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 | Year |
|---|---|---|---|
| Marteau, Valentin; Nemati, Niloofar; Handler, Kristina; Raju, Deeksha; Kirchmair, Alexander; Rieder, Dietmar; Soto, Erika Kvalem; Fotakis, Georgios; De Lange, Glenn; Carollo, Sandro | Single-cell integration and multi-modal profiling reveals phenotypes and spatial organization of neutrophils in colorectal cancer | Cancer Cell | 2026 |
| Weiler, Bradley Allen; Kron, Nicholas; Bonacolta, Anthony Mario; Vermeij, Mark JA; Baker, Andrew Charles; Del Campo, Javier | Temporal transcriptional rhythms govern coral-symbiont function and microbiome dynamics | Cell host & microbe | 2026 |
| Mäntylä, Sonja; Nurminen, Anssi; Huovinen, Sanna; Jaatinen, Serafiina; Haapaniemi, Teppo; Nurminen, Riikka; Hermelo, Ismaïl; Volz, Stefanie; Maaß, Kendra K; Pajtler, Kristian W | Genomic analysis of PLNTY-like tumor progression into epithelioid glioblastoma: a case report | Acta Neuropathologica Communications | 2026 |
| Tiihonen, Aliisa M; Salonen, Iida; Koivisto, Iina; Ritamäki, Anni S; Jaatinen, Serafiina; Hyvärinen, Tanja; Tilvis, Johanna; Kreutzer, Joose M; Karabiyik, Göktug; Mäntylä, Sonja | Hypoxia and Associated Acidosis Generate Cell-Type Specific Myeloid Responses in Glioblastoma | bioRxiv | 2026 |
| Hakkola, Sini; Peramaki, Anni; Kiviaho, Antti; Urbanucci, Alfonso; Nykter, Matti; Marttinen, Mikael | AR suppression rewires a SOX4 regulatory program to promote enzalutamide resistance in prostate cancer | bioRxiv | 2026 |
| Mäntylä, Elina; Korpela, Sanna; Rekonen, Anna; Hakkola, Sini; Karttunen, Jenni; Pörsti, Anni; Erämies, Sanni; Tadeu Arrojo Martins, Fábio; Davidsson, Roselia; Ojanen, Markus JT | Deep Invaginations of Nuclear Envelope Coordinate Spatial Organization of Chromatin in Epithelium | bioRxiv | 2026 |
| Akagha, Mojoyinola Joanna; Georgolopoulos, Grigorios; Martin, David; Meissl, Katrin; Amenitsch, Lena; Vogl, Claus; Farlik, Matthias; Fortelny, Nikolaus; Halbritter, Florian; Müller, Mathias | IFNγ shapes macrophage inflammatory responses by STAT1 isoform-specific epigenetic and transcriptional mechanisms | BMC genomics | 2026 |
| Robert, Jacques; Gosset, Lena; Vlachavas, Efstathios‐Iason; Lemaître, Gilles; Chatziioannou, Aristotelis; Puceat, Michel; Delom, Frederic; Fessart, Delphine | A mi RNA screen reveals a transcriptional network controlling the initiation of mammary organoids | The FEBS Journal | 2026 |
| Harray, Amelia J; Lucas, Andrew D; Herrmann, Susan E; Vlaskovsky, Philip S; Elagali, Ahmed; Seewoo, Bhedita J; Chan, Dick C; Chiarugi, Davide; Kulkarni, Rishabh; Trevenen, Michelle | Low-plastic diet and urinary levels of plastic-associated phthalates and bisphenols: the randomized controlled PERTH Trial | Nature Medicine | 2026 |
| 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 | 2025 |
| 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 | 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 | 2025 |
| 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 | 2025 |
| Micoli, Elia; Restelli, Facundo Ferrero; 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 |
| 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 | 2025 |
| Brunner, Elena; Damisch, Elisabeth; Groninger, Melanie Emma; Baschieri, Francesco; Tyckaert, François; Nommensen, Lukas; Neumann, Lucy; Fotakis, Georgios; Trajanoski, Zlatko; Schäfer, Georg | Unraveling the YAP1-TGFβ1 axis: a key driver of androgen receptor loss in prostate cancer-associated fibroblasts | Journal of Experimental & Clinical Cancer Research | 2025 |
| 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 | 2025 |
| Vlachavas, Efstathios‐Iason; Voutetakis, Konstantinos; Kosmidou, Vivian; Tsikalakis, Spyridon; Roditis, Spyridon; Pateas, Konstantinos; Kim, Ryangguk; Pagel, Kymberleigh; Wolf, Stephan; Warsow, Gregor | Molecular and functional profiling unravels targetable vulnerabilities in colorectal cancer | Molecular Oncology | 2025 |
| 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 |
| Uusi-Mäkelä, Joonas; Kauppinen, Maria; Seppälä, Janne; Jaatinen, Serafiina; Ryback, Birgitta; Rantapero, Tommi; Rodriguez-Martinez, Alejandra; Nykter, Matti; Rautajoki, Kirsi J | Tumor-associated long non-coding RNAs show variable expression across diffuse gliomas and effect on cell growth upon silencing in glioblastoma | Scientific Reports | 2025 |
| Song, Jie; Zhou, Yang; Hedman, Harald; Rantapero, Tommi; Landström, Maréne | Identification of progression markers for prostate cancer | Cell Cycle | 2025 |
| Erkan, Erdogan Pekcan; Hämäläinen, Emmi; Kolikova, Julia; Kuc, Kornelia; Ojala, Kalle; Kukkonen, Meiju; Hermelo, Ismail; Koskensalo, Selja; Tarvainen, Timo; Leppä, Alli | Sustained epithelial interferon signaling modulates incomplete pathologic response in colorectal cancer | bioRxiv | 2025 |
| Moradi, Elaheh; Vuorinen, Juuso; Rodriguez-Martinez, Alejandra; Pekkarinen, Meeri; Vulli, Miina; Lehtipuro, Suvi; Fey, Vidal; Tabaro, Francesco; Hartewig, Anja; Ampuja, Sinikka | Accurate classification of CNS tumors through DNA methylation data analysis of select genomic regions | medRxiv | 2025 |
| Sattari, Mina; Rauhala, Hanna; Latonen, Leena; Isaacs, William B; Nykter, Matti; Bova, G Steven; Kesseli, Juha; Visakorpi, Tapio | Identification of protein-coding genes associated with metastatic prostate cancer | Endocrine-Related Cancer | 2025 |
| Nikkola, Jussi; Ryyppö, Lauri; Vuorinen, Juuso; Moilanen, Lauri; Ahtiainen, Maarit; Pylvänäinen, Kirsi; Selin, Hanna; Virtanen, Tuomo; Nykter, Matti; Veitonmäki, Thea | Constrained hypermutation and absence of TERT promoter mutations in Lynch syndrome-associated urothelial cancer | Cell Reports | 2025 |
| Krossa, Sebastian; Andersen, Maria K; Sandholm, Elise M; Wess, Maximilian; Kiviaho, Antti; Sharma, Abhibhav; Hakkola, Sini; Hao, Yangyang; Alshalalfa, Mohammed; Davicioni, Elai | Spatial multi-omics identifies aggressive prostate cancer signatures highlighting pro-inflammatory chemokine activity in the tumor microenvironment | Nature communications | 2025 |
| Hormalainen, Kirsi; Marttila, Kaisa; Nykter, Matti; Uibu, Toomas; Ahvonen, Jarkko; Fey, Vidal; Keinänen, Mauri; Bärlund, Maarit; Jukkola, Arja | Comprehensive Genomic Profiling in Advanced Non‐Small Cell Lung Cancer: A Real‐World Cohort Study in Finland | Cancer Medicine | 2025 |
| Severson, Tesa M; Minnee, Emma; Zhu, Yanyun; Schuurman, Karianne; Nguyen, Holly M; Brown, Lisha G; Hakkola, Sini; Menezes, Renee; Gregoricchio, Sebastian; Kim, Yongsoo | Epigenetic profiling identifies markers of endocrine resistance and therapeutic options for metastatic castration-resistant prostate cancer | Cell Reports Medicine | 2025 |
| Psatha, Nikoletta; Sova, Pavel; Georgolopoulos, Grigorios; Paschoudi, Kiriaki; Iwata, Mineo; Bloom, Jordan; Ulyanova, Tatyana; Wang, Hao; Kirtsou, Alexandra; Vasiloudis, Ninos-Ioannis | Large-scale discovery of potent, compact and erythroid specific enhancers for gene therapy vectors | Nature Communications | 2025 |
| Vasiloudis, Ninos Ioannis; Paschoudi, Kiriaki; Beta, Christina; Georgolopoulos, Grigorios; Psatha, Nikoletta | Epigenetic Regulation of Erythropoiesis: From Developmental Programs to Therapeutic Targets | International Journal of Molecular Sciences | 2025 |
| Hunold, Pascal; Pizzolato, Giulia; Heramvand, Nadia; Kaiser, Laura; Barbiera, Giulia; van Ray, Olivia; Thomas, Roman; George, Julie; Peifer, Martin; Hänsel-Hertsch, Robert | DynaTag for efficient mapping of transcription factors in low-input samples and at single-cell resolution | Nature Communications | 2025 |
| Schwarzmüller, Luisa; Müller, Janina; Vlachavas, Efstathios-Iason; Beumers, Lukas; Fleischhacker, Lena; Burmester, Sara; Helm, Dominic; Körner, Cindy; Wiemann, Stefan | PAK1 activation drives divergent resistance mechanisms to aromatase inhibition and Tamoxifen in a luminal A breast cancer model | bioRxiv | 2025 |
| Zitta, Karina; Berndt, Rouven; Hess, Katharina; Fändrich, Fred; Gurvich, Olga; Sirviö, Katja; Kekarainen, Tuija; Hummitzsch, Lars; Wong, Yuk Lung; Sattler, Ole | Transcriptomic characterization of GMP-compliant regulatory macrophages (TRI-001) under inflammatory and hypoxic conditions: a comparative analysis across macrophage subtypes | Journal of Translational Medicine | 2025 |
| Furse, Samuel; Virtue, Samuel; Huang-Doran, Isabel; Vial-Puig, Antonio; Patterson-Cross, Ryan; Chiarugi, Davide; Stevenson, Philip C; Snowden, Stuart G; Koulman, Albert | The biosynthesis of lipids and control of lipid metabolism differs in male and female mammals | Royal Society Open Science | 2025 |
| Wise, James TF; Chiarugi, Davide; Chi, Jinhua; Wise Sr, John Pierce | Hexavalent chromium exposure impacts the metabolome of human lung fibroblast cells | Journal of Trace Elements in Medicine and Biology | 2025 |
| Furse, Samuel; Virtue, Samuel; Huang-Doran, Isabel; Vidal-Puig, Antonio; Chiarugi, Davide; Stevenson, Philip C; Snowden, Stuart G; Koulman, Albert | Systemic analyses show that the biosynthesis and spatial distribution of fatty acids, triglycerides and lipids differed in male and female mice and humans | Open Biology | 2025 |
| de Sande, Ana Hernández; Turunen, Tanja; Bouvy-Liivrand, Maria; Örd, Tiit; Palani, Senthil; Lahnalampi, Mari; Tundidor-Centeno, Celia; Liljenbäck, Heidi; Virta, Jenni; Niskanen, Henri | MicroRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution | Genome Medicine | 2025 |
| Krauß, Dana; Moreno-Viedma, Veronica; Adachi-Fernandez, Emi; de Sá Fernandes, Cristiano; Genger, Jakob-Wendelin; Fari, Ourania; Blauensteiner, Bernadette; Kirchhofer, Dominik; Bradaric, Nikolina; Gushchina, Valeriya | EGFR controls transcriptional and metabolic rewiring in KRASG12D colorectal cancer | EMBO molecular medicine | 2025 |
| Damisch, Elisabeth; Brunner, Elena; Nommensen, Lukas; Neumann, Lucy; Fotakis, Georgios; Trajanoski, Zlatko; Sopper, Sieghart; Schäfer, Georg; Puhr, Martin; Heidegger, Isabel | Optimised dissociation and multimodal profiling of prostate cancer stroma reveal fibromuscular cell heterogeneity with clinical correlates | Frontiers in Cell and Developmental Biology | 2025 |
| Boyd, Sonja; Mustamäki, Taru; Sjöblom, Nelli; Nordin, Arno; Tenca, Andrea; Jokelainen, Kalle; Rantapero, Tommi; Liuksiala, Thomas; Lahtinen, Laura; Kuopio, Teijo | NGS of brush cytology samples improves the detection of high-grade dysplasia and cholangiocarcinoma in patients with primary sclerosing cholangitis: A retrospective and prospective study | Hepatology communications | 2024 |
| Fonseca, Nicolette M; Maurice-Dror, Corinne; Herberts, Cameron; Tu, Wilson; Fan, William; Murtha, Andrew J; Kollmannsberger, Catarina; Kwan, Edmond M; Parekh, Karan; Schönlau, Elena | Prediction of plasma ctDNA fraction and prognostic implications of liquid biopsy in advanced prostate cancer | Nature communications | 2024 |
| Young, Benjamin D; Williamson, Olivia M; Kron, Nicholas S; Andrade Rodriguez, Natalia; Isma, Lys M; MacKnight, Nicholas J; Muller, Erinn M; Rosales, Stephanie M; Sirotzke, Stephanie M; Traylor-Knowles, Nikki | Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing | BMC genomics | 2024 |
| Kron, Nicholas S; Neuman, Benjamin W; Kumar, Sathish; Blackwelder, Patricia L; Vidal, Dayana; Walker-Phelan, Delphina Z; Gibbs, Patrick DI; Fieber, Lynne A; Schmale, Michael C | Expression dynamics of the aplysia abyssovirus | Virology | 2024 |
| 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 | 2024 |
| Dundr, Pavel; Machado-Lopez, Alba; Mas, Aymara; Věcková, Zuzana; Mára, Michal; Richtárová, Adéla; Matěj, Radoslav; Stružinská, Ivana; Kendall Bártů, Michaela; Němejcová, Kristýna | Uterine leiomyoma with RAD51B:: NUDT3 fusion: a report of 2 cases | Virchows Archiv | 2024 |
| e Ribeiro, Renan Ribeiro; 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 | 2024 |
| Kallio, Heini ML; Savolainen, Kalle; Virtanen, Tuomo; Ryyppö, Lauri; Selin, Hanna; Martikainen, Päivi; Staff, Synnöve; Kivinummi, Kati; Sipola, Joonatan; Vuorinen, Juuso | Sensitive circulating tumor DNA–based residual disease detection in epithelial ovarian cancer | Life science alliance | 2024 |
| Vesala, Laura; Basikhina, Yuliya; Tuomela, Tea; Nurminen, Anssi; Siukola, Emilia; Vale, Pedro F; Salminen, Tiina S | Mitochondrial perturbation in immune cells enhances cell-mediated innate immunity in Drosophila | BMC biology | 2024 |
| 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 | 2024 |
| 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 | 2024 |
| 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 | 2024 |
| 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 | 2024 |
| 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 | 2024 |
| Salenius, Karoliina; Väljä, Niina; Thusberg, Sini; Iris, Francois; Ladd-Acosta, Christine; Roos, Christophe; Nykter, Matti; Fasano, Alessio; Autio, Reija; Lin, Jake | Exploring autism spectrum disorder and co-occurring trait associations to elucidate multivariate genetic mechanisms and insights | BMC psychiatry | 2024 |
| 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 | 2024 |
| 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 | 2024 |
| 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 | 2024 |
| 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 | 2024 |
| Andersson-Rolf, Amanda; Groot, Kelvin; Korving, Jeroen; Begthel, Harry; Hanegraaf, Maaike AJ; VanInsberghe, Michael; Salmén, Fredrik; van den Brink, Stieneke; Lopez-Iglesias, Carmen; Peters, Peter J | Long-term in vitro expansion of a human fetal pancreas stem cell that generates all three pancreatic cell lineages | Cell | 2024 |
| 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 |
| 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 | 2024 |
| 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 | 2024 |
| 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 | |
| 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 | 2024 |
| 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 | 2024 |
| 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 | 2024 |
| 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 | 2024 |
| Hansson, Victor Chérouvrier; Cheng, Fang; Georgolopoulos, Grigorios; Mani, Katrin | Dichotomous Effects of Glypican-4 on Cancer Progression and Its Crosstalk with Oncogenes | International Journal of Molecular Sciences | 2024 |
| Obacz, Joanna; Archambeau, Jérôme; Lafont, Elodie; Nivet, Manon; Martin, Sophie; Aubry, Marc; Voutetakis, Konstantinos; Pineau, Raphael; Boniface, Rachel; Sicari, Daria | IRE1 endoribonuclease signaling promotes myeloid cell infiltration in glioblastoma | Neuro-oncology | 2024 |
| Li, Manci; Flack, Nicole; Larsen, Peter A | Multifaceted role of specialized neuropeptide-intensive neurons on the selective vulnerability to Alzheimer’s disease in the human brain | Biomolecules | 2024 |
| Fotakis, Georgios; Rieder, Dietmar; Loncova, Zuzana; Carollo, Sandro; Klieser, Eckhard; Neureiter, Daniel; Huemer, Florian; Hoegler, Sandra; Tomberger, Martina; Krogsdam, Anne | Conventional therapy induces tumor immunoediting and modulates the immune contexture in colorectal cancer | bioRxiv | 2024 |
| Mueller, Jonathan Wolf; Thomas, Patricia; Dalgaard, Louise Torp; da Silva Xavier, Gabriela | Sulfation pathways in the maintenance of functional beta-cell mass and implications for diabetes | Essays in biochemistry | 2024 |
| 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 | 2023 |
| Saralahti, Anni K; Harjula, Sanna-Kaisa E; Rantapero, Tommi; Uusi-Mäkelä, Meri IE; Kaasinen, Mikko; Junno, Maiju; Piippo, Hannaleena; Nykter, Matti; Lohi, Olli; Rounioja, Samuli | Characterization of the innate immune response to Streptococcus pneumoniae infection in zebrafish | PLoS Genetics | 2023 |
| 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 | 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 |
| 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 | 2023 |
| 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 | 2023 |
| 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 | 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 | 2023 |
| Simigdala, Nikiana; Chalari, Anna; Sklirou, Aimilia D; Chavdoula, Evangelia; Papafotiou, George; Melissa, Pelagia; Kafalidou, Aimilia; Paschalidis, Nikolaos; Pateras, Ioannis S; Athanasiadis, Emmanouil | Loss of Kmt2c in vivo leads to EMT, mitochondrial dysfunction and improved response to lapatinib in breast cancer | Cellular and Molecular Life Sciences | 2023 |
| 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 |
| Sandovici, Ionel; Mifsud, Borbala; Emery, Amy; Gulati, Pawan; Kentistou, Katherine A; Banu, Ayesha; Campbell, Niamh; Hardwick, Bryn S; Crooks, Alex T; Fernandez-Twinn, Denise S | Genome-wide analysis of promoter contacts identifies novel regulators of late-stage adipogenesis | bioRxiv | 2023 |
| Ojanen, Markus JT; Caro, Fernanda Munoz; Aittomäki, Saara; Ploquin, Mickaël J; Ortutay, Zsuzsanna; Pekkarinen, Meeri; Kesseli, Juha; Vähätupa, Maria; Määttä, Juuso; Nykter, Matti | FURIN regulates cytotoxic T‐lymphocyte effector function and memory cell transition in mice | European Journal of Immunology | 2023 |
| Sattari, Mina; Kohvakka, Annika; Moradi, Elaheh; Rauhala, Hanna; Urhonen, Henna; Isaacs, William B; Nykter, Matti; Murtola, Teemu J; Tammela, Teuvo LJ; Latonen, Leena | Identification of long noncoding RNAs with aberrant expression in prostate cancer metastases | Endocrine-related cancer | 2023 |
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| 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 | 2017 |
| 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 | 2017 |
| 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 | 2017 |
| 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 | 2017 |
| 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 | 2017 |
| Afyounian, Ebrahim; Annala, Matti; Nykter, Matti | Segmentum: a tool for copy number analysis of cancer genomes | BMC bioinformatics | 2017 |
| 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 | 2017 |
| 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 | 2017 |
| 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 | 2017 |
| 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 | 2017 |
| Yang, Meng; Topaloglu, Umit; Petty, W Jeffrey; Pagni, Matthew; Foley, Kristie L; Grant, Stefan C; Robinson, Mac; Bitting, Rhonda L; Thomas, Alexandra; Alistar, Angela T | Circulating mutational portrait of cancer: manifestation of aggressive clonal events in both early and late stages | Journal of hematology & oncology | 2017 |
| 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 | 2017 |
| 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 | 2017 |
| 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 | 2017 |
| Zhu, Lingyu; Kesseli, Juha; Nykter, Matti; Huttunen, Heikki | Predicting gene expression levels from histone modification signals with convolutional recurrent neural networks | European Medical and Biological Engineering Confernce | 2017 |
| 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 | 2017 |
| 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 | 2017 |
| 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 | 2017 |
| 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 | 2017 |
| Viana, Joana; Hannon, Eilis; Dempster, Emma; Pidsley, Ruth; Macdonald, Ruby; Knox, Olivia; Spiers, Helen; Troakes, Claire; Al-Saraj, Safa; Turecki, Gustavo | Schizophrenia-associated methylomic variation: molecular signatures of disease and polygenic risk burden across multiple brain regions | Human molecular genetics | 2017 |
| Giacomello, Stefania; Salmén, Fredrik; Terebieniec, Barbara K; Vickovic, Sanja; Navarro, José Fernandez; Alexeyenko, Andrey; Reimegård, Johan; McKee, Lauren S; Mannapperuma, Chanaka; Bulone, Vincent | Spatially resolved transcriptome profiling in model plant species | Nature plants | 2017 |
| Asp, Michaela; Salmén, Fredrik; Ståhl, Patrik L; Vickovic, Sanja; Felldin, Ulrika; Löfling, Marie; Fernandez Navarro, José; Maaskola, Jonas; Eriksson, Maria J; Persson, Bengt | Spatial detection of fetal marker genes expressed at low level in adult human heart tissue | Scientific reports | 2017 |
| Navarro, José Fernández; Sjöstrand, Joel; Salmén, Fredrik; Lundeberg, Joakim; Ståhl, Patrik L | ST Pipeline: an automated pipeline for spatial mapping of unique transcripts | Bioinformatics | 2017 |
| 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 | 2017 |
| 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 | 2016 |
| 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 | 2016 |
| 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 | 2016 |
| 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 | 2016 |
| 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 | 2016 |
| 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 | 2016 |
| 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 | 2016 |
| 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 | 2016 |
| 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 | 2016 |
| 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 | 2016 |
| 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 | 2016 |
| 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 | 2016 |
| Ulman, Vladimir; Svoboda, David; Nykter, Matti; Kozubek, Michal; Ruusuvuori, Pekka | Virtual cell imaging: A review on simulation methods employed in image cytometry | Cytometry Part A | 2016 |
| 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 | 2016 |
| Georgolopoulos, Grigorios; Parducci, Laura; Drouzas, Andreas D | A short phylogenetically informative cpDNA fragment for the identification of Pinus species | Biochemical Systematics and Ecology | 2016 |
| 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 | 2016 |
| Sin, Celine; Chiarugi, Davide; Valleriani, Angelo | Quantitative assessment of ribosome drop-off in E. coli | Nucleic acids research | 2016 |
| Sin, Celine; Chiarugi, Davide; Valleriani, Angelo | Degradation parameters from pulse-chase experiments | PLoS One | 2016 |
| Olarte, Carlos; Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana | A proof theoretic view of spatial and temporal dependencies in biochemical systems | Theoretical Computer Science | 2016 |
| 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 | 2016 |
| Laing, LV; Viana, Joana; Dempster, EL; Trznadel, M; Trunkfield, LA; Uren Webster, TM; Van Aerle, R; Paull, GC; Wilson, RJ; Mill, Jonathan | Bisphenol A causes reproductive toxicity, decreases dnmt1 transcription, and reduces global DNA methylation in breeding zebrafish (Danio rerio) | Epigenetics | 2016 |
| Hannon, Eilis; Spiers, Helen; Viana, Joana; Pidsley, Ruth; Burrage, Joe; Murphy, Therese M; Troakes, Claire; Turecki, Gustavo; O'donovan, Michael C; Schalkwyk, Leonard C | Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci | Nature neuroscience | 2016 |
| 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 | 2016 |
| 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 | 2016 |
| Ståhl, Patrik L; Salmén, Fredrik; Vickovic, Sanja; Lundmark, Anna; Navarro, José Fernández; Magnusson, Jens; Giacomello, Stefania; Asp, Michaela; Westholm, Jakub O; Huss, Mikael | Visualization and analysis of gene expression in tissue sections by spatial transcriptomics | Science | 2016 |
| Vickovic, Sanja; Ståhl, Patrik L; Salmén, Fredrik; Giatrellis, Sarantis; Westholm, Jakub Orzechowski; Mollbrink, Annelie; Navarro, José Fernández; Custodio, Joaquin; Bienko, Magda; Sutton, Lesley-Ann | Massive and parallel expression profiling using microarrayed single-cell sequencing | Nature communications | 2016 |
| Jemt, Anders; Salmén, Fredrik; Lundmark, Anna; Mollbrink, Annelie; Fernández Navarro, José; Ståhl, Patrik L; Yucel-Lindberg, Tülay; Lundeberg, Joakim | An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries | Scientific reports | 2016 |
| 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 | 2016 |
| Saralahti, Anni; Harjula, Sanna-Kaisa; Partanen, Essi; Rantapero, Tommi; Granberg, Kirsi; Lohi, Olli; Nykter, Matti; Rounioja, Samuli; Parikka, Mataleena; Rämet, Mika | A forward genetic screen for zebrafish genes involved in pneumococcal infection: P805 | Scandinavian Journal of Immunology | 2016 |
| Harjula, Sanna-Kaisa; Saralahti, Anni; Ojanen, Markus; Mathie, Heather; Halfpenny, Nicholas; Rantapero, Tommi; Granberg, Kirsi; Nykter, Matti; Lohi, Olli; Parikka, Mataleena | Genes affecting mycobacterial infection in zebrafish: P802 | Scandinavian Journal of Immunology | 2016 |
| Yli‐Hietanen, Jari; Ylipää, Antti; Yli‐Harja, Olli | Cancer research in the era of next‐generation sequencing and big data calls for intelligent modeling | Cancer Communications | 2015 |
| 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 | 2015 |
| 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 | 2015 |
| 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 | 2015 |
| 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 | 2015 |
| 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 | 2015 |
| 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 | 2015 |
| 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 | 2015 |
| 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 | 2015 |
| 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 | 2015 |
| 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 | 2015 |
| 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 | 2015 |
| 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 | 2015 |
| 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 | 2015 |
| 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 | 2015 |
| Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana; Olarte, Carlos | Verification of spatial and temporal modalities in biochemical systems | Electronic Notes in Theoretical Computer Science | 2015 |
| 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 | 2015 |
| Sin, Celine; Chiarugi, Davide; Valleriani, Angelo | Single-molecule modeling of mRNA degradation by miRNA: Lessons from data | BMC Systems Biology | 2015 |
| Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana; Olarte, Carlos; Torella, Luca | Modelling non-Markovian dynamics in biochemical reactions | BMC systems biology | 2015 |
| 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 | 2015 |
| Paradisi, Paolo; Allegrini, Paolo; Chiarugi, Davide | A renewal model for the emergence of anomalous solute crowding in liposomes | BMC systems biology | 2015 |
| Rading, M Michael; Sandmann, Michael; Steup, Martin; Chiarugi, Davide; Valleriani, Angelo | Weak correlation of starch and volume in synchronized photosynthetic cells | Physical Review E | 2015 |
| 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 | 2015 |
| Smedley, Damian; Haider, Syed; Durinck, Steffen; Pandini, Luca; Provero, Paolo; Allen, James; Arnaiz, Olivier; Awedh, Mohammad Hamza; Baldock, Richard; Barbiera, Giulia | The BioMart community portal: an innovative alternative to large, centralized data repositories | Nucleic acids research | 2015 |
| Koutsandreas, Theodoras; Pilalis, Eleftherios; Vlachavas, Efstathios Iason; Koczan, Dirk; Klippel, Sven; Dimitrakopoulou-Strauss, Antonia; Valavanis, Ioannis; Chatziioannou, Aristotelis | Making sense of the biological complexity through the platform-driven unification of the analytical and visualization tasks | 2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) | 2015 |
| 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 | 2014 |
| 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 | 2014 |
| 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 | 2014 |
| 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 | 2014 |
| 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 | 2014 |
| 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 | 2014 |
| Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana; Olarte, Carlos | A framework for modelling spatially dependent interactions of biological systems in CCP. | IWBBIO | 2014 |
| Bodei, Chiara; Brodo, Linda; Bruni, Roberto; Chiarugi, Davide | A flat process calculus for nested membrane interactions | Scientific Annals of Computer Science | 2014 |
| Pidsley, Ruth; Viana, Joana; Hannon, Eilis; Spiers, Helen; Troakes, Claire; Al-Saraj, Safa; Mechawar, Naguib; Turecki, Gustavo; Schalkwyk, Leonard C; Bray, Nicholas J | Methylomic profiling of human brain tissue supports a neurodevelopmental origin for schizophrenia | Genome biology | 2014 |
| 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 | 2014 |
| Ylipää, Antti; Yli-Harja, Olli; Zhang, Wei; Nykter, Matti | Characterization of aberrant pathways across human cancers | BMC systems biology | 2013 |
| 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 | 2013 |
| Annala, MJ; Parker, BC; Zhang, W; Nykter, M | Fusion genes and their discovery using high throughput sequencing | Cancer letters | 2013 |
| 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 | 2013 |
| 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 | 2013 |
| 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 | 2013 |
| 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 | 2013 |
| 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 | 2013 |
| 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 | 2013 |
| 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 | 2013 |
| 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 | 2013 |
| 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 | 2013 |
| 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 | 2013 |
| Manninen, Tapio; Huttunen, Heikki; Ruusuvuori, Pekka; Nykter, Matti | Leukemia prediction using sparse logistic regression | PloS one | 2013 |
| 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 | 2013 |
| Du, Xiaoling; Yang, Jilong; Ylipää, Antti; Zhu, Ze | RETRACTED ARTICLE: Genomic amplification and high expression of EGFR are key targetable oncogenic events in malignant peripheral nerve sheath tumor | Journal of hematology & oncology | 2013 |
| Mäki-Marttunen, Tuomo; Kesseli, Juha; Nykter, Matti | Balance between noise and information flow maximizes set complexity of network dynamics | PLoS One | 2013 |
| 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 | 2013 |
| 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 | 2013 |
| Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana; Guzman, Michell; Olarte, Carlos | Simulating signalling pathways with BioWayS | Electronic Notes in Theoretical Computer Science | 2013 |
| Dempster, Emma; Viana, Joana; Pidsley, Ruth; Mill, Jonathan | Epigenetic studies of schizophrenia: progress, predicaments, and promises for the future | Schizophrenia bulletin | 2013 |
| 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 | 2013 |
| 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 | 2012 |
| 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 | 2012 |
| 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 | 2012 |
| 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 | 2011 |
| 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 | 2011 |
| Yli-Harja, Olli; Ylipää, Antti; Nykter, Matti; Zhang, Wei | Cancer systems biology: signal processing for cancer research | Chinese Journal of Cancer | 2011 |
| 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 | 2011 |
| Annala, Matti; Laurila, Kirsti; Lähdesmäki, Harri; Nykter, Matti | A linear model for transcription factor binding affinity prediction in protein binding microarrays | PloS one | 2011 |
| 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 | 2011 |
| 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 | 2011 |
| 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 | 2011 |
| 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 | 2010 |
| Galas, David J; Nykter, Matti; Carter, Gregory W; Price, Nathan D; Shmulevich, Ilya | Biological information as set-based complexity | IEEE Transactions on Information Theory | 2010 |
| 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 | 2010 |
| 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 | 2009 |
| 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 | 2009 |
| 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 | 2009 |
| Bodei, Chiara; Bracciali, Andrea; Chiarugi, Davide | Control flow analysis for brane calculi | Electronic Notes in Theoretical Computer Science | 2009 |
| 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 | 2009 |
| 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 | 2009 |
| 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 |
| 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 | 2008 |
| 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 | 2008 |
| Bodei, Chiara; Bracciali, Andrea; Chiarugi, Davide | On deducing causality in metabolic networks | BMC bioinformatics | 2008 |
| 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 |
| Chiarugi, Davide; Degano, Pierpaolo; Marangoni, Roberto | A computational approach to the functional screening of genomes | PLoS Computational Biology | 2007 |
| 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 | 2007 |
| Koski, M Kristian; Hieta, Reija; Böllner, Claudia; Kivirikko, Kari I; Myllyharju, Johanna; Wierenga, Rik K | The active site of an algal prolyl 4-hydroxylase has a large structural plasticity | Journal of Biological Chemistry | 2007 |
| Nykter, Matti; Aho, Tommi; Ahdesmäki, Miika; Ruusuvuori, Pekka; Lehmussola, Antti; Yli-Harja, Olli | Simulation of microarray data with realistic characteristics | BMC bioinformatics | 2006 |
| 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 | 2006 |
| 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 | 2006 |
| 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 | 2006 |
| Chiarugi, Davide; Curti, Michele; Degano, Pierpaolo; Marangoni, Roberto | Vice: A virtual cell | International Conference on Computational Methods in Systems Biology | 2004 |
| 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 | 2004 |
| 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 | 2003 |
| 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 | 2003 |
| 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 | 2003 |
| 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 | 2002 |
