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.
| Authors | Title | Publication | Volume | Number | Pages | Year | Publisher |
|---|---|---|---|---|---|---|---|
| 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, Ltd | |
| 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 |
| 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 |
| 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 | |
| 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 |
| Pölönen, Petri; Mehtonen, Juha; Lin, Jake; Liuksiala, Thomas; Häyrynen, Sergei; Teppo, Susanna; Mäkinen, Artturi; Kumar, Ashwini; Malani, Disha; Pohjolainen, Virva; | Hemap: an interactive online resource for characterizing molecular phenotypes across hematologic malignancies | Cancer research | 79 | 10 | 2466-2479 | 2019 | American Association for Cancer Research |
| Annala, Matti; Vandekerkhove, Gillian; Khalaf, Daniel; Taavitsainen, Sinja; Beja, Kevin; Warner, Evan W; Sunderland, Katherine; Kollmannsberger, Christian; Eigl, Bernhard J; Finch, Daygen; | Circulating tumor DNA genomics correlate with resistance to abiraterone and enzalutamide in prostate cancer | Cancer discovery | 8 | 4 | 444-457 | 2018 | American Association for Cancer Research |
| 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 | |||
| 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 | 14083 | 2022 | Nature Publishing Group UK London |
| 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 | 17978 | 2017 | Nature Publishing Group UK London |
| 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 | 1-4 | 2015 | BioMed Central | |
| Taavitsainen, Sinja; Annala, Matti; Ledet, Elisa; Beja, Kevin; Miller, Patrick J; Moses, Marcus; Nykter, Matti; Chi, Kim N; Sartor, Oliver; Wyatt, Alexander W; | Evaluation of commercial circulating tumor DNA test in metastatic prostate cancer | JCO Precision Oncology | 3 | 1-9 | 2019 | American Society of Clinical Oncology | |
| Nykter, Matti; Aho, Tommi; Ahdesmäki, Miika; Ruusuvuori, Pekka; Lehmussola, Antti; Yli-Harja, Olli; | Simulation of microarray data with realistic characteristics | BMC bioinformatics | 7 | 1-17 | 2006 | BioMed Central | |
| 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 | 1-12 | 2017 | BioMed Central | |
| Ylipää, Antti; Yli-Harja, Olli; Zhang, Wei; Nykter, Matti; | Characterization of aberrant pathways across human cancers | BMC systems biology | 7 | 1-12 | 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 |
| Gundem, Gunes; Van Loo, Peter; Kremeyer, Barbara; Alexandrov, Ludmil B; Tubio, Jose MC; Papaemmanuil, Elli; Brewer, Daniel S; Kallio, Heini ML; Högnäs, Gunilla; Annala, Matti; | The evolutionary history of lethal metastatic prostate cancer | Nature | 520 | 7547 | 353-357 | 2015 | Nature Publishing Group UK London |
| 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 |
| 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 |
| Vandekerkhove, Gillian; Todenhöfer, Tilman; Annala, Matti; Struss, Werner J; Wong, Amanda; Beja, Kevin; Ritch, Elie; Brahmbhatt, Sonal; Volik, Stanislav V; Hennenlotter, Jörg; | Circulating tumor DNA reveals clinically actionable somatic genome of metastatic bladder cancer | Clinical Cancer Research | 23 | 21 | 6487-6497 | 2017 | American Association for Cancer Research |
| 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 | e141486 | 2021 | |
| 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 |
| 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 |
| 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 |
| 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 | |
| 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 |
| 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 |
| 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 | Springer Singapore Singapore |
| 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 | 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 | 122 | 2018 | Nature Publishing Group UK London |
| 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; Kohvakka, Annika; Annala, Matti; Latonen, Leena; Scaravilli, Mauro; Kartasalo, Kimmo; Leppänen, Simo-Pekka; Karakurt, Serdar; Seppälä, Janne; | Transcriptome sequencing reveals PCAT5 as a novel ERG-regulated long noncoding RNA in prostate cancer | Cancer research | 75 | 19 | 4026-4031 | 2015 | American Association for Cancer Research |
| 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 | |||||
| Lehtipuro, Suvi; Nykter, Matti; Granberg, Kirsi J; | Modes of immunosuppression in glioblastoma microenvironment | Oncotarget | 10 | 9 | 920 | 2019 | |
| 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 |
| Kukkonen, Konsta; Autio-Kimura, Bryn; Rauhala, Hanna; Kesseli, Juha; Nykter, Matti; Latonen, Leena; Visakorpi, Tapio; | Nonmalignant AR-positive prostate epithelial cells and cancer cells respond differently to androgen | Endocrine-Related Cancer | 29 | 12 | 717-733 | 2022 | Bioscientifica Ltd |
| 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 |
| 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 |
| 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 US New York |
| 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 | |
| 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 cancer | Cancer epidemiology, biomarkers & prevention | 22 | 12 | 2333-2344 | 2013 | American Association for Cancer Research |
| 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 | 5070 | 2020 | Nature Publishing Group UK London |
| 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 |
| Annala, Matti; Taavitsainen, Sinja; Khalaf, Daniel J; Vandekerkhove, Gillian; Beja, Kevin; Sipola, Joonatan; Warner, Evan W; Herberts, Cameron; Wong, Amanda; Fu, Simon; | Evolution of castration-resistant prostate cancer in ctDNA during sequential androgen receptor pathway inhibition | Clinical Cancer Research | 27 | 16 | 4610-4623 | 2021 | American Association for Cancer Research |
| 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 |
| 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 US New York |
| 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 | 44831 | 2017 | Nature Publishing Group UK London |
| 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 |
| 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 | 608 | 7921 | 199-208 | 2022 | Nature Publishing Group UK London |
| 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 | |
| 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: comparison of matched fresh frozen, FFPE, and PFPE tissues | The American Journal of Surgical Pathology | 42 | 1 | 103-115 | 2018 | LWW |
| 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 |
| 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 |
| Pekkarinen, Meeri; Nordfors, Kristiina; Uusi-Mäkelä, Joonas; Kytölä, Ville; Rauhala, Minna; Urhonen, Henna; Häyrynen, 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 | 2022.03. 14.483566 | 2022 | Cold Spring Harbor Laboratory | ||
| 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 |
| 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 |
| 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 US New York |
| 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 |
| 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 |
| Yang, Jilong; Ylipää, Antti; Sun, Yan; Zheng, Hong; Chen, Kexin; Nykter, Matti; Trent, Jonathan; Ratner, Nancy; Lev, Dina C; Zhang, Wei; | Genomic and molecular characterization of malignant peripheral nerve sheath tumor identifies the IGF1R pathway as a primary target for treatment | Clinical cancer research | 17 | 24 | 7563-7573 | 2011 | American Association for Cancer Research |
| 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 | 1-10 | 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 | 2022 | Elsevier | |
| 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 | |
| Afyounian, Ebrahim; Annala, Matti; Nykter, Matti; | Segmentum: a tool for copy number analysis of cancer genomes | BMC bioinformatics | 18 | 1-10 | 2017 | BioMed Central | |
| 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 |
| 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 |
| 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 | 3562 | 2019 | Nature Publishing Group UK London |
| 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 |
| 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 | 1-11 | 2017 | BioMed Central | |
| Veskimäe, K; Staff, S; Grönholm, A; Pesu, M; Laaksonen, M; Nykter, M; Isola, J; Mäenpää, J; | Assessment of PARP protein expression in epithelial ovarian cancer by ELISA pharmacodynamic assay and immunohistochemistry | Tumor Biology | 37 | 11991-11999 | 2016 | Springer Netherlands | |
| 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 | |
| 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 |
| 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 |
| 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 | |
| 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 |
| 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 | 184 | 2021 | Nature Publishing Group UK London |
| 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 |
| 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 |
| 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 | 13459 | 2022 | Nature Publishing Group UK London |
| 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 |
| 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 | 1-15 | 2017 | BioMed Central | |
| 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 cells associated with prostate cancer relapse | Nature communications | 12 | 1 | 5307 | 2021 | Nature Publishing Group UK London |
| Nykter, Matti; Price, Nathan D; Larjo, Antti; Aho, Tommi; Kauffman, Stuart A; Yli-Harja, Olli; Shmulevich, Ilya; | Critical networks exhibit maximal information diversity in structure-dynamics relationships | Physical review letters | 100 | 5 | 058702 | 2008 | American Physical Society |
| 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 | Taylor & Francis |
| Luoto, Suvi; Hermelo, Ismaïl; Vuorinen, Elisa M; Hannus, Paavo; Kesseli, Juha; Nykter, Matti; Granberg, Kirsi J; | Computational characterization of suppressive immune microenvironments in glioblastoma | Cancer research | 78 | 19 | 5574-5585 | 2018 | American Association for Cancer Research |
| 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 |
| 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; 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 | |
| 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 |
| 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 UK London |
| 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 |
| 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 |
| 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 | 1-17 | 2015 | BioMed Central | |
| 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 US New York |
| 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 |
| Nättinen, Janika; Jylhä, Antti; Aapola, Ulla; Enríquez-de-Salamanca, Amalia; Pinto-Fraga, José; López-Miguel, Alberto; González-García, María J; Stern, Michael E; Calonge, Margarita; Zhou, Lei; | Topical fluorometholone treatment and desiccating stress change inflammatory protein expression in tears | The Ocular Surface | 16 | 1 | 84-92 | 2018 | Elsevier |
| Du, Xiaoling; Yang, Jilong; Ylipää, Antti; Zhu, Ze; | Genomic amplification and high expression of EGFR are key targetable oncogenic events in malignant peripheral nerve sheath tumor | Journal of hematology & oncology | 6 | 1-12 | 2013 | BioMed Central | |
| Wyatt, AW; Annala, M; Beja, K; Parimi, S; Vandekerkhove, G; Warner, E; Zulfiqar, M; Finch, D; Oja, C; Vergidis, J; | Genomic alterations in circulating tumor DNA (ctDNA) are associated with clinical outcomes in treatment-naive metastatic castration-resistant prostate cancer (mCRPC) patients commencing androgen receptor (AR)-targeted therapy | Annals of Oncology | 27 | vi17 | 2016 | Elsevier | |
| 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 | 1-13 | 2017 | BioMed Central | |
| 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 UK London |
| 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 | 1-11 | 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 |
| Kytola, Ville; Topaloglu, Umit; Miller, Lance D; Bitting, Rhonda L; Goodman, Michael M; BDAgostino Jr, Ralph; 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 | |
| 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 |
| 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 | |
| Zhu, Lingyu; Kesseli, Juha; Nykter, Matti; Huttunen, Heikki; | Predicting gene expression levels from histone modification signals with convolutional recurrent neural networks | EMBEC & NBC 2017: Joint Conference of the European Medical and Biological Engineering Conference (EMBEC) and the Nordic-Baltic Conference on Biomedical Engineering and Medical Physics (NBC), Tampere, Finland, June 2017 | 555-558 | 2018 | Springer Singapore | ||
| 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 | 6-8 | 2011 | |||
| Ulman, Vladimír; Svoboda, David; Nykter, Matti; Kozubek, Michal; Ruusuvuori, Pekka; | Virtual cell imaging: A review on simulation methods employed in image cytometry | Cytometry Part A | 89 | 12 | 1057-1072 | 2016 | Wiley Online Library |
| 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 | djx118 | 2017 | Oxford University Press |
| 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 | |
| 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 | 40 | 11 | 1624-1633 | 2022 | Nature Publishing Group US New York |
| 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 | 1-10 | 2014 | BioMed Central | |
| 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 | 10360 | 2018 | Nature Publishing Group UK London |
| 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 |
| 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 |
| 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 | 1176 | 2018 | Nature Publishing Group UK London |
| 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 UK London |
| 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 | 2020.09. 08.287268 | 2020 | Cold Spring Harbor Laboratory | ||
| 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 | |
| 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 |
| 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 | 1-25 | 2020 | BioMed Central | |
| 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 | Am Heart Assoc |
| 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 development | Cancer discovery | 8 | 5 | 616-631 | 2018 | American Association for Cancer Research |
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| Chiarugi, Davide; Curti, Michele; Degano, Pierpaolo; Marangoni, Roberto; | Vice: A virtual cell | Computational Methods in Systems Biology: International Conference CMSB 2004, Paris, France, May 26-28, 2004, Revised Selected Papers | 207-220 | 2005 | Springer Berlin Heidelberg | ||
| Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana; Olarte, Carlos; | Verification of spatial and temporal modalities in biochemical systems | Electronic Notes in Theoretical Computer Science | 316 | 29-44 | 2015 | Elsevier | |
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| Bodei, Chiara; Bracciali, Andrea; Chiarugi, Davide; | Control flow analysis for brane calculi | Electronic Notes in Theoretical Computer Science | 227 | 59-75 | 2009 | Elsevier | |
| Furse, Samuel; Watkins, Adam J; Williams, Huw EL; Snowden, Stuart G; Chiarugi, Davide; Koulman, Albert; | Paternal nutritional programming of lipid metabolism is propagated through sperm and seminal plasma | Metabolomics | 18 | 2 | 13 | 2022 | Springer US New York |
| Pellegrinelli, Vanessa; Rodriguez-Cuenca, Segio; Rouault, Christine; Figueroa-Juarez, E; Schilbert, H; Virtue, S; Moreno-Navarrete, JM; Bidault, G; Vázquez-Borrego, MC; Dias, AR; | Dysregulation of macrophage PEPD in obesity determines adipose tissue fibro-inflammation and insulin resistance | Nature metabolism | 4 | 4 | 476-494 | 2022 | Nature Publishing Group UK London |
| Bodei, Chiara; Bortolussi, Luca; Chiarugi, Davide; Guerriero, Maria Luisa; Policriti, Alberto; Romanel, Alessandro; | On the impact of discreteness and abstractions on modelling noise in gene regulatory networks | Computational Biology and Chemistry | 56 | 98-108 | 2015 | Elsevier | |
| Lu, Yuning; Basatemur, Gemma; Scott, Ian C; Chiarugi, Davide; Clement, Marc; Harrison, James; Jugdaohsingh, Ravin; Yu, Xian; Newland, Stephen A; Jolin, Helen E; | Interleukin-33 signaling controls the development of iron-recycling macrophages | Immunity | 52 | 5 | 782-793. e5 | 2020 | Elsevier |
| Sin, Celine; Chiarugi, Davide; Valleriani, Angelo; | Single-molecule modeling of mRNA degradation by miRNA: Lessons from data | BMC Systems Biology | 9 | Suppl 3 | S2 | 2015 | BioMed Central London |
| Furse, Samuel; Watkins, Adam J; Hojat, Nima; Smith, James; Williams, Huw EL; Chiarugi, Davide; Koulman, Albert; | Lipid Traffic Analysis reveals the impact of high paternal carbohydrate intake on offsprings’ lipid metabolism | Communications Biology | 4 | 1 | 163 | 2021 | Nature Publishing Group UK London |
| Chiarugi, Davide; Falaschi, Moreno; Olarte, Carlos; Palamidessi, Catuscia; | Compositional modelling of signalling pathways in timed concurrent constraint programming | Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology | 414-417 | 2010 | |||
| Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana; Olarte, Carlos; Torella, Luca; | Modelling non-Markovian dynamics in biochemical reactions | BMC systems biology | 9 | 1-13 | 2015 | BioMed Central | |
| Adriaenssens, Alice E; Biggs, Emma K; Darwish, Tamana; Tadross, John; Sukthankar, Tanmay; Girish, Milind; Polex-Wolf, Joseph; Lam, Brain Y; Zvetkova, Ilona; Pan, Warren; | Glucose-dependent insulinotropic polypeptide receptor-expressing cells in the hypothalamus regulate food intake | Cell metabolism | 30 | 5 | 987-996. e6 | 2019 | Elsevier |
| Chiarugi, Davide; Falaschi, Moreno; Olarte, Carlos; Palamidessi, Catuscia; | A declarative view of signaling pathways | Programming Languages with Applications to Biology and Security: Essays Dedicated to Pierpaolo Degano on the Occasion of His 65th Birthday | 183-201 | 2015 | Springer International Publishing Cham | ||
| Paradisi, Paolo; Allegrini, Paolo; Chiarugi, Davide; | A renewal model for the emergence of anomalous solute crowding in liposomes | BMC Systems Biology | 9 | Suppl 3 | S7 | 2015 | BioMed Central London |
| Giacomini, Giorgia; Graziani, Caterina; Lachi, Veronica; Bongini, Pietro; Pancino, Niccolò; Bianchini, Monica; Chiarugi, Davide; Valleriani, Angelo; Andreini, Paolo; | A neural network approach for the analysis of reproducible ribo–seq profiles | Algorithms | 15 | 8 | 274 | 2022 | MDPI |
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| Chiarugi, Davide; Degano, Pierpaolo; Marangoni, Roberto; | A computational approach to the functional screening of genomes | PLoS Computational Biology | 3 | 9 | e174 | 2007 | Public Library of Science San Francisco, USA |
| Bodei, Chiara; Bracciali, Andrea; Chiarugi, Davide; | On deducing causality in metabolic networks | BMC bioinformatics | 9 | 1-10 | 2008 | BioMed Central | |
| Alvarez-Guaita, Anna; Patel, Satish; Lim, Koini; Haider, Afreen; Dong, Liang; Conway, Olivia J; Ma, Marcella KL; Chiarugi, Davide; Saudek, Vladimir; O’Rahilly, Stephen; | Phenotypic characterization of Adig null mice suggests roles for adipogenin in the regulation of fat mass accrual and leptin secretion | Cell reports | 34 | 10 | 2021 | Elsevier | |
| Furse, Samuel; Fernandez-Twinn, Denise S; Chiarugi, Davide; Koulman, Albert; Ozanne, Susan E; | Lipid metabolism is dysregulated before, during and after pregnancy in a mouse model of gestational diabetes | International journal of molecular sciences | 22 | 14 | 7452 | 2021 | MDPI |
| Sin, Celine; Chiarugi, Davide; Valleriani, Angelo; | Degradation parameters from pulse-chase experiments | PLoS One | 11 | 5 | e0155028 | 2016 | Public Library of Science San Francisco, CA USA |
| Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana; Guzman, Michell; Olarte, Carlos; | Simulating signalling pathways with BioWayS | Electronic Notes in Theoretical Computer Science | 293 | 17-34 | 2013 | Elsevier | |
| Furse, Samuel; Fernandez-Twinn, Denise S; Beeson, Jessica H; Chiarugi, Davide; Ozanne, Susan E; Koulman, Albert; | A mouse model of gestational diabetes shows dysregulated lipid metabolism post-weaning, after return to euglycaemia | Nutrition & Diabetes | 12 | 1 | 8 | 2022 | Nature Publishing Group UK London |
| Furse, Samuel; Virtue, Samuel; Snowden, Stuart G; Vidal-Puig, Antonio; Stevenson, Philip C; Chiarugi, Davide; Koulman, Albert; | Dietary PUFAs drive diverse system-level changes in lipid metabolism | Molecular Metabolism | 59 | 101457 | 2022 | Elsevier | |
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| Rading, M Michael; Sandmann, Michael; Steup, Martin; Chiarugi, Davide; Valleriani, Angelo; | Weak correlation of starch and volume in synchronized photosynthetic cells | Physical Review E | 91 | 1 | 012711 | 2015 | American Physical Society |
| Twinn, Denise; Beeson, Jesica; Chiarugi, Davide; Ozanne, Susan; Koulman, Albert; | A mouse model of gestational diabetes shows dysregulated lipid metabolism post-weaning, after return to euglycaemia | 2022 | Nature Publishing Group | ||||
| Olarte, Carlos; Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana; | A proof theoretic view of spatial and temporal dependencies in biochemical systems | Theoretical Computer Science | 641 | 25-42 | 2016 | Elsevier | |
| Chiarugi, Davide; Chinellato, M; Degano, Pierpaolo; Brutto, G Lo; Marangoni, Roberto; | Feedbacks and oscillations in the virtual cell VICE | International Conference on Computational Methods in Systems Biology | 93-107 | 2006 | Springer Berlin Heidelberg Berlin, Heidelberg | ||
| Hall, Zoe; Chiarugi, Davide; Charidemou, Evelina; Leslie, Jack; Scott, Emma; Pellegrinet, Luca; Allison, Michael; Mocciaro, Gabriele; Anstee, Quentin M; Evan, Gerard I; | Lipid remodeling in hepatocyte proliferation and hepatocellular carcinoma | Hepatology | 73 | 3 | 1028-1044 | 2021 | LWW |
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| Smith, Christopher; Patterson-Cross, Ryan; Woodward, Orla; Lewis, Jo; Chiarugi, Davide; Merkle, Florian; Gribble, Fiona; Reimann, Frank; Adriaenssens, Alice; | A comparative transcriptomic analysis of glucagon-like peptide-1 receptor-and glucose-dependent insulinotropic polypeptide receptor-expressing cells in the hypothalamus | Appetite | 174 | 106022 | 2022 | Academic Press | |
| Bodei, Chiara; Brodo, Linda; Bruni, Roberto; Chiarugi, Davide; | A flat process calculus for nested membrane interactions | Scientific Annals of Computer Science | 24 | 1 | 91-136 | 2014 | |
| Hannon, Eilis; Dempster, Emma; Viana, Joana; Burrage, Joe; Smith, Adam R; Macdonald, Ruby; St Clair, David; Mustard, Colette; Breen, Gerome; Therman, Sebastian; | An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation | Genome biology | 17 | 1-16 | 2016 | BioMed Central | |
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| Pidsley, Ruth; Fernandes, Cathy; Viana, Joana; Paya-Cano, Jose L; Liu, Lin; Smith, Rebecca G; Schalkwyk, Leonard C; Mill, Jonathan; | DNA methylation at the Igf2/H19 imprinting control region is associated with cerebellum mass in outbred mice | Molecular brain | 5 | 1-9 | 2012 | BioMed Central | |
| Kumsta, Robert; Marzi, Sarah J; Viana, Joana; Dempster, EL; Crawford, Bethany; Rutter, Michael; Mill, Jonathan; Sonuga-Barke, Edmund JS; | Severe psychosocial deprivation in early childhood is associated with increased DNA methylation across a region spanning the transcription start site of CYP2E1 | Translational psychiatry | 6 | 6 | e830-e830 | 2016 | Nature Publishing Group |
| Fisher, Helen L; Murphy, Therese M; Arseneault, Louise; Caspi, Avshalom; Moffitt, Terrie E; Viana, Joana; Hannon, Eilis; Pidsley, Ruth; Burrage, Joe; Dempster, Emma L; | Methylomic analysis of monozygotic twins discordant for childhood psychotic symptoms | Epigenetics | 10 | 11 | 1014-1023 | 2015 | Taylor & Francis |
| Viana, Joana; Pidsley, Ruth; Troakes, Claire; Spiers, Helen; Wong, Chloe CY; Al-Sarraj, Safa; Craig, Ian; Schalkwyk, Leonard; Mill, Jonathan; | Epigenomic and transcriptomic signatures of a Klinefelter syndrome (47, XXY) karyotype in the brain | epigenetics | 9 | 4 | 587-599 | 2014 | Taylor & Francis |
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| 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 |
| 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 | 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 | 1-19 | 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 | Elsevier |
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| 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 | Elsevier |
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| Nätkin, Reetta; Pennanen, Pasi; Syvälä, Heimo; Bläuer, Merja; Kesseli, Juha; Tammela, Teuvo LJ; Nykter, Matti; Murtola, Teemu J; | Adaptive and non-adaptive gene expression responses in prostate cancer during androgen deprivation | Plos one | 18 | 2 | e0281645 | 2023 | Public Library of Science San Francisco, CA USA |
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| Korvenlaita, Nea; Gómez‐Budia, Mireia; Scoyni, Flavia; Pistono, Cristiana; Giudice, Luca; Eamen, Shaila; Loppi, Sanna; de Sande, Ana Hernández; Huremagic, Benjamin; Bouvy‐Liivrand, Maria; | Dynamic release of neuronal extracellular vesicles containing miR‐21a‐5p is induced by hypoxia | Journal of extracellular vesicles | 12 | 1 | 12297 | 2023 | |
| Severson, Tesa M; Zhu, Yanyun; Prekovic, Stefan; Schuurman, Karianne; Nguyen, Holly M; Brown, Lisha G; Hakkola, Sini; Kim, Yongsoo; Kneppers, Jeroen; Linder, Simon; | Enhancer profiling identifies epigenetic markers of endocrine resistance and reveals therapeutic options for metastatic castration-resistant prostate cancer patients | medRxiv | 2023.02. 24.23286403 | 2023 | Cold Spring Harbor Laboratory Press | ||
| Aakula, Anna; Sharma, Mukund; Tabaro, Francesco; Nätkin, Reetta; Kamila, Jesse; Honkanen, Henrik; Schapira, Matthieu; Arrowsmith, Cheryl; Nykter, Matti; Westermarck, Jukka; | RAS and PP2A activities converge on epigenetic gene regulation | Life science alliance | 6 | 5 | 2023 | Life Science Alliance | |
| Moore, Jill E; Purcaro, Michael J; Pratt, Henry E; Epstein, Charles B; Shoresh, Noam; Adrian, Jessika; Kawli, Trupti; Davis, Carrie A; Dobin, Alexander; | Expanded encyclopaedias of DNA elements in the human and mouse genomes | Nature | 583 | 7818 | 699-710 | 2020 | Nature Publishing Group UK London |
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| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
| Häyrinen, Marjaana J; Kiiskilä, Jenni; Ranki, Annamari; Väkevä, Liisa; Barton, Henry J; Kuusisto, Milla EL; Porvari, Katja; Kuitunen, Hanne; Haapasaari, Kirsi-Maria; Teppo, Hanna-Riikka; | The transcription factor Twist1 has a significant role in mycosis fungoides (MF) cell biology: An RNA sequencing study of 40 MF cases | Cancers | 15 | 5 | 1527 | 2023 | MDPI |
| Cheng, Fang; Hansson, Victor Chérouvrier; Georgolopoulos, Grigorios; Mani, Katrin; | Attenuation of cancer proliferation by suppression of glypican-1 and its pleiotropic effects in neoplastic behavior | Oncotarget | 14 | 219 | 2023 | ||
| Papadopoulou, Anastasia; Karavalakis, George; Papadopoulou, Efthymia; Xochelli, Aliki; Bousiou, Zoi; Vogiatzoglou, Anastasios; Papayanni, Penelope-Georgia; Georgakopoulou, Aphrodite; Giannaki, Maria; Stavridou, Fani; | SARS-CoV-2-specific T cell therapy for severe COVID-19: a randomized phase 1/2 trial | Nature Medicine | 29 | 8 | 2019-2029 | 2023 | Nature Publishing Group US New York |
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| D’Amico, D; Fouassier, AM; Faitg, J; Hennighausen, N; Brandt, M; Konstantopoulos, D; Rinsch, C; Singh, A; | Topical application of urolithin A slows intrinsic skin aging and protects from UVB-mediated photodamage: findings from randomized clinical trials | medRxiv | 2023.06. 16.23291378 | 2023 | Cold Spring Harbor Laboratory Press | ||
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| Tikkanen, Tuomas; Leroy, Bernard; Fournier, Jean Louis; Risques, Rosa Ana; Malcikova, Jitka; Soussi, Thierry; | Seshat: a web service for accurate annotation, validation, and analysis of TP53 variants generated by conventional and next‐generation sequencing | Human mutation | 39 | 7 | 925-933 | 2018 | |
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| Alanen, Eljas; Heikkinen, Sanna; Nurminen, Riikka; Nykter, Matti; Haapasalo, Hannu; Hirvonen, Elli; Pitkäniemi, Janne; Rautajoki, Kirsi J; | Early-onset grade 2-3 diffuse gliomas and schwannomas increase the risk of central nervous system tumors among the patients’ relatives | Neuro-oncology advances | 5 | 1 | vdad008 | 2023 | Oxford University Press US |
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| Ketola, Kirsi; Kaljunen, Heidi; Taavitsainen, Sinja; Kaarijärvi, Roosa; Järvelä, Emmi; Rodríguez-Martín, Bernardo; Haase, Kerstin; Woodcock, Dan J; Tubio, Jose; Wedge, David C; | Subclone eradication analysis identifies targets for enhanced cancer therapy and reveals L1 retrotransposition as a dynamic source of cancer heterogeneity | Cancer research | 81 | 19 | 4901-4909 | 2021 | AACR |
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| Kron, Nicholas S; Fieber, Lynne A; | Aplysia neurons as a model of Alzheimer’s disease: Shared genes and differential expression | Journal of molecular neuroscience | 72 | 2 | 287-302 | 2022 | Springer US New York |
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| Punzon-Jimenez, Paula; Machado-Lopez, Alba; Perez-Moraga, Raul; Llera-Oyola, Jaime; Grases, Daniela; Galvez-Viedma, Marta; Sibai, Mustafa; Satorres-Perez, Elena; Lopez-Agullo, Susana; Badenes, Rafael; | Effect of aging on the human myometrium at single-cell resolution | Nature communications | 15 | 1 | 945 | 2024 | Nature Publishing Group UK London |
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| Montaldo, Elisa; Lusito, Eleonora; Bianchessi, Valentina; Caronni, Nicoletta; Scala, Serena; Basso-Ricci, Luca; Cantaffa, Carla; Masserdotti, Alice; Barilaro, Mattia; Barresi, Simona; | Cellular and transcriptional dynamics of human neutrophils at steady state and upon stress | Nature immunology | 23 | 10 | 1470-1483 | 2022 | Nature Publishing Group US New York |
| de Sande, Ana Hernández; Turunen, Tanja; Bouvy-Liivrand, Maria; Örd, Tiit; Palani, Senthil; Tundidor-Centeno, Celia; Liljenbäck, Heidi; Virta, Jenni; Smålander, Olli-Pekka; Sinkkonen, Lasse; | Cell-type-specific characterization of miRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution | bioRxiv | 2023.10. 09.561173 | 2023 | Cold Spring Harbor Laboratory | ||
| Ribeiro e Ribeiro, Renan; Sung, C James; Quddus, M Ruhul; | Synchronous Epidermodysplasia Verruciformis and Intraepithelial Lesion of the Vulva Is Caused by Coinfection With Alpha-Human Papillomavirus and Beta-Human Papillomavirus Genotypes and Facilitated by Mutations in Cell-Mediated Immunity Genes | Archives of Pathology & Laboratory Medicine | 148 | 9 | 1014-1021 | 2024 | the College of American Pathologists |
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| van Leeuwen, Wessel; VanInsberghe, Michael; Battich, Nico; Salmén, Fredrik; van Oudenaarden, Alexander; Rabouille, Catherine; | Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo | Cell reports methods | 2 | 6 | 2022 | Elsevier | |
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| Domènech-Moreno, Eva; Brandt, Anders; Lemmetyinen, Toni T; Wartiovaara, Linnea; Mäkelä, Tomi P; Ollila, Saara; | Tellu–an object-detector algorithm for automatic classification of intestinal organoids | Disease Models & Mechanisms | 16 | 3 | dmm049756 | 2023 | The Company of Biologists Ltd |
| Holmes, Andrew P; Wong, Shi Quan; Pulix, Michela; Johnson, Kirsty; Horton, Niamh S; Thomas, Patricia; de Magalhães, João Pedro; Plagge, Antonius; | Reductions in hypothalamic Gfap expression, glial cells and α-tanycytes in lean and hypermetabolic Gnasxl-deficient mice | Molecular brain | 9 | 1-13 | 2016 | Springer | |
| Dhayal, Shalinee; Zummo, Francesco P; Anderson, Matthew W; Thomas, Patricia; Welters, Hannah J; Arden, Catherine; Morgan, Noel G; | Differential effects of saturated and unsaturated fatty acids on autophagy in pancreatic β-cells | Journal of molecular endocrinology | 63 | 4 | 285-296 | 2019 | Bioscientifica Ltd |
| Thomas, Patricia; Leslie, Kaiyven A; Welters, Hannah J; Morgan, Noel G; | Long-chain saturated fatty acid species are not toxic to human pancreatic β-cells and may offer protection against pro-inflammatory cytokine induced β-cell death | Nutrition & Metabolism | 18 | 1-7 | 2021 | Springer | |
| Thomas, Patricia; Arden, Catherine; Corcoran, Jenna; Hacker, Christian; Welters, Hannah J; Morgan, Noel G; | Differential routing and disposition of the long-chain saturated fatty acid palmitate in rodent vs human beta-cells | Nutrition & diabetes | 12 | 1 | 22 | 2022 | Nature Publishing Group UK London |
| Campion, Richard; Bloxam, Leanne; Burrow, Kimberley; Brownridge, Philip J; Pentland, Daniel R; Thomas, Patricia; Gourlay, Campbell W; Eyers, Claire E; Barclay, Jeff W; Morgan, Alan; | Proteomic analysis of dietary restriction in yeast reveals a role for Hsp26 in replicative lifespan extension | Biochemical Journal | 478 | 24 | 4153-4167 | 2021 | Portland Press Ltd. |
| Namboori, Seema C; Thomas, Patricia; Ames, Ryan; Hawkins, Sophie; Garrett, Lawrence O; Willis, Craig RG; Rosa, Alessandro; Stanton, Lawrence W; Bhinge, Akshay; | Single-cell transcriptomics identifies master regulators of neurodegeneration in SOD1 ALS iPSC-derived motor neurons | Stem Cell Reports | 16 | 12 | 3020-3035 | 2021 | Elsevier |
| Drown, Melissa K; DeLiberto, Amanda N; Flack, Nicole; Doyle, Meghan; Westover, Alexander G; Proefrock, John C; Heilshorn, Sandra; D’Alessandro, Evan; Crawford, Douglas L; Faulk, Christopher; | Sequencing bait: Nuclear and mitogenome assembly of an abundant coastal tropical and subtropical fish, atherinomorus stipes | Genome biology and evolution | 14 | 8 | evac111 | 2022 | Oxford University Press |
| Flack, Nicole; Drown, Melissa; Walls, Carrie; Pratte, Jay; McLain, Adam; Faulk, Christopher; | Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul | NAR Genomics and Bioinformatics | 5 | 2 | lqad033 | 2023 | Oxford University Press |
| Melotto, Gloria; Jones, Megan W; Bosley, Kathryn; Flack, Nicole; Frank, Lexi E; Jacobson, Emily; Kipp, Evan J; Nelson, Sally; Ramirez, Mauricio; Walls, Carrie; | The genome of the soybean gall midge (Resseliella maxima) | G3: Genes, Genomes, Genetics | 13 | 4 | jkad046 | 2023 | Oxford University Press US |
| Flack, Nicole; Hughes, Lauren; Cassens, Jacob; Enriquez, Maya; Gebeyehu, Samrawit; Alshagawi, Mohammed; Hatfield, Jason; Kauffman, Anna; Brown, Baylor; Klaeui, Caitlin; | The genome of Przewalski’s horse (Equus ferus przewalskii) | G3: Genes, Genomes, Genetics | 14 | 8 | jkae113 | 2024 | Oxford University Press US |
| Colwell, Mathia L; Flack, Nicole; Rezabek, Amanda; Faulk, Christopher; | Intergenerational arsenic exposure on the mouse epigenome and metabolic physiology | Environmental and molecular mutagenesis | 64 | 2 | 72-87 | 2023 | Wiley Online Library |
| Rantapero, Tommi; | Bioinformatic analysis of next-generation sequencing data | gene | 59 | 1939 | |||
| Nurminen, Riikka; Afyounian, Ebrahim; Paunu, Niina; Katainen, Riku; Isomäki, Mari; Nurminen, Anssi; Scaravilli, Mauro; Tolppanen, Jenni; Fey, Vidal; Kivinen, Anni; | Previously reported CCDC26 risk variant and novel germline variants in GALNT13, AR, and MYO10 associated with familial glioma in Finland | Scientific Reports | 14 | 1 | 11562 | 2024 | Nature Publishing Group UK London |
| Hakola, Leena; Lund-Blix, Nicolai A; Takkinen, Hanna-Mari; Tapanainen, Heli; Niinistö, Sari; Korhonen, Tuuli E; Stene, Lars C; Hyöty, Heikki; Toppari, Jorma; Ilonen, Jorma; | Maternal gluten, cereal, and dietary fiber intake during pregnancy and lactation and the risk of islet autoimmunity and type 1 diabetes in the child | Clinical Nutrition ESPEN | 62 | 22-27 | 2024 | Elsevier | |
| Kivioja, Tomi; Posti, Jussi P; Sipilä, Jussi; Rauhala, Minna; Frantzen, Janek; Gardberg, Maria; Rahi, Melissa; Rautajoki, Kirsi; Nykter, Matti; Vuorinen, Ville; | Motor dysfunction as a primary symptom predicts poor outcome: multicenter study of glioma symptoms | Frontiers in Oncology | 13 | 1305725 | 2024 | Frontiers Media SA | |
| Kiviaho, Antti; Eerola, Sini K; Kallio, Heini ML; Andersen, Maria K; Hoikka, Miina; Tiihonen, Aliisa M; Salonen, Iida; Spotbeen, Xander; Giesen, Alexander; Parker, Charles TA; | Single cell and spatial transcriptomics highlight the interaction of club-like cells with immunosuppressive myeloid cells in prostate cancer | Nature Communications | 15 | 1 | 9949 | 2024 | Nature Publishing Group UK London |
| Uusi-Mäkelä, Meri; Harjula, Sanna-Kaisa Emilia; Junno, Maiju; Sillanpää, Alina; Nätkin, Reetta; Niskanen, Mirja Tellervo; Saralahti, Anni Karoliina; Nykter, Matti; Rämet, Mika; | The inflammasome adaptor pycard is essential for immunity against Mycobacterium marinum infection in adult zebrafish | Disease Models & Mechanisms | dmm. 052061 | 2025 | The Company of Biologists | ||
| Sipola, Joonatan; Munzur, Aslı D; Kwan, Edmond M; Seo, Clara CY; Hauk, Benjamin J; Parekh, Karan; Liao, Yi Jou; Bernales, Cecily Q; Donnellan, Gráinne; Bloise, Ingrid; | Plasma Cell–Free DNA Chromatin Immunoprecipitation Profiling Depicts Phenotypic and Clinical Heterogeneity in Advanced Prostate Cancer | Cancer Research | 85 | 4 | 791-807 | 2025 | American Association for Cancer Research |
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| Nikkola, Jussi; Ryyppö, Lauri; Vuorinen, Juuso; Kallio, Heini; Selin, Hanna; Jämsä, Pyry; Åkerla, Jonne; Virtanen, Tuomo; Pekkarinen, Tarmo; Kaipia, Antti; | Sensitive Detection of Urothelial Cancer via High-volume Urine DNA Analysis | European urology | 87 | 1 | 86-88 | 2025 | |
| Hermelo, Ismaïl; Virtanen, Tuomo; Salonen, Iida; Nätkin, Reetta; Keitaanniemi, Sofia; Tiihonen, Aliisa M; Lehtipuro, Suvi; Kummola, Laura; Raulamo, Ella; Nordfors, Kristiina; | Unsupervised clustering reveals noncanonical myeloid cell subsets in the brain tumor microenvironment | Cancer Immunology, Immunotherapy | 74 | 2 | 63 | 2025 | Springer |
| Pekkarinen, Meeri; Nordfors, Kristiina; Uusi-Mäkelä, Joonas; Kytölä, Ville; Hartewig, Anja; Huhtala, Laura; Rauhala, Minna; Urhonen, Henna; Häyrynen, Sergei; Afyounian, Ebrahim; | Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors | Life science alliance | 7 | 6 | 2024 | Life Science Alliance | |
| Hermelo, Ismaïl; Haapala, Ilkka; Mäkelä, Meri; Jacome Sanz, Dafne; Kontunen, Anton; Karjalainen, Markus; Müller, Philipp; Lehtimäki, Kai; Nykter, Matti; Frösén, Juhana; | Patient-derived glioma organoids real time identification of IDH mutation, 1p/19q-codeletion and CDKN2A/B homozygous deletion with differential ion mobility spectrometry | Journal of Neuro-Oncology | 171 | 3 | 691-703 | 2025 | Springer |
| Onfray, Constance; Chevolleau, Simon; Moinard, Eva; Girard, Océane; Mahadik, Kasturi; Allsop, Ryan; Georgolopoulos, Grigorios; Lavigne, Régis; Renoult, Ophélie; Aksoy, Irene; | Unraveling hallmark suitability for staging pre-and post-implantation stem cell models | Cell Reports | 43 | 5 | 2024 | Elsevier | |
| Onfray, Constance; Chevolleau, Simon; Moinard, Eva; Girard, Océane; Mahadik, Kasturi; Allsop, Ryan Nicolaas; Georgolopoulos, Grigorios; Lavigne, Regis; Renoult, Ophélie; Aksoy, Irene; | Deciphering Hallmark Combination Distinct for Peri-Implantation Stem Cell Models | 2023 | |||||
| Chérouvrier Hansson, Victor; Cheng, Fang; Georgolopoulos, Grigorios; Mani, Katrin; | Dichotomous Effects of Glypican-4 on Cancer Progression and Its Crosstalk with Oncogenes | International Journal of Molecular Sciences | 25 | 7 | 3945 | 2024 | MDPI |
| Micoli, Elia; Ferrero Restelli, Facundo; Barbiera, Giulia; Moors, Rani; Nouboers, Evelien; Du, Jessica Xinyun; Bertels, Hannah; Liu, Minhui; Konstantopoulos, Dimitris; Takeoka, Aya; | A single-cell transcriptomic atlas of developing inhibitory neurons reveals expanding and contracting modes of diversification. | bioRxiv | 2025.02. 19.636192 | 2025 | Cold Spring Harbor Laboratory | ||
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| Zeller, Peter; Blotenburg, Marloes; Bhardwaj, Vivek; de Barbanson, Buys Anton; Salmén, Fredrik; van Oudenaarden, Alexander; | T-ChIC: multi-omic detection of histone modifications and full-length transcriptomes in the same single cell | bioRxiv | 2024.05. 09.593364 | 2024 | Cold Spring Harbor Laboratory | ||
| Roth, Elisa C; Seitter, Hartwig; Ganglberger, Matthias; Zanetti, Lucia; Campiglio, Marta; Ortner, Nadine J; Fotakis, Georgios; Trajanoski, Zlatko; Koschak, Alexandra; | BPS2025–Voltage-gated calcium channels in mouse retinal bipolar cells | Biophysical Journal | 124 | 3 | 452a | 2025 | Elsevier |
| Rieder, Dietmar; Fotakis, Georgios; Ausserhofer, Markus; René, Geyeregger; Paster, Wolfgang; Trajanoski, Zlatko; Finotello, Francesca; | nextNEOpi: a comprehensive pipeline for computational neoantigen prediction | Bioinformatics | 38 | 4 | 1131-1132 | 2022 | Oxford University Press |
| Salcher, Stefan; Sturm, Gregor; Horvath, Lena; Untergasser, Gerold; Kuempers, Christiane; Fotakis, Georgios; Panizzolo, Elisa; Martowicz, Agnieszka; Trebo, Manuel; Pall, Georg; | High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer | Cancer cell | 40 | 12 | 1503-1520. e8 | 2022 | Elsevier |
| Plattner, Christina; Lamberti, Giorgia; Blattmann, Peter; Kirchmair, Alexander; Rieder, Dietmar; Loncova, Zuzana; Sturm, Gregor; Scheidl, Stefan; Ijsselsteijn, Marieke; Fotakis, Georgios; | Functional and spatial proteomics profiling reveals intra-and intercellular signaling crosstalk in colorectal cancer | Iscience | 26 | 12 | 2023 | Elsevier | |
| Heidegger, Isabel; Fotakis, Georgios; Offermann, Anne; Goveia, Jermaine; Daum, Sophia; Salcher, Stefan; Noureen, Asma; Timmer-Bosscha, Hetty; Schäfer, Georg; Walenkamp, Annemiek; | Comprehensive characterization of the prostate tumor microenvironment identifies CXCR4/CXCL12 crosstalk as a novel antiangiogenic therapeutic target in prostate cancer | Molecular cancer | 21 | 1 | 132 | 2022 | Springer |
| Marteau, Valentin; Nemati, Niloofar; Handler, Kristina; Raju, Deeksha; Soto, Erika Kvalem; Fotakis, Georgios; Carollo, Sandro; Boeck, Nina; Rossi, Alessia; Kirchmair, Alexander; | Single-cell integration and multi-modal profiling reveals phenotypes and spatial organization of neutrophils in colorectal cancer | bioRxiv | 2024.08. 26.609563 | 2024 | Cold Spring Harbor Laboratory | ||
| Sturm, Gregor; Szabo, Tamas; Fotakis, Georgios; Haider, Marlene; Rieder, Dietmar; Trajanoski, Zlatko; Finotello, Francesca; | Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data | Bioinformatics | 36 | 18 | 4817-4818 | 2020 | Oxford University Press |
| Seitter, Hartwig; Obkircher, Jana; Grabher, Patricia; Hartl, Julia; Zanetti, Lucia; Lux, Uwe Thorsten; Fotakis, Georgios; Fernández-Quintero, Monica L; Kaserer, Teresa; Koschak, Alexandra; | A novel calcium channel Cavβ2 splice variant with unique properties predominates in the retina | Journal of Biological Chemistry | 299 | 4 | 2023 | Elsevier | |
| Eigentler, Andrea; Handle, Florian; Schanung, Silvia; Degen, Antonia; Hackl, Hubert; Erb, Holger HH; Fotakis, Georgios; Hoefer, Julia; Ploner, Christian; Jöhrer, Karin; | Glucocorticoid treatment influences prostate cancer cell growth and the tumor microenvironment via altered glucocorticoid receptor signaling in prostate fibroblasts | Oncogene | 43 | 4 | 235-247 | 2024 | Nature Publishing Group UK London |
| Fotakis, Georgios; Rieder, Dietmar; Haider, Marlene; Trajanoski, Zlatko; Finotello, Francesca; | NeoFuse: predicting fusion neoantigens from RNA sequencing data | Bioinformatics | 36 | 7 | 2260-2261 | 2020 | Oxford University Press |
| Salcher, Stefan; Heidegger, Isabel; Untergasser, Gerold; Fotakis, Georgios; Scheiber, Alexandra; Martowicz, Agnieszka; Noureen, Asma; Krogsdam, Anne; Schatz, Christoph; Schäfer, Georg; | Comparative analysis of 10X Chromium vs. BD Rhapsody whole transcriptome single-cell sequencing technologies in complex human tissues | Heliyon | 10 | 7 | 2024 | Elsevier | |
| Brunner, Elena; Damisch, Elisabeth; Groninger, Melanie Emma; Nommensen, Lukas; Neumann, Lucy; Fotakis, Georgios; Trajanoski, Zlatko; Schäfer, Georg; Ploner, Christian; Karkampouna, Sofia; | Unraveling the YAP1-TGFβ1 axis: a key driver of androgen receptor loss in prostate cancer-associated fibroblasts | bioRxiv | 2025.02. 25.640167 | 2025 | Cold Spring Harbor Laboratory | ||
| Binenbaum, Ilona; Atamni, Hanifa Abu-Toamih; Fotakis, Georgios; Kontogianni, Georgia; Koutsandreas, Theodoros; Pilalis, Eleftherios; Mott, Richard; Himmelbauer, Heinz; Iraqi, Fuad A; Chatziioannou, Aristotelis A; | Container-aided integrative QTL and RNA-seq analysis of Collaborative Cross mice supports distinct sex-oriented molecular modes of response in obesity | BMC genomics | 21 | 1-13 | 2020 | Springer | |
| Vlachavas, Efstathios–Iason; Pilalis, Eleftherios; Papadodima, Olga; Koczan, Dirk; Willis, Stefan; Klippel, Sven; Cheng, Caixia; Pan, Leyun; Sachpekidis, Christos; Pintzas, Alexandros; | Radiogenomic analysis of F-18-fluorodeoxyglucose positron emission tomography and gene expression data elucidates the epidemiological complexity of colorectal cancer landscape | Computational and Structural Biotechnology Journal | 17 | 177-185 | 2019 | Elsevier | |
| Vlachavas, Efstathios Iason; Bohn, Jonas; Ueckert, Frank; Nuernberg, Sylvia; | A detailed catalogue of multi-omics methodologies for identification of putative biomarkers and causal molecular networks in translational cancer research | International journal of molecular sciences | 22 | 6 | 2822 | 2021 | MDPI |
| Yeles, Constantinos; Vlachavas, Efstathios-Iason; Papadodima, Olga; Pilalis, Eleftherios; Vorgias, Constantinos E; Georgakilas, Alexandros G; Chatziioannou, Aristotelis; | Integrative bioinformatic analysis of transcriptomic data identifies conserved molecular pathways underlying ionizing radiation-induced bystander effects (RIBE) | Cancers | 9 | 12 | 160 | 2017 | MDPI |
| Kontogianni, Georgia; Voutetakis, Konstantinos; Piroti, Georgia; Kypreou, Katerina; Stefanaki, Irene; Vlachavas, Efstathios Iason; Pilalis, Eleftherios; Stratigos, Alexander; Chatziioannou, Aristotelis; Papadodima, Olga; | A Comprehensive Analysis of Cutaneous Melanoma Patients in Greece Based on Multi-Omic Data | Cancers | 15 | 3 | 815 | 2023 | MDPI |
| Sumer, Oyku Ece; Schelzig, Korbinian; Jung, Janine; Li, Xiaoya; Moros, Janina; Schwarzmüller, Luisa; Sen, Ezgi; Karolus, Sabine; Wörner, Angelika; de Melo Costa, Verônica Rodrigues; | Selective arm-usage of pre-miR-1307 dysregulates angiogenesis and affects breast cancer aggressiveness | BMC biology | 23 | 1 | 25 | 2025 | Springer |
| Sumer, Oyku Ece; Schelzig, Korbinian; Jung, Janine; Li, Xiaoya; Moros, Janina; Schwarzmüller, Luisa; Sen, Ezgi; Karolus, Sabine; Wörner, Angelika; Nataraj, Nishanth Belugali; | Selective arm-usage of pre-miR-1307 dysregulates angiogenesis and contributes to breast cancer aggressiveness | 2023 | |||||
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| Lenherr-Frey, Daniel; Vrohlings, Melissa; Bouvy-Liivrand, Maria; Hieta, Reija; Shaw, Heather May; Lopes, Gilberto; Borras, Leonardo; Biswas, Swethajit; | In silico tumor immune microenvironment (TiME) analysis of non-small cell lung cancer (NSCLC) to inform clinical development of CDR404: A first-of-its-kind MAGE-A4 targeted T-cell engager. | 2024 | American Society of Clinical Oncology | ||||
| Kron, Nicholas S; Fieber, Lynne A; Baker, Lydia; Campbell, Catherine; Schmale, Michael C; | Host response to Aplysia Abyssovirus 1 in nervous system and gill | Developmental & Comparative Immunology | 159 | 105211 | 2024 | Elsevier | |
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| Traylor-Knowles, Nikki; Connelly, Michael T; Young, Benjamin D; Eaton, Katherine; Muller, Erinn M; Paul, Valerie J; Ushijima, Blake; DeMerlis, Allyson; Drown, Melissa K; Goncalves, Ashley; | Gene expression response to stony coral tissue loss disease transmission in M. cavernosa and O. faveolata from Florida | Frontiers in Marine Science | 8 | 681563 | 2021 | Frontiers Media SA | |
| Kron, Nicholas S; Young, Benjamin D; Drown, Melissa K; McDonald, M Danielle; | Long-read de novo genome assembly of Gulf toadfish (Opsanus beta) | BMC genomics | 25 | 1 | 871 | 2024 | Springer |
| Domènech‐Moreno, Eva; Lim, Wei‐Wen; Montrose, Melissa G; Sévigny, Myriam; Brandt, Anders; Lemmetyinen, Toni T; Viitala, Emma W; Mäkelä, Tomi P; Cook, Stuart A; Ollila, Saara; | Interleukin‐11 expressed in the polyp‐enriched fibroblast subset is a potential therapeutic target in Peutz‐Jeghers syndrome | The Journal of Pathology | 2025 | Wiley Online Library | |||
| Mulone, Alberto; Awad, Sherine; Chiarugi, Davide; Aldinucci, Marco; | Porting the Variant Calling Pipeline for NGS data in cloud-HPC environment | 2023 IEEE 47th Annual Computers, Software, and Applications Conference (COMPSAC) | 1858-1863 | 2023 | IEEE | ||
| Furse, Samuel; Martel, Carlos; Willer, David F; Stabler, Daniel; Fernandez-Twinn, Denise S; Scott, Jennifer; Patterson-Cross, Ryan; Watkins, Adam J; Virtue, Samuel; Prescott, Thomas AK; | Systemic analysis of lipid metabolism from individuals to multi-organism systems | Molecular Omics | 20 | 9 | 570-583 | 2024 | Royal Society of Chemistry |
| Awad, Sherine; Valleriani, Angelo; Chiarugi, Davide; | A data-driven estimation of the ribosome drop-off rate in S. cerevisiae reveals a correlation with the genes length | NAR Genomics and Bioinformatics | 6 | 2 | lqae036 | 2024 | Oxford University Press |
