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home:publications [19.11.2019 10:46]
Juha Kekäläinen 		home:publications [15.01.2024 13:53] (current)
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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.
  
-### 2019+## 2023
  
-Karttunen, J.; Heiskanen, M.; Lipponen, A.; Poulsen, D.; Pitkänen, A. **Extracellular Vesicles as Diagnostics and Therapeutics for Structural Epilepsies**, Int. J. Mol. Sci. 2019, 20(6), 1259; https://doi.org/10.3390/ijms20061259+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
  
-Failli M, Paananen J, Fortino V. **Prioritizing target-disease associations with novel safety and efficacy scoring methods**, //Sci Rep// 2019, https://doi.org/10.1038/s41598-019-46293-7+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
  
-Timonen O, Särkkä M, Fülöp T, Mattsson A, Kekäläinen J, Paananen J, **Varanto: variant enrichment analysis and annotation**, Bioinformatics 2019, https://doi.org/10.1093/bioinformatics/btz046+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, 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, https://doi.org/10.3390/ijms20215395+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 
  
-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**, //Cancer Research// 2019, https://doi.org/10.1158/0008-5472.CAN-18-2970+## 2022
  
-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**, +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.
-//Nucleic Acids Research// 2019, https://doi.org/10.1093/nar/gkz281+
  
 +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.
  
-### 2018+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 
 + 
 +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 
 + 
 +Ville Paakinaho, Joanna K Lempiäinen, Gianluca Sigismondo, Einari A Niskanen, Marjo Malinen, Tiina Jääskeläinen, Markku Varjosalo, Jeroen Krijgsveld, Jorma J Palvimo, **SUMOylation regulates the protein network and chromatin accessibility at glucocorticoid receptor-binding sites**, Nucleic Acids Research, Volume 49, Issue 4, 26 February 2021, Pages 1951–1971, https://doi.org/10.1093/nar/gkab032 
 + 
 +A.B.M. Kaiser Manjur, Joanna K. Lempiäinen, Marjo Malinen, Markku Varjosalo, Jorma J. Palvimo, Einari A. Niskanen, **BCOR modulates transcriptional activity of a subset of glucocorticoid receptor target genes involved in cell growth and mobility**, The Journal of Steroid Biochemistry and Molecular Biology, Volume 210, 2021, 105873, ISSN 0960-0760, https://doi.org/10.1016/j.jsbmb.2021.105873. 
 + 
 +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://doi.org/10.1038/s41388-021-01887-2 
 + 
 +Teemu J Rintala, Antonio Federico, Leena Latonen, Dario Greco, Vittorio Fortino, **A systematic comparison of data- and knowledge-driven approaches to disease subtype discovery**, Briefings in Bioinformatics, Volume 22, Issue 6, November 2021, bbab314, https://doi.org/10.1093/bib/bbab314 
 + 
 +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. 
 + 
 +Kärkkäinen, E., Heikkinen, S., Tengström, M., Kosma, V.-M., Mannermaa, A. and Hartikainen, J.M. (2021), **The debatable presence of PIWI-interacting RNAs in invasive breast cancer.**, Cancer Med, 10: 3593-3603. https://doi.org/10.1002/cam4.3915 
 + 
 +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, Päivi Pajukanta, Minna U. Kaikkonen, **Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease**, The American Journal of Human Genetics, Volume 108, Issue 3, 2021, Pages 411-430, ISSN 0002-9297, https://doi.org/10.1016/j.ajhg.2021.02.006 
 + 
 +Pierre R. Moreau, Vanesa Tomas Bosch, Maria Bouvy-Liivrand, Kadri Õunap, Tiit Örd, Heidi H. Pulkkinen, Petri Pölönen, Merja Heinäniemi, Seppo Ylä-Herttuala, Johanna P. Laakkonen, Suvi Linna-Kuosmanen, Minna U. Kaikkonen, **Profiling of Primary and Mature miRNA Expression in Atherosclerosis-Associated Cell Types**, Arteriosclerosis, Thrombosis, and Vascular Biology. 2021;41:2149–2167, https://doi.org/10.1161/ATVBAHA.121.315579 
 + 
 +Isidore Mushimiyimana, Vanesa Tomas Bosch, Henri Niskanen, Nicholas L. Downes, Pierre R. Moreau, Kiley Hartigan, Seppo Ylä-Herttuala, Nihay Laham-Karam, Minna U. Kaikkonen, **Genomic Landscapes of Noncoding RNAs Regulating VEGFA and VEGFC Expression in Endothelial Cells**, 2021, Molecular and Cellular Biology, e00594-20, 41, 7, https://doi.org/10.1128/MCB.00594-20 
 + 
 +Suvi Linna-Kuosmanen, Vanesa Tomas Bosch, Pierre R Moreau, Maria Bouvy-Liivrand, Henri Niskanen, Emilia Kansanen, Annukka Kivelä, Juha Hartikainen, Mikko Hippeläinen, Hannu Kokki, Pasi Tavi, Anna-Liisa Levonen, Minna U Kaikkonen, **NRF2 is a key regulator of endothelial microRNA expression under proatherogenic stimuli**, Cardiovascular Research, Volume 117, Issue 5, 1 May 2021, Pages 1339–1357, https://doi.org/10.1093/cvr/cvaa219 
 + 
 +Tanja Turunen, Ana Hernández de Sande, Petri Pölönen, Merja Heinäniemi, **Genome-wide analysis of primary microRNA expression using H3K36me3 ChIP-seq data**, Computational and Structural Biotechnology Journal, Volume 9, 2021, Pages 1944-1955, ISSN 2001-0370, https://doi.org/10.1016/j.csbj.2021.03.035 
 + 
 +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, 2021, https://doi.org/10.1016/j.jaci.2021.11.018. 
 + 
 +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://doi.org/10.1016/j.neuroimage.2021.117987 
 +  
 +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://doi.org/10.1093/nar/gkab032 
 + 
 +## 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://doi.org/10.3390/cells9112482. 
 +  
 +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://doi.org/10.1186/s13024-020-00415-2 
 + 
 +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's disease-associated protective Plcγ2-P522R variant promotes immune functions.** 
 +Mol Neurodegener. 2020 September. https://doi.org/10.1186/s13024-020-00402-7 
 + 
 +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://doi.org/10.1111/eos.12730 
 + 
 +Raittio E., Helakorpi S.,Suominen A.L., **Twenty‐five‐year follow‐up of educational differences in toothache prevalence**, January 2020, Community Dentistry And Oral Epidemiology 48(2), https://doi.org/10.1111/cdoe.12516 
 + 
 +Prakash M., Abdelaziz M., Zhang L., Strange B.A., Tohka J. **Quantitative Longitudinal Predictions of Alzheimer's Disease by Multi-Modal Predictive Learning** In: Alzheimer’s Disease Neuroimaging Initiative,  https://doi.org/10.3233/JAD-200906 
 + 
 +Valverde J.M., Shatillo A., De Feo R., Gröhn O., Sierra A., Tohka J. (2020) RatLesNetv2: **A Fully Convolutional Network for Rodent Brain Lesion Segmentation.** In: Frontiers in Neuroscience, vol 14, 1333. https://doi.org/10.3389/fnins.2020.610239 
 + 
 +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://doi.org/10.1007/978-3-030-32692-0_23 
 + 
 +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://doi.org/10.1186/s13073-020-00799-2 
 + 
 +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’s disease-associated protective Plcγ2-P522R variant promotes immune functions.**, Mol Neurodegeneration (2020). https://doi.org/10.1186/s13024-020-00402-7 
 + 
 +Pulkkinen, H.H., Kiema, M., Lappalainen, J.P. et al. **BMP6/TAZ-Hippo signaling modulates angiogenesis and endothelial cell response to VEGF.**, Angiogenesis (2020). https://doi.org/10.1007/s10456-020-09748-4 
 + 
 +Dufva O, Pölönen P, Brück O, et al. **Immunogenomic Landscape of Hematological Malignancies** [published online ahead of print, 2020 Jul 9]. Cancer Cell. 2020;S1535-6108(20)30275-0. https://doi.org/10.1016/j.ccell.2020.06.002 
 + 
 + Hanel, A; Carlberg, C.,**Skin Color and Vitamin D: An Update.**, Experimental dermatology. 2020, https://doi.org/10.1111/exd.14142 
 + 
 +Klåvus, A.; Kokla, M.; Noerman, S.; Koistinen, V.M.; Tuomainen, M.; Zarei, I.; Meuronen, T.; Häkkinen, M.R.; Rummukainen, S.; Farizah Babu, A.; Sallinen, T.; Kärkkäinen, O.; Paananen, J.; Broadhurst, D.; Brunius, C.; Hanhineva, K. **“notame”: Workflow for Non-Targeted LC–MS Metabolic Profiling.** Metabolites 2020, 10, 135, https://doi.org/10.3390/metabo10040135 
 + 
 +## 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://doi.org/10.1038/s41598-019-56683-6 
 + 
 +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://doi.org/10.1089/cmb.2019.0337 
 + 
 +Paananen, J; Fortino, V. **An omics perspective on drug target discovery platforms.**, //Brief Bioinform.// 2019 Nov, https://doi.org/10.1093/bib/bbz122 
 + 
 +Nikkilä A, Arvela H, Mehtonen J, Raitanen J, Heinäniemi M, Lohi O, Auvinen A. **Predicting residential radon concentrations in Finland: Model development, validation, and application to childhood leukemia.**, //Scand J Work Environ Health.// 2019 Nov, https://doi.org/10.5271/sjweh.3867 
 + 
 +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.**,  //BMC Cancer.// 2019 Nov 19, https://doi.org/10.1186/s12885-019-6339-0 
 + 
 +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://doi.org/10.3390/ijms20215395 
 + 
 +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.**, //Oncogene.// 2019 Aug, https://doi.org/10.1038/s41388-019-0956-6 
 + 
 +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://doi.org/10.1002/hep4.1413 
 + 
 +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.**, //Haematologica.// 2019 Jul, https://doi.org/10.3324/haematol.2018.214882 
 + 
 +Failli M, Paananen J, Fortino V. **Prioritizing target-disease associations with novel safety and efficacy scoring methods**, //Sci Rep// 2019 Jul, https://doi.org/10.1038/s41598-019-46293-7 
 + 
 +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**, //Cancer Research// 2019 May, https://doi.org/10.1158/0008-5472.CAN-18-2970 
 + 
 +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**, //Nucleic Acids Research// 2019 Apr, https://doi.org/10.1093/nar/gkz281 
 + 
 +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's disease-related pathology**, //Neurobiol Dis.// 2019 Apr, https://doi.org/10.1016/j.nbd.2018.12.009 
 + 
 +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.**, //Front Physiol.// 2019 Mar, https://doi.org/10.3389/fphys.2019.00224 
 + 
 +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.**, //Sci Rep.//, 2019 Mar, https://doi.org/10.1038/s41598-019-39215-0 
 + 
 +Karttunen, J.; Heiskanen, M.; Lipponen, A.; Poulsen, D.; Pitkänen, A. **Extracellular Vesicles as Diagnostics and Therapeutics for Structural Epilepsies**, //Int. J. Mol. Sci.// 2019 Mar; https://doi.org/10.3390/ijms20061259 
 + 
 +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.**, //Biochim Biophys Acta Gen Subj.//, 2019 Feb, https://doi.org/10.1016/j.bbagen.2018.11.012 
 + 
 +Timonen O, Särkkä M, Fülöp T, Mattsson A, Kekäläinen J, Paananen J. **Varanto: variant enrichment analysis and annotation**, Bioinformatics 2019 Jan, https://doi.org/10.1093/bioinformatics/btz046 
 + 
 + 
 +## 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,
Line 28: Line 179:
  
 Lewis, JD, Evans, AC, Tohka J. **T1 white/gray contrast as a predictor of chronological age, and an index of cognitive performance** //NeuroImage// 2018, https://doi.org/10.1016/j.neuroimage.2018.02.050 Lewis, JD, Evans, AC, Tohka J. **T1 white/gray contrast as a predictor of chronological age, and an index of cognitive performance** //NeuroImage// 2018, https://doi.org/10.1016/j.neuroimage.2018.02.050
- 
-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's disease-related pathology**, //Neurobiol Dis.// 2019, https://doi.org/10.1016/j.nbd.2018.12.009 
  
 Martiskainen H, Takalo M, Solomon A, Stančáková A, Marttinen M, Martiskainen H, Takalo M, Solomon A, Stančáková A, Marttinen M,
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 Lakkisto P, Laivuori H. **Fetal Microsatellite in the Heme Oxygenase 1 Promoter Is Associated With Severe and Early-Onset Preeclampsia** , //Hypertension// 2018, https://doi.org/10.1161/HYPERTENSIONAHA.117.10425. Lakkisto P, Laivuori H. **Fetal Microsatellite in the Heme Oxygenase 1 Promoter Is Associated With Severe and Early-Onset Preeclampsia** , //Hypertension// 2018, https://doi.org/10.1161/HYPERTENSIONAHA.117.10425.
  
-### 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://doi.org/10.1007/s40142-017-0115-8 Paananen, J. **Bioinformatics in the Identification of Novel Targets and Pathways in Neurodegenerative Diseases**, Curr Genet Med Rep (2017) 5:15–21, https://doi.org/10.1007/s40142-017-0115-8
home/publications.1574153171.txt.gz · Last modified: 19.11.2019 10:46 by Juha Kekäläinen

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