Scientific references

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

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

Authors Title Publication Volume Number Pages Year Publisher
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
Pekkarinen, Meeri; Nordfors, Kristiina; Uusi-Makela, Joonas; Kytola, Ville; Rauhala, Minna; Urhonen, Henna; Hayrynen, Sergei; Afyounian, Ebrahim; Yli-Harja, Olli; Zhang, Wei; Integrative DNA methylation analysis of pediatric brain tumors reveals tumor type-specific developmental trajectories and epigenetic signatures of malignancy bioRxiv 2022 Cold Spring Harbor Laboratory
Ruusuvuori, Pekka; Valkonen, Masi; Kartasalo, Kimmo; Valkonen, Mira; Visakorpi, Tapio; Nykter, Matti; Latonen, Leena; Spatial analysis of histology in 3D: quantification and visualization of organ and tumor level tissue environment Heliyon 8 1 e08762 2022 Elsevier
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
Hamis, Sara; Somervuo, Panu; Agren, J Arvid; Tadele, Dagim Shiferaw; Kesseli, Juha; Scott, Jacob G; Nykter, Matti; Gerlee, Philip; Finkelshtein, Dmitri; Ovaskainen, Otso; Spatial cumulant models enable spatially informed treatment strategies and analysis of local interactions in cancer systems bioRxiv 2022 Cold Spring Harbor Laboratory
Aakula, Anna; Sharma, Mukund; Tabaro, Francesco; Honkanen, Henrik; Schapira, Matthieu; Arrowsmith, Cheryl; Nykter, Matti; Westermarck, Jukka; RAS and PP2A activities converge on epigenetic gene regulation bioRxiv 2022 Cold Spring Harbor Laboratory
Cerqueira, Juliana Xavier de Miranda; Saavalainen, Paivi; Kurppa, Kalle; Laurikka, Pilvi; Huhtala, Heini; Nykter, Matti; Koskinen, Lotta LE; Yohannes, Dawit A; Kilpelainen, Elina; Shcherban, Anastasia; Coeliac disease phenotypic variation unraveled by disease-susceptibility loci in a deeply phenotyped Finnish cohort EUROPEAN JOURNAL OF HUMAN GENETICS 30 SUPPL 1 586-586 2022 SPRINGERNATURE CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND
Zijlmans, Dick W; Talon, Irene; Verhelst, Sigrid; Bendall, Adam; Van Nerum, Karlien; Javali, Alok; Malcolm, Andrew A; van Knippenberg, Sam SFA; Biggins, Laura; To, San Kit; Integrated multi-omics reveal polycomb repressive complex 2 restricts human trophoblast induction Nature cell biology 24 6 858-871 2022 Nature Publishing Group
Cao, Shaolong; Wang, Jennifer R; Ji, Shuangxi; Yang, Peng; Dai, Yaoyi; Guo, Shuai; Montierth, Matthew D; Shen, John Paul; Zhao, Xiao; Chen, Jingxiao; Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression Nature biotechnology 1-10 2022 Nature Publishing Group
Sharma, Mukund; Aakula, Anna; Tabaro, Francesco; Pavic, Karolina; Huhtaniemi, Riikka; Nykter, Matti; Westermarck, Jukka; Chromatin repressor complex as a converge point of RAS and PP2A activities in lung cancer Cancer Research 82 12_Supplement 2958-2958 2022 The American Association for Cancer Research
Taavitsainen, Sinja; Engedal, Nikolai; Cao, Shaolong; Handle, Florian; Erickson, Andrew; Prekovic, Stefan; Wetterskog, Daniel; Tolonen, Teemu; Vuorinen, Elisa M; Kiviaho, Antti; Single-cell transcriptome and chromatin sequencing uncover gene expression and gene regulatory patterns associated with enzalutamide resistance Cancer Research 82 12_Supplement 401-401 2022 The American Association for Cancer Research
Herberts, Cameron; Annala, Matti; Sipola, Joonatan; Ng, Sarah W; Chen, Xinyi E; Nurminen, Anssi; Korhonen, Olga; Munzur, Aslı D; Beja, Kevin; Schönlau, Elena; Clonal architecture and evolution of treatment-resistant prostate cancer via deep whole-genome ctDNA sequencing Cancer Research 82 12_Supplement 3625-3625 2022 The American Association for Cancer Research
Papadopoulou, Anastasia; Stavridou, Fani; Giannaki, Maria; Paschoudi, Kiriaki; Chatzopoulou, Fani; Gavriilaki, Eleni; Georgolopoulos, Grigorios; Anagnostopoulos, Achilles; Yannaki, Evangelia; Robust SARS-COV-2-specific T-cell immune memory persists long-term in immunocompetent individuals post BNT162b2 double shot Heliyon 8 7 e09863 2022 Elsevier
Roumelioti, Fani; Tzaferis, Christos; Konstantopoulos, Dimitris; Papadopoulou, Dimitra; Prados, Alejandro; Sakkou, Maria; Liakos, Anastasios; Chouvardas, Panagiotis; Meletakos, Theodore; Pandis, Yiannis; miR-221/222 drive synovial fibroblast expansion and pathogenesis of TNF-mediated arthritis bioRxiv 2022 Cold Spring Harbor Laboratory
Herberts, Cameron; Annala, Matti; Sipola, Joonatan; Ng, Sarah WS; Chen, Xinyi E; Nurminen, Anssi; Korhonen, Olga V; Munzur, Aslı D; Beja, Kevin; Schönlau, Elena; Deep whole-genome ctDNA chronology of treatment-resistant prostate cancer Nature 608 7921 199-208 2022 Nature Publishing Group
Armaka, Marietta; Konstantopoulos, Dimitris; Tzaferis, Christos; Lavigne, Matthieu D; Sakkou, Maria; Liakos, Anastasios; Sfikakis, Petros P; Dimopoulos, Meletios A; Fousteri, Maria; Kollias, George; Single-cell multimodal analysis identifies common regulatory programs in synovial fibroblasts of rheumatoid arthritis patients and modeled TNF-driven arthritis Genome medicine 14 1 1-25 2022 BioMed Central
Koivisto, Maria; Tolvanen, Tuomas A; Toimela, Tarja; Miinalainen, Ilkka; Kiviaho, Antti; Kesseli, Juha; Nykter, Matti; Eklund, Lauri; Heinonen, Tuula; Functional human cell-based vascularised cardiac tissue model for biomedical research and testing Scientific reports 12 1 1-13 2022 Nature Publishing Group
Psatha, N; Sova, P; Georgolopoulos, G; Iwata, M; Paschoudi, K; Kirtsou, A; Ulyanova, T; Stamatoyannopoulos, JA; Yannaki, E; Papayannopoulou, T; P1437: NOVEL ERYTHROID ENHANCERS IMPROVE GENE THERAPY VECTORS FOR BETA-HEMOGLOBINOPATHIES HemaSphere 6 1320-1321 2022 LWW
Rautajoki, Kirsi J; Jaatinen, Serafiina; Tiihonen, Aliisa M; Annala, Matti; Vuorinen, Elisa M; Kivinen, Anni; Rauhala, Minna J; Maass, Kendra K; Pajtler, Kristian W; Yli-Harja, Olli; PTPRD and CNTNAP2 as markers of tumor aggressiveness in oligodendrogliomas Scientific reports 12 1 1-11 2022 Nature Publishing Group
Pham, Thi Xuan Ai; Panda, Amitesh; Kagawa, Harunobu; Ertekin, Cankat; Georgolopoulos, Grigorios; van Knippenberg, Sam SFA; Allsop, Ryan Nicolaas; Bruneau, Alexandre; Chui, Jonathan Sai-Hong; Vanheer, Lotte; Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells Cell stem cell 29 9 1346-1365. e10 2022 Cell Press
Detsika, Maria G; Sakkou, Maria; Triantafyllidou, Vaso; Konstantopoulos, Dimitris; Grigoriou, Eirini; Psarra, Katherina; Jahaj, Edison; Dimpoulou, Ioanna; Orfanos, Stylianos E; Tsirogianni, Alexandra; Upregulation of CD55 complement regulator in distinct PBMC subpopulations of COVID-19 patients is associated with suppression of interferon responses. bioRxiv 2022 Cold Spring Harbor Laboratory
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
Du, Xiaoling; Yang, Jilong; Ylipää, Antti; Zhu, Ze; Retraction Note: Genomic amplification and high expression of EGFR are key targetable oncogenic events in malignant peripheral nerve sheath tumor Journal of Hematology & Oncology 15 2022 BioMed Central
Hannon, Eilis; Jeffries, Aaron R; Policicchio, Stefania; Viana, Joana; Leung, Szi Kay; Dempster, Emma; Mill, Jonathan; 42. LEVERAGING A BESPOKE CORTICAL TRANSCRIPTOME TO ASSESS THE ROLE OF ALTERNATIVE SPLICING IN SCHIZOPHRENIA European Neuropsychopharmacology 63 e67-e68 2022 Elsevier
Lagarto, José Reis; Marques, Herminia; Viana, Joana; Brito, Rita; Fradão, Sandra; Projeto Piloto de desmaterialização de manuais escolares e de outros recursos educativos digitais My Research 2022: Comunicar saberes no presente global| Disseminating knowledge in the global present 2022
Costa, Fernando Albuquerque; Paz, Ana; Pereira, Carolina; Cruz, Elisabete; Soromenho, Gilda; Viana, Joana; DE AVALIAÇÃO DA IMPLEMENTAÇÃO DAS APRENDIZAGENS ESSENCIAIS 2022
de OLIVEIRA, Artur Cunha Nogueira; Viana, Joana; Uso de tecnologias digitais no ensino de cartografia no Sistema Colégio Militar do Brasil Revista Ibero-Americana de Estudos em Educação 1785-1805 2022
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 1-11 2022 Springer
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
Poole, Kenneth; Chappell, Daniel; Sano, Hiroshige; Chiarugi, Davide; D'Amore, Simona; Baker, Olivia; Page, Kathleen; Ramaswami, Uma; Johannesdottir, Fj; Cox, Timothy; Radiographic cortical thickness index predicts fragility fracture in Gaucher disease 2022 Radiological Society of North America
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
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 1-10 2022 Nature Publishing Group
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
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
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-expressing cells in the hypothalamus Appetite 174 106022 2022 Elsevier
Cangiano, Mario; Grudniewska, Magda; Salji, Mark J; Nykter, Matti; Jenster, Guido; Urbanucci, Alfonso; Granchi, Zoraide; Janssen, Bart; Hamilton, Graham; Leung, Hing Y; Gene regulation network analysis on human prostate orthografts highlights a potential role for the JMJD6 regulon in clinical prostate cancer Cancers 13 9 2094 2021 MDPI
Filppu, Pauliina; Ramanathan, Jayendrakishore Tanjore; Granberg, Kirsi J; Gucciardo, Erika; Haapasalo, Hannu; Lehti, Kaisa; Nykter, Matti; Le Joncour, Vadim; Laakkonen, Pirjo; CD109-GP130 interaction drives glioblastoma stem cell plasticity and chemoresistance through STAT3 activity JCI insight 6 9 2021 American Society for Clinical Investigation
Cerqueira, Juliana XM; Saavalainen, Päivi; Kurppa, Kalle; Laurikka, Pilvi; Huhtala, Heini; Nykter, Matti; LE Koskinen, Lotta; Yohannes, Dawit A; Kilpeläinen, Elina; Shcherban, Anastasia; Independent and cumulative coeliac disease-susceptibility loci are associated with distinct disease phenotypes Journal of Human Genetics 66 6 613-623 2021 Nature Publishing Group
Rajamäki, Kristiina; Taira, Aurora; Katainen, Riku; Välimäki, Niko; Kuosmanen, Anna; Plaketti, Roosa-Maria; Seppälä, Toni T; Ahtiainen, Maarit; Wirta, Erkki-Ville; Vartiainen, Emilia; Genetic and epigenetic characteristics of inflammatory bowel Disease–Associated colorectal cancer Gastroenterology 161 2 592-607 2021 WB Saunders
Kukkonen, Konsta; Taavitsainen, Sinja; Huhtala, Laura; Uusi-Makela, Joonas; Granberg, Kirsi J; Nykter, Matti; Urbanucci, Alfonso; Chromatin and epigenetic dysregulation of prostate cancer development, progression, and therapeutic response Cancers 13 13 3325 2021 MDPI
Cao, Shaolong; Wang, Jennifer R; Ji, Shuangxi; Yang, Peng; Montierth, Matthew D; Guo, Shuai; Shen, John Paul; Zhao, Xiao; Chen, Jingxiao; Lee, Jaewon James; Tumor cell total mRNA expression shapes the molecular and clinical phenotype of cancer bioRxiv 2020.09. 30.306795 2021 Cold Spring Harbor Laboratory
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
Ketola, Kirsi; Kaljunen, Heidi; Taavitsainen, Sinja; Kaarijärvi, Roosa; Järvelä, Emmi; Rodriguez Martin, Bernardo; Haase, Kerstin; Woodcock, Dan J; Tubio, Jose; Wedge, David C; Subclone eradication analysis identifies targets for enhanced cancer therapy and reveals L1 retrotransposition as a dynamic source of cancer heterogeneity Cancer Research 81 19 4901-4909 2021 American Association for Cancer Research
Taavitsainen, Sinja; Engedal, Nikolai; Cao, Shaolong; Handle, Florian; Erickson, Andrew; Prekovic, Stefan; Wetterskog, Daniel; Tolonen, Teemu; Vuorinen, EM; Kiviaho, Antti; Single-cell ATAC and RNA sequencing reveal pre-existing and persistent subpopulations of cells associated with relapse of prostate cancer bioRxiv 2021 Cold Spring Harbor Laboratory
Vandekerkhove, Gillian; Lavoie, Jean-Michel; Annala, Matti; Murtha, Andrew J; Sundahl, Nora; Walz, Simon; Sano, Takeshi; Taavitsainen, Sinja; Ritch, Elie; Fazli, Ladan; Plasma ctDNA is a tumor tissue surrogate and enables clinical-genomic stratification of metastatic bladder cancer Nature communications 12 1 1-12 2021 Nature Publishing Group
Taavitsainen, S; Engedal, Nikolai; Cao, S; Handle, Florian; Erickson, A; Prekovic, Stefan; Wetterskog, D; Tolonen, T; Vuorinen, EM; Kiviaho, A; Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse Nature communications 12 1 1-16 2021 Nature Publishing Group
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
Annala, Matti; Taavitsainen, Sinja; Khalaf, Daniel J; Vandekerkhove, Gillian; Beja, Kevin; Sipola, Joonatan; Warner, Evan W; Herberts, Cameron; Wong, Amanda; Fu, Simon; Evolution of Castration-Resistant Prostate Cancer in ctDNA during Sequential Androgen Receptor Pathway InhibitionProstate Cancer Evolution during Sequential AR Inhibition Clinical Cancer Research 27 16 4610-4623 2021 American Association for Cancer Research
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
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
Rooda, Ilmatar; Kaselt, Birgitta; Liivrand, Maria; Smolander, Olli-Pekka; Salumets, Andres; Velthut-Meikas, Agne; Hsa-mir-548 family expression in human reproductive tissues BMC genomic data 22 1 1-13 2021 Springer
Moreau, Pierre R; Tomas Bosch, Vanesa; Bouvy-Liivrand, Maria; Õunap, Kadri; Örd, Tiit; Pulkkinen, Heidi H; Pölönen, Petri; Heinäniemi, Merja; Ylä-Herttuala, Seppo; Laakkonen, Johanna P; Profiling of primary and mature miRNA expression in atherosclerosis-associated cell types Arteriosclerosis, thrombosis, and vascular biology 41 7 2149-2167 2021 Lippincott Williams & Wilkins Hagerstown, MD
Loppi, Sanna; Korhonen, Paula; Bouvy‐Liivrand, Maria; Caligola, Simone; Turunen, Tiia A; Turunen, Mikko P; Hernandez de Sande, Ana; Kołosowska, Natalia; Scoyni, Flavia; Rosell, Anna; Peripheral inflammation preceeding ischemia impairs neuronal survival through mechanisms involving miR‐127 in aged animals Aging Cell 20 1 e13287 2021
Linna-Kuosmanen, Suvi; Tomas Bosch, Vanesa; Moreau, Pierre R; Bouvy-Liivrand, Maria; Niskanen, Henri; Kansanen, Emilia; Kivelä, Annukka; Hartikainen, Juha; Hippeläinen, Mikko; Kokki, Hannu; NRF2 is a key regulator of endothelial microRNA expression under proatherogenic stimuli Cardiovascular research 117 5 1339-1357 2021 Oxford University Press
Simao, Felipe A; Hieta, Reija; Pulman, Jane A; Madonna, Gabriele; Ascierto, Paolo Antonio; Lewensohn, Rolf; Masucci, Giuseppe V; SRF-CLICAL: An approach for patient risk stratification using random forest models bioRxiv 2021 Cold Spring Harbor Laboratory
Manni, Mosè; Berkeley, Matthew R; Seppey, Mathieu; Simão, Felipe A; Zdobnov, Evgeny M; BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes Molecular Biology and Evolution 38 10 4647-4654 2021 Oxford University Press
Madonna, Gabriele; Masucci, Giuseppe V; Capone, Mariaelena; Mallardo, Domenico; Grimaldi, Antonio Maria; Simeone, Ester; Vanella, Vito; Festino, Lucia; Palla, Marco; Scarpato, Luigi; Clinical Categorization Algorithm (CLICAL) and Machine Learning Approach (SRF-CLICAL) to Predict Clinical Benefit to Immunotherapy in Metastatic Melanoma Patients: Real-World Evidence from the Istituto Nazionale Tumori IRCCS Fondazione Pascale, Napoli, Italy Cancers 13 16 4164 2021 MDPI
Verta, Jukka-Pekka; Barton, Henry J; Pritchard, Victoria; Primmer, Craig R; Genetic Drift Dominates Genome-Wide Regulatory Evolution Following an Ancient Whole-Genome Duplication in Atlantic Salmon Genome biology and evolution 13 5 evab059 2021 Oxford University Press
Barton, Henry J; Zeng, Kai; The effective population size modulates the strength of GC biased gene conversion in two passerines bioRxiv 2021 Cold Spring Harbor Laboratory
Georgolopoulos, Grigorios; Psatha, Nikoletta; Iwata, Mineo; Nishida, Andrew; Som, Tannishtha; Yiangou, Minas; Stamatoyannopoulos, John A; Vierstra, Jeff; Discrete regulatory modules instruct hematopoietic lineage commitment and differentiation Nature communications 12 1 1-15 2021 Nature Publishing Group
Georgolopoulos, Grigorios; Psatha, Nikoletta; Iwata, Mineo; Nishida, Andrew; Som, Tannishtha; Yiangou, Minas; Stamatoyannopoulos, John A; Vierstra, Jeff; Chromatin dynamics during hematopoiesis reveal discrete regulatory modules instructing differentiation Biorxiv 2020.04. 02.022566 2021 Cold Spring Harbor Laboratory
Psatha, Nikoletta; Georgakopoulou, Aphrodite; Li, Chang; Nandakumar, Vivek; Georgolopoulos, Grigorios; Acosta, Reyes; Paschoudi, Kiriaki; Nelson, Jemma; Chee, Daniel; Athanasiadou, Anastasia; Enhanced HbF reactivation by multiplex mutagenesis of thalassemic CD34+ cells in vitro and in vivo blood 138 17 1540-1553 2021 American Society of Hematology
Stefos, Georgios C; Szantai, Eszter; Konstantopoulos, Dimitris; Samiotaki, Martina; Fousteri, Maria; aniFOUND: analysing the associated proteome and genomic landscape of the repaired nascent non-replicative chromatin Nucleic acids research 49 11 e64-e64 2021 Oxford University Press
Zannikou, Markella; Barbayianni, Ilianna; Fanidis, Dionysios; Grigorakaki, Theodora; Vlachopoulou, Evlalia; Konstantopoulos, Dimitris; Fousteri, Maria; Nikitopoulou, Ioanna; Kotanidou, Anastasia; Kaffe, Eleanna; MAP3K8 Regulates Cox-2–Mediated Prostaglandin E2 Production in the Lung and Suppresses Pulmonary Inflammation and Fibrosis The Journal of Immunology 206 3 607-620 2021 Am Assoc Immnol
Armaka, Marietta; Konstantopoulos, Dimitris; Tzaferis, Christos; Lavigne, Matthieu D; Sakkou, Maria; Liakos, Anastasios; Sfikakis, Petros P; Dimopoulos, Meletios A; Fousteri, Maria; Kollias, George; Single-cell chromatin and transcriptome dynamics of Synovial Fibroblasts transitioning from homeostasis to pathology in modelled TNF-driven arthritis bioRxiv 2021 Cold Spring Harbor Laboratory
Viana, Joana; Peralta, Helena; Online learning: From the curriculum for all to the curriculum for each individual. Journal of New Approaches in Educational Research 10 1 122-136 2021 ERIC
Viana, Joana; Fradão, Sandra; Peralta, Helena; Soromenho, Gilda; Aprender e Ensinar a Distância em Tempo de Pandemia 2021
Costa, Fernando A; Raleiras, Mónica; Viana, Joana; 12 PEDAGOGICAL PRINCIPLES FOR THE USE OF GAMIFICATION IN HIGHER EDUCATION Proceedings of ICERI2021 Conference 8 9th 2021
Marques, Herminia; Viana, Joana; Lagarto, José; Brito, Rita; Projeto-piloto de desmaterialização de manuais escolares e de outros recursos educativos digitais: relatório final Projeto-piloto de desmaterialização de manuais escolares e de outros recursos educativos digitais: relatório final 2021 Direção-Geral da Educação
Raleiras, Mónica; Costa, Fernando A; Viana, Joana; Students' Approaches to Learning in a Gamified Course in Higher Education 2021 19th International Conference on Information Technology Based Higher Education and Training (ITHET) 1-7 2021 IEEE
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 1-12 2021 Nature Publishing Group
Carobbio, Stefania; Guenantin, Anne-Claire; Bahri, Myriam; Rodriguez-Fdez, Sonia; Honig, Floris; Kamzolas, Ioannis; Samuelson, Isabella; Long, Kathleen; Awad, Sherine; Lukovic, Dunja; Unraveling the Developmental Roadmap toward Human Brown Adipose Tissue Stem cell reports 16 3 641-655 2021 Elsevier
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 108810 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
Furse, Samuel; Watkins, Adam; Hojat, Nima; Smith, James; Williams, Huw; Chiarugi, Davide; Stevenson, Philip; Koulman, Albert; Traffic Analysis Reveals the Impact of Dietary Intake on Lipid Metabolism The FASEB Journal 35 2021 Wiley Online Library
Furse, S; Watkins, AJ; Hojat, N; Smith, J; Williams, HEL; Chiarugi, D; Code for: Lipid traffic analysis reveals the impact of high paternal carbohydrate intake on offsprings’ lipid metabolism 2021
Furse, S; Watkins, AJ; Hojat, N; Smith, J; Williams, HEL; Chiarugi, D; PMC free article PubMed][Google Scholar] 2021
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 Wiley Online Library
Scaravilli, Mauro; Afyounian, Ebrahim; Nykter, Matti; Visakorpi, Tapio; Latonen, Leena; Integrative proteomics of prostate cancer Current Opinion in Endocrine and Metabolic Research 10 43-49 2020 Elsevier
Granberg, Kirsi Johanna; Tuominen, Joonas; Nordfors, Kristiina; Pekkarinen, Meeri; Kytölä, Ville; Häyrynen, Sergei; Afyounian, Ebrahim; Lohi, Olli; Helen, Pauli; Kesseli, Juha; Abstract LB-173: DNA methylation analysis reveals epigenetic regulation of neural differentiation in AT/RTs Cancer Research 80 16_Supplement LB-173-LB-173 2020 The American Association for Cancer Research
Tanjore Ramanathan, Jayendrakishore; Lehtipuro, Suvi; Sihto, Harri; Tóvári, József; Reiniger, Lilla; Téglási, Vanda; Moldvay, Judit; Nykter, Matti; Haapasalo, Hannu; Le Joncour, Vadim; Prostate‐specific membrane antigen expression in the vasculature of primary lung carcinomas associates with faster metastatic dissemination to the brain Journal of cellular and molecular medicine 24 12 6916-6927 2020 Wiley Online Library
Gundem, Gunes; Van Loo, Peter; Kremeyer, Barbara; Alexandrov, Ludmil B; Tubio, Jose; Papaemmanuil, Elli; Brewer, Daniel S; Kallio, Heini ML; Hägnäs, Gunilla; Annala, Matti; Author Correction: The evolutionary history of lethal metastatic prostate cancer (Nature,(2015), 520, 7547,(353-357), 10.1038/nature14347) 2020 Springer US
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
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
Woodcock, DJ; Riabchenko, Ekaterina; Taavitsainen, Sinja; Kankainen, Matti; Gundem, Gunes; Brewer, DS; Ellonen, Pekka; Lepistö, Maija; Golubeva, YA; Warner, AC; Prostate cancer evolution from multilineage primary to single lineage metastases with implications for liquid biopsy Nature communications 11 1 1-13 2020 Nature Publishing Group
Gundem, Gunes; Van Loo, Peter; Kremeyer, Barbara; Alexandrov, Ludmil B; Tubio, JMC; Papaemmanuil, Elli; Brewer, Daniel S; Kallio, Heini ML; Hagnas, Gunilla; Annala, Matti; The evolutionary history of lethal metastatic prostate cancer (vol 87, pg 511, 2020) Nature 584 7820 E18-E18 2020 Macmillan Publishers Ltd., London, England
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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
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
Warner, Evan; Yip, Steven; Annala, Matti; Wang, Gang; Angeles, Arkhjamil; Beigi, Arshia; Schönlau, Elena; Wong, Amanda; Taavitsainen, Sinja; Vandekerkhove, Gillian; Abstract PR09: Frequency and etiology of ctDNA-positive metastatic prostate cancer with BRCA2, ATM, or CDK12 mutations Clinical Cancer Research 26 11_Supplement PR09-PR09 2020 The American Association for Cancer Research
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
Gundem, Gunes; Van Loo, Peter; Kremeyer, Barbara; Alexandrov, Ludmil B; Tubio, Jose; Papaemmanuil, Elli; Brewer, Daniel S; Kallio, Heini ML; Hägnäs, Gunilla; Annala, Matti; Author Correction: The evolutionary history of lethal metastatic prostate cancer Nature 584 7820 E18-E18 2020 Nature Publishing Group
Warner, Evan; Yip, Steven; Annala, Matti; Wang, Gang; Angeles, Arkhjamil; Beigi, Arshia; Schonlau, Elena; Wong, Amanda; Taavitsainen, Sinja; Vandekerkhove, Gillian; Frequency and etiology of ctDNA-positive metastatic prostate cancer with BRCA2, ATM, or CDK12 mutations CLINICAL CANCER RESEARCH 26 11 30-30 2020 AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA …
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
Raittinen, Paavo VH; Pennanen, Pasi; Syvälä, Heimo; Bläuer, Merja; Ikonen, Niina; Nätkin, Reetta; Nykter, Matti; Tammela, Teuvo; Ilmonen, Pauliina; Murtola, Teemu T; Genetic landscape changes in metastatic prostate cancer after sequential steps of androgen targeted therapy Cancer Research 80 16_Supplement 5913-5913 2020 The American Association for Cancer Research
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
Uusi-Mäkelä, Joonas; Afyounian, Ebrahim; Tabaro, Francesco; Häkkinen, Tomi; Lussana, Alessandro; Shcherban, Anastasia; Annala, Matti; Nurminen, Riikka; Kivinummi, Kati; Tammela, Teuvo LJ; Chromatin accessibility analysis uncovers regulatory element landscape in prostate cancer progression bioRxiv 2020 Cold Spring Harbor Laboratory
Mehtonen, Juha; Teppo, Susanna; Lahnalampi, Mari; Kokko, Aleksi; Kaukonen, Riina; Oksa, Laura; Bouvy-Liivrand, Maria; Malyukova, Alena; Mäkinen, Artturi; Laukkanen, Saara; Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities Genome medicine 12 1 1-25 2020 Springer
Oeyen, Jan Philip; Baa-Puyoulet, Patrice; Benoit, Joshua B; Beukeboom, Leo W; Bornberg-Bauer, Erich; Buttstedt, Anja; Calevro, Federica; Cash, Elizabeth I; Chao, Hsu; Charles, Hubert; Sawfly genomes reveal evolutionary acquisitions that fostered the mega-radiation of parasitoid and eusocial Hymenoptera Genome biology and evolution 12 7 1099-1188 2020 Oxford University Press
Manni, Mosè; Simao, Felipe A; Robertson, Hugh M; Gabaglio, Marco A; Waterhouse, Robert M; Misof, Bernhard; Niehuis, Oliver; Szucsich, Nikolaus U; Zdobnov, Evgeny M; The genome of the blind soil-dwelling and ancestrally wingless dipluran campodea augens: a key reference hexapod for studying the emergence of insect innovations Genome biology and evolution 12 1 3534-3549 2020 Oxford University Press
Rotenberg, Dorith; Baumann, Aaron A; Ben-Mahmoud, Sulley; Christiaens, Olivier; Dermauw, Wannes; Ioannidis, Panagiotis; Jacobs, Chris GC; Vargas Jentzsch, Iris M; Oliver, Jonathan E; Poelchau, Monica F; Genome-enabled insights into the biology of thrips as crop pests BMC biology 18 1 1-37 2020 BioMed Central
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
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
Rantapero, Tommi; Developing a Framework for Analysis of Next-Generation Sequencing Data in Cancer Genetics and Epigenetics 2020 Tampere University
Ulyanova, Tatyana; Georgolopoulos, Grigorios; Papayannopoulou, Thalia; Reappraising the role of α5 integrin and the microenvironmental support in stress erythropoiesis Experimental hematology 81 16-31. e4 2020 Elsevier
Konstantopoulos, D; Tzaferis, C; Sakkou, M; Liakos, A; Lavigne, M; Karamitros, D; Fousteri, M; Armaka, M; Kollias, G; OP0099 FUNCTIONAL MAPPING OF SYNOVIAL FIBROBLAST POPULATIONS IN HEALTH AND ARTHRITIC DISEASE: INSIGHTS INTO THE PATHOGENIC REMODELING OF SYNOVIAL MICROENVIRONMENT 2020 BMJ Publishing Group Ltd
Liakos, Anastasios; Konstantopoulos, Dimitris; Lavigne, Matthieu D; Fousteri, Maria; Continuous transcription initiation guarantees robust repair of all transcribed genes and regulatory regions Nature communications 11 1 1-16 2020 Nature Publishing Group
Morianos, Ioannis; Trochoutsou, Aikaterini I; Papadopoulou, Gina; Semitekolou, Maria; Banos, Aggelos; Konstantopoulos, Dimitris; Manousopoulou, Antigoni; Kapasa, Maria; Wei, Ping; Lomenick, Brett; Activin-A limits Th17 pathogenicity and autoimmune neuroinflammation via CD39 and CD73 ectonucleotidases and Hif1-α–dependent pathways Proceedings of the National Academy of Sciences 117 22 12269-12280 2020 National Acad Sciences
Ori, APS; Wang, T; Pulit, SL; Strengman, E; Viana, J; Mill, J; de Jong, S; Ophoff, RA; Integrative genomic strategies applied to a lymphoblast cell line model reveal specific transcriptomic signatures associated with clozapine response bioRxiv 2020 Cold Spring Harbor Laboratory
Policicchio, Stefania; Washer, Sam; Viana, Joana; Iatrou, Artemis; Burrage, Joe; Hannon, Eilis; Turecki, Gustavo; Kaminsky, Zachary; Mill, Jonathan; Dempster, Emma L; Genome-wide DNA methylation meta-analysis in the brains of suicide completers Translational psychiatry 10 1 1-13 2020 Nature Publishing Group
Almeida, Marta; Viana, Joana; Carvalho, Luís Miguel; Processos e Sentidos da Regulação Transnacional da Profissão Docente: uma análise das Cimeiras Internacionais sobre a Profissão Docente (2011-2017) Currículo sem Fronteiras 20 1 62-84 2020
Raleiras, M; Viana, J; Costa, F; Adaptive gamification models in higher education: Is there a place for self-regulated learning? Proceedings of EDULEARN20 Conference 6 7th 2020
Viana, Joana; Wildman, Nick; Hannon, Eilis; Farbos, Audrey; Neill, Paul O’; Moore, Karen; Van Aerle, Ronny; Paull, Greg; Santos, Eduarda; Mill, Jonathan; Clozapine-induced transcriptional changes in the zebrafish brain npj Schizophrenia 6 1 1-11 2020 Nature Publishing Group
Costa, Fernando Albuquerque; Viana, Joana; Raleiras, Mónica; What do higher education students have to say about gamification? International Conference in Methodologies and intelligent Systems for Techhnology Enhanced Learning 56-65 2020 Springer
Viana, Joana; Peralta, Helena; Aprender na era digital: Do currículo para todos ao currículo de cada um: Learning in the digital age: from the curriculum for everyone to the curriculum of each Revista Portuguesa de Educação 33 1 137-157 2020
Viana, Joana; Burrage, Joe; Hanon, Eilis; Mill, Jonathan; Dempster, EL; Murphy, Therese M; Genome-wide DNA methylation meta-analysis in the brains of suicide completers 2020 Nature Publishing Group
Responsáveis, Investigadores; Costa, Estela; de Almeida, Marta Mateus; Colaboradores, Investigadores; Dorotea, Nuno; Viana, Joana; Estudo de avaliação da reorganização do calendário escolar 2020
Responsáveis, Investigadoras; Costa, Estela; de Almeida, Marta Mateus; Viana, Joana; Relatório de avaliação da reorganização do calendário escolar 2020
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
Hall, Zoe; Leslie, Jack; Scott, Emma; Chiarugi, Davide; Charidemou, Evelina; Pelligrinet, Luca; Evan, Gerard; Allison, Michael; Vidal-Puig, Antonio; Anstee, Quentin; Phospholipid metabolism rewiring in liver regeneration and hepatocellular carcinoma Journal of Hepatology 73 S15-S16 2020 Elsevier
Furse, Samuel; Watkins, Adam J; Chiarugi, Davide; Hojat, Nima; Smith, James; Williams, Huw EL; Koulman, Albert; Revealing grand-paternal programming of lipid metabolism using a novel computational tool BioRxiv 2020 Cold Spring Harbor Laboratory
Valleriani, Angelo; Chiarugi, Davide; A workbench for the translational control of gene expression bioRxiv 2020 Cold Spring Harbor Laboratory
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
Granberg, Kirsi J; Raita, Annina; Lehtinen, Birgitta; Tiihonen, Aliisa M; Kesseli, Juha; Annala, Matti; Rodriguez-Martinez, Alejandra; Nordfors, Kristiina; Zhang, Wei; Visakorpi, Tapio; Moderate-to-strong expression of FGFR3 and TP53 alterations in a subpopulation of choroid plexus tumors. Histology and Histopathology 35 7 673-680 2019
Yang, Jilong; Ylipää, Antti; Sun, Yan; Zheng, Hong; Chen, Kexin; Nykter, Matti; Trent, Jonathan; Ratner, Nancy; Lev, Dina C; Zhang, Wei; Editor's Note: Genomic and Molecular Characterization of Malignant Peripheral Nerve Sheath Tumor Identifies the IGF1R Pathway as a Primary Target for Treatment Clinical Cancer Research 25 10 3195-3195 2019 AACR
Scaravilli, Mauro; Kohvakka, Annika; Ruusuvuori, Pekka; Afyounian, Ebrahim; Nykter, Matti; Visakorpi, Tapio; Latonen, Leena; Integrative proteomic analysis of prostate cancer reveals distinct regulation of RNA binding proteins during disease progression Cancer Research 79 13_Supplement 4393-4393 2019 The American Association for Cancer Research
Lehtipuro, Suvi; Nykter, Matti; Granberg, Kirsi J; Modes of immunosuppression in glioblastoma microenvironment Oncotarget 10 9 920 2019 Impact Journals, LLC
Pölönen, Petri; Mehtonen, Juha; Lin, Jake; Liuksiala, Thomas; Häyrynen, Sergei; Teppo, Susanna; Mäkinen, Artturi; Kumar, Ashwini; Malani, Disha; Pohjolainen, Virva; Hemap: An Interactive Online Resource for Characterizing Molecular Phenotypes across Hematologic MalignanciesOrganizing Molecular Diversity of Hematologic Malignancies Cancer research 79 10 2466-2479 2019 American Association for Cancer Research
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
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
Ruusuvuori, Pekka; Kartasalo, Kimmo; Valkonen, Mira; Valkonen, Masi; Visakorpi, Tapio; Nykter, Matti; Latonen, Leena; 3D reconstruction and quantitative analysis of histology for prostate cancer Cancer Research 79 13_Supplement 46-46 2019 The American Association for Cancer Research
Cangiano, M; Leung, H; Janssen, B; Nykter, M; Jenster, G; A transcription factor activity profile as a prognostic signature for androgen deprivation therapy resistance predisposition in prostate cancer patients European Urology Supplements 18 8 e3048-e3049 2019 Elsevier
Viiri, Leena E; Rantapero, Tommi; Kiamehr, Mostafa; Alexanova, Anna; Oittinen, Mikko; Viiri, Keijo; Niskanen, Henri; Nykter, Matti; Kaikkonen, Minna U; Aalto-Setälä, Katriina; Extensive reprogramming of the nascent transcriptome during iPSC to hepatocyte differentiation Scientific reports 9 1 1-12 2019 Nature Publishing Group
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
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
Tuominen, Joonas I; Afyounian, Ebrahim; Tabaro, Francesco; Häkkinen, Tomi; Shcherban, Anastasia; Annala, Matti; Kivinummi, Kati; Tammela, Teuvo; Kesseli, Juha; Latonen, Leena; Abstract LB-096: Chromatin alterations in human prostate cancer Cancer Research 79 13_Supplement LB-096-LB-096 2019 The American Association for Cancer Research
Sattari, M; Kohvakka, A; Urhonen, H; Moradi, E; Rauhala, H; Nykter, M; Latonen, L; Bova, GS; Kesseli, J; Visakorpi, T; Identification of novel long non-coding RNA based biomarkers in prostate cancer European Urology Supplements 18 8 e3078 2019 Elsevier
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
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
Moreau, Pierre; Ord, Tiit; Lonnberg, Tapio; Bouvy-Liivrand, Maria; Aavik, Einari; Yla-Herttuala, Seppo; Heinaniemi, Merja; Kaikkonen-Maatta, Minna; Dissecting the Roles of Altered Cell Type Composition and Cell Specific Responses to Proatherogenic Stimuli in Contributing to Global Gene Expression Changes in Atherosclerotic Aorta JOURNAL OF VASCULAR RESEARCH 56 54-54 2019 KARGER ALLSCHWILERSTRASSE 10, CH-4009 BASEL, SWITZERLAND
Korhonen, Matti; Maliniemi, Pilvi; Impola, Ulla; Liivrand, Maria; Heinaniemi, Merja; Nascent Transcripts of Target-Activated CD19-CAR-T Cells Reveal Early Activation of the C-REL and NF kappa B Pathway MOLECULAR THERAPY 27 4 460-460 2019 CELL PRESS 50 HAMPSHIRE ST, FLOOR 5, CAMBRIDGE, MA 02139 USA
Waterhouse, Robert M; Seppey, Mathieu; Simão, Felipe A; Zdobnov, Evgeny M; Using BUSCO to assess insect genomic resources Insect genomics 59-74 2019 Springer
Kriventseva, Evgenia V; Kuznetsov, Dmitry; Tegenfeldt, Fredrik; Manni, Mosè; Dias, Renata; Simão, Felipe A; Zdobnov, Evgeny M; OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs Nucleic acids research 47 D1 D807-D811 2019 Oxford University Press
Zeng, Kai; Jackson, Benjamin C; Barton, Henry J; Methods for estimating demography and detecting between-locus differences in the effective population size and mutation rate Molecular biology and evolution 36 2 423-433 2019 Oxford University Press
Barton, Henry Juho; Characterising the impact of directional forces on genomic variation 2019 University of Sheffield
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
Zajitschek, Felix; Georgolopoulos, Grigorios; Vourlou, Anna; Ericsson, Maja; Zajitschek, Susanne RK; Friberg, Urban; Maklakov, Alexei A; Evolution under dietary restriction decouples survival from fecundity in Drosophila melanogaster females The Journals of Gerontology: Series A 74 10 1542-1548 2019 Oxford University Press US
Vallianou, Ioanna; Christofi, Panayiota; Varvaraki, Angeliki; Psatha, Nikoletta; Georgolopoulos, Grigorios; Georgakopoulou, Afrodite; Papayanni, Penelope; Anagnostopoulos, Achilles; Yannaki, Evangelia; UM171 Efficiently Expands Genetically Modified Haematopoietic Stem Cells from Mobilized Blood and Transduces Preferentially the Erythroid Lineage Molecular Therapy 27 4 456-456 2019 Elsevier (Cell Press)
Psatha, Nikoleta; Sova, Pavel; Georgolopoulos, Grigorios; Navas, Pat; Stamatoyannopoulos, John A; Vierstra, Jeff; Papayannopoulou, Thalia; Stamatoyannopoulos, George; Identifying Novel Erythroid Specific Enhancers to Optimize Transgene Expression in Beta Globin Gene Therapy Molecular Therapy 27 4 416-417 2019 Elsevier (Cell Press)
Georgolopoulos, G; Iwata, M; Nishida, A; Som, T; Yiangou, M; Stamatoyannopoulos, JA; Vierstra, J; PF454 DENSE TEMPORAL PROFILING OF EPIGENETIC EVENTS REVEALS TWO DISCRETE PROGRAMS THAT GOVERN HUMAN ERYTHROPOIESIS HemaSphere 3 S1 179 2019 LWW
Georgolopoulos, Grigorios; Iwata, Mineo; Psatha, Nikoletta; Yiangou, Minas; Vierstra, Jeff; Unbiased phenotypic identification of functionally distinct hematopoietic progenitors Journal of Biological Research-Thessaloniki 26 1 1-5 2019 Springer
Liakos, Anastasios; Konstantopoulos, Dimitris; Lavigne, Matthieu D; Fousteri, Maria; Continuous transcription initiation guarantees robust repair of transcribed genes and regulatory regions in response to DNA damage bioRxiv 712364 2019 Cold Spring Harbor Laboratory
Liakos, A; Konstantopoulos, D; Spyropoulou, Z; Fousteri, M; Lavigne, MD; Elucidating the role of active transcription in keeping genome integrity in check BRITISH JOURNAL OF DERMATOLOGY 180 6 E217-E217 2019 WILEY 111 RIVER ST, HOBOKEN 07030-5774, NJ USA
Yusuf, Leeban; Heatley, Matthew; Palmer, Joseph PG; Barton, Henry J; Cooney, Christopher R; Goßmann, Toni; Non-coding rather than coding regions underpin avian bill shape diversification at macroevolutionary scales bioRxiv 2019
Viana, Joana; Mansell, Georgina; Jager, Amanda; Mogavero, Floriana; Walker, Sophie; Huzard, Damien; Zoratto, Francesca; Macri, Simone; Hannon, Eilis; Laviola, Giovanni; Genetic And Epigenetic Signatures Of Aggression In Three Distinct Rodent Models European Neuropsychopharmacology 29 CONF 1225-1226 2019 Elsevier
Policicchio, Stefania; Viana, Joana; Iatrou, Artemis; Hannon, Eilis; Burrage, Joe; Turecki, Gustavo; Kaminsky, Zachary; Mill, Jonathan; Dempster, Emma; Murphy, Therese; SA68SUICIDE-ASSOCIATED DNA METHYLATION CHANGES IN POST-MORTEM BRAIN SAMPLES: A META-ANALYSIS European Neuropsychopharmacology 29 S1225 2019 Elsevier
Viana, Joana; Hannon, Eilis; van Aerle, Ronny; Dempster, Emma; Paull, Gregory; Santos, Eduarda; Mill, Jonathan; A ZEBRAFISH MODEL OF CLOZAPINE EXPOSURE: DRUG-INDUCED TRANSCRIPTOMIC CHANGES IN THE BRAIN European Neuropsychopharmacology 29 S782 2019 Elsevier
Viana, Joana; Coelho, Conceição; A percorrer o caminho da transformação (digital) na escola... o professor como agente de mudança! Intersaberes 2019 Curitiba
Viana, Joana; EDUCAÇÃO DIGITAL (NÃO FORMAL) Omnia 9 1 17-24 2019
Mill, Jonathan; Hannon, Eilis; Spiers, Helen; Wong, Chloe Chung Yi; Viana, Joana; O'Donovan, Michael; Schalkwyk, Leo; Bray, Nick; Regulatory Genomic Variation In The Developing Brain: Relevance To Neuropsychiatric Phenotypes European Neuropsychopharmacology 29 S772-S773 2019 Elsevier
de Almeida, Marta Mateus; Viana, Joana; Sanches, Tatiana; Paz, Ana Luísa; Tendências recentes da investigação internacional sobre pedagogia do ensino superior: uma revisão da literatura Revista Lusófona de Educação 45 45 2019
Costa, FA; Viana, J; Tréz, T; Gonçalves, C; Cruz, E; Pereira, C; Learning Activities Design Based on the Concept of Learning With Technologies EDULEARN19 Proceedings 4066-4073 2019 IATED
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
Roberts, Geoffrey P; Larraufie, Pierre; Richards, Paul; Kay, Richard G; Galvin, Sam G; Miedzybrodzka, Emily L; Leiter, Andrew; Li, H Joyce; Glass, Leslie L; Ma, Marcella KL; Comparison of human and murine enteroendocrine cells by transcriptomic and peptidomic profiling Diabetes 68 5 1062-1072 2019 Am Diabetes Assoc
Luoto, Suvi; Hermelo, Ismaïl; Vuorinen, Elisa; Hannus, Paavo; Kesseli, Juha; Nykter, Matti; Granberg, Kirsi; TMIC-30. computational characterization of suppressive immune microenvironments in glioblastoma Neuro-Oncology 20 Suppl 6 vi262 2018 Oxford University Press
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, Matti; Taavitsainen, Sinja; Vandekerkhove, Gillian; Bacon, Jack VW; Beja, Kevin; Chi, Kim N; Nykter, Matti; Wyatt, Alexander W; Frequent mutation of the FOXA1 untranslated region in prostate cancer Communications biology 1 1 1-8 2018 Nature Publishing Group
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
Mäntylä, S; Haapasalo, J; Ilvesaro, J; Nordfors, K; Isola, J; Haapasalo, H; Nykter, M; Granberg, K; P04. 78 Ultrarapid FGFR3 immunostaining for diagnosis of gliomas harboring FGFR3 gene fusions Neuro-Oncology 20 Suppl 3 iii298 2018 Oxford University Press
Tuominen, Joonas; Häkkinen, Tomi; Annala, Matti; Kivinummi, Kati; Tammela, Teuvo; Latonen, Leena; Granberg, Kirsi; Visakorpi, Tapio; Nykter, Matti; Abstract A077: Chromatin state alterations in human prostate cancer progression Cancer Research 78 16_Supplement A077-A077 2018 The American Association for Cancer Research
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
Kohvakka, Annika; Shcherban, Anastasia; Kivinummi, Kati K; Annala, Matti; Urbanucci, Alfonso; Nykter, Matti; Visakorpi, Tapio; Discovery of an androgen-responsive long noncoding RNA that associates with progression of ERG-overexpressing prostate cancers Cancer Research 78 13_Supplement 2476-2476 2018 The American Association for Cancer Research
Högnäs, Gunilla; Kivinummi, Kati; Kallio, Heini ML; Hieta, Reija; Ruusuvuori, Pekka; Koskenalho, Antti; Kesseli, Juha; Tammela, Teuvo LJ; Riikonen, Jarno; Ilvesaro, Joanna; Feasibility of prostate paxgene fixation for molecular research and diagnostic surgical pathology The American Journal of Surgical Pathology 42 1 103-115 2018 Wolters Kluwer
Annala, Matti; Vandekerkhove, Gillian; Khalaf, Daniel; Taavitsainen, Sinja; Beja, Kevin; Warner, Evan W; Sunderland, Katherine; Kollmannsberger, Christian; Eigl, Bernhard J; Finch, Daygen; Circulating Tumor DNA Genomics Correlate with Resistance to Abiraterone and Enzalutamide in Prostate CancerctDNA and Resistance to AR-Targeted Therapy Cancer discovery 8 4 444-457 2018 American Association for Cancer Research
Nordfors, Kristiina; Haapasalo, Joonas; Afyounian, Ebrahim; Tuominen, Joonas; Annala, Matti; Häyrynen, Sergei; Karhu, Ritva; Helén, Pauli; Lohi, Olli; Nykter, Matti; Erratum: Whole-exome sequencing identifies germline mutation in TP53 and ATRX in a child with genomically aberrant AT/RT and her mother with anaplastic astrocytoma Cold Spring Harbor Molecular Case Studies 4 3 2018 Cold Spring Harbor Laboratory Press
Aapola, U; Mikhailova, A; Nykter, M; Zhou, L; Beuerman, R; Uusitalo, H; Comparison of itraq and swath in a clinical study with multiple time points 2018 BioMed Central Ltd
Ruusuvuori, Pekka; Valkonen, Mira; Kartasalo, Kimmo; Visakorpi, Tapio; Nykter, Matti; Latonen, Leena; Abstract B077: 3D reconstruction and machine learning-based analysis of prostate cancer from histologic images Cancer Research 78 16_Supplement B077-B077 2018 The American Association for Cancer Research
Luoto, Suvi; Hermelo, Ismaïl; Vuorinen, Elisa M; Hannus, Paavo; Kesseli, Juha; Nykter, Matti; Granberg, Kirsi J; Computational Characterization of Suppressive Immune Microenvironments in GlioblastomaComputational Analysis of Immune Responses in Glioblastoma Cancer research 78 19 5574-5585 2018 American Association for Cancer Research
Latonen, Leena; Afyounian, Ebrahim; Jylhä, Antti; Nättinen, Janika; Aapola, Ulla; Annala, Matti; Kivinummi, Kati; Tammela, Teuvo; Beuerman, Roger W; Uusitalo, Hannu; Abstract A020: Integrative analysis of the proteome in primary and advanced prostate cancer Cancer Research 78 16_Supplement A020-A020 2018 The American Association for Cancer Research
Granberg, Kirsi Johanna; Annala, Matti; Jaatinen, Serafiina; Haapasalo, Joonas; Yli-Harja, Olli; Haapasalo, Hannu; Zhang, Wei; Nykter, Matti; Gatekeeper inactivation drives glioma progression into secondary glioblastoma Cancer Research 78 13_Supplement 3427-3427 2018 The American Association for Cancer Research
Latonen, Leena; Afyounian, Ebrahim; Jylha, Antti; Nattinen, Janika; Aapola, Ulla; Annala, Matti; Kivinummi, Kati; Tammela, Teuvo; Beuerman, Roger W; Uusitalo, Hannu; Integrative analysis of the proteome in primary and advanced prostate cancer. CANCER RESEARCH 78 16 34-34 2018 AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA …
Portero-Otin, Manuel; Nykter, Matti; Lushchak, Oleh; Navas, Placido; Pamplona, Reinald; Sanz, Alberto; Essential physiological differences characterise short-and long-lived strains of Drosophila melanogaster 2018
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
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
Latonen, Leena; Nykter, Matti; Visakorpi, Tapio; Proteomics of prostate cancer–revealing how cancer cells master their messy genomes Oncoscience 5 7-8 216 2018 Impact Journals, LLC
Ruusuvuori, Pekka; Valkonen, Mira; Kartasalo, Kimmo; Visakorpi, Tapio; Nykter, Matti; Latonen, Leena; 3D reconstruction and machine learning-based analysis of prostate cancer from histologic images. CANCER RESEARCH 78 16 120-121 2018 AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA …
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
Lin, Jake; Kimura, Bryn Y; Oikarinen, Sami; Nykter, Matti; Bioinformatics Assembling and Assessment of Novel Coxsackievirus B1 Genome The Human Virome 261-272 2018 Springer
Martínez, Alejandra Rodríguez; Vuorinen, Elisa M; Shcherban, Anastasia; Rajala, Nina K; Nykter, Matti; Kallioniemi, Anne; ZNF414 as a functionally relevant transcription factor in pancreatic and breast cancer cells Cancer Research 78 13_Supplement 3353-3353 2018 The American Association for Cancer Research
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
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
Jylhä, Antti; Nättinen, Janika; Aapola, Ulla; Mikhailova, Alexandra; Nykter, Matti; Zhou, Lei; Beuerman, Roger; Uusitalo, Hannu; Comparison of iTRAQ and SWATH in a clinical study with multiple time points Clinical Proteomics 15 1 1-11 2018 BioMed Central
Hermelo, I; Haapasalo, J; Nordfors, K; Haapasalo, H; Nykter, M; Granberg, K; P01. 143 Unravelling the immune response components landscape in diffuse gliomas using immunophenotyping approach Neuro-Oncology 20 Suppl 3 iii265 2018 Oxford University Press
Dufva, Olli; Pölönen, Petri; Brück, Oscar; Keränen, Mikko A; Mehtonen, Juha; Siitonen, Sanna M; Leivonen, Suvi-Katri; Meriranta, Leo; Leppa, Sirpa; Nykter, Matti; Immunogenomic Landscape of Hematological Malignancies 2018 American Society of Hematology Washington, DC
Tammela, T; Latonen, L; Afyounian, E; Jylhä, A; Nättinen, J; Aapola, U; Annala, M; Kivinummi, K; Beuerman, R; Uusitalo, H; Integrative analysis of the proteome in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression European Urology Supplements 17 2 e159 2018 Elsevier
Harjula, Sanna-Kaisa E; Ojanen, Markus JT; Taavitsainen, Sinja; Nykter, Matti; Rämet, Mika; Interleukin 10 mutant zebrafish have an enhanced interferon gamma response and improved survival against a Mycobacterium marinum infection Scientific reports 8 1 1-17 2018 Nature Publishing Group
Latonen, Leena; Afyounian, Ebrahim; Jylhä, Antti; Nättinen, Janika; Aapola, Ulla; Annala, Matti; Kivinummi, Kati K; Tammela, Teuvo TL; Beuerman, Roger W; Uusitalo, Hannu; Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression Nature communications 9 1 1-13 2018 Nature Publishing Group
de Bock, Charles E; Demeyer, Sofie; Degryse, Sandrine; Verbeke, Delphine; Sweron, Bram; Gielen, Olga; Vandepoel, Roel; Vicente, Carmen; Vanden Bempt, Marlies; Dagklis, Antonis; HOXA9 Cooperates with Activated JAK/STAT Signaling to Drive Leukemia DevelopmentHOXA9 and Mutant JAK3 Cooperation in Leukemia Cancer discovery 8 5 616-631 2018 American Association for Cancer Research
Moreau, Pierre R; Örd, Tiit; Downes, Nicholas L; Niskanen, Henri; Bouvy-Liivrand, Maria; Aavik, Einari; Ylä-Herttuala, Seppo; Kaikkonen, Minna U; Transcriptional profiling of hypoxia-regulated non-coding RNAs in human primary endothelial cells Frontiers in Cardiovascular Medicine 5 159 2018 Frontiers Media SA
Bister, Nea; Eamen, Shaila; Huremagic, Benjamin; Korhonen, Paula; Loppi, Sanna; Scoyni, Flavia; Konttinen, Henna; Cheng, Lesley; Vella, Laura J; Bouvy-Liivrand, Maria; Ischaemia-related conditions induce secretion of miR-21-5p-containing extracellular vesicles that alter microglial activation Journal of Extracellular Vesicles 7 159-160 2018 Taylor & Francis Ltd.
Waterhouse, Robert M; Seppey, Mathieu; Simão, Felipe A; Manni, Mosè; Ioannidis, Panagiotis; Klioutchnikov, Guennadi; Kriventseva, Evgenia V; Zdobnov, Evgeny M; BUSCO applications from quality assessments to gene prediction and phylogenomics Molecular biology and evolution 35 3 543-548 2018 Oxford University Press
Simão, Felipe A; Seppey, Mathieu; Waterhouse, Robert M; Manni, Mose; Ioannidis, Panagiotis; Klioutchnikov, Guennadi; Sierro, Nicolas; Ivanov, Nikolai V; Kriventseva, Evgenia V; Zdobnov, Evgeny M; BUSCO v3: Expanded Plant Coverage and Utilities Beyond Benchmarking. Plant and Animal Genome XXVI Conference (January 13-17, 2018) 2018 PAG
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Barton, Henry J; Zeng, Kai; New methods for inferring the distribution of fitness effects for INDELs and SNPs Molecular Biology and Evolution 35 6 1536-1546 2018 Oxford University Press
Havunen, Riikka; Santos, João M; Sorsa, Suvi; Rantapero, Tommi; Lumen, Dave; Siurala, Mikko; Airaksinen, Anu J; Cervera-Carrascon, Victor; Tähtinen, Siri; Kanerva, Anna; Abscopal effect in non-injected tumors achieved with cytokine-armed oncolytic adenovirus Molecular Therapy-Oncolytics 11 109-121 2018 Elsevier
Kaikkonen, Elina; Rantapero, Tommi; Zhang, Qin; Taimen, Pekka; Laitinen, Virpi; Kallajoki, Markku; Jambulingam, Dhanaprakash; Ettala, Otto; Knaapila, Juha; Boström, Peter J; ANO7 is associated with aggressive prostate cancer International journal of cancer 143 10 2479-2487 2018 Wiley Online Library
Semitekolou, Maria; Morianos, Ioannis; Banos, Aggelos; Konstantopoulos, Dimitris; Adamou-Tzani, Marina; Sparwasser, Tim; Xanthou, Georgina; Dendritic cells conditioned by activin A–induced regulatory T cells exhibit enhanced tolerogenic properties and protect against experimental asthma Journal of Allergy and Clinical Immunology 141 2 671-684. e7 2018 Elsevier
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Diogo, Ana Matias; Silva, Pedro; Viana, Joana; Children's use of ICT, family mediation, and social inequalities Issues in Educational Research 28 1 61-76 2018
Viana, J; Santos, A Moura; Mooc learners: who are they and what are their perspectives? INTED2018 Proceedings. 12th International Technology, Education and Development Conference 2018
Laing, LV; Viana, J; Dempster, EL; Webster, TM Uren; van Aerle, R; Mill, Jonathan; Santos, EM; Sex-specific transcription and DNA methylation profiles of reproductive and epigenetic associated genes in the gonads and livers of breeding zebrafish Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 222 16-25 2018 Elsevier
Valkonen, Mira; Kartasalo, Kimmo; Liimatainen, Kaisa; Nykter, Matti; Latonen, Leena; Ruusuvuori, Pekka; Dual structured convolutional neural network with feature augmentation for quantitative characterization of tissue histology Proceedings of the IEEE International Conference on Computer Vision Workshops 27-35 2017
Kivinummi, Kati; Urbanucci, Alfonso; Leinonen, Katri; Tammela, Teuvo LJ; Annala, Matti; Isaacs, William B; Bova, G Steven; Nykter, Matti; Visakorpi, Tapio; The expression of AURKA is androgen regulated in castration-resistant prostate cancer Scientific reports 7 1 1-11 2017 Nature Publishing Group
Lehtinen, Birgitta; Raita, Annina; Kesseli, Juha; Annala, Matti; Nordfors, Kristiina; Yli-Harja, Olli; Zhang, Wei; Visakorpi, Tapio; Nykter, Matti; Haapasalo, Hannu; Clinical association analysis of ependymomas and pilocytic astrocytomas reveals elevated FGFR3 and FGFR1 expression in aggressive ependymomas BMC cancer 17 1 1-12 2017 Springer
Urbanucci, Alfonso; Barfeld, Stefan J; Kytölä, Ville; Itkonen, Harri M; Coleman, Ilsa M; Vodák, Daniel; Sjöblom, Liisa; Sheng, Xia; Tolonen, Teemu; Minner, Sarah; Androgen receptor deregulation drives bromodomain-mediated chromatin alterations in prostate cancer Cell reports 19 10 2045-2059 2017 Elsevier
Valkonen, Mira; Kartasalo, Kimmo; Liimatainen, Kaisa; Nykter, Matti; Latonen, Leena; Ruusuvuori, Pekka; Metastasis detection from whole slide images using local features and random forests Cytometry Part A 91 6 555-565 2017 Wiley Online Library
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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
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
Valkonen, Mira; Ruusuvuori, Pekka; Kartasalo, Kimmo; Nykter, Matti; Visakorpi, Tapio; Latonen, Leena; Analysis of spatial heterogeneity in normal epithelium and preneoplastic alterations in mouse prostate tumor models Scientific reports 7 1 1-10 2017 Nature Publishing Group
Afyounian, Ebrahim; Annala, Matti; Nykter, Matti; Segmentum: a tool for copy number analysis of cancer genomes BMC bioinformatics 18 1 1-10 2017 Springer
Lin, Jake; Kramna, Lenka; Autio, Reija; Hyöty, Heikki; Nykter, Matti; Cinek, Ondrej; Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples BMC genomics 18 1 1-11 2017 Springer
Vandekerkhove, Gillian; Todenhöfer, Tilman; Annala, Matti; Struss, Werner J; Wong, Amanda; Beja, Kevin; Ritch, Elie; Brahmbhatt, Sonal; Volik, Stanislav V; Hennenlotter, Jörg; Circulating Tumor DNA Reveals Clinically Actionable Somatic Genome of Metastatic Bladder CancerctDNA Alterations in Metastatic Bladder Cancer Clinical Cancer Research 23 21 6487-6497 2017 American Association for Cancer Research
Ampuja, M; Rantapero, T; Rodriguez-Martinez, A; Palmroth, M; Alarmo, EL; Nykter, M; Kallioniemi, A; Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer BMC genomics 18 1 1-15 2017 BioMed Central
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
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
Jylhä, Antti; Nattinen, Janika; Aapola, Ulla; Nykter, Matti; Beuerman, Roger W; Uusitalo, Hannu MT; Tear proteome provides basis for patient stratification after switching to a unpreserved glaucoma medication Investigative Ophthalmology & Visual Science 58 8 2115-2115 2017 The Association for Research in Vision and Ophthalmology
Yang, Meng; Topaloglu, Umit; Petty, W Jeffrey; Pagni, Matthew; Foley, Kristie L; Grant, Stefan C; Robinson, Mac; Bitting, Rhonda L; Thomas, Alexandra; Alistar, Angela T; Circulating mutational portrait of cancer: manifestation of aggressive clonal events in both early and late stages Journal of hematology & oncology 10 1 1-13 2017 BioMed Central
Kytola, Ville; Topaloglu, Umit; Miller, Lance D; Bitting, Rhonda L; Goodman, Michael M; DAgostino Jr, Ralph B; Desnoyers, Rodwige J; Albright, Carol; Yacoub, George; Qasem, Shadi A; Mutational landscapes of smoking-related cancers in Caucasians and African Americans: precision oncology perspectives at Wake Forest Baptist Comprehensive Cancer Center Theranostics 7 11 2914 2017 Ivyspring International Publisher
Annala, Matti; Struss, Werner J; Warner, Evan W; Beja, Kevin; Vandekerkhove, Gillian; Wong, Amanda; Khalaf, Daniel; Seppälä, Irma-Liisa; So, Alan; Lo, Gregory; Treatment outcomes and tumor loss of heterozygosity in germline DNA repair–deficient prostate cancer European urology 72 1 34-42 2017 Elsevier
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
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Tammela, T; Kallio, H; Annala, M; Brofeldt, A; Hieta, R; Kivinummi, K; Nykter, M; Lilja, H; Bova, G; Visakorpi, T; Neoadjuvant hormonal therapies induce the expression of AR transcript variants European Urology Supplements 3 16 e255-e256 2017
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
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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
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Simão, Felipe A; Waterhouse, Robert M; Ioannidis, Panagiotis; Kriventseva, Evgenia V; Zdobnov, Evgeny M; Supplementary online material 2017
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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
Psatha, Nikoletta; Georgolopoulos, Grigorios; Phelps, Susan; Papayannopoulou, Thalia; Brief report: a differential transcriptomic profile of ex vivo expanded adult human hematopoietic stem cells empowers them for engraftment better than their surface phenotype Stem cells translational medicine 6 10 1852-1858 2017 Oxford University Press
Georgolopoulos, Grigorios; Iwata, Mineo; Nishida, Andrew; Som, Tannishtha; Stamatoyannopoulos, John A; Vierstra, Jeff; Comprehensive Identification of Cis-and Trans-Elements Driving Human Hematopoiesis Blood 130 3774 2017 Elsevier
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Viana, Joana; Peralta, Helena; Costa, F; Digital Non-formal Education as an Opportunity to Transform School Better e-learning for innovation in education 197-214 2017 ÖzKaracan Matbaacılık
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 26 1 210-225 2017 Oxford University Press
Wong, Chloe Chung Yi; Parikshak, Neel; Spiers, Helen; Brays, Nicholas J; Lysenko, Laura; Troakes, Claire; Viana, Joana; Hannon, Eilis; Schalkwyk, Leo; Geschwind, Daniel; METHYLOMIC ANALYSIS OF AUTISM BRAIN: DISEASE ASSOCIATED VARIATION AND SUPPORT FOR A NEURODEVELOPMENTAL COMPONENT TO ETIOLOGY EUROPEAN NEUROPSYCHOPHARMACOLOGY 27 S233-S233 2017 ELSEVIER SCIENCE BV PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS
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Viana, Joana; Pidsley, Ruth; Hannon, Eilis; Spiers, Helen; Troakes, Claire; Al-Saraj, Safa; Mechawar, Naguib; Turecki, Gustavo; Schalkwyk, Leo; Bray, Nicholas J; INVESTIGATING EPIGENOMIC REGULATION IN SCHIZOPHRENIA EUROPEAN NEUROPSYCHOPHARMACOLOGY 27 S263-S263 2017 ELSEVIER SCIENCE BV PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS
Costa, F; Cruz, Elisabete; Viana, Joana; Pereira, Carolina; O processo de desenvolvimento de dinâmicas de educação digital de adultos Atas do XXII Colóquio da AFIRSE Portugal. Lisboa: AFIRSE Portugal 286-301 2017
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Costa, Fernando Albuquerque; Viana, Joana; Tréz, Ticiana; Gonçalves, Catarina; Cruz, Elisabete; Desenho de atividades de aprendizagem baseado no conceito de aprender com tecnologias CONFERÊNCIA INTERNACIONAL CHALLENGES 2017
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Viana, Joana; Costa, Fernando Albuquerque; Peralta, Helena; Aprendizagens pessoais em contextos informais: oportunidades criadas pela Internet Revista Observatório 3 4 190-231 2017 Universidade Federal do Tocantins
Viana, Joana; Wildman, Nick; Paull, Gregory; Santos, Eduarda; Mill, Jonathan; BEHAVIOURAL AND TRANSCRIPTOMIC CORRELATES WITH CLOZAPINE RESPONSE IN ZEBRAFISH EUROPEAN NEUROPSYCHOPHARMACOLOGY 27 S202-S202 2017 ELSEVIER SCIENCE BV PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS
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
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Ylipää, A; Kivinummi, KK; Annala, MJ; Kartasalo, K; Latonen, L; Leppänen, SP; Scaravilli, M; Zhang, W; Tammela, TLJ; Visakorpi, T; 299 Novel prostate cancer specific transcripts identified using RNA-seq European Urology Supplements 1 13 e299 2014
Ruusuvuori, Pekka; Lin, Jake; Scott, Adrian C; Tan, Zhihao; Sorsa, Saija; Kallio, Aleksi; Nykter, Matti; Yli-Harja, Olli; Shmulevich, Ilya; Dudley, Aimée M; Quantitative analysis of colony morphology in yeast BioTechniques 56 1 18-27 2014 Future Science
Liuksiala, Thomas; Teittinen, Kaisa; Granberg, Kirsi; Heinäniemi, Merja; Annala, Matti; Ylipää, Antti; Mäki, Markku; Nykter, Matti; Lohi, Olli; Large scale gene expression analysis identifies key oncogenic pathways across hematological malignancies Cancer Research 74 19_Supplement 2363-2363 2014 The American Association for Cancer Research
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
Yang, Jilong; Annala, Matti; Ji, Ping; Wang, Guowen; Zheng, Hong; Codgell, David; Du, Xiaoling; Fang, Zhiwei; Sun, Baocun; Nykter, Matti; Recurrent LRP1-SNRNP25 and KCNMB4-CCND3 fusion genes promote tumor cell motility in human osteosarcoma Journal of hematology & oncology 7 1 1-10 2014 Springer
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
Granberg, Kirsi J; Lehtinen, Birgitta; Annala, Matti J; Haapasalo, Hannu; Nykter, Matti; Zhang, Wei; Abstract LB-92: Using immunohistochemistry to evaluate FGFR3 gene fusion recurrence and clinical associations in astrocytomas Cancer Research 74 19_Supplement LB-92-LB-92 2014 The American Association for Cancer Research
Gerard, Deborah; Bouvy-Liivrand, Maria; Sinkkonen, Lasse; Sauter, Thomas; TIME-COURSE ANALYSIS OF GENE EXPRESSION DYNAMICS OF ADIPOGENESIS AND OSTEOBLASTOGENESIS Bioinformatics: Integrating data, teams and disciplines 17 2014
Liivrand, Maria; Modelling and global analysis of transcript profiles reveals dynamic roles for microRNAs in transcriptional networks controlling lineage commitment. 2014 University of Luxembourg,​ Luxembourg,​​ Luxembourg
Bouvy-Liivrand, Maria; Heinäniemi, Merja; John, Elisabeth; Schneider, Jochen G; Sauter, Thomas; Sinkkonen, Lasse; Combinatorial regulation of lipoprotein lipase by microRNAs during mouse adipogenesis RNA biology 11 1 76-91 2014 Taylor & Francis
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 15 10 1-11 2014 BioMed Central
Silva, Pedro; Diogo, Ana Matias; Coelho, Conceição; Fernandes, Conceição; Viana, Joana; Crianças e TIC: Uma relação desigualmente construída na família Entre crise e euforia: Práticas e políticas educativas no Brasil e em Portugal 737-771 2014 Universidade do Porto, Faculdade de Letras
Viana, Joana; Branco, Eloísa; Costa, F; Que tecnologias digitais têm e usam as crianças entre 7 e 13 anos de uma escola de Lisboa Proceedings of the Atas digitais do III Congresso Internacional das TIC na Educação/ticEDUCA 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 9 4 587-599 2014 Taylor & Francis
Paradisi, Paolo; Chiarugi, Davide; Biochemical Reactions as Renewal Processes: the case of mRNA Degradation. IWBBIO 1574-1576 2014
Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana; Olarte, Carlos; A framework for modelling spatially dependent interactions of biological systems in CCP. IWBBIO 912-923 2014
Zhang, Wei; Parker, Brittany C; Annala, Matti J; Cogdell, David; Granberg, Kirsi; Sun, Yan; Ji, Ping; Li, Xia; Gumin, Joy; Zheng, Hong; The tumorigenic fusion FGFR3-TACC3 escapes miR-99a regulation in glioblastoma. Cancer Research 73 8_Supplement 5311-5311 2013 American Association for Cancer Research
Ylipää, Antti; Yli-Harja, Olli; Zhang, Wei; Nykter, Matti; Characterization of aberrant pathways across human cancers BMC systems biology 7 1 1-12 2013 BioMed Central
Yang, Da; Sun, Yan; Hu, Limei; Zheng, Hong; Ji, Ping; Pecot, Chad V; Zhao, Yanrui; Reynolds, Sheila; Cheng, Hanyin; Rupaimoole, Rajesha; Integrated analyses identify a master microRNA regulatory network for the mesenchymal subtype in serous ovarian cancer Cancer cell 23 2 186-199 2013 Elsevier
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
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
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
Annala, Matti J; Waltering, Kati K; Ylipää, Antti; Kartasalo, Kimmo; Tuppurainen, Kirsi; Karakurt, Serdar; Latonen, Leena; Saramäki, Outi; Leppänen, Simo-Pekka; Seppälä, Janne; Integrative sequencing reveals novel alterations in untreated and castration resistant prostate cancer. Cancer Research 73 8_Supplement 5217-5217 2013 American Association for Cancer Research
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
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
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
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
Patel, Lalit R; Nykter, Matti; Chen, Kexin; Zhang, Wei; Cancer genome sequencing: understanding malignancy as a disease of the genome, its conformation, and its evolution Cancer letters 340 2 152-160 2013 Elsevier
Lin, Jake; Kreisberg, Richard; Kallio, Aleksi; Dudley, Aimée M; Nykter, Matti; Shmulevich, Ilya; May, Patrick; Autio, Reija; POMO-Plotting Omics analysis results for Multiple Organisms BMC genomics 14 1 1-10 2013 BioMed Central
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
Zhang, Wei; Nykter, Matti; Chen, Kexin; Next generation sequencing applications in cancer research Cancer letters 340 2 149-150 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 123 2 2013 Am Soc Clin Investig
Leinonen, Katri A; Saramäki, Outi R; Furusato, Bungo; Kimura, Takahiro; Takahashi, Hiroyuki; Egawa, Shin; Suzuki, Hiroyoshi; Keiger, Kerri; Ho Hahm, Sung; Isaacs, William B; Loss of PTEN Is Associated with Aggressive Behavior in ERG-Positive Prostate CancerExpression of ERG in Prostate Cancer Cancer epidemiology, biomarkers & prevention 22 12 2333-2344 2013 American Association for Cancer Research
Hytonen, Vesa P; Nykter, Matti; Uusimaki, Marko; Ramet, Mika; Parikka, Mataleena; Hannu Turpeinen, Anna Oksanen, Virpi 2013
Zhang; Nykter, Matti; Kexin, Chen; Featuring the guest editor special issue genome sequencing CANCER LETTERS 340 2 151-151 2013 ELSEVIER IRELAND LTD ELSEVIER HOUSE, BROOKVALE PLAZA, EAST PARK SHANNON, CO …
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
Du, Xiaoling; Yang, Jilong; Ylipää, Antti; Zhu, Ze; Genomic amplification and high expression of EGFR are key targetable oncogenic events in malignant peripheral nerve sheath tumor Journal of hematology & oncology 6 1 1-12 2013 BioMed Central
Siltanen, Sanna; Fischer, Daniel; Rantapero, Tommi; Laitinen, Virpi; Mpindi, John Patrick; Kallioniemi, Olli; Wahlfors, Tiina; Schleutker, Johanna; ARLTS1 and prostate cancer risk-analysis of expression and regulation PLoS One 8 8 e72040 2013 Public Library of Science San Francisco, USA
Laitinen, Virpi H; Wahlfors, Tiina; Saaristo, Leena; Rantapero, Tommi; Pelttari, Liisa M; Kilpivaara, Outi; Laasanen, Satu-Leena; Kallioniemi, Anne; Nevanlinna, Heli; Aaltonen, Lauri; HOXB13 G84E mutation in Finland: population-based analysis of prostate, breast, and colorectal cancer risk Cancer epidemiology, biomarkers & prevention 22 3 452-460 2013 American Association for Cancer Research
Anantharajan, Jothi; Koski, M Kristian; Kursula, Petri; Hieta, Reija; Bergmann, Ulrich; Myllyharju, Johanna; Wierenga, Rik K; The structural motifs for substrate binding and dimerization of the α subunit of collagen prolyl 4-hydroxylase Structure 21 12 2107-2118 2013 Elsevier
Costa, Fernando Albuquerque; Rodriguez, Carla; Cruz, Elisabete; Gomes, Nádia; Santos, Cátia; Viana, Joana; Peralta, Helena; Branco, Eloísa; Fradão, Sandra; On track for a digital school 2013 IEEE 63rd Annual Conference International Council for Education Media (ICEM) 1-12 2013 IEEE
Dempster, Emma; Viana, Joana; Pidsley, Ruth; Mill, Jonathan; Epigenetic studies of schizophrenia: progress, predicaments, and promises for the future Schizophrenia bulletin 39 1 11-16 2013 Oxford University Press US
Costa, Fernando Albuquerque; Rodriguez, Carla; Cruz, Elisabete; Peralta, Helena; Viana, Joana; Fradão, Sandra; Branco, Eloisa; Gomes, Nádia; Santos, Cátia; Subgrupo de investigação em Educação, Tecnologia e Sociedade Anais dos Workshops do Congresso Brasileiro de Informática na Educação 2 1 2013
Silva, Pedro; Viana, Joana; Coelho, Conceição; Fernandes, Conceição; Crianças, Computadores e Jogos: um estudo de caso Edição em CD-Rom]. In Maria João Gomes, António José Osório, Altina Ramos, Bento Duarte da Silva & Luís Valente (Orgs.), Atas da VIII Conferência Internacional de Tecnologias de Informação e Comunicação na Educação, Challenges 2013
Costa, Fernando Albuquerque; Rodriguez, Carla; Cruz, Elisabete; Gomes, Nádia; Santos, Cátia; Viana, Joana; Peralta, Helena; Branco, Eloísa; Fradão, Sandra; A caminho de uma escola digital VII Conferência Internacional de TIC na Educação 2013
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
Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana; Marangoni, Roberto; Olarte, Carlos; Stochastic modelling of non Markovian Dynamics in Biochemical Reactions. IWBBIO 537-544 2013
Sarbu, Septimia; Kesseli, Juha; Nykter, Matti; Quantifying the relationship between the structure and the dynamics of random Boolean networks from time series data Ninth International Workshop on Computational Systems Biology, WCSB 2012, June 4-6, Ulm, Germany 75 2012
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
Ylipää, Antti; Zhang, Wei; Nykter, Matti; A characterization of pathway aberrations across human cancers Cancer Research 72 8_Supplement 4939-4939 2012 American Association for Cancer Research
Rane, Jayant K; Pellacani, Davide; Droop, Alastair P; Ylipää, Antti; Stower, Michael J; Simms, Matthew S; Mann, Vincet M; Visakorpi, Tapio; Collins, Anne T; Maitland, Norman J; Elucidation of dynamic prostate epithelial hierarchy: Insights into transcriptional and epigenetic regulatory mechanisms Cancer Research 72 8_Supplement 5198-5198 2012 American Association for Cancer Research
John, Elisabeth; Wienecke-Baldacchino, Anke; Liivrand, Maria; Heinäniemi, Merja; Carlberg, Carsten; Sinkkonen, Lasse; Dataset integration identifies transcriptional regulation of microRNA genes by PPARγ in differentiating mouse 3T3-L1 adipocytes Nucleic acids research 40 10 4446-4460 2012 Oxford University Press
Rantapero, Tommi; Bioinformatic analysis of next-generation sequencing data 2012
Diogo, Ana Matias; Silva, Pedro; Gomes, Carlos; Coelho, Conceição; Fernandes, Conceição; Viana, Joana; Educação, desigualdades sociais e usos do computador Magalhães: uma pesquisa comparativa VII Congresso Português de Sociologia 1-25 2012 APS, Associação Portuguesa de Sociologia
Viana, Joana; Os jovens e a web 2.0: uma conexão ou um mito Atas do II Congresso Internacional TIC e Educação 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 5 1 1-9 2012 Springer
Costa, Fernando Albuquerque; Viana, Joana; Cruz, Elisabete; The management of a PLE from the Perspective of Higher Education Students 62 International Council for Educational Media Conference 317-323 2012 ICEM
Viana, Joana; Silva, Pedro; Coelho, Conceição; Fernandes, Conceição; Sobre os usos do computador Magalhães pelos alunos II Congresso Internacional TIC e Educação 2012
Bodei, Chiara; Brodo, Linda; Chiarugi, Davide; Control Flow Analysis of Generalised Boolean Networks Electronic Notes in Theoretical Computer Science 284 3-22 2012 Elsevier
Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana; Guzman, Michell; Olarte, Carlos; Simulating signalling pathways through BioWays Proc. of CS2BIO 2012
Yang, Jilong; Ylipää, Antti; Sun, Yan; Zheng, Hong; Chen, Kexin; Nykter, Matti; Trent, Jonathan; Ratner, Nancy; Lev, Dina C; Zhang, Wei; Genomic and Molecular Characterization of Malignant Peripheral Nerve Sheath Tumor Identifies the IGF1R Pathway as a Primary Target for TreatmentTargeting IGF1R in MPNST Clinical cancer research 17 24 7563-7573 2011 American Association for Cancer Research
Kesseli, Juha; Hahne, Lauri; Yli-Harja, Olli; Shmulevich, Ilya; Nykter, Matti; Structure-Dynamics Relationships in Biological Networks Information Processing and Biological Systems 153-178 2011 Springer
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
Erkkilä, Timo; Kreisberg, Richard; Reynolds, Sheila; Thorsson, Vesteinn; Lin, Jake; Torkkola, Kari; Bressler, Ryan; Bernard, Brady; Ruusuvuori, Pekka; Annala, Matti; Integrated views into cancer regulomes reveal regulatory hot spots The 11th SocBiN Conference, Helsinki, Finland 2011
Yli-Harja, Olli; Ylipää, Antti; Nykter, Matti; Zhang, Wei; Cancer systems biology: signal processing for cancer research Chinese journal of cancer 30 4 221 2011 BioMed Central
Chen, Kexin; Cheng, Hanyin; Zhang, Lina; Cogdell, David E; Zheng, Hong; Schetter, Aaron J; Nykter, Matti; Harris, Curtis C; Hamilton, Stanley R; Zhang, Wei; Circulating plasma MiR-141 is a novel biomarker for metastatic colon cancer and predicts poor prognosis Cancer Research 71 8_Supplement 1145-1145 2011 American Association for Cancer Research
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
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
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
Kauppi, Jukka-Pekka; Nykter, Matti; Niemi, Jari; Clustering Method for Data Having Outliers and Clusters with Varying Sizes and Densities 2011
Hahne, Lauri; Kesseli, Juha; Nykter, Matti; Evaluation of compressors for estimating normalized compression distance Eight International Workshop on Computational Systems Biology, WCSB 2011, June 6-8, Zurich, Switzerland. TICSP series 53-56 2011 WCSB 2011
Mäki-Marttunen, Tuomo; Kesseli, Juha; Kauffman, Stuart; Yli-Harja, Olli; Nykter, Matti; Of the complexity of Boolean network state trajectories 2011 WCSB 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 30 1 27 2011 BioMed Central
Ylipää, Antti; Waltering, Kati; Zhang, Wei; Visakorpi, Tapio; Nykter, Matti; A systems approach into studying the changes in genetic regulation during prostate cancer progression Cancer Research 71 8_Supplement 4906-4906 2011 American Association for Cancer Research
Costa, Fernando Albuquerque; Viana, Joana; Cruz, Elisabete; Recursos educativos para uma aprendizagem autónoma e significativa. Algumas características essenciais XI Congreso Internacional Galego-Portugués de Psicopedagoxía 1609-1615 2011 Universidade de A Coruña
Silva, Pedro; Coelho, Conceição; Fernandes, Conceição; Viana, Joana; Usos do Computador Magalhães entre a Escola e a Família: notas de uma pesquisa sociológica Actas da VII conferência internacional de tecnologias de informação e comunicação na educação" Challenges 2011: perspectivas de inovação 2011
Costa, Fernando Albuquerque; Cruz, Elisabete; Viana, Joana; A gestão de um PLE na perspectiva de estudantes do ensino superior VII Conferência Internacional de Tecnologias de Informação e Comunicação na Educação, Challenges 2011 323-333 2011 Centro de Competência da Universidade do Minho
Ylipää, Antti; Yli-Harja, Olli; Zhang, Wei; Nykter, Matti; From genetic markers to characteristic regulators in soft-tissue sarcomas Proceedings of the Seventh International Workshop on Computational Systems Biology, WCSB 2010, Luxembourg, June 16-18, 2010. TICSP Series 4 2010
Annala, Matti; Laurila, Kirsti; Nykter, Matti; Harri, L; A linear model for transcription factor binding affinity prediction in PBM microarrays RECOMB The 7th Annual RECOMB Satellite on Regulatory Genomics, the 6th Annual RECOMB Satellite on Systems Biology, and the 5th Annual DREAM reverse engineering challenges 2010
Heinäniemi, M; Nykter, Matti; Wienecke, A; Sinkkonen, L; Schmitz, M; Zhou, J; Kauffman, S; Huang, S; Shmulevich, I; Carlberg, C; Systematic identification of lineage determining transcriptional regulation from public gene expression profiles Proceedings of the Seventh International Workshop on Computational Systems Biology, WCSB 2010, Luxembourg, June 16-18, 2010. TICSP Series 2 2010
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
Ylipaa, Antti; Nykter, Matti; Shmulevich, Ilya; Zhang, Wei; An investigation of the regulation of cellular processes in glioblastoma multiforme via integrated analysis of paired microRNA and gene expression profiles Cancer Research 70 8_Supplement 2008-2008 2010 American Association for Cancer Research
Kivinen, Virpi; Nykter, Matti; Yli-Harja, Olli; Shmulevich, Ilya; Classifier design with pathway based feature selection Proceedings of the Seventh International Workshop on Computational Systems Biology, WCSB 2010, Luxembourg, June 16-18, 2010. TICSP Series 4 2010
Annala, Matti; Yli-Harja, Olli; Shmulevich, Ilya; Nykter, Matti; Improving correlation between microarrays and transcriptome sequencing through probeset analysis Proceedings of the Seventh International Workshop on Computational Systems Biology, WCSB 2010, Luxembourg, June 16-18, 2010 15-18 2010 Tampere University of Technology
Nykter, Matti; Ruusuvuori, Pekka; Carlberg, Carsten; Yli-Harja, Olli; Seventh International Workshop on Computational Systems Biology, WCSB 2010, June 16-18, 2010, Luxembourg 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 56 2 667-677 2010 IEEE
Costa, Fernando Albuquerque; Cruz, Elisabete; Viana, Joana; Managing personal learning environments: the voice of the students The PLE Conference 1-12 2010 The PLE Conference
Silva, PEDRO; Coelho, CONCEIÇÃO; Fernandes, CONCEIÇÃO; Viana, JOANA; O computador Magalhães entre a escola e a família: notas preliminares de uma pesquisa sociológica Atas do I Encontro Internacional TIC e Educação TicEduca 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 414-417 2010
Bodei, Chiara; Bracciali, Andrea; Chiarugi, Davide; Gori, Roberta; A taxonomy of causality-based biological properties arXiv preprint arXiv:1002.4067 2010
Ylipää, A; Nykter, M; Yli-Harja, O; Zhang, W; Shmulevich, I; Association of genetic features with pathways using multiple high-throughput data Abstracts of the 2009 Joint RECOMB Satellite Conference on Regulatory Genomics-Systems Biology-Dream4, Boston, USA, 2-6 December 2009 291 2009
Litvak, Vladimir; Ramsey, Stephen A; Rust, Alistair G; Zak, Daniel E; Kennedy, Kathleen A; Lampano, Aaron E; Nykter, Matti; Shmulevich, Ilya; Aderem, Alan; Role of the transcription factor C/EBPδ in a regulatory circuit that discriminates between transient and persistent Toll-like receptor 4-induced signals Nature immunology 10 4 437 2009 NIH Public Access
Ylipää, Antti; Nykter, Matti; Trent, Jonathan; Zhang, Wei; Yli-Harja, Olli; A gene copy number based classifier for gastrointestinal stromal tumors and leiomyosarcomas Sixth International Workshop on Computational Systems Biology, WCSB 2009, June 10-12, 2009, Aarhus, Denmark 21 2009
Larjo, Antti; Pettinen, Antti; Kong, Lingjia; Yaroslavsky, Leonid; Äijö, Tarmo; Kim, Harold D; O'Shea, Erin K; Chowdhury, Sharif; Lia, Kang; Millera, Eric D; Journal Club is held in room TB219 (19.01.-29.06. 2010) about once a week on Tuesdays at 14.15. Changes are possible. Order and exact date after next 2 forthcoming presentation are temporary and for reference only. Credits policy: 70% attendance of one semaster+ 2 presentation (in total) could gain 3 credits, 70% attendance of one semaster+ 1 presentation (in total) could gain 2 credits BMC Systems Biology 3 100 2009
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
Kesseli, Juha; Ribeiro, Andre S; Nykter, Matti; Measuring Information Propagation and Processing in Biological Systems Open Information Management: Applications of Interconnectivity and Collaboration 190-226 2009 IGI Global
Nykter, Matti; Kesseli, Juha; Shmulevich, Ilya; Dynamical systems analysis of stack filters arXiv preprint arXiv:0907.4551 2009
Kivinen, V; Nykter, M; Martin, D; Yli-Harja, O; Shmulevich, I; Selection of an optimal set of blood biomarker proteins Abstracts of the 2009 Joint RECOMB Satellite Conference on Regulatory Genomics-Systems Biology-Dream4, Boston, USA, 2-6 December 2009 254 2009
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
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
Koski, M Kristian; Hieta, Reija; Hirsilä, Maija; Rönkä, Anna; Myllyharju, Johanna; Wierenga, Rik K; The crystal structure of an algal prolyl 4-hydroxylase complexed with a proline-rich peptide reveals a novel buried tripeptide binding motif Journal of Biological Chemistry 284 37 25290-25301 2009 ASBMB
Viana, Joana; O papel dos ambientes online no desenvolvimento da aprendizagem informal 2009
Viana, Joana; Portal E-ESCOLA:[http://www. e-escola. pt] Educação, Formação & Tecnologias-ISSN 1646-933X 2 1 123-126 2009
Bodei, Chiara; Bracciali, Andrea; Chiarugi, Davide; Control flow analysis for brane calculi Electronic Notes in Theoretical Computer Science 227 59-75 2009 Elsevier
Falaschi, Moreno; Chiarugi, Davide; Degano, Pierpaolo; Marangoni, Roberto; UNIVERSITA DEGLI STUDI DI SIENA 2009
Erkkilä, Timo; Nykter, Matti; Lähdesmäki, Harri; Ahdesmäki, Miika; Yli-Harja, Olli; Testing for differential expression in simulated and real cdna microarray data using frequentist and bayesian methods Fifth International Workshop on Computational Systems Biology (WCSB08) 2008
Kivinen, Virpi; Nykter, Matti; Ylipää, Antti; Hu, Limei; Cogdell, David; Hunt, Kelly; Zhang, Wei; Yli-Harja, Olli; Relationships between genetic aberrations and gene expression levels in gastrointestinal tract tumors Proceedings of the Fifth International Workshop on Computational Systems Biology, WCSB 2008, Leipzig, Germany, 11-13 June 2008 77-80 2008
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 100 5 58702 2008 APS
Ylipaa, Antti; Nykter, Matti; Kivinen, Virpi; Hu, Limei; Cogdell, David; Hunt, Kelly; Zhang, Wei; Yli-Harja, Olli; Finding common aberrations in array CGH data 2008 3rd International Symposium on Communications, Control and Signal Processing 1199-1204 2008 IEEE
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
Pettinen, Antti; Mäkiraatikka, E; Manninen, Tiina; Smolander, O; Ylipää, A; Hituri, Katri; Linne, M; Evaluation of deterministic and stochastic simulation tools for cellular signaling Frontiers in Neuroinformatics 2008
Saarinen, A; Ylipää, A; Yli-Harja, O; Linne, M; Computational methods for stochastic modeling and parameter fitting of models based on Hodgkin-Huxley formalism Front. Neuroinform. Conference Abstract: Neuroinformatics 2008
Mäkiraatikka, E; Manninen, T; Saarinen, A; Ylipää, A; Teppola, H; Hituri, K; Pettinen, A; Linne, ML; Kemiallisten reaktioiden mallintaminen ja tietokonesimulaatiot Solubiologi 26 1 21-28 2008
Costa, Fernando Albuquerque; Viseu, Sofia; Viana, Joana; Trigo, Ana Paula; Estratégias de desenvolvimento de materiais de auto-aprendizagem: Projectos e-Student e e-escola Atas do IX Congresso da SPCE 782-801 2008 Sociedade Portuguesa de Ciências da Educação
Bodei, Chiara; Bracciali, Andrea; Chiarugi, Davide; On deducing causality in metabolic networks BMC bioinformatics 9 4 1-10 2008 Springer
Chiarugi, Davide; Degano, Pierpaolo; Klinken, Jan Bert Van; Marangoni, Roberto; Cells in silico: a holistic approach International School on Formal Methods for the Design of Computer, Communication and Software Systems 366-386 2008 Springer
Leppä, Sirpa; Taskinen, Minna; Sommarhem, Antti; Elonen, Erkki; Nykter, Matti; Monni, Outi; Timonen, Tuomo; Hautaniemi, Sampsa; Karjalainen-Lindsberg, Marja-Liisa; Meri, Seppo; STAT5 Signaling Is Associated with the Outcome of Follicular and Mantle Cell Lymphoma Patients Treated with Immunochemotherapy. 2007 American Society of Hematology
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
Ruusuvuori, Pekka; Nykter, Matti; Makiraatikka, Eeva; Lehmussola, Antti; Korpelainen, Tomi; Erkkila, Timo; Yli-Harja, Olli; Microarray simulator as educational tool 2007 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society 5919-5922 2007 IEEE
Mäkiraatikka, Eeva; Manninen, Tiina; Saarinen, Antti; Ylipää, Antti; Teppola, Heidi; Hituri, Katri; Pettinen, Antti; Yli-Harja, Olli; Linne, Marja-Leena; Stochastic simulation tools for cellular signaling: survey, evaluation, and quantitative analysis Proceedings of the 2nd Conference on Foundations of Systems Biology in Engineering (FOSBE 2007), eds F. Allgöwer and M. Reuss (Stuttgart) 171-176 2007
Manninen, Tiina; Saarinen, Antti; Ylipää, Antti; Linne, Marja-Leena; Yli-Harja, Olli; Ruohonen, Keijo; Sequential Monte Carlo based maximum likelihood estimation for calcium binding reactions Proc. of the 2nd Conference on Foundations of Systems Biology in Engineering (FOSBE 2007) 189-194 2007
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
Koski, M Kristian; Hieta, Reija; Bollner, Claudia; Kivirikko, Kari I; Myllyharju, Johanna; Wierenga, Rik K; The active site of an algal prolyl 4-hydroxylase has a large structural plasticity Journal of Biological Chemistry 282 51 37112-37123 2007 ASBMB
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; A toolkit supporting formal reasoning about causality in metabolic networks Network Tools and Applications in Biology 2007
Nykter, Matti; Aho, Tommi; Ahdesmäki, Miika; Ruusuvuori, Pekka; Lehmussola, Antti; Yli-Harja, Olli; Simulation of microarray data with realistic characteristics BMC bioinformatics 7 1 1-17 2006 BioMed Central
Nykter, Matti; Signal processing methods and information approach to systems biology 2006 Tampere University of Technology
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
Campbell, Sharon E; Stone, William; Zhang, Wei; Taylor, Ellen; Nykter, Matti; Lippman, Scott; Krishnan, Koyamangalath; Alpha-and gamma-tocopherol regulate different sets of genes in the human colon cancer cell line, HCT-116. Cancer Research 66 8_Supplement 1181-1181 2006 American Association for Cancer Research
Nykter, Matti; Kesseli, Juha; Shmulevich, Ilya; Yli-Harja, Olli; Analyzing Boolean network dynamics using attractor basin structure 4th TICSP WORKSHOP ON COMPUTATIONAL SYSTEMS BIOLOGY, WCSB 2006 69 2006 Citeseer
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
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
Nykter, Matti; Yli-Harja, Olli; Shmulevich, Ilya; Normalized compression distance for gene expression analysis Workshop on Genomic Signal Processing and Statistics (GENSIPS)(May 2005) 2005 Citeseer
Nykter, M; Yli-Harja, O; Shmulevich, I; The similarity metric in network analysis Proceedings of The 3rd TICSP Workshop on Computational Systems Biology, WCSB 2005, Tampere, Finland, 13-14 June 2005 63-64 2005
Nykter, Matti; Feature selection for Lymphoma outcome prediction Proceedings of the 2nd TICSP Workshop on Computational Systems Biology, WCSB'2004, Silja Opera, Helsinki-St. Petersburg, 14-16 June 2004 51-52 2004
Niemistö, Antti; Nykter, Matti; Aho, Tommi; Jalovaara, Henna; Marjanen, Kalle; Ahdesmäki, Miika; Ruusuvuori, Pekka; Tiainen, Mikko; Linne, Marja-Leena; Yli-Harja, Olli; Distribution estimation of synchronized budding yeast population Proceedings of the winter international synposium on Information and communication technologies 1-6 2004
Harjunpää, Antti; Nykter, Matti; Monni, Outi; Karjalainen-Lindsberg, Marja-Liisa; Hemmer, Samuli; Yli-Harja, Olli; Meri, Seppo; Leppä, Sirpa; The Use of Gene-Expression Profiling to Predict Outcome of Follicular Lymphoma Patients Treated with Rituximab and Chemotherapy. Blood 104 11 1395 2004 Elsevier
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
Chiarugi, Davide; Curti, Michele; Degano, Pierpaolo; Marangoni, Roberto; Vice: A virtual cell International Conference on Computational Methods in Systems Biology 207-220 2004 Springer
Nykter, M; Kesseli, J; Aho, T; Yli-Harja, O; On estimation of statistical characteristics of microarray data Proceedings of the 2003 Finnish Signal Processing Symposium, FINSIG'03, Tampere, Finland, 19 May 2003 222-226 2003 TICSP
Hieta, Reija; Prolyl 4-hydroxylase: Structural and Functional Characterization of the Peptide-substrate-binding Domain of the Human Enzyme, and Cloning and Characterization of a Plant Enzyme with Unique Properties 2003 Oulun yliopisto
Hieta, Reija; Kukkola, Liisa; Permi, Perttu; Pirila, Paivi; Kivirikko, Kari I; Kilpelainen, Ilkka; Myllyharju, Johanna; PROTEIN STRUCTURE AND FOLDING-The Peptide-Substrate-binding Domain of Human Collagen Prolyl 4-Hydroxylases. BACKBONE ASSIGNMENTS, SECONDARY STRUCTURE, AND BINDING OF PROLINE-RICH PEPTIDES. Journal of Biological Chemistry 278 37 34966-34974 2003 Baltimore [etc.]
Hieta, Reija; Kukkola, Liisa; Permi, Perttu; Pirilä, Päivi; Kivirikko, Kari I; Kilpeläinen, Ilkka; Myllyharju, Johanna; The peptide-substrate-binding domain of human collagen prolyl 4-hydroxylases: backbone assignments, secondary structure, and binding of proline-rich peptides Journal of Biological Chemistry 278 37 34966-34974 2003 ASBMB
Pekkala, Mira; Hieta, Reija; Kursula, Petri; Kivirikko, Kari I; Wierenga, Rik K; Myllyharju, Johanna; Crystallization of the proline-rich-peptide binding domain of human type I collagen prolyl 4-hydroxylase Acta Crystallographica Section D: Biological Crystallography 59 5 940-942 2003 International Union of Crystallography
Kukkola, Liisa; Hieta, Reija; Kivirikko, Kari I; Myllyharju, Johanna; Identification and characterization of a third human, rat, and mouse collagen prolyl 4-hydroxylase isoenzyme Journal of Biological Chemistry 278 48 47685-47693 2003 ASBMB
Hieta, Reija; Myllyharju, Johanna; ENZYME CATALYSIS AND REGULATION-Cloning and characterization of a low molecular weight prolyl 4-hydroxylase from Arabidopsis thaliana. Effective hydroxylation of proline-rich, collagen-like, and Journal of Biological Chemistry 277 26 23965-23971 2002 Baltimore [etc.]
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
Kivirikko, Kari; Myllyharju, Johanna; Kukkola, Liisa; Hieta, Reija; Alpha (III) subunit for prolyl 4-hydroxylase 2002 Google Patents

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