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 | 1-17 | 2006 | BioMed Central |
| 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 | 1-12 | 2017 | BioMed Central |
| Ylipää, Antti; Yli-Harja, Olli; Zhang, Wei; Nykter, Matti; | Characterization of aberrant pathways across human cancers | BMC systems biology | 7 | 1 | 1-12 | 2013 | BioMed Central |
| 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 | Endocrine Abstracts | 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 | 10 | 43-49 | 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 | Proceedings of the Seventh International Workshop on Computational Systems Biology, WCSB 2010, Luxembourg, June 16-18, 2010. TICSP Series | 4 | 2010 | |||
| 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 | 1 | 1-14 | 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 | Elsevier |
| 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'2004, Silja Opera, Helsinki-St. Petersburg, 14-16 June 2004 | 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 | Blood | 128 | 22 | 1725 | 2016 | Content Repository Only! |
| 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, Antti; Mäkiraatikka, Eeva; Manninen, Tiina; Smolander, O; Ylipää, Antti; Hituri, Katri; 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 | Elsevier |
| 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 | American Association for Cancer Research |
| 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; Halonen, Pasi; Kohonen, Pekka; Fey, Vidal; Grafström, Roland; Perälä, Merja; Kallioniemi, Olli; Iljin, Kristiina; | Drugs with known pharmacological profiles, such as monensin, disulfiram and salinomycin, show cancer-selective inhibition of prostate cancer cell growth by increasing oxidative stress | European Journal of Cancer: Supplement | 8 | 5 | 61-62 | 2010 | Elsevier |
| 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 | Endocrine Abstracts | 42 | 2016 | BioScientifica | ||
| Ruusuvuori, P; Nykter, M; Latonen, L; | 712 Processing of stacked histological tissue sections in digital pathology | European Journal of Cancer | 3 | 51 | S131 | 2015 | |
| 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 | Endocrine Abstracts | 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 | 2009 | |||
| 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 | 1 | 1-10 | 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 | Blood | 126 | 23 | 3646 | 2015 | Content Repository Only! |
| 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 Netherlands |
| 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 San Francisco, USA |
| 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 | 2005 | Elsevier |
| 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, Dordrecht | ||
| 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; Kleivi Sahlberg, Kristine; 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 San Francisco, USA |
| 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 | 12 | 7 | 1099-1188 | 2020 | Oxford University 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 | 1-10 | 2017 | BioMed Central |
| 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 | 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 | American Society of Plant Biologists |
| 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 | Blood | 126 | 23 | 4805 | 2015 | Content Repository Only! |
| 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 | Elsevier |
| 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 | 1-11 | 2017 | BioMed Central |
| 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 Netherlands |
| 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 |
| 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 | 1 | 13 | e299 | 2014 | |
| Nykter, Matti; Ruusuvuori, Pekka; Carlberg, Carsten; Yli-Harja, Olli; | Seventh International Workshop on Computational Systems Biology, WCSB 2010, June 16-18, 2010, Luxembourg | 2010 | |||||
| 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 | Proceedings of the Fifth International Workshop on Computational Systems Biology, WCSB 2008, Leipzig, Germany, 11-13 June 2008 | 77-80 | 2008 | |||
| 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 | Elsevier |
| 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 |
| 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 | 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 | 1-15 | 2017 | BioMed Central |
| 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 | Elsevier |
| 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 | Proceedings of the Seventh International Workshop on Computational Systems Biology, WCSB 2010, Luxembourg, June 16-18, 2010. TICSP Series | 4 | 2010 | |||
| 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 | Elsevier |
| 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 | 78 | 6 | 834-844 | 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, 3: 15 PM-5: 15 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 | Humana Press, New York, NY | ||
| 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 | 39 | 30 | 5241-5251 | 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 | American Association for Cancer Research | ||||
| 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 | 1-17 | 2015 | BioMed Central |
| 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 | BMC biology | 18 | 1 | 1-37 | 2020 | BioMed Central |
| 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 | ||
| 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. | Blood | 110 | 11 | 2626 | 2007 | Content Repository Only! |
| 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 | vi17 | 2016 | Elsevier | |
| 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 | |||||
| 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 | 3 | 15 | e1074 | 2016 | |
| 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 | 3 | 16 | e909-e910 | 2017 | |
| 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 | 1-11 | 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 | Friedrich-Schiller-Universität Jena | ||||
| 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 | 2011 | WCSB 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 | |
| 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 | 3 | 16 | e255-e256 | 2017 | |
| 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 | 69 | 8 | 1416-1422 | 2020 | BMJ Publishing Group |
| Dufva, Olli; Pölönen, Petri; Brück, Oscar; Keränen, Mikko AI; Klievink, Jay; Mehtonen, Juha; Huuhtanen, Jani; Kumar, Ashwini; Malani, Disha; Siitonen, Sanna; | Immunogenomic landscape of hematological malignancies | Cancer Cell | 38 | 3 | 380-399. e13 | 2020 | Cell Press |
| 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 | 1-10 | 2014 | BioMed Central |
| 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; Bollner, 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 | Elsevier |
| 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 | 24 | 12 | 6916-6927 | 2020 | |
| 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 | Elsevier |
| 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 San Francisco, USA |
| 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 | 233-236 | 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 | American Society of Plant Biologists |
| 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 | 2017 | 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 Berlin Heidelberg |
| 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, 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 |
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| Nykter, M; Yli-Harja, O; Shmulevich, I; | The similarity metric in network analysis | Proceedings of The 3rd TICSP Workshop on Computational Systems Biology, WCSB 2005, Tampere, Finland, 13-14 June 2005 | 63-64 | 2005 | |||
| Kauppi, Jukka-Pekka; Nykter, Matti; Niemi, Jari; | Clustering Method for Data Having Outliers and Clusters with Varying Sizes and Densities | 2011 | |||||
| Annala, Matti; Yli-Harja, Olli; Shmulevich, Ilya; Nykter, Matti; | Improving correlation between microarrays and transcriptome sequencing through probeset analysis | Proceedings of the Seventh International Workshop on Computational Systems Biology, WCSB 2010, Luxembourg, June 16-18, 2010 | 15-18 | 2010 | Tampere University of Technology | ||
| Nykter, M; Kesseli, J; Aho, T; Yli-Harja, O; | On estimation of statistical characteristics of microarray data | Proceedings of the 2003 Finnish Signal Processing Symposium, FINSIG'03, Tampere, Finland, 19 May 2003 | 222-226 | 2003 | TICSP | ||
| Kivinen, V; Nykter, M; Martin, D; Yli-Harja, O; Shmulevich, I; | Selection of an optimal set of blood biomarker proteins | Abstracts of the 2009 Joint RECOMB Satellite Conference on Regulatory Genomics-Systems Biology-Dream4, Boston, USA, 2-6 December 2009 | 254 | 2009 | |||
| Annala, Matti; Laurila, Kirsti; Nykter, Matti; Harri, L; | A linear model for transcription factor binding affinity prediction in PBM microarrays | RECOMB The 7th Annual RECOMB Satellite on Regulatory Genomics, the 6th Annual RECOMB Satellite on Systems Biology, and the 5th Annual DREAM reverse engineering challenges | 2010 | ||||
| Mäkiraatikka, E; Manninen, T; Saarinen, A; Ylipää, A; Teppola, H; Hituri, K; Pettinen, A; Linne, ML; | Kemiallisten reaktioiden mallintaminen ja tietokonesimulaatiot | Solubiologi | 26 | 1 | 21-28 | 2008 | |
| Filppu, Pauliina; Ramanathan, Jayendrakishore Tanjore; Granberg, Kirsi J; Gucciardo, Erika; Haapasalo, Hannu; Lehti, Kaisa; Nykter, Matti; Le Joncour, Vadim; Laakkonen, Pirjo; | CD109-GP130 interaction drives glioblastoma stem cell plasticity and chemoresistance through STAT3 activity | JCI insight | 2021 | ||||
| Owens, Dominic DG; Anselmi, Giorgio; Oudelaar, A Marieke; Downes, Damien J; Cavallo, Alessandro; Harman, Joe R; Schwessinger, Ron; Bucakci, Akin; Greder, Lucas; De Ornellas, Sara; | Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development | bioRxiv | 2021 | Cold Spring Harbor Laboratory | |||
| Pavlaki, Ioanna; Shapiro, Michael; Pisignano, Giuseppina; Telenius, Jelena; Descalzo, Silvia Munoz; Williams, Robert J; Hughes, Jim Raymond; Vance, Keith W; | Chromatin interaction maps identify Wnt responsive cis-regulatory elements coordinating Paupar-Pax6 expression in neuronal cells | bioRxiv | 2021 | Cold Spring Harbor Laboratory | |||
| Annala, Matti; Taavitsainen, Sinja; Khalaf, Daniel J; Vandekerkhove, Gillian; Beja, Kevin; Sipola, Joonatan; Warner, Evan W; Herberts, Cameron; Wong, Amanda; Fu, Simon; | Evolution of castration-resistant prostate cancer in ctDNA during sequential androgen receptor pathway inhibition | Clinical Cancer Research | 27 | 16 | 4610-4623 | 2021 | American Association for Cancer Research |
| Neto, Felipe Aristides Simao; Hieta, Reija; Pulman, Jane Ann; Madonna, Gabriele; Ascierto, Paolo; Lewensohn, Rolf; Masucci, Giuseppe; | SRF-CLICAL: an approach for patient risk stratification using random forest models | bioRxiv | 2021 | Cold Spring Harbor Laboratory | |||
| FA, Simao Neto; Hieta, R; Pulman, JA; Madonna, G; Ascierto, P; Lewensohn, R; Masucci, G; | SRF-CLICAL: an approach for patient risk stratification using random forest models | 2021 | |||||
| Iljin, Kristiina; Fey, Vidal; | Monensin Is a Potent Inducer of Oxidative Stress and Inhibitor of Androgen Signaling Leading to Apoptosis in Pro... | 2010 | |||||
| Bozhilov, Yavor K; Downes, Damien J; Telenius, Jelena; Oudelaar, A Marieke; Olivier, Emmanuel N; Mountford, Joanne C; Hughes, Jim R; Gibbons, Richard J; Higgs, Douglas R; | A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker | Nature Communications | 12 | 1 | 1-13 | 2021 | Nature Publishing Group |
| Manni, Mosè; Berkeley, Matthew R; Seppey, Mathieu; Simao, Felipe A; Zdobnov, Evgeny M; | BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes | arXiv preprint arXiv:2106.11799 | 2021 | ||||
| Tsakonas, Georgios; Martín-Bernabé, Alfonso; Rounis, Konstantinos; Moreno-Ruiz, Pablo; Botling, Johan; De Petris, Luigi; Ylipää, Antti; Mezheyeuski, Artur; Micke, Patrick; Östman, Arne; | High Density of NRF2 Expression in Malignant Cells Is Associated with Increased Risk of CNS Metastasis in Early-Stage NSCLC | Cancers | 13 | 13 | 3151 | 2021 | Multidisciplinary Digital Publishing Institute |
| 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; | Correction to: Genome-enabled insights into the biology of thrips as crop pests | BMC biology | 18 | 1 | 1-2 | 2020 | BioMed Central |
| Jacome Sanz, Dafne; Saralahti, Anni K; Pekkarinen, Meeri; Kesseli, Juha; Nykter, Matti; Rämet, Mika; Ojanen, Markus JT; Pesu, Marko; | Proprotein convertase subtilisin/kexin type 9 regulates the production of acute‐phase reactants from the liver | Liver International | 41 | 10 | 2511-2522 | 2021 | |
| Kukkonen, Konsta; Taavitsainen, Sinja; Huhtala, Laura; Uusi-Makela, Joonas; Granberg, Kirsi J; Nykter, Matti; Urbanucci, Alfonso; | Chromatin and epigenetic dysregulation of prostate cancer development, progression, and therapeutic response | Cancers | 13 | 13 | 3325 | 2021 | Multidisciplinary Digital Publishing Institute |
| Jasu, Juho; Tolonen, Teemu; Antonarakis, Emmanuel S; Beltran, Himisha; Halabi, Susan; Eisenberger, Mario A; Carducci, Michael A; Loriot, Yohann; Van der Eecken, Kim; Lolkema, Martijn; | Combined longitudinal clinical and autopsy phenomic assessment in lethal metastatic prostate cancer: recommendations for advancing precision medicine | European urology open science | 30 | 47-62 | 2021 | Elsevier | |
| King, Andrew J; Songdej, Duantida; Downes, Damien J; Beagrie, Robert A; Liu, Siyu; Buckley, Megan; Hua, Peng; Suciu, Maria C; Oudelaar, A Marieke; Hanssen, Lars LP; | Reactivation of a developmentally silenced embryonic globin gene | Nature communications | 12 | 1 | 1-15 | 2021 | Nature Publishing Group |
| Isaacs, Isaac; | User Menu | ||||||
| Ketola, Kirsi; Kaljunen, Heidi; Taavitsainen, Sinja; Kaarijärvi, Roosa; Järvelä, Emmi; Rodríguez-Martín, Bernardo; Haase, Kerstin; Woodcock, Dan J; Tubio, Jose; Wedge, David C; | Subclone eradication analysis identifies targets for enhanced cancer therapy and reveals L1 retrotransposition as a dynamic source of cancer heterogeneity | Cancer Research | 81 | 19 | 4901-4909 | 2021 | American Association for Cancer Research |
| Taavitsainen, S; Engedal, N; Cao, S; Handle, F; Erickson, A; Prekovic, S; Wetterskog, D; Tolonen, T; Vuorinen, EM; Kiviaho, A; | Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse | Nature communications | 12 | 1 | 1-16 | 2021 | Nature Publishing Group |
| Fey, Vidal; Jambulingam, Dhanaprakash; Sara, Henri; Heron, Samuel; Sipeky, Csilla; Schleutker, Johanna; | BioCPR–A Tool for Correlation Plots | Data | 6 | 9 | 97 | 2021 | Multidisciplinary Digital Publishing Institute |
| Moreau, Pierre R; Tomas Bosch, Vanesa; Bouvy-Liivrand, Maria; Õunap, Kadri; Örd, Tiit; Pulkkinen, Heidi H; Pölönen, Petri; Heinäniemi, Merja; Ylä-Herttuala, Seppo; Laakkonen, Johanna P; | Profiling of Primary and Mature miRNA Expression in Atherosclerosis Associated Cell Types | Arteriosclerosis, thrombosis, and vascular biology | ATVBAHA. 121.315579 | 2021 | Am Heart Assoc | ||
| Loppi, Sanna; Korhonen, Paula; Bouvy‐Liivrand, Maria; Caligola, Simone; Turunen, Tiia A; Turunen, Mikko P; Hernandez de Sande, Ana; Kołosowska, Natalia; Scoyni, Flavia; Rosell, Anna; | Peripheral inflammation preceeding ischemia impairs neuronal survival through mechanisms involving miR‐127 in aged animals | Aging cell | 20 | 1 | e13287 | 2021 | Wiley Online Library |
| Bister, Nea; Eamen, Shaila; Huremagic, Benjamin; Korhonen, Paula; Loppi, Sanna; Scoyni, Flavia; Konttinen, Henna; Cheng, Lesley; Vella, Laura J; Bouvy-Liivrand, Maria; | Ischaemia-related conditions induce secretion of miR-21-5p-containing extracellular vesicles that alter microglial activation | Journal of Extracellular Vesicles | 7 | 159-160 | 2018 | Taylor & Francis Ltd. | |
| Verta, Jukka-Pekka; Barton, Henry J; Pritchard, Victoria; Primmer, Craig R; | Genetic Drift Dominates Genome-Wide Regulatory Evolution Following an Ancient Whole-Genome Duplication in Atlantic Salmon | Genome biology and evolution | 13 | 5 | evab059 | 2021 | Oxford University Press |
| Hayes, Kai; Barton, Henry J; Zeng, Kai; | A study of faster-Z evolution in the great tit (Parus major) | Genome biology and evolution | 12 | 3 | 210-222 | 2020 | Oxford University Press |
| Zeng, Kai; Jackson, Benjamin C; Barton, Henry J; | Methods for estimating demography and detecting between-locus differences in the effective population size and mutation rate | Molecular biology and evolution | 36 | 2 | 423-433 | 2019 | Oxford University Press |
| Barton, Henry Juho; | Characterising the impact of directional forces on genomic variation | 2019 | University of Sheffield | ||||
| Kim, J‐M; Santure, AW; Barton, Henry J; Quinn, JL; Cole, Eleanor F; Great Tit HapMap Consortium; Visser, ME; Sheldon, BC; Groenen, MAM; van Oers, K; | A high‐density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour | Molecular ecology resources | 18 | 4 | 877-891 | 2018 | Wiley Online Library |
| Barton, Henry J; Zeng, Kai; | The impact of natural selection on short insertion and deletion variation in the great tit genome | Genome biology and evolution | 11 | 6 | 1514-1524 | 2019 | Oxford University Press |
| Kim, Jun-Mo; Santure, Anna W; Barton, Henry J; Quinn, John L; Cole, Eleanor F; Visser, Marcel E; Sheldon, Ben C; Groenen, M; van Oers, Kees; Slate, Jon; | Data from: A high density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour | 2018 | |||||
| Corcoran, Padraic; Gossmann, Toni I; Barton, Henry J; Slate, Jon; Zeng, Kai; | Determinants of the efficacy of natural selection on coding and noncoding variability in two passerine species (vol 9, pg 2987, 2017) | GENOME BIOLOGY AND EVOLUTION | 10 | 4 | 1062-1062 | 2018 | OXFORD UNIV PRESS GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND |
| Olofsson, Jill K; Dunning, Luke T; Lundgren, Marjorie R; Barton, Henry J; Thompson, John; Cuff, Nicholas; Ariyarathne, Menaka; Yakandawala, Deepthi; Sotelo, Graciela; Zeng, Kai; | Population-specific selection on standing variation generated by lateral gene transfers in a grass | Current Biology | 29 | 22 | 3921-3927. e5 | 2019 | Elsevier |
| Barton, Henry J; Zeng, Kai; | The effective population size modulates the strength of GC biased gene conversion in two passerines | bioRxiv | 2021 | Cold Spring Harbor Laboratory | |||
| Corcoran, Pádraic; Gossmann, Toni I; Barton, Henry J; Great Tit HapMap Consortium; Slate, Jon; Zeng, Kai; | Determinants of the efficacy of natural selection on coding and noncoding variability in two passerine species | Genome biology and evolution | 9 | 11 | 2987-3007 | 2017 | Oxford University Press |
| Barton, Henry J; Zeng, Kai; | New methods for inferring the distribution of fitness effects for INDELs and SNPs | Molecular biology and evolution | 35 | 6 | 1536-1546 | 2018 | Oxford University Press |
| Barton, HJ; Bond, A; Boot, JR; Brandon, DR; O’Brien, A; | The relationship between development of lung inflammation and changes in bone marrow populations in guinea-pigs following inhaled antigen challenge | International Archives of Allergy and Immunology | 96 | 1 | 1-11 | 1991 | Karger Publishers |
| Yusuf, Leeban; Heatley, Matthew C; Palmer, Joseph PG; Barton, Henry J; Cooney, Christopher R; Gossmann, Toni I; | Noncoding regions underpin avian bill shape diversification at macroevolutionary scales | Genome research | 30 | 4 | 553-565 | 2020 | Cold Spring Harbor Lab |
