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 | |
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| 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 |
| Nurminen, R; Afyounian, E; Tuominen, J; Scaravilli, M; Saarinen, M; Annala, M; Paunu, N; Haapasalo, H; Nykter, M; Granberg, KJ; | Identification of predisposing germline variants in familial glioma | EUROPEAN JOURNAL OF HUMAN GENETICS | 28 | SUPPL 1 | 517-518 | 2020 | SPRINGERNATURE CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND |
| 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 | |||||
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| 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 | |||
| Kim, J‐M; Santure, AW; Barton, Henry J; Quinn, JL; Cole, Eleanor F; Great Tit HapMap Consortium; Visser, ME; Sheldon, BC; Groenen, MAM; van Oers, K; | A high‐density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour | Molecular Ecology Resources | 18 | 4 | 877-891 | 2018 | Wiley Online Library |
| Kim, Jun-Mo; Santure, Anna W; Barton, Henry J; Quinn, John L; Cole, Ella F; Visser, Marcel E; Sheldon, Ben C; Groenen, M; Slate, J; | Data from: A high-density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour | 2018 | University of Sheffield | ||||
| Corcoran, Padraic; Gossmann, Toni I; Barton, Henry J; Slate, Jon; Zeng, Kai; | Determinants of the efficacy of natural selection on coding and noncoding variability in two passerine species (vol 9, pg 2987, 2017) | GENOME BIOLOGY AND EVOLUTION | 10 | 4 | 1062-1062 | 2018 | OXFORD UNIV PRESS GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND |
| 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 |
| Hieta, Reija; | Studying androgen receptor gene aberrations in prostate cancer using targeted DNA and RNA sequencing panels | 2018 | |||||
| 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 |
| Lund, Riikka J; Rahkonen, Nelly; Malonzo, Maia; Kauko, Leni; Emani, Maheswara Reddy; Kivinen, Virpi; Närvä, Elisa; Kemppainen, Esko; Laiho, Asta; Skottman, Heli; | RNA polymerase III subunit POLR3G regulates specific subsets of polyA+ and smallRNA transcriptomes and splicing in human pluripotent stem cells | Stem Cell Reports | 8 | 5 | 1442-1454 | 2017 | Cell Press |
| 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 | |
| Zhu, Lingyu; Kesseli, Juha; Nykter, Matti; Huttunen, Heikki; | Predicting Gene Expression Levels from Histone Modification Signals with Convolutional Recurrent Neural Networks | EMBEC & NBC 2017 | 555-558 | 2017 | Springer | ||
| 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 | |
| Wyatt, Alexander W; Annala, Matti; Aggarwal, Rahul; Beja, Kevin; Feng, Felix; Youngren, Jack; Foye, Adam; Lloyd, Paul; Nykter, Matti; Beer, Tomasz M; | Concordance of circulating tumor DNA and matched metastatic tissue biopsy in prostate cancer | JNCI: Journal of the National Cancer Institute | 109 | 12 | 2017 | Oxford University Press | |
| 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 |
| Bouvy-Liivrand, Maria; Hernández de Sande, Ana; Pölönen, Petri; Mehtonen, Juha; Vuorenmaa, Tapio; Niskanen, Henri; Sinkkonen, Lasse; Kaikkonen, Minna Unelma; Heinäniemi, Merja; | Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture | Nucleic acids research | 45 | 17 | 9837-9849 | 2017 | Oxford University Press |
| Zdobnov, Evgeny M; Tegenfeldt, Fredrik; Kuznetsov, Dmitry; Waterhouse, Robert M; Simão, Felipe A; Ioannidis, Panagiotis; Seppey, Mathieu; Loetscher, Alexis; Kriventseva, Evgenia V; | OrthoDB v9. 1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs | Nucleic acids research | 45 | D1 | D744-D749 | 2017 | Oxford University Press |
| Simão, Felipe A; Waterhouse, Robert M; Ioannidis, Panagiotis; Kriventseva, Evgenia V; Zdobnov, Evgeny M; | Supplementary online material | 2017 | |||||
| Ioannidis, Panagiotis; Simao, Felipe A; Waterhouse, Robert M; Manni, Mosè; Seppey, Mathieu; Robertson, Hugh M; Misof, Bernhard; Niehuis, Oliver; Zdobnov, Evgeny M; | Genomic features of the damselfly Calopteryx splendens representing a sister clade to most insect orders | Genome biology and evolution | 9 | 2 | 415-430 | 2017 | Oxford University Press |
| 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 | |
| Lavigne, Matthieu D; Konstantopoulos, Dimitris; Ntakou-Zamplara, Katerina Z; Liakos, Anastasios; Fousteri, Maria; | Global unleashing of transcription elongation waves in response to genotoxic stress restricts somatic mutation rate | Nature communications | 8 | 1 | 1-15 | 2017 | Nature Publishing Group |
| Tousa, Sofia; Semitekolou, Maria; Morianos, Ioannis; Banos, Aggelos; Trochoutsou, Aikaterini I; Brodie, Tess M; Poulos, Nikolaos; Samitas, Konstantinos; Kapasa, Maria; Konstantopoulos, Dimitris; | Activin-A co-opts IRF4 and AhR signaling to induce human regulatory T cells that restrain asthmatic responses | Proceedings of the National Academy of Sciences | 114 | 14 | E2891-E2900 | 2017 | National Acad Sciences |
| 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 | |
| Marzi, Sarah; Kumsta, Robert; Viana, Joana; Rutter, Michael; Mills, Jonathan; Sonuga-Barke, Edmund; | SEVERE PSYCHOSOCIAL DEPRIVATION IN EARLY CHILDHOOD IS ASSOCIATED WITH HYPERMETHYLATION ACROSS A REGION OF THE CYP2E1 GENE | EUROPEAN NEUROPSYCHOPHARMACOLOGY | 27 | S232-S233 | 2017 | ELSEVIER SCIENCE BV PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS | |
| 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 | |||
| Hannon, Eilis; Spiers, Helen; Viana, Joana; Pidsley, Ruth; Burrage, Joe; Murphy, Therese; Troakes, Claire; Turecki, Gustavo; O'Donovan, Michael; Schalkwyk, Leonard; | Methylation quantitative trait loci (mQTL) in the developing human brain and their enrichment in genomic regions associated with schizophrenia | EUROPEAN NEUROPSYCHOPHARMACOLOGY | 27 | S307-S308 | 2017 | ELSEVIER SCIENCE BV PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS | |
| 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 | ||||
| Viana, Joana; Costa, Fernando Albuquerque; Peralta, Helena; | PERSONAL LEARNING IN INFORMAL CONTEXTS: opportunities created by the Internet | 2017 | |||||
| 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 |
| Ruusuvuori, Pekka; Valkonen, Mira; Kartasalo, Kimmo; Visakorpi, Tapio; Latonen, Leena; Nykter, Matti; | Histological modeling of prostate cancer | Endocrine Abstracts | 42 | 2016 | Bioscientifica | ||
| Bova, G Steven; Kallio, Heini ML; Annala, Matti; Kivinummi, Kati; Högnäs, Gunilla; Häyrynen, Sergei; Rantapero, Tommi; Kivinen, Virpi; Isaacs, William B; Tolonen, Teemu; | Integrated clinical, whole-genome, and transcriptome analysis of multisampled lethal metastatic prostate cancer | Molecular Case Studies | 2 | 3 | a000752 | 2016 | Cold Spring Harbor Laboratory Press |
| Granberg, Kirsi J; Annala, Matti; Lehtinen, Birgitta; Kesseli, Juha; Haapasalo, Joonas; Yli-Harja, Olli; Visakorpi, Tapio; Haapasalo, Hannu; Nykter, Matti; Zhang, Wei; | Strong FGFR3 staining is a marker for FGFR3 fusions and poor prognosis in diffuse gliomas | Cancer Research | 76 | 14_Supplement | 5011-5011 | 2016 | The American Association for Cancer Research |
| Cordova, Zuzet Martinez; Grönholm, Anna; Kytölä, Ville; Taverniti, Valentina; Hämäläinen, Sanna; Aittomäki, Saara; Niininen, Wilhelmiina; Junttila, Ilkka; Ylipää, Antti; Nykter, Matti; | Myeloid cell expressed proprotein convertase FURIN attenuates inflammation | Oncotarget | 7 | 34 | 54392 | 2016 | Impact Journals, LLC |
| Valkonen, Mira; Nykter, Matti; Visakorpi, Tapio; Latonen, Leena; | Health figures: an open source JavaScript library for health data visualization./Ledesma, Andres; Al-Musawi, Mohammed; Nieminen, Hannu. In: BMC Medical Informatics and Decision Making, Vol. 16, No. 1, 38, 22.03. 2016. Research output: Scientific-peer-review› Article | BMC Medical Informatics and Decision Making | 16 | 1 | 38 | 2016 | |
| Dufva, Olli; Pölönen, Petri; Keränen, Mikko A; Liuksiala, Thomas; Lin, Jake; Mehtonen, Juha; Häyrynen, Sergei; Granberg, Kirsi; Nykter, Matti; Lohi, Olli; | Pan-Hematopoietic Cancer Gene Expression Analysis Identifies Immunologically Active Acute Myeloid Leukemia Subtypes | Blood | 128 | 22 | 1725 | 2016 | Elsevier |
| Kallio, Heini ML; Annala, Matti; Brofeldt, Anniina; Hieta, Reija; Kivinummi, Kati; Tammela, Teuvo; Nykter, Matti; Lilja, Hans G; Bova, G Steven; Visakorpi, Tapio; | Next generation sequencing panels to predict response to hormonal therapy in prostate cancer | Endocrine Abstracts | 42 | 2016 | Bioscientifica | ||
| Nurminen, Riikka; Rantapero, Tommi; Wong, Swee C; Fischer, Daniel; Lehtonen, Rainer; Tammela, Teuvo LJ; Nykter, Matti; Visakorpi, Tapio; Wahlfors, Tiina; Schleutker, Johanna; | Expressional profiling of prostate cancer risk SNPs at 11q13. 5 identifies DGAT2 as a new target gene | Genes, Chromosomes and Cancer | 55 | 8 | 661-673 | 2016 | Wiley Online Library |
| Kohvakka, Annika; Kivinummi, Kati; Kytola, Ville; Ylipaa, Antti; Annala, Matti; Urbanucci, Alfonso; Nykter, Matti; Visakorpi, Tapio; | Expression of a novel androgen-regulated long noncoding RNA correlates with progression-free survival in prostate cancer patients | Endocrine Abstracts | 42 | 2016 | Bioscientifica | ||
| Kartasalo, Kimmo; Latonen, Leena; Visakorpi, Tapio; Nykter, Matti; Ruusuvuori, Pekka; | Benchmarking of algorithms for 3D tissue reconstruction | 2016 IEEE International Conference on Image Processing (ICIP) | 2360-2364 | 2016 | IEEE | ||
| Häyrynen, Sergei; Nykter, Matti; | Pan-cancer analysis of alternative splicing patterns and association to genomic aberrations | Cancer Research | 76 | 14_Supplement | 1513-1513 | 2016 | The American Association for Cancer Research |
| Urbanucci, Alfonso; Barfeld, Stefan; Kytola, Ville; Vodak, Daniel; Sjoblom, Liisa; Tolonen, Teemu; Minner, Sarah; Burdelski, Christoph; Kivinummi, Kati K; Kregel, Steven; | Chromatin relaxation is a feature of advanced prostate cancer | Endocrine Abstracts | 42 | 2016 | Bioscientifica | ||
| Uusitalo, Hannu MT; Jylhä, Antti; Nättinen, Janika; Vaajanen, Anu; Härkönen, Miihkali; Nykter, Matti; Zhou, Lei; Beuerman, Roger W; | Conjunctival tissue proteome demonstrates abnormal expression of wound response proteins in glaucoma patients | Investigative Ophthalmology & Visual Science | 57 | 12 | 2924-2924 | 2016 | The Association for Research in Vision and Ophthalmology |
| Veskimäe, K; Staff, S; Grönholm, A; Pesu, M; Laaksonen, M; Nykter, M; Isola, J; Mäenpää, J; | Assessment of PARP protein expression in epithelial ovarian cancer by ELISA pharmacodynamic assay and immunohistochemistry | Tumor Biology | 37 | 9 | 11991-11999 | 2016 | Springer |
| Chua, Corrine Yingxuan; Liu, Yuexin; Granberg, Kirsi J; Hu, Limei; Haapasalo, Hannu; Annala, Matti J; Cogdell, David E; Verploegen, Maartje; Moore, Lynette M; Fuller, Gregory N; | IGFBP2 potentiates nuclear EGFR–STAT3 signaling | Oncogene | 35 | 6 | 738-747 | 2016 | Nature Publishing Group |
| Harjula, Sanna-Kaisa; Saralahti, Anni; Ojanen, Markus; Mathie, Heather; Halfpenny, Nicholas; Rantapero, Tommi; Granberg, Kirsi; Nykter, Matti; Lohi, Olli; Parikka, Mataleena; | Genes affecting mycobacterial infection in zebrafish | SCANDINAVIAN JOURNAL OF IMMUNOLOGY | 83 | 5 | 383-383 | 2016 | WILEY-BLACKWELL 111 RIVER ST, HOBOKEN 07030-5774, NJ USA |
| Saralahti, Anni; Harjula, Sanna-Kaisa; Partanen, Essi; Rantapero, Tommi; Granberg, Kirsi; Lohi, Olli; Nykter, Matti; Rounioja, Samuli; Parikka, Mataleena; Ramet, Mika; | A forward genetic screen for zebrafish genes involved in pneumococcal infection | SCANDINAVIAN JOURNAL OF IMMUNOLOGY | 83 | 5 | 384-384 | 2016 | WILEY-BLACKWELL 111 RIVER ST, HOBOKEN 07030-5774, NJ USA |
| Wyatt, Alexander W; Azad, Arun A; Volik, Stanislav V; Annala, Matti; Beja, Kevin; McConeghy, Brian; Haegert, Anne; Warner, Evan W; Mo, Fan; Brahmbhatt, Sonal; | Genomic alterations in cell-free DNA and enzalutamide resistance in castration-resistant prostate cancer | JAMA oncology | 2 | 12 | 1598-1606 | 2016 | American Medical Association |
| Luoto, Suvi; Kesseli, Juha; Nykter, Matti; Granberg, Kirsi J; | Different immune cell responses are associated with glioblastoma subclassification and typical genetic alterations | Cancer Research | 76 | 14_Supplement | 4148-4148 | 2016 | The American Association for Cancer Research |
| Ruusuvuori, Pekka; Valkonen, Mira; Nykter, Matti; Visakorpi, Tapio; Latonen, Leena; | Feature-based analysis of mouse prostatic intraepithelial neoplasia in histological tissue sections | Journal of pathology informatics | 7 | 1 | 5 | 2016 | Elsevier |
| Teppo, Susanna; Laukkanen, Saara; Liuksiala, Thomas; Nordlund, Jessica; Oittinen, Mikko; Teittinen, Kaisa; Grönroos, Toni; St-Onge, Pascal; Sinnett, Daniel; Syvänen, Ann-Christine; | Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemia | Genome research | 26 | 11 | 1468-1477 | 2016 | Cold Spring Harbor Lab |
| Polonen, P; Mehtonen, J; Lin, J; Liuksiala, T; Hayrinen, S; Teppo, S; May, P; Hautamaki, V; Granberg, K; Lohi, O; | MOLECULAR CLASSIFICATION AND COMPARATIVE ANALYSIS OF ACUTE MYELOID LEUKEMIA MULTI-OMICS DATA USING THE INTERACTIVE HEMAP RESOURCE | HAEMATOLOGICA | 101 | 205-205 | 2016 | FERRATA STORTI FOUNDATION VIA GIUSEPPE BELLI 4, 27100 PAVIA, ITALY | |
| Gronroos, T; Teppo, S; Mehtonen, J; Laukkanen, S; Liuksiala, T; Nykter, M; Heinaniemi, M; Lohi, O; | OVEREXPRESSION OF PTP4A3 IN ETV6-RUNX1 ACUTE LEUKEMIA | HAEMATOLOGICA | 101 | 347-347 | 2016 | FERRATA STORTI FOUNDATION VIA GIUSEPPE BELLI 4, 27100 PAVIA, ITALY | |
| Sjöblom, Liisa; Saramäki, Outi; Annala, Matti; Leinonen, Katri; Nättinen, Janika; Tolonen, Teemu; Wahlfors, Tiina; Nykter, Matti; Bova, G Steven; Schleutker, Johanna; | Microseminoprotein-beta expression in different stages of prostate cancer | PloS one | 11 | 3 | e0150241 | 2016 | Public Library of Science San Francisco, CA USA |
| Wyatt, AW; Annala, M; Beja, K; Parimi, S; Vandekerkhove, G; Warner, E; Zulfiqar, M; Finch, D; Oja, C; Vergidis, J; | Genomic alterations in circulating tumor DNA (ctDNA) are associated with clinical outcomes in treatment-naive metastatic castration-resistant prostate cancer (mCRPC) patients commencing androgen receptor (AR)-targeted therapy | Annals of Oncology | 27 | vi17 | 2016 | Elsevier | |
| Sjöblom, L; Saramäki, O; Annala, M; Leinonen, K; Nättinen, J; Tolonen, T; Wahlfors, T; Nykter, M; Bova, G; Schleutker, J; | 1074 Microseminoprotein-beta expression in different stages of prostate cancer | European Urology Supplements | 3 | 15 | e1074 | 2016 | |
| Ulman, Vladimír; Svoboda, David; Nykter, Matti; Kozubek, Michal; Ruusuvuori, Pekka; | Virtual cell imaging: A review on simulation methods employed in image cytometry | Cytometry Part A | 89 | 12 | 1057-1072 | 2016 | Wiley Online Library |
| Mehtonen, J; Polonen, P; Lin, J; Liuksiala, T; Hayrynen, S; Teppo, S; May, P; Hautamaki, V; Granberg, K; Lohi, O; | COMPARATIVE ANALYSIS OF GENE REGULATORY NETWORKS IN LYMPHOID LEUKEMIAS USING THE INTERACTIVE HEMAP RESOURCE | HAEMATOLOGICA | 101 | 25-25 | 2016 | FERRATA STORTI FOUNDATION VIA GIUSEPPE BELLI 4, 27100 PAVIA, ITALY | |
| Heinäniemi, Merja; Vuorenmaa, Tapio; Teppo, Susanna; Kaikkonen, Minna U; Bouvy-Liivrand, Maria; Mehtonen, Juha; Niskanen, Henri; Zachariadis, Vasilios; Laukkanen, Saara; Liuksiala, Thomas; | Transcription-coupled genetic instability marks acute lymphoblastic leukemia structural variation hotspots | Elife | 5 | e13087 | 2016 | eLife Sciences Publications Limited | |
| Waterhouse, Robert; Tenan, Mirna; Simão, Felipe A; Ioannidis, Panagiotis; Kriventseva, Evgenia V; Zdobnov, Evgeny M; | Large-scale gene functional inference through orthology | F1000Research | 5 | 2016 | |||
| Hoy, Marjorie A; Waterhouse, Robert M; Wu, Ke; Estep, Alden S; Ioannidis, Panagiotis; Palmer, William J; Pomerantz, Aaron F; Simao, Felipe A; Thomas, Jainy; Jiggins, Francis M; | Genome sequencing of the phytoseiid predatory mite Metaseiulus occidentalis reveals completely atomized Hox genes and superdynamic intron evolution | Genome biology and evolution | 8 | 6 | 1762-1775 | 2016 | Oxford University Press |
| Laitinen, Virpi H; Akinrinade, Oyediran; Rantapero, Tommi; Tammela, Teuvo LJ; Wahlfors, Tiina; Schleutker, Johanna; | Germline copy number variation analysis in Finnish families with hereditary prostate cancer | The Prostate | 76 | 3 | 316-324 | 2016 | Wiley Online Library |
| Georgolopoulos, Grigorios; Parducci, Laura; Drouzas, Andreas D; | A short phylogenetically informative cpDNA fragment for the identification of Pinus species | Biochemical Systematics and Ecology | 66 | 166-172 | 2016 | Elsevier | |
| Zajitschek, Felix; Zajitschek, Susanne RK; Canton, Cindy; Georgolopoulos, Grigorios; Friberg, Urban; Maklakov, Alexei A; | Evolution under dietary restriction increases male reproductive performance without survival cost | Proceedings of the Royal Society B: Biological Sciences | 283 | 1825 | 20152726 | 2016 | The Royal Society |
| Jiang, Yuxiang; Oron, Tal Ronnen; Clark, Wyatt T; Bankapur, Asma R; D’Andrea, Daniel; Lepore, Rosalba; Funk, Christopher S; Kahanda, Indika; Verspoor, Karin M; Ben-Hur, Asa; | An expanded evaluation of protein function prediction methods shows an improvement in accuracy | Genome biology | 17 | 1 | 1-19 | 2016 | BioMed Central |
| Hannon, Eilis; Dempster, Emma; Viana, Joana; Burrage, Joe; Smith, Adam R; Macdonald, Ruby; St Clair, David; Mustard, Colette; Breen, Gerome; Therman, Sebastian; | An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation | Genome biology | 17 | 1 | 1-16 | 2016 | BioMed Central |
| Laing, LV; Viana, Joana; Dempster, EL; Trznadel, M; Trunkfield, LA; Uren Webster, TM; Van Aerle, R; Paull, GC; Wilson, RJ; Mill, Jonathan; | Bisphenol A causes reproductive toxicity, decreases dnmt1 transcription, and reduces global DNA methylation in breeding zebrafish (Danio rerio) | Epigenetics | 11 | 7 | 526-538 | 2016 | Taylor & Francis |
| Santos, Ana Moura; Viana, Joana; | Mooc técnico: desafios do desenho curricular e da produção de conteúdos multimédia | 2016 | |||||
| Hannon, Eilis; Spiers, Helen; Viana, Joana; Pidsley, Ruth; Burrage, Joe; Murphy, Therese M; Troakes, Claire; Turecki, Gustavo; O'donovan, Michael C; Schalkwyk, Leonard C; | Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci | Nature neuroscience | 19 | 1 | 48-54 | 2016 | Nature Publishing Group |
| Santos, A Moura; Viana, Joana; | From design to production: First course experiences within mooc tÉcnico | ICERI2016 Proceedings. 9th annual International Conference of Education, Research and Innovation | 2016 | ||||
| Da Silva, Alexandre Guedes; Santos, Ana Moura; Costa, Fernando Albuquerque; Viana, Joana; | Enhancing MOOC videos: Design and production strategies | Research Track | 107 | 2016 | |||
| Kumsta, Robert; Marzi, Sarah J; Viana, Joana; Dempster, EL; Crawford, Bethany; Rutter, Michael; Mill, Jonathan; Sonuga-Barke, Edmund JS; | Severe psychosocial deprivation in early childhood is associated with increased DNA methylation across a region spanning the transcription start site of CYP2E1 | Translational psychiatry | 6 | 6 | e830-e830 | 2016 | Nature Publishing Group |
| Viana, Joana Andreia Domingues; | Currículo em contextos informais: contributos para a (re) conceptualização do conceito de currículo a partir de aprendizagens online | 2016 | Universidade de Lisboa (Portugal) | ||||
| Sin, Celine; Chiarugi, Davide; Valleriani, Angelo; | Quantitative assessment of ribosome drop-off in E. coli | Nucleic acids research | 44 | 6 | 2528-2537 | 2016 | Oxford University Press |
| Sin, Celine; Chiarugi, Davide; Valleriani, Angelo; | Degradation parameters from pulse-chase experiments | PLoS one | 11 | 5 | e0155028 | 2016 | Public Library of Science San Francisco, CA USA |
| Olarte, Carlos; Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana; | A proof theoretic view of spatial and temporal dependencies in biochemical systems | Theoretical Computer Science | 641 | 25-42 | 2016 | Elsevier | |
| Vega, Carlos Alberto Olarte; Chiarugi, Davide; Hermith, Diana; Falaschi, Moreno; | A proof theoretic view of spatial and temporal dependencies in biochemical systems | 2016 | Elsevier | ||||
| Gundem, Gunes; Van Loo, Peter; Kremeyer, Barbara; Alexandrov, Ludmil B; Tubio, Jose; Papaemmanuil, Elli; Brewer, Daniel S; Kallio, Heini ML; Högnäs, Gunilla; Annala, Matti; | The evolutionary history of lethal metastatic prostate cancer | Nature | 520 | 7547 | 353-357 | 2015 | Nature Publishing Group |
| Scaravilli, Mauro; Porkka, Kati P; Brofeldt, Anniina; Annala, Matti; Tammela, Teuvo LJ; Jenster, Guido W; Nykter, Matti; Visakorpi, Tapio; | MiR‐1247‐5p is overexpressed in castration resistant prostate cancer and targets MYCBP2 | The Prostate | 75 | 8 | 798-805 | 2015 | Wiley Online Library |
| Veskimäe, Kristina; Staff, Synnöve; Tabaro, Francesco; Nykter, Matti; Isola, Jorma; Mäenpää, Johanna; | Microarray analysis of differentially expressed genes in ovarian and fallopian tube epithelium from risk‐reducing salpingo‐oophorectomies | Genes, Chromosomes and Cancer | 54 | 5 | 276-287 | 2015 | Wiley Online Library |
| Turner, Kristen M; Sun, Youting; Ji, Ping; Granberg, Kirsi J; Bernard, Brady; Hu, Limei; Cogdell, David E; Zhou, Xinhui; Yli-Harja, Olli; Nykter, Matti; | Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression | Proceedings of the National Academy of Sciences | 112 | 11 | 3421-3426 | 2015 | National Acad Sciences |
| Ylipää, Antti; Kivinummi, Kati; Annala, Matti; Kohvakka, Annika; Latonen, Leena; Scaravilli, Mauro; Kartasalo, Kimmo; Leppänen, Simo-Pekka; Karakurt, Serdar; Seppälä, Janne; | Transcriptome sequencing reveals PCAT5-new ERG-regulated non-coding transcript in prostate cancer | Cancer Research | 75 | 15_Supplement | 148-148 | 2015 | The American Association for Cancer Research |
| Jylhä, Antti; Aapola, Ulla; Nättinen, Janika; Nykter, Matti; Beuerman, Roger W; Uusitalo, Hannu MT; | Tear proteome reveals predictive biomarkers for clinical improvement in glaucoma patients switching from preserved to preservative free medication | Investigative Ophthalmology & Visual Science | 56 | 7 | 3674-3674 | 2015 | The Association for Research in Vision and Ophthalmology |
| Kallio, Heini ML; Annala, Matti; Kivinummi, Kati; Högnäs, Gunilla; Gundem, Gunes; Wedge, David C; Van Loo, Peter; Heyn, Holger; Emmert-Buck, Michael R; Isaacs, William B; | Clonal evolution of a lethal prostate cancer: Integrated whole genome analysis case study | Cancer Research | 75 | 15_Supplement | 3883-3883 | 2015 | The American Association for Cancer Research |
| Nordfors, Kristiina; Haapasalo, Joonas; Mäkelä, Katri; Granberg, Kirsi J; Nykter, Matti; Korja, Miikka; Paavonen, Timo; Haapasalo, Hannu; Soini, Ylermi; | Twist predicts poor outcome of patients with astrocytic glioma | Journal of clinical pathology | 68 | 11 | 905-912 | 2015 | BMJ Publishing Group |
| Kaukoniemi, Kirsi M; Rauhala, Hanna E; Scaravilli, Mauro; Latonen, Leena; Annala, Matti; Vessella, Robert L; Nykter, Matti; Tammela, Teuvo LJ; Visakorpi, Tapio; | Epigenetically altered miR‐193b targets cyclin D1 in prostate cancer | Cancer medicine | 4 | 9 | 1417-1425 | 2015 | Wiley Online Library |
| Ruusuvuori, P; Nykter, M; Latonen, L; | 712 Processing of stacked histological tissue sections in digital pathology | European Journal of Cancer | 3 | 51 | S131 | 2015 | |
| Laukkanen, Saara; Liuksiala, Thomas; Nykter, Matti; Heinäniemi, Merja; Lohi, Olli; | Identification of Novel Drug Targets in T-Cell Acute Lymphoblastic Leukemia | Blood | 126 | 23 | 3646 | 2015 | Elsevier |
| Ylipää, Antti; Kivinummi, Kati; Kohvakka, Annika; Annala, Matti; Latonen, Leena; Scaravilli, Mauro; Kartasalo, Kimmo; Leppänen, Simo-Pekka; Karakurt, Serdar; Seppälä, Janne; | Transcriptome Sequencing Reveals PCAT5 as a Novel ERG-Regulated Long Noncoding RNA in Prostate CancerPCAT5: An ERG-Regulated lncRNA | Cancer research | 75 | 19 | 4026-4031 | 2015 | American Association for Cancer Research |
| Sarbu, Septimia; Shmulevich, Ilya; Yli-Harja, Olli; Nykter, Matti; Kesseli, Juha; | Mapping dynamical states to structural classes for Boolean networks using a classification algorithm | 2015 23rd European Signal Processing Conference (EUSIPCO) | 160-164 | 2015 | IEEE | ||
| Abeshouse, Adam; Ahn, Jaeil; Akbani, Rehan; Ally, Adrian; Amin, Samirkumar; Andry, Christopher D; Annala, Matti; Aprikian, Armen; Armenia, Joshua; Arora, Arshi; | The molecular taxonomy of primary prostate cancer | Cell | 163 | 4 | 1011-1025 | 2015 | Elsevier |
| Liuksiala, Thomas; Granberg, Kirsi; Häyrynen, Sergei; Mehtonen, Juha; Pölönen, Petri; Teppo, Susanna; Lin, Jake; Laukkanen, Saara; May, Patrick; Nykter, Matti; | Mapping the Gene Expression Diversity Across Hematological and Lymphoid Malignancies | Blood | 126 | 23 | 4805 | 2015 | Elsevier |
| Annala, Matti; Kivinummi, Kati; Tuominen, Joonas; Karakurt, Serdar; Granberg, Kirsi; Latonen, Leena; Ylipää, Antti; Sjöblom, Liisa; Ruusuvuori, Pekka; Saramäki, Outi; | Recurrent SKIL-activating rearrangements in ETS-negative prostate cancer | Oncotarget | 6 | 8 | 6235 | 2015 | Impact Journals, LLC |
| Li, Xia; Liu, Yuexin; Granberg, Kirsi J; Wang, Qinhao; Moore, Lynette M; Ji, Ping; Gumin, Joy; Sulman, Erik P; Calin, George A; Haapasalo, Hannu; | Two mature products of MIR-491 coordinate to suppress key cancer hallmarks in glioblastoma | Oncogene | 34 | 13 | 1619-1628 | 2015 | Nature Publishing Group |
| Rane, Jayant K; Ylipää, Antti; Adamson, Rachel; Mann, Vincent M; Simms, Matthew S; Collins, Anne T; Visakorpi, Tapio; Nykter, Matti; Maitland, Norman J; | Construction of therapeutically relevant human prostate epithelial fate map by utilising miRNA and mRNA microarray expression data | British journal of cancer | 113 | 4 | 611-615 | 2015 | Nature Publishing Group |
| Rane, Jayant K; Scaravilli, Mauro; Ylipää, Antti; Pellacani, Davide; Mann, Vincent M; Simms, Matthew S; Nykter, Matti; Collins, Anne T; Visakorpi, Tapio; Maitland, Norman J; | MicroRNA expression profile of primary prostate cancer stem cells as a source of biomarkers and therapeutic targets | European urology | 67 | 1 | 7-10 | 2015 | Elsevier |
| Marttila, Saara; Kananen, Laura; Häyrynen, Sergei; Jylhävä, Juulia; Nevalainen, Tapio; Hervonen, Antti; Jylhä, Marja; Nykter, Matti; Hurme, Mikko; | Ageing-associated changes in the human DNA methylome: genomic locations and effects on gene expression | BMC genomics | 16 | 1 | 1-17 | 2015 | BioMed Central |
| Veskimae, K; Staff, S; Tabaro, F; Nykter, M; Isola, J; Maenpaa, J; | MICROARRAY ANALYSIS OF DIFFERENTIALLY EXPRESSED GENES IN OVARIAN AND FALLOPIAN TUBE EPITHELIUM FROM RISK-REDUCING SALPINGO-OOPHORECTOMIES PUBLISHED: GENES CHROMOSOMES CANCER. 2015 FEB 23 | INTERNATIONAL JOURNAL OF GYNECOLOGICAL CANCER | 25 | 9 | 576-576 | 2015 | LIPPINCOTT WILLIAMS & WILKINS TWO COMMERCE SQ, 2001 MARKET ST, PHILADELPHIA … |
| Annala, M; Kivinummi, K; Tuominen, J; Latonen, L; Ylipää, A; Saramäki, O; Kaukoniemi, KM; Karakurt, S; Yli-Harja, O; Vessella, RL; | 165 Recurrent SKIL-activating rearrangements in ETS-negative prostate cancer | European Urology Supplements | 2 | 14 | e165 | 2015 | |
| Kuusisto, Kirsi M; Rantapero, Tommi; Kankuri-Tammilehto, Minna; Nykter, Matti; Laasanen, Satu-Leena; Schleutker, Johanna; | Abstract LB-284: Exome sequencing of high-risk Finnish hereditary breast and breast-ovarian cancer families | Cancer Research | 75 | 15_Supplement | LB-284-LB-284 | 2015 | The American Association for Cancer Research |
| Yli-Hietanen, Jari; Ylipää, Antti; Yli-Harja, Olli; | Cancer research in the era of next-generation sequencing and big data calls for intelligent modeling | Chinese journal of cancer | 34 | 3 | 1-4 | 2015 | BioMed Central |
| Liuksiala, Thomas Edward; | Blood Cancer Lineage Identification: A Machine Learning Approach | 2015 | |||||
| Simão, Felipe A; Waterhouse, Robert M; Ioannidis, Panagiotis; Kriventseva, Evgenia V; Zdobnov, Evgeny M; | BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs | Bioinformatics | 31 | 19 | 3210-3212 | 2015 | Oxford University Press |
| Kriventseva, Evgenia V; Tegenfeldt, Fredrik; Petty, Tom J; Waterhouse, Robert M; Simao, Felipe A; Pozdnyakov, Igor A; Ioannidis, Panagiotis; Zdobnov, Evgeny M; | OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software | Nucleic acids research | 43 | D1 | D250-D256 | 2015 | Oxford University Press |
| Neafsey, Daniel E; Waterhouse, Robert M; Abai, Mohammad R; Aganezov, Sergey S; Alekseyev, Max A; Allen, James E; Amon, James; Arcà, Bruno; Arensburger, Peter; Artemov, Gleb; | Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes | Science | 347 | 6217 | 1258522 | 2015 | American Association for the Advancement of Science |
| Laitinen, Virpi H; Rantapero, Tommi; Fischer, Daniel; Vuorinen, Elisa M; Tammela, Teuvo LJ; Practical Consortium; Wahlfors, Tiina; Schleutker, Johanna; | Fine‐mapping the 2q37 and 17q11. 2‐q22 loci for novel genes and sequence variants associated with a genetic predisposition to prostate cancer | International journal of cancer | 136 | 10 | 2316-2327 | 2015 | Wiley Online Library |
| Costa, Fernando Albuquerque; Viana, Joana; Cruz, Elisabete; Pereira, Carolina; | Digital literacy of adults education needs for the full exercise of citizenship | 2015 International Symposium on Computers in Education (SIIE) | 92-96 | 2015 | IEEE | ||
| Costa, Fernando Albuquerque; Cruz, Elisabete; Viana, Joana; Brito, Rita; Rodriguez, Carla; | Conceções e expectativas de professores e educadores de infância a propósito do conceito de escola digital | 2015 | Challenges | ||||
| Costa, Fernando Albuquerque; Moura Santos, Ana; Silva, AG; Viana, Joana; | Guiões para desenho de cursos MOOC | MEC. Experiências de Inovação Didática no Ensino Superior. Lisboa: MEC | 327-342 | 2015 | |||
| Santos, Ana Moura; Costa, F; Viana, Joana; Silva, AG; | Estratégias para Desenho e Produção de Vídeos para Cursos em formato MOOC | Actas da IX Conferência Internacional de Tecnologias de Informação e Comunicação na Educação, Challenges | 828-840 | 2015 | sn | ||
| Fisher, Helen L; Murphy, Therese M; Arseneault, Louise; Caspi, Avshalom; Moffitt, Terrie E; Viana, Joana; Hannon, Eilis; Pidsley, Ruth; Burrage, Joe; Dempster, Emma L; | Methylomic analysis of monozygotic twins discordant for childhood psychotic symptoms | Epigenetics | 10 | 11 | 1014-1023 | 2015 | Taylor & Francis |
| Silva, Pedro; Diogo, Ana Matias; Coelho, Conceição; Fernandes, Conceição; Viana, Joana; | Children's practices of ICT and social inequalities: on the uses of the Magalhães computer in two school communities | Digital literacy, technology and social inclusion | 345-375 | 2015 | Húmus | ||
| Costa, F; Cruz, Elisabete; Viana, Joana; Pereira, Carolina; | Literacia Digital de Adultos: Contributos para o desenvolvimento de dinâmicas de formação | Atas do Seminário Internacional de Informática Educativa (SIIE) | 169-175 | 2015 | Instituto Politécnico de Setúbal | ||
| RAMOS, DOÓJ; DE ALMEIDA, MM; VIANA, J; SANCHES, T; PAZ, AL; | RECENT TRENDS OF INTERNATIONAL RESEARCH ON HIGHER EDUCATION PEDAGOGY: A LITERATURE REVIEW | LUSOFONA DE EDUCACAO Издательство: University of Lusophone Humanities and Technology | 2015 | ||||
| Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana; Olarte, Carlos; | Verification of spatial and temporal modalities in biochemical systems | Electronic Notes in Theoretical Computer Science | 316 | 29-44 | 2015 | Elsevier | |
| Falaschi, Moreno; Hermith, Diana; Chiarugi, Davide; Vega, Carlos Alberto Olarte; | Verification of spatial and temporal modalities in biochemical systems | 2015 | Elsevier | ||||
| Bodei, Chiara; Bortolussi, Luca; Chiarugi, Davide; Guerriero, Maria Luisa; Policriti, Alberto; Romanel, Alessandro; | On the impact of discreteness and abstractions on modelling noise in gene regulatory networks | Computational Biology and Chemistry | 56 | 98-108 | 2015 | Elsevier | |
| Sin, Celine; Chiarugi, Davide; Valleriani, Angelo; | Single-molecule modeling of mRNA degradation by miRNA: Lessons from data | BMC Systems Biology | 9 | 3 | 1-9 | 2015 | Springer |
| Chiarugi, Davide; Falaschi, Moreno; Hermith, Diana; Olarte, Carlos; Torella, Luca; | Modelling non-Markovian dynamics in biochemical reactions | BMC systems biology | 9 | 3 | 1-13 | 2015 | Springer |
| Chiarugi, Davide; Falaschi, Moreno; Olarte, Carlos; Palamidessi, Catuscia; | A declarative view of signaling pathways | Programming Languages with Applications to Biology and Security | 183-201 | 2015 | Springer | ||
| Paradisi, Paolo; Allegrini, Paolo; Chiarugi, Davide; | A renewal model for the emergence of anomalous solute crowding in liposomes | BMC Systems Biology | 9 | 3 | 1-8 | 2015 | Springer |
| Rading, M Michael; Sandmann, Michael; Steup, Martin; Chiarugi, Davide; Valleriani, Angelo; | Weak correlation of starch and volume in synchronized photosynthetic cells | Physical Review E | 91 | 1 | 12711 | 2015 | APS |
| Huang, Qilai; Whitington, Thomas; Gao, Ping; Lindberg, Johan F; Yang, Yuehong; Sun, Jielin; Väisänen, Marja-Riitta; Szulkin, Robert; Annala, Matti; Yan, Jian; | A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding | Nature genetics | 46 | 2 | 126-135 | 2014 | Nature Publishing Group |
| 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 |
