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Publications

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

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, Heikkinen S, Norton L. The Diabetes Gene and Wnt Pathway Effector TCF7L2 Regulates Adipocyte Development and Function, Diabetes 2018, https://doi.org/10.2337/db17-0318.

Niskanen H, Tuszynska I, Zaborowski R, Heinäniemi M, Ylä-Herttuala S, Wilczynski B, Kaikkonen MU.Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regions Nucleic Acids Res. 2018, 10.1093/nar/gkx1214.

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

Martiskainen H, Takalo M, Solomon A, Stančáková A, Marttinen M, Natunen T, Haapasalo A, Herukka SK, Kuusisto J, Soininen H, Kivipelto M, Laakso M, Hiltunen M. Decreased plasma C-reactive protein levels in APOE ε4 allele carriers, Ann Clin Transl Neurol. 2018. https://doi.org/10.1002/acn3.639.

Kaartokallio T, Utge S, Klemetti MM, Paananen J, Pulkki K, Romppanen J, Tikkanen I, Heinonen S, Kajantie E, Kere J, Kivinen K, Pouta A, 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

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.txt · Last modified: 10.03.2022 15:35 by Administrator