng, Hong; Codgell, David; Du, Xiaoling; Fang, Zhiwei; Sun, Baocun; Nykter, Matti; Recurrent LRP1-SNRNP25 and KCNMB4-CCND3 fusion genes promote tumor cell motility in human osteosarcoma Journal of hematology & oncology 7 1 76 2014 Springer
Tammela, T; Latonen, L; Afyounian, E; Jylhä, A; Nättinen, J; Aapola, U; Annala, M; Kivinummi, K; Beuerman, R; Uusitalo, H; Integrative analysis of the proteome in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression European Urology Supplements 17 2 e159 2018 Elsevier
Cantisani, Maria Carmela; Parascandolo, Alessia; Perälä, Merja; Allocca, Chiara; Fey, Vidal; Sahlberg, Niko; Merolla, Francesco; Basolo, Fulvio; Laukkanen, Mikko O; Kallioniemi, Olli Pekka; A loss-of-function genetic screening identifies novel mediators of thyroid cancer cell viability Oncotarget 7 19 28510 2016 Impact Journals, LLC
Koski, M Kristian; Hieta, Reija; Böllner, Claudia; Kivirikko, Kari I; Myllyharju, Johanna; Wierenga, Rik K; The active site of an algal prolyl 4-hydroxylase has a large structural plasticity Journal of Biological Chemistry 282 51 37112-37123 2007 ASBMB
Tanjore Ramanathan, Jayendrakishore; Lehtipuro, Suvi; Sihto, Harri; Tóvári, József; Reiniger, Lilla; Téglási, Vanda; Moldvay, Judit; Nykter, Matti; Haapasalo, Hannu; Le Joncour, Vadim; Prostate‐specific membrane antigen expression in the vasculature of primary lung carcinomas associates with faster metastatic dissemination to the brain Journal of Cellular and Molecular Medicine 2019 Wiley Online Library
Annala, M; Kivinummi, K; Tuominen, J; Latonen, L; Ylipää, A; Saramäki, O; Kaukoniemi, KM; Karakurt, S; Yli-Harja, O; Vessella, RL; 165 Recurrent SKIL-activating rearrangements in ETS-negative prostate cancer European Urology Supplements 2 14 e165 2015
Rantapero, Tommi; Bioinformatic analysis of next-generation sequencing data 2012
Kukkola, Liisa; Hieta, Reija; Kivirikko, Kari I; Myllyharju, Johanna; Identification and characterization of a third human, rat, and mouse collagen prolyl 4-hydroxylase isoenzyme Journal of Biological Chemistry 278 48 47685-47693 2003 ASBMB
Mehtonen, J; Polonen, P; Lin, J; Liuksiala, T; Hayrynen, S; Teppo, S; May, P; Hautamaki, V; Granberg, K; Lohi, O; COMPARATIVE ANALYSIS OF GENE REGULATORY NETWORKS IN LYMPHOID LEUKEMIAS USING THE INTERACTIVE HEMAP RESOURCE HAEMATOLOGICA 101 25-25 2016 FERRATA STORTI FOUNDATION VIA GIUSEPPE BELLI 4, 27100 PAVIA, ITALY
Vandekerkhove, Gillian; Struss, Werner J; Annala, Matti; Kallio, Heini ML; Khalaf, Daniel; Warner, Evan W; Herberts, Cameron; Ritch, Elie; Beja, Kevin; Loktionova, Yulia; Circulating tumor DNA abundance and potential utility in de novo metastatic prostate cancer European urology 75 4 667-675 2019 Elsevier
Harjula, Sanna-Kaisa E; Ojanen, Markus JT; Taavitsainen, Sinja; Nykter, Matti; Rämet, Mika; Interleukin 10 mutant zebrafish have an enhanced interferon gamma response and improved survival against a Mycobacterium marinum infection Scientific reports 8 1 1-17 2018 Nature Publishing Group
Mäki-Marttunen, Tuomo; Kesseli, Juha; Nykter, Matti; Balance between noise and information flow maximizes set complexity of network dynamics PLoS One 8 3 e56523 2013 Public Library of Science
Ylipää, Antti; Waltering, Kati; Zhang, Wei; Visakorpi, Tapio; Nykter, Matti; A systems approach into studying the changes in genetic regulation during prostate cancer progression 2011 AACR
Nykter, Matti; Lähdesmäki, Harri; Rust, Alistair; Thorsson, Vesteinn; Shmulevich, Ilya; A data integration framework for prediction of transcription factor targets: a BCL6 case study Annals of the New York Academy of Sciences 1158 205 2009 NIH Public Access
Simão, Felipe A; Waterhouse, Robert M; Ioannidis, Panagiotis; Kriventseva, Evgenia V; Zdobnov, Evgeny M; Supplementary online material 2017
Nykter, Matti; Price, Nathan D; Aldana, Maximino; Ramsey, Stephen A; Kauffman, Stuart A; Hood, Leroy E; Yli-Harja, Olli; Shmulevich, Ilya; Gene expression dynamics in the macrophage exhibit criticality Proceedings of the National Academy of Sciences 105 6 1897-1900 2008 National Acad Sciences
Kivirikko, Kari; Myllyharju, Johanna; Kukkola, Liisa; Hieta, Reija; Alpha (III) subunit for prolyl 4-hydroxylase 2002 Google Patents
Liuksiala, Thomas; Teittinen, KJ; Granberg, Kirsi; Heinäniemi, Merja; Annala, Matti; Mäki, Markku; Nykter, Matti; Lohi, Olli; Overexpression of SNORD114-3 marks acute promyelocytic leukemia Leukemia 28 1 233 2014 Nature Publishing Group
Latonen, Leena; Afyounian, Ebrahim; Jylhä, Antti; Nättinen, Janika; Aapola, Ulla; Annala, Matti; Kivinummi, Kati K; Tammela, Teuvo TL; Beuerman, Roger W; Uusitalo, Hannu; Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression Nature communications 9 1 1-13 2018 Nature Publishing Group
Pölönen, Petri; Deen, Ashik Jawahar; Leinonen, Hanna M; Jyrkkänen, Henna-Kaisa; Kuosmanen, Suvi; Mononen, Mimmi; Jain, Ashish; Tuomainen, Tomi; Pasonen-Seppänen, Sanna; Hartikainen, Jaana M; Nrf2 and SQSTM1/p62 jointly contribute to mesenchymal transition and invasion in glioblastoma Oncogene 38 50 7473-7490 2019 Nature Publishing Group
Määttä, Kirsi; Rantapero, Tommi; Lindström, Anna; Nykter, Matti; Kankuri-Tammilehto, Minna; Laasanen, Satu-Leena; Schleutker, Johanna; Whole-exome sequencing of Finnish hereditary breast cancer families European Journal of Human Genetics 25 1 85-93 2017 Nature Publishing Group
Ruusuvuori, Pekka; Nykter, Matti; Makiraatikka, Eeva; Lehmussola, Antti; Korpelainen, Tomi; Erkkila, Timo; Yli-Harja, Olli; Microarray Simulator as Educational Tool 2007 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society 5919-5922 2007 IEEE
Kuusisto, Kirsi M; Rantapero, Tommi; Kankuri-Tammilehto, Minna; Nykter, Matti; Laasanen, Satu-Leena; Schleutker, Johanna; Abstract LB-284: Exome sequencing of high-risk Finnish hereditary breast and breast-ovarian cancer families 2015 AACR
Granberg, Kirsi J; Lehtinen, Birgitta; Annala, Matti J; Haapasalo, Hannu; Nykter, Matti; Zhang, Wei; Abstract LB-92: Using immunohistochemistry to evaluate FGFR3 gene fusion recurrence and clinical associations in astrocytomas 2014 AACR
Duffy, David J; Krstic, Aleksandar; Schwarzl, Thomas; Halasz, Melinda; Iljin, Kristiina; Fey, Dirk; Haley, Bridget; Whilde, Jenny; Haapa-Paananen, Saija; Fey, Vidal; Wnt signalling is a bi-directional vulnerability of cancer cells Oncotarget 7 37 60310 2016 Impact Journals, LLC
Ioannidis, Panagiotis; Simao, Felipe A; Waterhouse, Robert M; Manni, Mosè; Seppey, Mathieu; Robertson, Hugh M; Misof, Bernhard; Niehuis, Oliver; Zdobnov, Evgeny M; Genomic features of the damselfly Calopteryx splendens representing a sister clade to most insect orders Genome biology and evolution 9 2 415-430 2017 Oxford University Press
Basenko, Evelina Y; Pulman, Jane A; Shanmugasundram, Achchuthan; Harb, Omar S; Crouch, Kathryn; Starns, David; Warrenfeltz, Susanne; Aurrecoechea, Cristina; Stoeckert, Christian J; Kissinger, Jessica C; FungiDB: an integrated bioinformatic resource for fungi and oomycetes Journal of Fungi 4 1 39 2018 Multidisciplinary Digital Publishing Institute
Pulman, Jane; A transcriptomics approach to understanding polymorphic and transcript level differences linked to isoquinoline alkaloid production in triploid varieties of Narcissus pseudonarcissus 2014 University of Liverpool
Zienkiewicz, Agnieszka; Zienkiewicz, Krzysztof; Poliner, Eric; Pulman, Jane A; Du, Zhi-Yan; Stefano, Giovanni; Tsai, Chia-Hong; Horn, Patrick; Feussner, Ivo; Farre, Eva M; The Microalga Nannochloropsis during transition from quiescence to autotrophy in response to nitrogen availability Plant Physiology 182 2 819-839 2020 Am Soc Plant Biol
Huot, B; Castroverde, CDM; Velásquez, AC; Hubbard, E; Pulman, JA; Yao, J; Childs, KL; Tsuda, K; Montgomery, BL; He, SY; Dual impact of elevated temperature on plant defence and bacterial virulence in Arabidopsis
Huot, Bethany; Castroverde, Christian Danve M; Velásquez, André C; Hubbard, Emily; Pulman, Jane A; Yao, Jian; Childs, Kevin L; Tsuda, Kenichi; Montgomery, Beronda L; He, Sheng Yang; Dual impact of elevated temperature on plant defence and bacterial virulence in Arabidopsis Nature communications 8 1 1-12 2017 Nature Publishing Group
Wiersma, Andrew T; Pulman, Jane A; Brown, Linda K; Cowger, Christina; Olson, Eric L; Identification of Pm58 from Aegilops tauschii Theoretical and Applied Genetics 130 6 1123-1133 2017 Springer
Poliner, Eric; Pulman, Jane A; Zienkiewicz, Krzysztof; Childs, Kevin; Benning, Christoph; Farré, Eva M; A toolkit for Nannochloropsis oceanica CCMP 1779 enables gene stacking and genetic engineering of the eicosapentaenoic acid pathway for enhanced long‐chain polyunsaturated fatty acid production Plant biotechnology journal 16 1 298-309 2018 Wiley Online Library
Aurrecoechea, Cristina; Barreto, Ana; Basenko, Evelina Y; Brestelli, John; Brunk, Brian P; Cade, Shon; Crouch, Kathryn; Doherty, Ryan; Falke, Dave; Fischer, Steve; EuPathDB: the eukaryotic pathogen genomics database resource Nucleic acids research 45 D1 D581-D591 2017 Oxford University Press
Bowman, Megan J; Pulman, Jane A; Liu, Tiffany L; Childs, Kevin L; A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa BMC bioinformatics 18 1 1-15 2017 BioMed Central
Basenko, E; Pulman, J; Shanmugasundram, A; Harb, OS; Crouch, K; Starns, D; Warrenfeltz, S; Aurrecoechea, C; Stoeckert Jr, CJ; Kissinger, JC; FungiDB: an integrated bioinformatic resource for fungi and oomycetes. J. Fungi (Basel) 4: 39 2018
Haldenby, Sam; Bronowski, Christina; Nelson, Charlotte; Kenny, John; Martinez-Rodriguez, Carmen; Chaudhuri, Roy; Williams, Nicola J; Forbes, Ken; Strachan, Norval J; Pulman, Jane; Increasing prevalence of a fluoroquinolone resistance mutation amongst Campylobacter jejuni isolates from four human infectious intestinal disease studies in the United Kingdom Plos one 15 1 e0227535 2020 Public Library of Science San Francisco, CA USA
Pulman, Jane A; Childs, Kevin L; Sgambelluri, R Michael; Walton, Jonathan D; Expansion and diversification of the MSDIN family of cyclic peptide genes in the poisonous agarics Amanita phalloides and A. bisporigera BMC genomics 17 1 1-14 2016 BioMed Central
Luukinen, Hanna; Hammarén, Milka Marjut; Vanha-aho, Leena-Maija; Svorjova, Aleksandra; Kantanen, Laura; Järvinen, Sampsa; Luukinen, Bruno Vincent; Dufour, Eric; Rämet, Mika; Hytönen, Vesa Pekka; Priming of innate antimycobacterial immunity by heat-killed Listeria monocytogenes induces sterilizing response in the adult zebrafish tuberculosis model Disease models & mechanisms 11 1 2018 The Company of Biologists Ltd
Aspatwar, Ashok; Becker, Holger M; Parvathaneni, Nanda Kumar; Hammaren, Milka; Svorjova, Aleksandra; Barker, Harlan; Supuran, Claudiu T; Dubois, Ludwig; Lambin, Philippe; Parikka, Mataleena; Nitroimidazole-based inhibitors DTP338 and DTP348 are safe for zebrafish embryos and efficiently inhibit the activity of human CA IX in Xenopus oocytes Journal of enzyme inhibition and medicinal chemistry 33 1 1064-1073 2018 Taylor & Francis