Scientific references

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

For a visual summary of our team's publication record, see our blog post What do we publish?

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
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
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. Cancer Research 73 8_Supplement 5311-5311 2013 American Association for Cancer Research
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 35 7 673-680 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 Springer
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 TreatmentTargeting IGF1R in MPNST Clinical cancer research 17 24 7563-7573 2011 American Association for Cancer Research
Ruusuvuori, Pekka; Valkonen, Mira; Kartasalo, Kimmo; Visakorpi, Tapio; Latonen, Leena; Nykter, Matti; Histological modeling of prostate cancer Endocrine Abstracts 42 2016 Bioscientifica
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
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; 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
Cangiano, Mario; Grudniewska, Magda; Salji, Mark J; Nykter, Matti; Jenster, Guido; Urbanucci, Alfonso; Granchi, Zoraide; Janssen, Bart; Hamilton, Graham; Leung, Hing Y; Gene regulation network analysis on human prostate orthografts highlights a potential role for the JMJD6 regulon in clinical prostate cancer Cancers 13 9 2094 2021 MDPI
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 6 9 2021 American Society for Clinical Investigation
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
Granberg, Kirsi Johanna; Tuominen, Joonas; Nordfors, Kristiina; Pekkarinen, Meeri; Kytölä, Ville; Häyrynen, Sergei; Afyounian, Ebrahim; Lohi, Olli; Helen, Pauli; Kesseli, Juha; Abstract LB-173: DNA methylation analysis reveals epigenetic regulation of neural differentiation in AT/RTs Cancer Research 80 16_Supplement LB-173-LB-173 2020 The American Association for Cancer Research
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 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
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
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 Cancer Research 76 14_Supplement 5011-5011 2016 The American Association for Cancer Research
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
Turpeinen, Hannu; Oksanen, Anna; Kivinen, Virpi; Kukkurainen, Sampo; Uusimäki, Annemari; Rämet, Mika; Parikka, Mataleena; Hytönen, Vesa P; Nykter, Matti; Pesu, Marko; Proprotein convertase subtilisin/kexin type 7 (PCSK7) is essential for the zebrafish development and bioavailability of transforming growth factor β1a (TGFβ1a) Journal of Biological Chemistry 288 51 36610-36623 2013 ASBMB
Cordova, Zuzet Martinez; Grönholm, Anna; Kytölä, Ville; Taverniti, Valentina; Hämäläinen, Sanna; Aittomäki, Saara; Niininen, Wilhelmiina; Junttila, Ilkka; Ylipää, Antti; Nykter, Matti; Myeloid cell expressed proprotein convertase FURIN attenuates inflammation Oncotarget 7 34 54392 2016 Impact Journals, LLC
Nykter, Matti; Feature selection for Lymphoma outcome prediction Proceedings of the 2nd TICSP Workshop on Computational Systems Biology, WCSB'2004, Silja Opera, Helsinki-St. Petersburg, 14-16 June 2004 51-52 2004
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 San Francisco, USA
Gundem, Gunes; Van Loo, Peter; Kremeyer, Barbara; Alexandrov, Ludmil B; Tubio, Jose; Papaemmanuil, Elli; Brewer, Daniel S; Kallio, Heini ML; Hägnäs, Gunilla; Annala, Matti; Author Correction: The evolutionary history of lethal metastatic prostate cancer (Nature,(2015), 520, 7547,(353-357), 10.1038/nature14347) 2020 Springer US
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
Cerqueira, Juliana XM; Saavalainen, Päivi; Kurppa, Kalle; Laurikka, Pilvi; Huhtala, Heini; Nykter, Matti; LE Koskinen, Lotta; Yohannes, Dawit A; Kilpeläinen, Elina; Shcherban, Anastasia; Independent and cumulative coeliac disease-susceptibility loci are associated with distinct disease phenotypes Journal of Human Genetics 66 6 613-623 2021 Nature Publishing Group
Rajamäki, Kristiina; Taira, Aurora; Katainen, Riku; Välimäki, Niko; Kuosmanen, Anna; Plaketti, Roosa-Maria; Seppälä, Toni T; Ahtiainen, Maarit; Wirta, Erkki-Ville; Vartiainen, Emilia; Genetic and epigenetic characteristics of inflammatory bowel Disease–Associated colorectal cancer Gastroenterology 161 2 592-607 2021 WB Saunders
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 Cell Press
Nykter, Matti; Signal processing methods and information approach to systems biology 2006 Tampere University of Technology
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 Elsevier
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
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 Cancer Research 75 15_Supplement 148-148 2015 The American Association for Cancer Research
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
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
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 Cancer Research 79 13_Supplement 4393-4393 2019 The American Association for Cancer Research
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 MDPI
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. Cancer Research 73 8_Supplement 5217-5217 2013 American Association for Cancer Research
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 MalignanciesOrganizing Molecular Diversity of 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 Cancer Research 75 15_Supplement 3883-3883 2015 The American Association for Cancer Research
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
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 Elsevier
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 MDPI
Cao, Shaolong; Wang, Jennifer R; Ji, Shuangxi; Yang, Peng; Montierth, Matthew D; Guo, Shuai; Shen, John Paul; Zhao, Xiao; Chen, Jingxiao; Lee, Jaewon James; Tumor cell total mRNA expression shapes the molecular and clinical phenotype of cancer bioRxiv 2020.09. 30.306795 2021 Cold Spring Harbor Laboratory
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
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
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
Woodcock, DJ; Riabchenko, Ekaterina; Taavitsainen, Sinja; Kankainen, Matti; Gundem, Gunes; Brewer, DS; Ellonen, Pekka; Lepistö, Maija; Golubeva, YA; Warner, AC; Prostate cancer evolution from multilineage primary to single lineage metastases with implications for liquid biopsy Nature communications 11 1 1-13 2020 Nature Publishing Group
Ruusuvuori, P; Nykter, M; Latonen, L; 712 Processing of stacked histological tissue sections in digital pathology European Journal of Cancer 3 51 S131 2015
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
Ylipää, A; Nykter, M; Yli-Harja, O; Zhang, W; Shmulevich, I; Association of genetic features with pathways using multiple high-throughput data Abstracts of the 2009 Joint RECOMB Satellite Conference on Regulatory Genomics-Systems Biology-Dream4, Boston, USA, 2-6 December 2009 291 2009
Heinäniemi, M; Nykter, Matti; Wienecke, A; Sinkkonen, L; Schmitz, M; Zhou, J; Kauffman, S; Huang, S; Shmulevich, I; Carlberg, C; Systematic identification of lineage determining transcriptional regulation from public gene expression profiles Proceedings of the Seventh International Workshop on Computational Systems Biology, WCSB 2010, Luxembourg, June 16-18, 2010. TICSP Series 2 2010
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
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 Cancer Research 78 16_Supplement A077-A077 2018 The American Association for Cancer Research
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
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
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 Wiley Online Library
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 Elsevier
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 Cancer Research 78 13_Supplement 2476-2476 2018 The American Association for Cancer Research
Erkkilä, Timo; Kreisberg, Richard; Reynolds, Sheila; Thorsson, Vesteinn; Lin, Jake; Torkkola, Kari; Bressler, Ryan; Bernard, Brady; Ruusuvuori, Pekka; Annala, Matti; Integrated views into cancer regulomes reveal regulatory hot spots The 11th SocBiN Conference, Helsinki, Finland 2011
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
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
LB Almeida, Bilena; M. Bahrudeen, Mohamed N; Chauhan, Vatsala; Dash, Suchintak; Kandavalli, Vinodh; Häkkinen, Antti; Lloyd-Price, Jason; SD Cristina, Palma; Baptista, Ines SC; Gupta, Abhishekh; The transcription factor network of E. coli steers global responses to shifts in RNAP concentration Nucleic Acids Research 50 12 6801-6819 2022 Oxford University Press
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 CancerPCAT5: An ERG-Regulated lncRNA Cancer research 75 19 4026-4031 2015 American Association for Cancer Research
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
Ketola, Kirsi; Kaljunen, Heidi; Taavitsainen, Sinja; Kaarijärvi, Roosa; Järvelä, Emmi; Rodriguez Martin, 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
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
Pekkarinen, Meeri; Nordfors, Kristiina; Uusi-Makela, Joonas; Kytola, Ville; Rauhala, Minna; Urhonen, Henna; Hayrynen, Sergei; Afyounian, Ebrahim; Yli-Harja, Olli; Zhang, Wei; Integrative DNA methylation analysis of pediatric brain tumors reveals tumor type-specific developmental trajectories and epigenetic signatures of malignancy bioRxiv 2022 Cold Spring Harbor Laboratory
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 CancerctDNA and Resistance to AR-Targeted Therapy Cancer discovery 8 4 444-457 2018 American Association for Cancer Research
Ruusuvuori, Pekka; Kartasalo, Kimmo; Valkonen, Mira; Valkonen, Masi; Visakorpi, Tapio; Nykter, Matti; Latonen, Leena; 3D reconstruction and quantitative analysis of histology for prostate cancer Cancer Research 79 13_Supplement 46-46 2019 The American Association for Cancer Research
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
Taavitsainen, Sinja; Engedal, Nikolai; Cao, Shaolong; Handle, Florian; Erickson, Andrew; Prekovic, Stefan; Wetterskog, Daniel; Tolonen, Teemu; Vuorinen, EM; Kiviaho, Antti; Single-cell ATAC and RNA sequencing reveal pre-existing and persistent subpopulations of cells associated with relapse of prostate cancer bioRxiv 2021 Cold Spring Harbor Laboratory
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
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
Aapola, U; Mikhailova, A; Nykter, M; Zhou, L; Beuerman, R; Uusitalo, H; Comparison of itraq and swath in a clinical study with multiple time points 2018 BioMed Central Ltd
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 San Francisco, USA
Häyrynen, Sergei; Nykter, Matti; Pan-cancer analysis of alternative splicing patterns and association to genomic aberrations Cancer Research 76 14_Supplement 1513-1513 2016 The American Association for Cancer Research
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 Cancer Research 78 16_Supplement B077-B077 2018 The American Association for Cancer Research
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
Gundem, Gunes; Van Loo, Peter; Kremeyer, Barbara; Alexandrov, Ludmil B; Tubio, JMC; Papaemmanuil, Elli; Brewer, Daniel S; Kallio, Heini ML; Hagnas, Gunilla; Annala, Matti; The evolutionary history of lethal metastatic prostate cancer (vol 87, pg 511, 2020) Nature 584 7820 E18-E18 2020 Macmillan Publishers Ltd., London, England
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 Endocrine Abstracts 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
Luoto, Suvi; Hermelo, Ismaïl; Vuorinen, Elisa M; Hannus, Paavo; Kesseli, Juha; Nykter, Matti; Granberg, Kirsi J; Computational Characterization of Suppressive Immune Microenvironments in GlioblastomaComputational Analysis of Immune Responses in Glioblastoma Cancer research 78 19 5574-5585 2018 American Association for Cancer Research
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
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 Cancer Research 78 16_Supplement A020-A020 2018 The American Association for Cancer Research
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
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
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
Ruusuvuori, Pekka; Valkonen, Masi; Kartasalo, Kimmo; Valkonen, Mira; Visakorpi, Tapio; Nykter, Matti; Latonen, Leena; Spatial analysis of histology in 3D: quantification and visualization of organ and tumor level tissue environment Heliyon 8 1 e08762 2022 Elsevier
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
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 Springer
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
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 Citeseer
Rodriguez-Martinez, Alejandra; Vuorinen, Elisa M; Shcherban, Anastasia; Uusi-Mäkelä, Joonas; Rajala, Nina KM; Nykter, Matti; Kallioniemi, Anne; Novel ZNF414 activity characterized by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1865 3 194811 2022 Elsevier
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 Cancer Research 78 13_Supplement 3427-3427 2018 The American Association for Cancer Research
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 Elsevier
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 …
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 Cancer Research 71 8_Supplement 1145-1145 2011 American Association for Cancer Research
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 San Francisco, USA
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 Springer
Veskimäe, K; Staff, S; Grönholm, A; Pesu, M; Laaksonen, M; Nykter, M; Isola, J; Mäenpää, J; Assessment of PARP protein expression in epithelial ovarian cancer by ELISA pharmacodynamic assay and immunohistochemistry Tumor Biology 37 9 11991-11999 2016 Springer
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 San Francisco, USA
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 CancerctDNA Alterations in Metastatic Bladder Cancer Clinical Cancer Research 23 21 6487-6497 2017 American Association for Cancer Research
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 Cancer Research 70 8_Supplement 2008-2008 2010 American Association for Cancer Research
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
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
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
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
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
Vandekerkhove, Gillian; Lavoie, Jean-Michel; Annala, Matti; Murtha, Andrew J; Sundahl, Nora; Walz, Simon; Sano, Takeshi; Taavitsainen, Sinja; Ritch, Elie; Fazli, Ladan; Plasma ctDNA is a tumor tissue surrogate and enables clinical-genomic stratification of metastatic bladder cancer Nature communications 12 1 1-12 2021 Nature Publishing Group
Mäki-Marttunen, Tuomo; Aćimović, 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 Research Foundation
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
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 SCANDINAVIAN JOURNAL OF IMMUNOLOGY 83 5 383-383 2016 WILEY-BLACKWELL 111 RIVER ST, HOBOKEN 07030-5774, NJ USA
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
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
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
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
Zhang, Wei; Nykter, Matti; Chen, Kexin; Next generation sequencing applications in cancer research Cancer letters 340 2 149-150 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 Cancer Research 76 14_Supplement 4148-4148 2016 The American Association for Cancer Research
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
Kauppi, Jukka-Pekka; Nykter, Matti; Niemi, Jari; Clustering Method for Data Having Outliers and Clusters with Varying Sizes and Densities 2011
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
Taavitsainen, S; Engedal, Nikolai; Cao, S; Handle, Florian; Erickson, A; Prekovic, Stefan; 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
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 58702 2008 APS
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 1 5 2016 Elsevier
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 Cancer Research 79 13_Supplement LB-096-LB-096 2019 The American Association for Cancer Research
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
Nurminen, R; Afyounian, E; Tuominen, J; Scaravilli, M; Saarinen, M; Annala, M; Paunu, N; Haapasalo, H; Nykter, M; Granberg, KJ; Identification of predisposing germline variants in familial glioma EUROPEAN JOURNAL OF HUMAN GENETICS 28 SUPPL 1 517-518 2020 SPRINGERNATURE CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND
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
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
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
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
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 …
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
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. Cancer Research 66 8_Supplement 1181-1181 2006 American Association for Cancer Research
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
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
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
Annala, M; Fu, S; Bacon, JVW; Sipola, J; Iqbal, N; Ferrario, C; Ong, M; Wadhwa, D; Hotte, SJ; Lo, G; Cabazitaxel versus abiraterone or enzalutamide in poor prognosis metastatic castration-resistant prostate cancer: a multicentre, randomised, open-label, phase II trial Annals of Oncology 32 7 896-905 2021 Elsevier
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 Washington, DC
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. Blood 104 11 1395 2004 Elsevier
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 Clinical Cancer Research 26 11_Supplement PR09-PR09 2020 The American Association for Cancer Research
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
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
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
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 Cancer Research 78 13_Supplement 3353-3353 2018 The American Association for Cancer Research
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
Hautamäki, V; Nykter, M; Heinäniemi, M; Nykter, Matti; Data-driven characterization of molecular phenotypes across heterogenous sample collections
Leinonen, Katri A; Saramäki, Outi R; Furusato, Bungo; Kimura, Takahiro; Takahashi, Hiroyuki; Egawa, Shin; Suzuki, Hiroyoshi; Keiger, Kerri; Ho Hahm, Sung; Isaacs, William B; Loss of PTEN Is Associated with Aggressive Behavior in ERG-Positive Prostate CancerExpression of ERG in Prostate Cancer Cancer epidemiology, biomarkers & prevention 22 12 2333-2344 2013 American Association for Cancer Research
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
Itkonen, Harri M; Coleman, Ilsa M; Urbanucci, Alfonso; Barfeld, Stefan J; Kytölä, Ville; Itkonen, Harri M; Coleman, Ilsa M; Vodák, Daniel; Sjöblom, Liisa; Sheng, Xia; Let us know how access to this document benefits yo u
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
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
Gundem, Gunes; Van Loo, Peter; Kremeyer, Barbara; Alexandrov, Ludmil B; Tubio, Jose; Papaemmanuil, Elli; Brewer, Daniel S; Kallio, Heini ML; Hägnäs, Gunilla; Annala, Matti; Author Correction: The evolutionary history of lethal metastatic prostate cancer Nature 584 7820 E18-E18 2020 Nature Publishing Group
Nykter, Matti; Ruusuvuori, Pekka; Carlberg, Carsten; Yli-Harja, Olli; Seventh International Workshop on Computational Systems Biology, WCSB 2010, June 16-18, 2010, Luxembourg 2010
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
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
Hahne, Lauri; Kesseli, Juha; Nykter, Matti; Evaluation of compressors for estimating normalized compression distance Eight International Workshop on Computational Systems Biology, WCSB 2011, June 6-8, Zurich, Switzerland. TICSP series 53-56 2011 WCSB 2011
Zhang; Nykter, Matti; Kexin, Chen; Featuring the guest editor special issue genome sequencing CANCER LETTERS 340 2 151-151 2013 ELSEVIER IRELAND LTD ELSEVIER HOUSE, BROOKVALE PLAZA, EAST PARK SHANNON, CO …
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
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
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 InhibitionProstate Cancer Evolution during Sequential AR Inhibition Clinical Cancer Research 27 16 4610-4623 2021 American Association for Cancer Research
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 Cancer Research 74 19_Supplement 2363-2363 2014 The American Association for Cancer Research
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
Yang, Mi; Petralia, Francesca; Li, Zhi; Li, Hongyang; Ma, Weiping; Song, Xiaoyu; Kim, Sunkyu; Lee, Heewon; Yu, Han; Lee, Bora; Community assessment of the predictability of cancer protein and phosphoprotein levels from genomics and transcriptomics Cell systems 11 2 186-195. e9 2020 Elsevier
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
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
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
Raittinen, Paavo VH; Pennanen, Pasi; Syvälä, Heimo; Bläuer, Merja; Ikonen, Niina; Nätkin, Reetta; Nykter, Matti; Tammela, Teuvo; Ilmonen, Pauliina; Murtola, Teemu T; Genetic landscape changes in metastatic prostate cancer after sequential steps of androgen targeted therapy Cancer Research 80 16_Supplement 5913-5913 2020 The American Association for Cancer Research
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 Eight International Workshop on Computational Systems Biology, WCSB 2011, June 6-8, Zurich, Switzerland. TICSP series 137-140 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 Wiley Online Library
Tammela, T; Kallio, H; Annala, M; Brofeldt, A; Hieta, R; Kivinummi, K; Nykter, M; Lilja, H; Bova, G; Visakorpi, T; Neoadjuvant hormonal therapies induce the expression of AR transcript variants European Urology Supplements 3 16 e255-e256 2017
Dufva, Olli; Pölönen, Petri; Brück, Oscar; Keränen, Mikko A; Mehtonen, Juha; Siitonen, Sanna M; Leivonen, Suvi-Katri; Meriranta, Leo; Leppa, Sirpa; Nykter, Matti; Immunogenomic Landscape of Hematological Malignancies 2018 American Society of Hematology Washington, DC
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
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
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
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
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 Cancer Research 72 8_Supplement 4939-4939 2012 American Association for Cancer Research
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 Springer
Tammela, T; Latonen, L; Afyounian, E; Jylhä, A; Nättinen, J; Aapola, U; Annala, M; Kivinummi, K; Beuerman, R; Uusitalo, H; Integrative analysis of the proteome in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression European Urology Supplements 17 2 e159 2018 Elsevier
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
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 Cancer Research 71 8_Supplement 4906-4906 2011 American Association for Cancer Research
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 1 205-214 2009 Wiley Online Library
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
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; Jawahar Deen, Ashik; 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
Uusi-Mäkelä, Joonas; Afyounian, Ebrahim; Tabaro, Francesco; Häkkinen, Tomi; Lussana, Alessandro; Shcherban, Anastasia; Annala, Matti; Nurminen, Riikka; Kivinummi, Kati; Tammela, Teuvo LJ; Chromatin accessibility analysis uncovers regulatory element landscape in prostate cancer progression bioRxiv 2020 Cold Spring Harbor Laboratory
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 Cancer Research 75 15_Supplement LB-284-LB-284 2015 The American Association for Cancer Research
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 Cancer Research 74 19_Supplement LB-92-LB-92 2014 The American Association for Cancer Research
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
Yli-Hietanen, Jari; Ylipää, Antti; Yli-Harja, Olli; Cancer research in the era of next-generation sequencing and big data calls for intelligent modeling Chinese journal of cancer 34 3 1-4 2015 BioMed Central
YLIPÄÄ, ANTTI; SARJALLISET MONTE CARLO-MENETELMÄT STOKAS-TISEN HODGKIN–HUXLEY-MALLIN PARAMETRIEN ESTI-MOINNISSA
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
Pettinen, Antti; Mäkiraatikka, E; Manninen, Tiina; Smolander, O; Ylipää, A; Hituri, Katri; Linne, M; Evaluation of deterministic and stochastic simulation tools for cellular signaling Frontiers in Neuroinformatics 2008
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
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
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 MDPI
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 Cancer Research 72 8_Supplement 5198-5198 2012 American Association for Cancer Research
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
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
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
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
Liuksiala, Thomas Edward; Blood Cancer Lineage Identification: A Machine Learning Approach 2015
Rooda, Ilmatar; Kaselt, Birgitta; Liivrand, Maria; Smolander, Olli-Pekka; Salumets, Andres; Velthut-Meikas, Agne; Hsa-mir-548 family expression in human reproductive tissues BMC genomic data 22 1 1-13 2021 Springer
de Bock, Charles E; Demeyer, Sofie; Degryse, Sandrine; Verbeke, Delphine; Sweron, Bram; Gielen, Olga; Vandepoel, Roel; Vicente, Carmen; Vanden Bempt, Marlies; Dagklis, Antonis; HOXA9 Cooperates with Activated JAK/STAT Signaling to Drive Leukemia DevelopmentHOXA9 and Mutant JAK3 Cooperation in Leukemia Cancer discovery 8 5 616-631 2018 American Association for Cancer Research
John, Elisabeth; Wienecke-Baldacchino, Anke; Liivrand, Maria; Heinaniemi, Merja; Carlberg, Carsten; Sinkkonen, Lasse; Dataset integration identifies transcriptional regulation of microRNA genes by PPARc in differentiating mouse 3T3-L1 adipocytes
Mehtonen, Juha; Teppo, Susanna; Lahnalampi, Mari; Kokko, Aleksi; Kaukonen, Riina; Oksa, Laura; Bouvy-Liivrand, Maria; Malyukova, Alena; Mäkinen, Artturi; Laukkanen, Saara; Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities Genome medicine 12 1 1-25 2020 Springer
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 41 7 2149-2167 2021 Lippincott Williams & Wilkins Hagerstown, MD
John, Elisabeth; Wienecke-Baldacchino, Anke; Liivrand, Maria; Heinäniemi, Merja; Carlberg, Carsten; Sinkkonen, Lasse; Dataset integration identifies transcriptional regulation of microRNA genes by PPARγ in differentiating mouse 3T3-L1 adipocytes Nucleic acids research 40 10 4446-4460 2012 Oxford University Press
Gerard, Deborah; Bouvy-Liivrand, Maria; Sinkkonen, Lasse; Sauter, Thomas; TIME-COURSE ANALYSIS OF GENE EXPRESSION DYNAMICS OF ADIPOGENESIS AND OSTEOBLASTOGENESIS Bioinformatics: Integrating data, teams and disciplines 17 2014
Moreau, Pierre; Ord, Tiit; Lonnberg, Tapio; Bouvy-Liivrand, Maria; Aavik, Einari; Yla-Herttuala, Seppo; Heinaniemi, Merja; Kaikkonen-Maatta, Minna; Dissecting the Roles of Altered Cell Type Composition and Cell Specific Responses to Proatherogenic Stimuli in Contributing to Global Gene Expression Changes in Atherosclerotic Aorta JOURNAL OF VASCULAR RESEARCH 56 54-54 2019 KARGER ALLSCHWILERSTRASSE 10, CH-4009 BASEL, SWITZERLAND
Korhonen, Matti; Maliniemi, Pilvi; Impola, Ulla; Liivrand, Maria; Heinaniemi, Merja; Nascent Transcripts of Target-Activated CD19-CAR-T Cells Reveal Early Activation of the C-REL and NF kappa B Pathway MOLECULAR THERAPY 27 4 460-460 2019 CELL PRESS 50 HAMPSHIRE ST, FLOOR 5, CAMBRIDGE, MA 02139 USA
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
Moreau, Pierre R; Örd, Tiit; Downes, Nicholas L; Niskanen, Henri; Bouvy-Liivrand, Maria; Aavik, Einari; Ylä-Herttuala, Seppo; Kaikkonen, Minna U; Transcriptional profiling of hypoxia-regulated non-coding RNAs in human primary endothelial cells Frontiers in Cardiovascular Medicine 5 159 2018 Frontiers Media SA
Linna-Kuosmanen, Suvi; Tomas Bosch, Vanesa; Moreau, Pierre R; Bouvy-Liivrand, Maria; Niskanen, Henri; Kansanen, Emilia; Kivelä, Annukka; Hartikainen, Juha; Hippeläinen, Mikko; Kokki, Hannu; NRF2 is a key regulator of endothelial microRNA expression under proatherogenic stimuli Cardiovascular research 117 5 1339-1357 2021 Oxford University Press
Liivrand, Maria; Modelling and global analysis of transcript profiles reveals dynamic roles for microRNAs in transcriptional networks controlling lineage commitment. 2014 University of Luxembourg,​ Luxembourg,​​ Luxembourg
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.
Bouvy-Liivrand, Maria; Hernández de Sande, Ana; Pölönen, Petri; Mehtonen, Juha; Vuorenmaa, Tapio; Niskanen, Henri; Sinkkonen, Lasse; Kaikkonen, Minna Unelma; Heinäniemi, Merja; Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture Nucleic acids research 45 17 9837-9849 2017 Oxford University Press
Bouvy-Liivrand, Maria; Heinäniemi, Merja; John, Elisabeth; Schneider, Jochen G; Sauter, Thomas; Sinkkonen, Lasse; Combinatorial regulation of lipoprotein lipase by microRNAs during mouse adipogenesis RNA biology 11 1 76-91 2014 Taylor & Francis
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
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
Simao, Felipe A; Hieta, Reija; Pulman, Jane A; Madonna, Gabriele; Ascierto, Paolo Antonio; Lewensohn, Rolf; Masucci, Giuseppe V; SRF-CLICAL: An approach for patient risk stratification using random forest models bioRxiv 2021 Cold Spring Harbor Laboratory
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
Zdobnov, Evgeny M; Tegenfeldt, Fredrik; Kuznetsov, Dmitry; Waterhouse, Robert M; Simão, 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
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
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
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
Simão, Felipe A; Utilities of OrthoDB and BUSCO Plant and Animal Genome XXVI Conference (January 13-17, 2018) PAG
Manni, Mosè; Berkeley, Matthew R; Seppey, Mathieu; Simão, 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 Molecular Biology and Evolution 38 10 4647-4654 2021 Oxford University Press
Madonna, Gabriele; Masucci, Giuseppe V; Capone, Mariaelena; Mallardo, Domenico; Grimaldi, Antonio Maria; Simeone, Ester; Vanella, Vito; Festino, Lucia; Palla, Marco; Scarpato, Luigi; Clinical Categorization Algorithm (CLICAL) and Machine Learning Approach (SRF-CLICAL) to Predict Clinical Benefit to Immunotherapy in Metastatic Melanoma Patients: Real-World Evidence from the Istituto Nazionale Tumori IRCCS Fondazione Pascale, Napoli, Italy Cancers 13 16 4164 2021 MDPI
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
Waterhouse, Robert M; Seppey, Mathieu; Simão, Felipe A; Zdobnov, Evgeny M; Using BUSCO to assess insect genomic resources Insect genomics 59-74 2019 Springer
Waterhouse, Robert; Tenan, Mirna; Simão, Felipe A; Ioannidis, Panagiotis; Kriventseva, Evgenia V; Zdobnov, Evgeny M; Large-scale gene functional inference through orthology F1000Research 5 2016
Rotenberg, Dorith; Baumann, Aaron A; Ben-Mahmoud, Sulley; Christiaens, Olivier; Dermauw, Wannes; Ioannidis, Panagiotis; Jacobs, Chris GC; Vargas Jentzsch, Iris M; 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
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 1258522 2015 American Association for the Advancement of Science
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
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
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
Simão, Felipe A; Waterhouse, Robert M; Ioannidis, Panagiotis; Kriventseva, Evgenia V; Zdobnov, Evgeny M; Supplementary online material 2017
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
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, Ella F; Visser, Marcel E; Sheldon, Ben C; Groenen, M; Slate, J; 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 University of Sheffield
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
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
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 San Francisco, USA
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 _
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, biomarkers & prevention 22 3 452-460 2013 American Association for Cancer Research
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
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
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
Rantapero, Tommi; Developing a Framework for Analysis of Next-Generation Sequencing Data in Cancer Genetics and Epigenetics 2020 Tampere University
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
Rantapero, Tommi; Bioinformatic analysis of next-generation sequencing data 2012
Georgolopoulos, Grigorios; Psatha, Nikoletta; Iwata, Mineo; Nishida, Andrew; Som, Tannishtha; Yiangou, Minas; Stamatoyannopoulos, John A; Vierstra, Jeff; Discrete regulatory modules instruct hematopoietic lineage commitment and differentiation Nature communications 12 1 1-15 2021 Nature Publishing Group
Georgolopoulos, Grigorios; Psatha, Nikoletta; Iwata, Mineo; Nishida, Andrew; Som, Tannishtha; Yiangou, Minas; Stamatoyannopoulos, John A; Vierstra, Jeff; Chromatin dynamics during hematopoiesis reveal discrete regulatory modules instructing differentiation Biorxiv 2020.04. 02.022566 2021 Cold Spring Harbor Laboratory
Psatha, Nikoletta; Georgolopoulos, Grigorios; Phelps, Susan; Papayannopoulou, Thalia; Brief report: a differential transcriptomic profile of ex vivo expanded adult human hematopoietic stem cells empowers them for engraftment better than their surface phenotype Stem cells translational medicine 6 10 1852-1858 2017 Oxford University Press
Georgolopoulos, Grigorios; Parducci, Laura; Drouzas, Andreas D; A short phylogenetically informative cpDNA fragment for the identification of Pinus species Biochemical Systematics and Ecology 66 166-172 2016 Elsevier
Psatha, Nikoletta; Georgakopoulou, Aphrodite; Li, Chang; Nandakumar, Vivek; Georgolopoulos, Grigorios; Acosta, Reyes; Paschoudi, Kiriaki; Nelson, Jemma; Chee, Daniel; Athanasiadou, Anastasia; Enhanced HbF reactivation by multiplex mutagenesis of thalassemic CD34+ cells in vitro and in vivo blood 138 17 1540-1553 2021 American Society of Hematology
Zajitschek, Felix; Georgolopoulos, Grigorios; Vourlou, Anna; Ericsson, Maja; Zajitschek, Susanne RK; Friberg, Urban; Maklakov, Alexei A; Evolution under dietary restriction decouples survival from fecundity in Drosophila melanogaster females The Journals of Gerontology: Series A 74 10 1542-1548 2019 Oxford University Press US
Vallianou, Ioanna; Christofi, Panayiota; Varvaraki, Angeliki; Psatha, Nikoletta; Georgolopoulos, Grigorios; Georgakopoulou, Afrodite; Papayanni, Penelope; Anagnostopoulos, Achilles; Yannaki, Evangelia; UM171 Efficiently Expands Genetically Modified Haematopoietic Stem Cells from Mobilized Blood and Transduces Preferentially the Erythroid Lineage Molecular Therapy 27 4 456-456 2019 Elsevier (Cell Press)
Zajitschek, Felix; Zajitschek, Susanne RK; Canton, Cindy; Georgolopoulos, Grigorios; Friberg, Urban; Maklakov, Alexei A; Evolution under dietary restriction increases male reproductive performance without survival cost Proceedings of the Royal Society B: Biological Sciences 283 1825 20152726 2016 The Royal Society
Psatha, Nikoleta; Sova, Pavel; Georgolopoulos, Grigorios; Navas, Pat; Stamatoyannopoulos, John A; Vierstra, Jeff; Papayannopoulou, Thalia; Stamatoyannopoulos, George; Identifying Novel Erythroid Specific Enhancers to Optimize Transgene Expression in Beta Globin Gene Therapy Molecular Therapy 27 4 416-417 2019 Elsevier (Cell Press)
Georgolopoulos, Grigorios; Iwata, Mineo; Nishida, Andrew; Som, Tannishtha; Stamatoyannopoulos, John A; Vierstra, Jeff; Comprehensive Identification of Cis-and Trans-Elements Driving Human Hematopoiesis Blood 130 3774 2017 Elsevier
Ulyanova, Tatyana; Georgolopoulos, Grigorios; Papayannopoulou, Thalia; Reappraising the role of α5 integrin and the microenvironmental support in stress erythropoiesis Experimental hematology 81 16-31. e4 2020 Elsevier
Georgolopoulos, G; Iwata, M; Nishida, A; Som, T; Yiangou, M; Stamatoyannopoulos, JA; Vierstra, J; PF454 DENSE TEMPORAL PROFILING OF EPIGENETIC EVENTS REVEALS TWO DISCRETE PROGRAMS THAT GOVERN HUMAN ERYTHROPOIESIS HemaSphere 3 S1 179 2019 LWW
Georgolopoulos, Grigorios; Iwata, Mineo; Psatha, Nikoletta; Yiangou, Minas; Vierstra, Jeff; Unbiased phenotypic identification of functionally distinct hematopoietic progenitors Journal of Biological Research-Thessaloniki 26 1 1-5 2019 Springer
Stefos, Georgios C; Szantai, Eszter; Konstantopoulos, Dimitris; Samiotaki, Martina; Fousteri, Maria; aniFOUND: analysing the associated proteome and genomic landscape of the repaired nascent non-replicative chromatin Nucleic acids research 49 11 e64-e64 2021 Oxford University Press
Lavigne, Matthieu D; Konstantopoulos, Dimitris; Ntakou-Zamplara, Katerina Z; Liakos, Anastasios; Fousteri, Maria; Global unleashing of transcription elongation waves in response to genotoxic stress restricts somatic mutation rate Nature communications 8 1 1-15 2017 Nature Publishing Group
Tousa, Sofia; Semitekolou, Maria; Morianos, Ioannis; Banos, Aggelos; Trochoutsou, Aikaterini I; Brodie, Tess M; Poulos, Nikolaos; Samitas, Konstantinos; Kapasa, Maria; Konstantopoulos, Dimitris; Activin-A co-opts IRF4 and AhR signaling to induce human regulatory T cells that restrain asthmatic responses Proceedings of the National Academy of Sciences 114 14 E2891-E2900 2017 National Acad Sciences
Konstantopoulos, D; Tzaferis, C; Sakkou, M; Liakos, A; Lavigne, M; Karamitros, D; Fousteri, M; Armaka, M; Kollias, G; OP0099 FUNCTIONAL MAPPING OF SYNOVIAL FIBROBLAST POPULATIONS IN HEALTH AND ARTHRITIC DISEASE: INSIGHTS INTO THE PATHOGENIC REMODELING OF SYNOVIAL MICROENVIRONMENT 2020 BMJ Publishing Group Ltd
Liakos, Anastasios; Konstantopoulos, Dimitris; Lavigne, Matthieu D; Fousteri, Maria; Continuous transcription initiation guarantees robust repair of transcribed genes and regulatory regions in response to DNA damage bioRxiv 712364 2019 Cold Spring Harbor Laboratory
Zannikou, Markella; Barbayianni, Ilianna; Fanidis, Dionysios; Grigorakaki, Theodora; Vlachopoulou, Evlalia; Konstantopoulos, Dimitris; Fousteri, Maria; Nikitopoulou, Ioanna; Kotanidou, Anastasia; Kaffe, Eleanna; MAP3K8 Regulates Cox-2–Mediated Prostaglandin E2 Production in the Lung and Suppresses Pulmonary Inflammation and Fibrosis The Journal of Immunology 206 3 607-620 2021 Am Assoc Immnol
Liakos, A; Konstantopoulos, D; Spyropoulou, Z; Fousteri, M; Lavigne, MD; Elucidating the role of active transcription in keeping genome integrity in check BRITISH JOURNAL OF DERMATOLOGY 180 6 E217-E217 2019 WILEY 111 RIVER ST, HOBOKEN 07030-5774, NJ USA
Armaka, Marietta; Konstantopoulos, Dimitris; Tzaferis, Christos; Lavigne, Matthieu D; Sakkou, Maria; Liakos, Anastasios; Sfikakis, Petros P; Dimopoulos, Meletios A; Fousteri, Maria; Kollias, George; Single-cell chromatin and transcriptome dynamics of Synovial Fibroblasts transitioning from homeostasis to pathology in modelled TNF-driven arthritis bioRxiv 2021 Cold Spring Harbor Laboratory
Semitekolou, Maria; Morianos, Ioannis; Banos, Aggelos; Konstantopoulos, Dimitris; Adamou-Tzani, Marina; Sparwasser, Tim; Xanthou, Georgina; Dendritic cells conditioned by activin A–induced regulatory T cells exhibit enhanced tolerogenic properties and protect against experimental asthma Journal of Allergy and Clinical Immunology 141 2 671-684. e7 2018 Elsevier
Liakos, Anastasios; Konstantopoulos, Dimitris; Lavigne, Matthieu D; Fousteri, Maria; Continuous transcription initiation guarantees robust repair of all transcribed genes and regulatory regions Nature communications 11 1 1-16 2020 Nature Publishing Group
Morianos, Ioannis; Trochoutsou, Aikaterini I; Papadopoulou, Gina; Semitekolou, Maria; Banos, Aggelos; Konstantopoulos, Dimitris; Manousopoulou, Antigoni; Kapasa, Maria; Wei, Ping; Lomenick, Brett; Activin-A limits Th17 pathogenicity and autoimmune neuroinflammation via CD39 and CD73 ectonucleotidases and Hif1-α–dependent pathways Proceedings of the National Academy of Sciences 117 22 12269-12280 2020 National Acad Sciences
Hieta, Reija; Studying androgen receptor gene aberrations in prostate cancer using targeted DNA and RNA sequencing panels 2018
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
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.]
Hieta, Reija; Kukkola, Liisa; Permi, Perttu; Pirilä, Päivi; Kivirikko, Kari I; Kilpeläinen, Ilkka; Myllyharju, Johanna; The peptide-substrate-binding domain of human collagen prolyl 4-hydroxylases: backbone assignments, secondary structure, and binding of proline-rich peptides Journal of Biological Chemistry 278 37 34966-34974 2003 ASBMB
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)
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.]
Jiang, Yuxiang; Oron, Tal Ronnen; Clark, Wyatt T; Bankapur, Asma R; D’Andrea, Daniel; Lepore, Rosalba; Funk, Christopher S; Kahanda, Indika; Verspoor, Karin M; Ben-Hur, Asa; Availability: This version is available at: http://porto. polito. it/2649752/since: September 2016
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
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
Jiang, Yuxiang; Oron, Tal Ronnen; Clark, Wyatt T; Bankapur, Asma R; D’Andrea, Daniel; Lepore, Rosalba; Funk, Christopher S; Kahanda, Indika; Verspoor, Karin M; Ben-Hur, Asa; An expanded evaluation of protein function prediction methods shows an improvement in accuracy Genome biology 17 1 1-19 2016 BioMed Central
Hieta, Reija; Myllyharju, Johanna; Cloning and characterization of a low molecular weight prolyl 4-hydroxylase from Arabidopsis thaliana: effective hydroxylation of proline-rich, collagen-like, and hypoxia-inducible transcription factor α-like peptides Journal of Biological Chemistry 277 26 23965-23971 2002 ASBMB
Koski, M Kristian; Hieta, Reija; Hirsilä, Maija; Rönkä, Anna; Myllyharju, Johanna; Wierenga, Rik K; The crystal structure of an algal prolyl 4-hydroxylase complexed with a proline-rich peptide reveals a novel buried tripeptide binding motif Journal of Biological Chemistry 284 37 25290-25301 2009 ASBMB
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
Pekkala, Mira; Hieta, Reija; Bergmann, Ulrich; Kivirikko, Kari I; Wierenga, Rik K; Myllyharju, Johanna; The peptide-substrate-binding domain of collagen prolyl 4-hydroxylases is a tetratricopeptide repeat domain with functional aromatic residues Journal of Biological Chemistry 279 50 52255-52261 2004 ASBMB
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 ASBMB
Kukkola, Liisa; Hieta, Reija; Kivirikko, Kari I; Myllyharju, Johanna; Identification and characterization of a third human, rat, and mouse collagen prolyl 4-hydroxylase isoenzyme Journal of Biological Chemistry 278 48 47685-47693 2003 ASBMB
Kivirikko, Kari; Myllyharju, Johanna; Kukkola, Liisa; Hieta, Reija; Alpha (III) subunit for prolyl 4-hydroxylase 2002 Google Patents
Hamis, Sara; Somervuo, Panu; Agren, J Arvid; Tadele, Dagim Shiferaw; Kesseli, Juha; Scott, Jacob G; Nykter, Matti; Gerlee, Philip; Finkelshtein, Dmitri; Ovaskainen, Otso; Spatial cumulant models enable spatially informed treatment strategies and analysis of local interactions in cancer systems bioRxiv 2022 Cold Spring Harbor Laboratory
Aakula, Anna; Sharma, Mukund; Tabaro, Francesco; Honkanen, Henrik; Schapira, Matthieu; Arrowsmith, Cheryl; Nykter, Matti; Westermarck, Jukka; RAS and PP2A activities converge on epigenetic gene regulation bioRxiv 2022 Cold Spring Harbor Laboratory
Cerqueira, Juliana Xavier de Miranda; Saavalainen, Paivi; Kurppa, Kalle; Laurikka, Pilvi; Huhtala, Heini; Nykter, Matti; Koskinen, Lotta LE; Yohannes, Dawit A; Kilpelainen, Elina; Shcherban, Anastasia; Coeliac disease phenotypic variation unraveled by disease-susceptibility loci in a deeply phenotyped Finnish cohort EUROPEAN JOURNAL OF HUMAN GENETICS 30 SUPPL 1 586-586 2022 SPRINGERNATURE CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND
Yusuf, Leeban; Heatley, Matthew; Palmer, Joseph PG; Barton, Henry J; Cooney, Christopher R; Goßmann, Toni; Non-coding rather than coding regions underpin avian bill shape diversification at macroevolutionary scales bioRxiv 2019
Zijlmans, Dick W; Talon, Irene; Verhelst, Sigrid; Bendall, Adam; Van Nerum, Karlien; Javali, Alok; Malcolm, Andrew A; van Knippenberg, Sam SFA; Biggins, Laura; To, San Kit; Integrated multi-omics reveal polycomb repressive complex 2 restricts human trophoblast induction Nature cell biology 24 6 858-871 2022 Nature Publishing Group
Cao, Shaolong; Wang, Jennifer R; Ji, Shuangxi; Yang, Peng; Dai, Yaoyi; Guo, Shuai; Montierth, Matthew D; Shen, John Paul; Zhao, Xiao; Chen, Jingxiao; Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression Nature biotechnology 1-10 2022 Nature Publishing Group
Sharma, Mukund; Aakula, Anna; Tabaro, Francesco; Pavic, Karolina; Huhtaniemi, Riikka; Nykter, Matti; Westermarck, Jukka; Chromatin repressor complex as a converge point of RAS and PP2A activities in lung cancer Cancer Research 82 12_Supplement 2958-2958 2022 The American Association for Cancer Research
Taavitsainen, Sinja; Engedal, Nikolai; Cao, Shaolong; Handle, Florian; Erickson, Andrew; Prekovic, Stefan; Wetterskog, Daniel; Tolonen, Teemu; Vuorinen, Elisa M; Kiviaho, Antti; Single-cell transcriptome and chromatin sequencing uncover gene expression and gene regulatory patterns associated with enzalutamide resistance Cancer Research 82 12_Supplement 401-401 2022 The American Association for Cancer Research
Herberts, Cameron; Annala, Matti; Sipola, Joonatan; Ng, Sarah W; Chen, Xinyi E; Nurminen, Anssi; Korhonen, Olga; Munzur, Aslı D; Beja, Kevin; Schönlau, Elena; Clonal architecture and evolution of treatment-resistant prostate cancer via deep whole-genome ctDNA sequencing Cancer Research 82 12_Supplement 3625-3625 2022 The American Association for Cancer Research
Papadopoulou, Anastasia; Stavridou, Fani; Giannaki, Maria; Paschoudi, Kiriaki; Chatzopoulou, Fani; Gavriilaki, Eleni; Georgolopoulos, Grigorios; Anagnostopoulos, Achilles; Yannaki, Evangelia; Robust SARS-COV-2-specific T-cell immune memory persists long-term in immunocompetent individuals post BNT162b2 double shot Heliyon 8 7 e09863 2022 Elsevier
Roumelioti, Fani; Tzaferis, Christos; Konstantopoulos, Dimitris; Papadopoulou, Dimitra; Prados, Alejandro; Sakkou, Maria; Liakos, Anastasios; Chouvardas, Panagiotis; Meletakos, Theodore; Pandis, Yiannis; miR-221/222 drive synovial fibroblast expansion and pathogenesis of TNF-mediated arthritis bioRxiv 2022 Cold Spring Harbor Laboratory
Herberts, Cameron; Annala, Matti; Sipola, Joonatan; Ng, Sarah WS; Chen, Xinyi E; Nurminen, Anssi; Korhonen, Olga V; Munzur, Aslı D; Beja, Kevin; Schönlau, Elena; Deep whole-genome ctDNA chronology of treatment-resistant prostate cancer Nature 1-10 2022 Nature Publishing Group
Armaka, Marietta; Konstantopoulos, Dimitris; Tzaferis, Christos; Lavigne, Matthieu D; Sakkou, Maria; Liakos, Anastasios; Sfikakis, Petros P; Dimopoulos, Meletios A; Fousteri, Maria; Kollias, George; Single-cell multimodal analysis identifies common regulatory programs in synovial fibroblasts of rheumatoid arthritis patients and modeled TNF-driven arthritis Genome medicine 14 1 1-25 2022 BioMed Central
Koivisto, Maria; Tolvanen, Tuomas A; Toimela, Tarja; Miinalainen, Ilkka; Kiviaho, Antti; Kesseli, Juha; Nykter, Matti; Eklund, Lauri; Heinonen, Tuula; Functional human cell-based vascularised cardiac tissue model for biomedical research and testing Scientific reports 12 1 1-13 2022 Nature Publishing Group
Psatha, N; Sova, P; Georgolopoulos, G; Iwata, M; Paschoudi, K; Kirtsou, A; Ulyanova, T; Stamatoyannopoulos, JA; Yannaki, E; Papayannopoulou, T; P1437: NOVEL ERYTHROID ENHANCERS IMPROVE GENE THERAPY VECTORS FOR BETA-HEMOGLOBINOPATHIES HemaSphere 6 1320-1321 2022 LWW
Rautajoki, Kirsi J; Jaatinen, Serafiina; Tiihonen, Aliisa M; Annala, Matti; Vuorinen, Elisa M; Kivinen, Anni; Rauhala, Minna J; Maass, Kendra K; Pajtler, Kristian W; Yli-Harja, Olli; PTPRD and CNTNAP2 as markers of tumor aggressiveness in oligodendrogliomas Scientific Reports 12 1 1-11 2022 Nature Publishing Group

Try our new Virtual Bioinformatics Core service!

End-of-year offer 2022