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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.
 +
 +## 2024
 +Sallamaari Siponen, Balamuralikrishna Jayaprakash, Anna-Maria Hokajärvi, Vicente Gomez-Alvarez, Jenni Inkinen, Ivan Ryzhikov, Pia Räsänen, Jenni Ikonen, Anna Pursiainen, Ari Kauppinen, Mikko Kolehmainen, Jussi Paananen, Eila Torvinen, Ilkka T. Miettinen, Tarja Pitkänen, **Composition of active bacterial communities and presence of opportunistic pathogens in disinfected and non-disinfected drinking water distribution systems in Finland**,
 +Water Research, Volume 248, 2024, 120858, ISSN 0043-1354, https://doi.org/10.1016/j.watres.2023.120858.
 +
 +## 2023
 +
 +Juho Mononen, Mari Taipale, Marjo Malinen, Bharadwaja Velidendla, Einari Niskanen, Anna-Liisa Levonen, Anna-Kaisa Ruotsalainen, Sami Heikkinen, **Genetic variation is a key determinant of chromatin accessibility and drives differences in the regulatory landscape of C57BL/6J and 129S1/SvImJ mice**, Nucleic Acids Research, 2023;, gkad1225, https://doi.org/10.1093/nar/gkad1225
 +
 +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://doi.org/10.1093/nar/gkad1126
 +
 +Csader, S.; Ismaiah, M.J.; Kuningas, T.; Heinäniemi, M.; Suhonen, J.; Männistö, V.; Pentikäinen, H.; Savonen, K.; Tauriainen, M.-M.; Galano, J.-M.; et al. **Twelve Weeks of High-Intensity Interval Training Alters Adipose Tissue Gene Expression but Not Oxylipin Levels in People with Non-Alcoholic Fatty Liver Disease**. Int. J. Mol. Sci. 2023, 24, 8509. https://doi.org/10.3390/ijms24108509
 +
 +Lipponen, A.; Kajevu, N.; Natunen, T.; Ciszek, R.; Puhakka, N.; Hiltunen, M.; Pitkänen, A. **Gene Expression Profile as a Predictor of Seizure Liability**. Int. J. Mol. Sci. 2023, 24, 4116. https://doi.org/10.3390/ijms24044116 
 +
 +## 2022
 +
 +Samms RJ, Cheng CC, Fourcaudot M, Heikkinen S, Khattab A, Adams J, Cersosimo E, Triplitt C, Puckett C, Tsintzas K, Adams AC, Abdul-Ghani MA, DeFronzo RA, Norton L. **FGF21 contributes to metabolic improvements elicited by combination therapy with exenatide and pioglitazone in patients with type 2 diabetes** Am J Physiol Endocrinol Metab. 2022 Aug 1;323(2):E123-E132. doi: 10.1152/ajpendo.00050.2022. Epub 2022 Jun 20. PMID: 35723225; PMCID: PMC9291413.
 +
 +Kainulainen K, Takabe P, Heikkinen S, Aaltonen N, de la Motte C, Rauhala L, Durst FC, Oikari S, Hukkanen T, Rahunen E, Ikonen E, Hartikainen JM, Ketola K, Pasonen-Seppänen S. **M1 Macrophages Induce Protumor Inflammation in Melanoma Cells through TNFR-NF-κB Signaling** J Invest Dermatol. 2022 Nov;142(11):3041-3051.e10. doi: 10.1016/j.jid.2022.04.024. Epub 2022 May 14. PMID: 35580697.
 +
 +Kärkkäinen E, Heikkinen S, Tengström M, Kosma VM, Mannermaa A, Hartikainen JM. **Expression profiles of small non-coding RNAs in breast cancer tumors characterize clinicopathological features and show prognostic and predictive potential** Sci Rep. 2022 Dec 30;12(1):22614. doi: 10.1038/s41598-022-26954-w. PMID: 36585466; PMCID: PMC9803687.
 +
 +Raittio, E, Sofi-Mahmudi, A, Uribe, SE. **Research transparency in dental research: A programmatic analysis**. Eur J Oral Sci. 2023; 131:e12908. https://doi.org/10.1111/eos.12908 
 +
 +Ghahremani, Morteza and Khateri, Mohammad and Sierra, Alejandra and Tohka, Jussi, **Adversarial Distortion Learning for Medical Image Denoising**, https://doi.org/10.48550/arxiv.2204.14100
 +
 +Hanel, A.; Carlberg, C. **Time-Resolved Gene Expression Analysis Monitors the Regulation of Inflammatory Mediators and Attenuation of Adaptive Immune Response by Vitamin D**. Int. J. Mol. Sci. 2022, 23, 911. https://doi.org/10.3390/ijms23020911 
 +
 +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://doi.org/10.1093/bioinformatics/btac463
 +
 +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, Volume 158, 2022, 106997, ISSN 0160-4120, https://doi.org/10.1016/j.envint.2021.106997
 +
 +Jäntti, H., Sitnikova, V., Ishchenko, Y. et al. **Microglial amyloid beta clearance is driven by PIEZO1 channels**. J Neuroinflammation 19, 147 (2022). https://doi.org/10.1186/s12974-022-02486-y
 +
 +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://doi.org/10.1007/s12021-022-09607-1
 +
 +
 +Oksa, L.; Mäkinen, A.; Nikkilä, A.; Hyvärinen, N.; Laukkanen, S.; Rokka, A.; Haapaniemi, P.; Seki, M.; Takita, J.; Kauko, O.; Heinäniemi, M.; Lohi, O. **Arginine Methyltransferase PRMT7 Deregulates Expression of RUNX1 Target Genes in T-Cell Acute Lymphoblastic Leukemi**a. Cancers 2022, 14, 2169. https://doi.org/10.3390/cancers14092169 
 +
 +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, Michelle A Kelliher, Caroline A. Heckman, Olli Lohi, David M Langenau; **Combination therapies to inhibit LCK tyrosine kinase and mTOR signaling in T-cell Acute Lymphoblastic Leukemia**. Blood 2022; blood.2021015106. doi: https://doi.org/10.1182/blood.2021015106
 +
 +Céline Vandamme, Marja Rytkönen-Nissinen, Tapio Lönnberg, Jukka Randell, Rauno J. Harvima, Tuure Kinnunen, Tuomas Virtanen,
 +**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://doi.org/10.1016/j.jaci.2021.11.018.
 +
 +Timo A. Lakka, Kirsikka Aittola, Elina Järvelä-Reijonen, Tanja Tilles-Tirkkonen, Reija Männikkö, Niina Lintu, Leila Karhunen, Marjukka Kolehmainen, Marja Harjumaa, Elina Mattila, Riia Järvenpää, Miikka Ermes, Santtu Mikkonen, Janne Martikainen, Kaisa Poutanen, Ursula Schwab, Pilvikki Absetz, Jaana Lindström, Jussi Pihlajamäki,
 +**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://doi.org/10.1016/j.lanepe.2022.100527.
  
 ## 2021 ## 2021
 +
 +A. Abdollahzadeh, A. Sierra and J. Tohka, **Cylindrical Shape Decomposition for 3D Segmentation of Tubular Objects**, in IEEE Access, vol. 9, pp. 23979-23995, 2021, http://dx.doi.org/10.1109/ACCESS.2021.3056958
 +
 +Prakash, Mithilesh et al. **Quantitative Longitudinal Predictions of Alzheimer’s Disease by Multi-Modal Predictive Learning**. 1 Jan. 2021 : 1533 – 1546. http://dx.doi.org/10.3233/JAD-200906
 +
 +Petteri Stenroos, Tiina Pirttimäki, Jaakko Paasonen, Ekaterina Paasonen, Raimo A Salo, Hennariikka Koivisto, Teemu Natunen, Petra Mäkinen, Teemu Kuulasmaa, Mikko Hiltunen, Heikki Tanila, Olli Gröhn, **Isoflurane affects brain functional connectivity in rats 1 month after exposure**, NeuroImage, Volume 234, 2021, 117987, ISSN 053-8119, https://doi.org/10.1016/j.neuroimage.2021.117987.
  
 Chen, J., Spracklen, C.N., Marenne, G. et al. **The trans-ancestral genomic architecture of glycemic traits.** Nat Genet 53, 840–860 (2021). https://doi.org/10.1038/s41588-021-00852-9 Chen, J., Spracklen, C.N., Marenne, G. et al. **The trans-ancestral genomic architecture of glycemic traits.** Nat Genet 53, 840–860 (2021). https://doi.org/10.1038/s41588-021-00852-9
home/publications.1646916393.txt.gz · Last modified: 10.03.2022 14:46 by Administrator

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