Please find below annual lists of the publications that took advantage of the services provided by Bioinformatics Center.

L. Cattelani, V. Fortino, Triple and quadruple optimization for feature selection in cancer biomarker discovery, Journal of Biomedical Informatics, Volume 159, 2024, 104736, ISSN 1532-0464, https://doi.org/10.1016/j.jbi.2024.104736.

Vandad Imani, Carlos Sevilla-Salcedo, Elaheh Moradi, Vittorio Fortino, Jussi Tohka, Multi-objective genetic algorithm for multi-view feature selection, Applied Soft Computing, 2024, 112332, ISSN 1568-4946, https://doi.org/10.1016/j.asoc.2024.112332.

Saarela A, Timonen O, Kirjavainen J, Liu Y, Silvennoinen K, Mervaala E, et al. Novel LAMC3 pathogenic variant enriched in Finnish population causes malformations of cortical development and severe epilepsy. Epileptic Disord. 2024; 26: 498–509. https://doi.org/10.1002/epd2.20244

Selvarajan, I., Kiema, M., Huang, R. T., Li, J., Zhu, J., Pölönen, P., Örd, T., Õunap, K., Godiwala, M., Golebiewski, A. K., Ravindran, A., Mäklin, K., Toropainen, A., Stolze, L. K., Arce, M., Magnusson, P. U., White, S., Romanoski, C. E., Heinäniemi, M., Laakkonen, J. P., … Kaikkonen, M. U. (2024). Coronary Artery Disease Risk Variant Dampens the Expression of CALCRL by Reducing HSF Binding to Shear Stress Responsive Enhancer in Endothelial Cells In Vitro. Arteriosclerosis, thrombosis, and vascular biology, 44(6), 1330–1345. https://doi.org/10.1161/ATVBAHA.123.318964

Teemu J Rintala, Francesco Napolitano, Vittorio Fortino, Multi-task deep latent spaces for cancer survival and drug sensitivity prediction, Bioinformatics, Volume 40, Issue Supplement_2, September 2024, Pages ii182–ii189, https://doi.org/10.1093/bioinformatics/btae388

Rintala TJ, Fortino V (2024) COPS: A novel platform for multi-omic disease subtype discovery via robust multi-objective evaluation of clustering algorithms. PLOS Computational Biology 20(8): e1012275. https://doi.org/10.1371/journal.pcbi.1012275

Aarthi Ravindran, Lari Holappa, Henri Niskanen, Ilya Skovorodkin, Susanna Kaisto, Mustafa Beter, Miika Kiema, Ilakya Selvarajan, Valtteri Nurminen, Einari Aavik, Rédouane Aherrahrou, Sanna Pasonen-Seppänen, Vittorio Fortino, Johanna P Laakkonen, Seppo Ylä-Herttuala, Seppo Vainio, Tiit Örd, Minna U Kaikkonen, Translatome profiling reveals Itih4 as a novel smooth muscle cell–specific gene in atherosclerosis, Cardiovascular Research, 2024;, cvae028, https://doi.org/10.1093/cvr/cvae028

Lewis, J.D., Imani, V. & Tohka, J. Intelligence and cortical morphometry: caveats in brain-behavior associations. Brain Struct Funct (2024). https://doi.org/10.1007/s00429-024-02792-6

Juan Miguel Valverde, Artem Shatillo, Jussi Tohka, Sauron U-Net: Simple automated redundancy elimination in medical image segmentation via filter pruning, Neurocomputing, Volume 594, 2024, 127817, ISSN 0925-2312, https://doi.org/10.1016/j.neucom.2024.127817.

Jokelainen, O., Rintala, T.J., Fortino, V. et al. Differential expression analysis identifies a prognostically significant extracellular matrix–enriched gene signature in hyaluronan-positive clear cell renal cell carcinoma. Sci Rep 14, 10626 (2024). https://doi.org/10.1038/s41598-024-61426-3

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.

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

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 Leukemia. 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.

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

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

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

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