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home:publications [09.12.2019 10:44] Teemu Kuulasmaa [2019] |
home:publications [12.12.2023 12:58] Administrator |
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Please find below annual lists of the publications that took advantage of the services provided by Bioinformatics Center. | Please find below annual lists of the publications that took advantage of the services provided by Bioinformatics Center. | ||
+ | ## 2023 | ||
+ | Laura Helminen, Jasmin Huttunen, Melina Tulonen, Niina Aaltonen, Einari A Niskanen, Jorma J Palvimo, Ville Paakinaho, **Chromatin accessibility and pioneer factor FOXA1 restrict glucocorticoid receptor action in prostate cancer**, Nucleic Acids Research, 2023;, gkad1126, https:// | ||
- | ### 2019 | + | Csader, S.; Ismaiah, M.J.; Kuningas, T.; Heinäniemi, |
- | Karttunen, J.; Heiskanen, M.; Lipponen, A.; Poulsen, D.; Pitkänen, A. **Extracellular Vesicles | + | Lipponen, A.; Kajevu, N.; Natunen, T.; Ciszek, R.; Puhakka, N.; Hiltunen, M.; Pitkänen, A. **Gene Expression Profile |
- | Failli M, Paananen J, Fortino V. **Prioritizing target-disease associations with novel safety and efficacy scoring methods**, //Sci Rep// 2019, https:// | + | ## 2022 |
- | Timonen O, Särkkä | + | Samms RJ, Cheng CC, Fourcaudot |
- | Lipponen A, Natunen T, Hujo M, Ciszek R, Hämäläinen E, Tohka J, Hiltunen M, Paananen J, Poulsen D, Kansanen | + | Kainulainen K, Takabe P, Heikkinen S, Aaltonen N, de la Motte C, Rauhala L, Durst FC, Oikari S, Hukkanen T, Rahunen |
- | Pölönen P, Mehtonen J, Lin J, Liuksiala T, Häyrynen | + | Kärkkäinen E, Heikkinen |
- | Mehtonen J, Pölönen P, Häyrynen S, Lin J, Liuksiala T, Granberg K, Lohi O, Hautamäki V, Nykter M, Heinäniemi M. **Data-driven characterization of molecular phenotypes across heterogenous sample collections**, | + | Raittio, E, Sofi-Mahmudi, A, Uribe, SE. **Research transparency in dental research: A programmatic analysis**. Eur J Oral Sci. 2023; 131: |
- | //Nucleic Acids Research// 2019, https:// | + | |
- | Ngo Trong T, Mehtonen J, González G, Kramer R, Hautamäki V, Heinäniemi M. **Semisupervised Generative Autoencoder | + | Ghahremani, Morteza and Khateri, Mohammad and Sierra, Alejandra and Tohka, Jussi, **Adversarial Distortion Learning |
- | Nikkilä A, Arvela H, Mehtonen J, Raitanen J, Heinäniemi M, Lohi O, Auvinen | + | Hanel, A.; Carlberg, C. **Time-Resolved Gene Expression Analysis Monitors the Regulation of Inflammatory Mediators |
- | Sallinen H, Janhonen S, Pölönen P, Niskanen H, Liu OH, Kivelä A, Hartikainen JM, Anttila M, Heinäniemi M, Ylä-Herttuala S, Kaikkonen MU. **Comparative transcriptome analysis of matched primary and distant metastatic ovarian carcinoma.**, | + | Luca Cattelani, Vittorio Fortino, **Improved NSGA-II algorithms for multi-objective biomarker discovery, Bioinformatics**, Volume 38, Issue Supplement_2, September 2022, Pages ii20–ii26, https:// |
- | Pölönen P, Jawahar Deen A, Leinonen HM, Jyrkkänen HK, Kuosmanen S, Mononen M, Jain A, Tuomainen T, Pasonen-Seppänen S, Hartikainen JM, Mannermaa A, Nykter M, Tavi P, Johansen T, Heinäniemi M, Levonen AL. **Nrf2 and SQSTM1/p62 jointly contribute | + | Maria-Elisa Nordberg, Martin Täubel, Sami Heikkinen, Kaisa Jalkanen, Arto Köliö, Marianne Stranger, Hanna Leppänen, Anne Hyvärinen, Kati Huttunen, **Toxicological transcriptome of human airway constructs after exposure |
- | // | + | |
- | Kuusanmäki H, Leppä AM, Pölönen P, Kontro M, Dufva O, Deb D, Yadav B, Brück O, Kumar A, Everaus | + | Jäntti, H., Sitnikova, V., Ishchenko, Y. et al. **Microglial amyloid beta clearance is driven by PIEZO1 channels**. J Neuroinflammation 19, 147 (2022). https:// |
+ | Valverde, J.M., Shatillo, A., De Feo, R. et al. **Automatic Cerebral Hemisphere Segmentation in Rat MRI with Ischemic Lesions via Attention-based Convolutional Neural Networks**. Neuroinform (2022). https:// | ||
- | ### 2018 | + | |
+ | Oksa, L.; Mäkinen, A.; Nikkilä, A.; Hyvärinen, N.; Laukkanen, S.; Rokka, A.; Haapaniemi, P.; Seki, M.; Takita, J.; Kauko, O.; Heinäniemi, | ||
+ | |||
+ | Saara Laukkanen, Alexandra Bacquelaine Veloso, Chuan Yan, Laura Oksa, Eric J. Alpert, Daniel Do, Noora Hyvärinen, Karin McCarthy, Abhinav Adhikari, Qiqi Yang, Sowmya Iyer, Sara P. Garcia, Annukka Pello, Tanja Ruokoranta, Sanni Moisio, Sadiksha Adhikari, Jeffrey A. Yoder, Kayleigh Mary Gallagher, Lauren Whelton, James R. Allen, Alexander Hai Jin, Siebe Loontiens, Merja Heinäniemi, | ||
+ | |||
+ | Céline Vandamme, Marja Rytkönen-Nissinen, | ||
+ | **Single-cell characterization of dog allergen–specific T cells reveals TH2 heterogeneity in allergic individuals**, | ||
+ | Journal of Allergy and Clinical Immunology, | ||
+ | Volume 149, Issue 5, | ||
+ | 2022, | ||
+ | Pages 1732-1743.e15, | ||
+ | ISSN 0091-6749, | ||
+ | https:// | ||
+ | |||
+ | Timo A. Lakka, Kirsikka Aittola, Elina Järvelä-Reijonen, | ||
+ | **Real-world effectiveness of digital and group-based lifestyle interventions as compared with usual care to reduce type 2 diabetes risk – A stop diabetes pragmatic randomised trial, | ||
+ | The Lancet Regional Health - Europe **, | ||
+ | 2022, | ||
+ | 100527, | ||
+ | ISSN 2666-7762, | ||
+ | https:// | ||
+ | |||
+ | ## 2021 | ||
+ | |||
+ | A. Abdollahzadeh, | ||
+ | |||
+ | Prakash, Mithilesh et al. **Quantitative Longitudinal Predictions of Alzheimer’s Disease by Multi-Modal Predictive Learning**. 1 Jan. 2021 : 1533 – 1546. http:// | ||
+ | |||
+ | Petteri Stenroos, Tiina Pirttimäki, | ||
+ | |||
+ | Chen, J., Spracklen, C.N., Marenne, G. et al. **The trans-ancestral genomic architecture of glycemic traits.** Nat Genet 53, 840–860 (2021). https:// | ||
+ | |||
+ | Ville Paakinaho, Joanna K Lempiäinen, | ||
+ | |||
+ | A.B.M. Kaiser Manjur, Joanna K. Lempiäinen, | ||
+ | |||
+ | Launonen, KM., Paakinaho, V., Sigismondo, G. et al. **Chromatin-directed proteomics-identified network of endogenous androgen receptor in prostate cancer cells.** Oncogene 40, 4567–4579 (2021). https:// | ||
+ | |||
+ | Teemu J Rintala, Antonio Federico, Leena Latonen, Dario Greco, Vittorio Fortino, **A systematic comparison of data- and knowledge-driven approaches to disease subtype discovery**, | ||
+ | |||
+ | Maria-Elisa Nordberg, Martin Täubel, Sami Heikkinen, Kaisa Jalkanen, Arto Köliö, Marianne Stranger, Hanna Leppänen, Anne Hyvärinen, Kati Huttunen, **Toxicological transcriptome of human airway constructs after exposure to indoor air particulate matter: In search of relevant pathways of moisture damage-associated health effects**, Environment International, | ||
+ | |||
+ | Kärkkäinen, | ||
+ | |||
+ | Ilakya Selvarajan, Anu Toropainen, Kristina M. Garske, Maykel López Rodríguez, Arthur Ko, Zong Miao, Dorota Kaminska, Kadri Õunap, Tiit Örd, Aarthi Ravindran, Oscar H. Liu, Pierre R. Moreau, Ashik Jawahar Deen, Ville Männistö, Calvin Pan, Anna-Liisa Levonen, Aldons J. Lusis, Sami Heikkinen, Casey E. Romanoski, Jussi Pihlajamäki, | ||
+ | |||
+ | Pierre R. Moreau, Vanesa Tomas Bosch, Maria Bouvy-Liivrand, | ||
+ | |||
+ | Isidore Mushimiyimana, | ||
+ | |||
+ | Suvi Linna-Kuosmanen, | ||
+ | |||
+ | Tanja Turunen, Ana Hernández de Sande, Petri Pölönen, Merja Heinäniemi, | ||
+ | |||
+ | Céline Vandamme, Marja Rytkönen-Nissinen, | ||
+ | |||
+ | Stenroos P, Pirttimäki T, Paasonen J, Paasonen E, Salo RA, Koivisto H, Natunen T, Mäkinen P, Kuulasmaa T, Hiltunen M, Tanila H, Gröhn O., **Isoflurane affects brain functional connectivity in rats 1 month after exposure.**, | ||
+ | Neuroimage. 2021 March, https:// | ||
+ | |||
+ | Paakinaho V, Lempiäinen JK, Sigismondo G, Niskanen EA, Malinen M, Jääskeläinen T, Varjosalo M, Krijgsveld J, Palvimo JJ., **SUMOylation regulates the protein network and chromatin accessibility at glucocorticoid receptor-binding sites.**, Nucleic Acids Res. 2021 February. https:// | ||
+ | |||
+ | ## 2020 | ||
+ | Marttinen M, Ferreira CB, Paldanius KMA, Takalo M, Natunen T, Mäkinen P, Leppänen L, Leinonen V, Tanigaki K, Kang G, Hiroi N, Soininen H, Rilla K, Haapasalo A, Hiltunen M., **Presynaptic Vesicle Protein SEPTIN5 Regulates the Degradation of APP C-Terminal Fragments and the Levels of Aβ.** | ||
+ | Cells. 2020 November. https:// | ||
+ | |||
+ | Natunen T, Martiskainen H, Marttinen M, Gabbouj S, Koivisto H, Kemppainen S, Kaipainen S, Takalo M, Svobodová H, Leppänen L, Kemiläinen B, Ryhänen S, Kuulasmaa T, Rahunen E, Juutinen S, Mäkinen P, Miettinen P, Rauramaa T, Pihlajamäki J, Haapasalo A, Leinonen V, Tanila H, Hiltunen M., **Diabetic phenotype in mouse and humans reduces the number of microglia around β-amyloid plaques.** | ||
+ | Mol Neurodegener. 2020 November. https:// | ||
+ | |||
+ | Takalo M, Wittrahm R, Wefers B, Parhizkar S, Jokivarsi K, Kuulasmaa T, Mäkinen P, Martiskainen H, Wurst W, Xiang X, Marttinen M, Poutiainen P, Haapasalo A, Hiltunen M, Haass C., **The Alzheimer' | ||
+ | Mol Neurodegener. 2020 September. https:// | ||
+ | |||
+ | Raittio E., Huumonen S., Suominen A.L., **Is the technical quality of root fillings associated with socioeconomic status? A cross‐sectional study among Finnish adults**, August 2020, European Journal Of Oral Sciences 128(5), https:// | ||
+ | |||
+ | Raittio E., Helakorpi S.,Suominen A.L., **Twenty‐five‐year follow‐up of educational differences in toothache prevalence**, | ||
+ | |||
+ | Prakash M., Abdelaziz M., Zhang L., Strange B.A., Tohka J. **Quantitative Longitudinal Predictions of Alzheimer' | ||
+ | |||
+ | Valverde J.M., Shatillo A., De Feo R., Gröhn O., Sierra A., Tohka J. (2020) RatLesNetv2: | ||
+ | |||
+ | Valverde J.M., Shatillo A., De Feo R., Gröhn O., Sierra A., Tohka J. (2019) **Automatic Rodent Brain MRI Lesion Segmentation with Fully Convolutional Networks.** In: Suk HI., Liu M., Yan P., Lian C. (eds) Machine Learning in Medical Imaging. MLMI 2019. Lecture Notes in Computer Science, vol 11861. Springer, Cham. https:// | ||
+ | |||
+ | Mehtonen J., Teppo S., Lahnalampi M., Kokko A., Kaukonen R., Oksa L., Bouvy-Liivrand M., Malyukova A., Mäkinen A., Laukkanen S., Mäkinen P., Rounioja S., Ruusuvuori P., Sangfelt O., Lund R., Lönnberg T, Lohi O. & Heinäniemi M. **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 Med 12, 99 (2020). https:// | ||
+ | |||
+ | Takalo, M., Wittrahm, R., Wefers, B., Parhizkar, S., Jokivarsi, K., Kuulasmaa, T., Mäkinen, P., Martiskainen, | ||
+ | |||
+ | Pulkkinen, H.H., Kiema, M., Lappalainen, | ||
+ | |||
+ | Dufva O, Pölönen P, Brück O, et al. **Immunogenomic Landscape of Hematological Malignancies** [published online ahead of print, 2020 Jul 9]. Cancer Cell. 2020; | ||
+ | |||
+ | | ||
+ | |||
+ | Klåvus, A.; Kokla, M.; Noerman, S.; Koistinen, V.M.; Tuomainen, M.; Zarei, I.; Meuronen, T.; Häkkinen, M.R.; Rummukainen, | ||
+ | |||
+ | ## 2019 | ||
+ | |||
+ | Das Gupta, S., Lipponen, A., Paldanius, K.M.A. et al. **Dynamics of clusterin protein expression in the brain and plasma following experimental traumatic brain injury.** Sci Rep 9, 20208 (2019), https:// | ||
+ | |||
+ | Ngo Trong T, Mehtonen J, González G, Kramer R, Hautamäki V, Heinäniemi M. **Semisupervised Generative Autoencoder for Single-Cell Data.**, //J Comput Biol.// 2019 Dec, https:// | ||
+ | |||
+ | Paananen, J; Fortino, V. **An omics perspective on drug target discovery platforms.**, | ||
+ | |||
+ | Nikkilä A, Arvela H, Mehtonen J, Raitanen J, Heinäniemi M, Lohi O, Auvinen A. **Predicting residential radon concentrations in Finland: Model development, | ||
+ | |||
+ | Sallinen H, Janhonen S, Pölönen P, Niskanen H, Liu OH, Kivelä A, Hartikainen JM, Anttila M, Heinäniemi M, Ylä-Herttuala S, Kaikkonen MU. **Comparative transcriptome analysis of matched primary and distant metastatic ovarian carcinoma.**, | ||
+ | |||
+ | Lipponen A, Natunen T, Hujo M, Ciszek R, Hämäläinen E, Tohka J, Hiltunen M, Paananen J, Poulsen D, Kansanen E, Ndode-Ekane XE, Levonen AL, Pitkänen A. **In Vitro and In Vivo Pipeline for Validation of Disease-Modifying Effects of Systems Biology-Derived Network Treatments for Traumatic Brain Injury—Lessons Learned**, //Int. J. Mol. Sci.// 2019 Oct, https:// | ||
+ | |||
+ | Pölönen P, Jawahar Deen A, Leinonen HM, Jyrkkänen HK, Kuosmanen S, Mononen M, Jain A, Tuomainen T, Pasonen-Seppänen S, Hartikainen JM, Mannermaa A, Nykter M, Tavi P, Johansen T, Heinäniemi M, Levonen AL. **Nrf2 and SQSTM1/p62 jointly contribute to mesenchymal transition and invasion in glioblastoma.**, | ||
+ | |||
+ | Benhammou JN, Ko A, Alvarez M, Kaikkonen MU, Rankin C, Garske KM, Padua D, Bhagat Y, Kaminska D, Kärjä V, Pihlajamäki J, Pisegna JR, Pajukanta P. **Novel Lipid Long Intervening Noncoding RNA, Oligodendrocyte Maturation-Associated Long Intergenic Noncoding RNA, Regulates the Liver Steatosis Gene Stearoyl-Coenzyme A Desaturase As an Enhancer RNA.**, //Hepatol Commun.// 2019 Aug, https:// | ||
+ | |||
+ | Kuusanmäki H, Leppä AM, Pölönen P, Kontro M, Dufva O, Deb D, Yadav B, Brück O, Kumar A, Everaus H, Gjertsen BT, Heinäniemi M, Porkka K, Mustjoki S, Heckman CA. **Phenotype-based drug screening reveals association between venetoclax response and differentiation stage in acute myeloid leukemia.**, | ||
+ | |||
+ | Failli M, Paananen J, Fortino V. **Prioritizing target-disease associations with novel safety and efficacy scoring methods**, //Sci Rep// 2019 Jul, https:// | ||
+ | |||
+ | Pölönen P, Mehtonen J, Lin J, Liuksiala T, Häyrynen S, Teppo S, Mäkinen A, Kumar A, Malani D, Pohjolainen V, Porkka K, Heckman CA, May P, Hautamäki V, Granberg K, Lohi O, Nykter M, Heinäniemi M. **Hemap: An interactive online resource for characterizing molecular phenotypes across hematologic malignancies**, | ||
+ | |||
+ | Mehtonen J, Pölönen P, Häyrynen S, Lin J, Liuksiala T, Granberg K, Lohi O, Hautamäki V, Nykter M, Heinäniemi M. **Data-driven characterization of molecular phenotypes across heterogenous sample collections**, | ||
+ | |||
+ | Marttinen M, Paananen J, Neme A, Mitra V, Takalo M, Natunen T, Paldanius KMA, Mäkinen P, Bremang M, Kurki MI, Rauramaa T, Leinonen V, Soininen H, Haapasalo A, Pike I, Hiltunen M **A multiomic approach to characterize the temporal sequence in Alzheimer' | ||
+ | |||
+ | Jauhiainen S, Laakkonen JP, Ketola K, Toivanen PI, Nieminen T, Ninchoji T, Levonen AL, Kaikkonen MU, Ylä-Herttuala S. **Axon Guidance-Related Factor FLRT3 Regulates VEGF-Signaling and Endothelial Cell Function.**, | ||
+ | |||
+ | Viiri LE, Rantapero T, Kiamehr M, Alexanova A, Oittinen M, Viiri K, Niskanen H, Nykter M, Kaikkonen MU, Aalto-Setälä K. **Extensive reprogramming of the nascent transcriptome during iPSC to hepatocyte differentiation.**, | ||
+ | |||
+ | Karttunen, J.; Heiskanen, M.; Lipponen, A.; Poulsen, D.; Pitkänen, A. **Extracellular Vesicles as Diagnostics and Therapeutics for Structural Epilepsies**, | ||
+ | |||
+ | Gurzeler E, Aavik E, Laine A, Valkama T, Niskanen H, Huusko J, Kaikkonen MU, Ylä-Herttuala S. **Therapeutic effects of rosuvastatin in hypercholesterolemic prediabetic mice in the absence of low density lipoprotein receptor.**, | ||
+ | |||
+ | Timonen O, Särkkä M, Fülöp T, Mattsson A, Kekäläinen J, Paananen J. **Varanto: variant enrichment analysis and annotation**, | ||
+ | |||
+ | |||
+ | ## 2018 | ||
Chen X, Ayala I, Shannon C, Fourcaudot M, Acharya NK, Jenkinson CP, | Chen X, Ayala I, Shannon C, Fourcaudot M, Acharya NK, Jenkinson CP, | ||
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Lewis, JD, Evans, AC, Tohka J. **T1 white/gray contrast as a predictor of chronological age, and an index of cognitive performance** // | Lewis, JD, Evans, AC, Tohka J. **T1 white/gray contrast as a predictor of chronological age, and an index of cognitive performance** // | ||
- | |||
- | Marttinen M, Paananen J, Neme A, Mitra V, Takalo M, Natunen T, | ||
- | Paldanius KMA, Mäkinen P, Bremang M, Kurki MI, Rauramaa T, Leinonen V, | ||
- | Soininen H, Haapasalo A, Pike I, Hiltunen M **A multiomic approach to characterize the temporal sequence in Alzheimer' | ||
Martiskainen H, Takalo M, Solomon A, Stančáková A, Marttinen M, | Martiskainen H, Takalo M, Solomon A, Stančáková A, Marttinen M, | ||
Line 52: | Line 181: | ||
Lakkisto P, Laivuori H. **Fetal Microsatellite in the Heme Oxygenase 1 Promoter Is Associated With Severe and Early-Onset Preeclampsia** , // | Lakkisto P, Laivuori H. **Fetal Microsatellite in the Heme Oxygenase 1 Promoter Is Associated With Severe and Early-Onset Preeclampsia** , // | ||
- | ### 2017 or earlier | + | ## 2017 or earlier |
Paananen, J. **Bioinformatics in the Identification of Novel Targets and Pathways in Neurodegenerative Diseases**, Curr Genet Med Rep (2017) 5:15–21, https:// | Paananen, J. **Bioinformatics in the Identification of Novel Targets and Pathways in Neurodegenerative Diseases**, Curr Genet Med Rep (2017) 5:15–21, https:// |