Genomics and Mechanisms in Translational Medicine Doctoral Programme

FTLD Patient–Derived Fibroblasts Show Defective Mitochondrial Function and Accumulation of p62

Autorzy: Stina Leskelä; Dorit Hoffmann; Hannah Rostalski; Nadine Huber; Rebekka Wittrahm; Päivi Hartikainen; Ville E. Korhonen; Ville Leinonen; Mikko Hiltunen; Eino Solje; Anne M. Remes; Anne M. Remes; Annakaisa Haapasalo
Opublikowane w: Molecular Neurobiology, Numer 58, 2021, Strona(/y) 5438-5458, ISSN 0893-7648
Wydawca: Humana Press, Inc.
DOI: 10.1007/s12035-021-02475-x

The Alzheimer’s disease-associated protective Plcγ2-P522R variant promotes immune functions

Autorzy: Mari Takalo, Rebekka Wittrahm, Benedikt Wefers, Samira Parhizkar, Kimmo Jokivarsi, Teemu Kuulasmaa, Petra Mäkinen, Henna Martiskainen, Wolfgang Wurst, Xianyuan Xiang, Mikael Marttinen, Pekka Poutiainen, Annakaisa Haapasalo, Mikko Hiltunen, and Christian Haass
Opublikowane w: Molecular Neurodegeneration, Numer 15, 2020, Strona(/y) 52, ISSN 1750-1326
Wydawca: BioMed Central
DOI: 10.1186/s13024-020-00402-7

GFAP as a biomarker in frontotemporal dementia and primary psychiatric disorders: diagnostic and prognostic performance

Autorzy: Katisko K, Cajanus A, Huber N, Jääskeläinen O, Kokkola T, Kärkkäinen V, Rostalski H, Hartikainen P, Koivisto AM, Hannonen S, Lehtola JM, Korhonen VE, Helisalmi S, Koivumaa-Honkanen H, Herukka SK, Remes AM, Solje E, Haapasalo A
Opublikowane w: Journal of Neurology, Neurosurgery and Psychiatry, Numer vol. 92, no. 12, 2021, Strona(/y) 1-8, ISSN 0022-3050
Wydawca: BMJ Publishing Group
DOI: 10.1136/jnnp-2021-326487

C9orf72 proteins regulate autophagy and undergo autophagosomal or proteasomal degradation in a cell type-dependent manner

Autorzy: Leskelä; Huber; Rostalski; Natunen; Remes; Takalo; Hiltunen; Haapasalo
Opublikowane w: Cells, Numer 84, 2019, Strona(/y) E1233, ISSN 2073-4409
Wydawca: MDPI
DOI: 10.3390/cells8101233

PI3Kβ inhibition enhances ALK-inhibitor sensitivity in ALK-rearranged lung cancer

Autorzy: Sarang S. Talwelkar, Mikko I. Mäyränpää, Julia Schüler, Nora Linnavirta, Annabrita Hemmes, Simone Adinolfi, Matti Kankainen, Wolfgang Sommergruber, Anna-Liisa Levonen, Jari Räsänen, Aija Knuuttila, Emmy W. Verschuren, Krister Wennerberg
Opublikowane w: Molecular Oncology, 2022, ISSN 1574-7891
Wydawca: Elsevier BV
DOI: 10.1002/1878-0261.13342

Indolepropionic Acid, a Gut Bacteria-Produced Tryptophan Metabolite and the Risk of Type 2 Diabetes and Non-Alcoholic Fatty Liver Disease

Autorzy: Sehgal, R., de Mello, V. D., Männistö, V., Lindström, J., Tuomilehto, J., Pihlajamäki, J., Uusitupa, M
Opublikowane w: Nutrients, Numer 14(21), 2022, Strona(/y) 1-18, ISSN 2072-6643
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu14214695

A consensus protocol for functional connectivity analysis in the rat brain

Autorzy: Joanes Grandjean, Gabriel Desrosiers-Gregoire, Cynthia Anckaerts, Diego Angeles-Valdez, Fadi Ayad, David A. Barrière, Ines Blockx, Aleksandra Bortel, Margaret Broadwater, Beatriz M. Cardoso, Marina Célestine, Jorge E. Chavez-Negrete, Sangcheon Choi, Emma Christiaen, Perrin Clavijo, Luis Colon-Perez, Samuel Cramer, Tolomeo Daniele, Elaine Dempsey, Yujian Diao, Arno Doelemeyer, David Dopfel, Lenka
Opublikowane w: Nature Neuroscience, 2023, ISSN 1097-6256
Wydawca: Nature Publishing Group
DOI: 10.1038/s41593-023-01286-8

Convolutional Neural Networks Enable Robust Automatic Segmentation of the Rat Hippocampus in MRI After Traumatic Brain Injury

Autorzy: "De Feo, Riccardo; Hä mä lä inen, Elina; Manninen, Eppu; Immonen, Riikka; Valverde, Juan Miguel; Ndode-Ekane, Xavier Ekolle; Grö hn, Olli; Pitkä nen, Asla; Tohka, Jussi"
Opublikowane w: Frontiers in Neurology, Numer 13, 2022, Strona(/y) 820267, ISSN 1664-2295
Wydawca: Frontiers Research Foundation
DOI: 10.3389/fneur.2022.820267

Region-wise loss for biomedical image segmentation

Autorzy: J.M. Valverde, J. Tohka
Opublikowane w: Pattern Recognition, Numer 136, 2023, Strona(/y) 109208, ISSN 0031-3203
Wydawca: Pergamon Press
DOI: 10.1016/j.patcog.2022.109208

Characterization of a functional endothelial super-enhancer that regulates ADAMTS18 and angiogenesis

Autorzy: Isidore Mushimiyimana, Henri Niskanen, Mustafa Beter, Johanna P Laakkonen, Minna U Kaikkonen, Seppo Ylä-Herttuala, Nihay Laham-Karam
Opublikowane w: Nucleic Acids Research, Numer vol. 49, no. 14, 2021, Strona(/y) 8078-8096, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkab633

Serum aromatic and branched-chain amino acids associated with NASH demonstrate divergent associations with serum lipids

Autorzy: de Mello VD, Sehgal R, Männistö V, Klåvus A, Nilsson E, Perfilyev A, Kaminska D, Miao Z, Pajukanta P, Ling C, Hanhineva K, Pihlajamäki J.
Opublikowane w: Liver International, Numer 41, 2021, Strona(/y) 754-763, ISSN 1478-3231
Wydawca: John Wiley & Sons Ltd
DOI: 10.1111/liv.14743

Deficient neurotransmitter systems and synaptic function in frontotemporal lobar degeneration—Insights into disease mechanisms and current therapeutic approaches

Autorzy: Nadine Huber, Sonja Korhonen, Dorit Hoffmann, Stina Leskelä, Hannah Rostalski, Anne M. Remes, Paavo Honkakoski, Eino Solje, Annakaisa Haapasalo
Opublikowane w: Molecular Psychiatry, Numer 27, 2022, Strona(/y) 1300-1309, ISSN 1359-4184
Wydawca: Nature Publishing Group
DOI: 10.1038/s41380-021-01384-8

Automated joint skull-stripping and segmentation with Multi-Task U-Net in large mouse brain MRI databases

Autorzy: Riccardo De Feo, Artem Shatillo, Alejandra Sierra, Juan Miguel Valverde, Olli Gröhn, Federico Giove, Jussi Tohka
Opublikowane w: NeuroImage, Numer 229, 2021, Strona(/y) 117734, ISSN 1053-8119
Wydawca: Academic Press
DOI: 10.1016/j.neuroimage.2021.117734

MECP2 Increases the Pro-Inflammatory Response of Microglial Cells and Phosphorylation at Serine 423 Regulates Neuronal Gene Expression upon Neuroinflammation.

Autorzy: Rebekka Wittrahm; Mari Takalo; Mikael Marttinen; Teemu Kuulasmaa; Petra Mäkinen; Susanna Kemppainen; Henna Martiskainen; Tuomas Rauramaa; Ian Pike; Ville Leinonen; Teemu Natunen; Annakaisa Haapasalo; Mikko Hiltunen
Opublikowane w: Cells, Numer 10, 2021, Strona(/y) 860, ISSN 2073-4409
Wydawca: MDPI
DOI: 10.3390/cells10040860

Hypoxia-Mediated Regulation of Histone Demethylases Affects Angiogenesis-Associated Functions in Endothelial Cells

Autorzy: Liu, O. H. F., Kiema, M., Beter, M., Ylä-Herttuala, S., Laakkonen, J. P., & Kaikkonen, M. U.
Opublikowane w: Arteriosclerosis, Thrombosis, and Vascular Biology, Numer 40, 2020, Strona(/y) 2665-2667, ISSN 1079-5642
Wydawca: Lippincott Williams & Wilkins Ltd.
DOI: 10.1161/atvbaha.120.315214

Transfer Learning in Magnetic Resonance Brain Imaging: A Systematic Review.

Autorzy: Juan Miguel Valverde; Vandad Imani; Ali Abdollahzadeh; Riccardo De Feo; Mithilesh Prakash; Robert Ciszek; Jussi Tohka
Opublikowane w: Journal of Imaging, Numer 7, 2021, Strona(/y) 66, ISSN 2313-433X
Wydawca: MDPI
DOI: 10.3390/jimaging7040066

Indole-3-Propionic Acid, a Gut-Derived Tryptophan Metabolite, Associates with Hepatic Fibrosis

Autorzy: Sehgal, Ratika, Mariana Ilha, Maija Vaittinen, Dorota Kaminska, Ville Männistö, Vesa Kärjä, Marjo Tuomainen, Kati Hanhineva, Stefano Romeo, Päivi Pajukanta, Jussi Pihlajamäki, and Vanessa D. de Mello
Opublikowane w: Nutrients, Numer 13, 2021, Strona(/y) 3509, ISSN 2072-6643
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu13103509

Light sedation with short habituation time for large-scale functional magnetic resonance imaging studies in rats

Autorzy: Lenka Dvořáková, Petteri Stenroos, Ekaterina Paasonen, Raimo A. Salo, Jaakko Paasonen, Olli Gröhn
Opublikowane w: NMR in Biomedicine, Numer vol. 35, no. 6, 2021, Strona(/y) 1-13, ISSN 0952-3480
Wydawca: John Wiley & Sons Inc.
DOI: 10.1002/nbm.4679

Astrocytes and Microglia as Potential Contributors to the Pathogenesis of C9orf72 Repeat Expansion-Associated FTLD and ALS

Autorzy: Hannah Rostalski, Stina Leskelä, Nadine Huber, Kasper Katisko, Antti Cajanus, Eino Solje, Mikael Marttinen, Teemu Natunen, Anne M. Remes, Mikko Hiltunen, Annakaisa Haapasalo
Opublikowane w: Frontiers in Neuroscience, Numer 13, 2019, ISSN 1662-453X
Wydawca: Frontiers Media SA
DOI: 10.3389/fnins.2019.00486

RatLesNetv2: A Fully Convolutional Network for Rodent Brain Lesion Segmentation

Autorzy: "Juan Miguel Valverde,; Artem, Shatillo; De Feo, Riccardo; Olli, Grö hn; Alejandra, Sierra; Jussi, Tohka"
Opublikowane w: Frontiers in Neuroscience, Numer 14, 2020, Strona(/y) 610239, ISSN 1662-453X
Wydawca: Frontiers Media S.A.
DOI: 10.3389/fnins.2020.610239

C9orf72 hexanucleotide repeat expansion leads to altered neuronal and dendritic spine morphology and synaptic dysfunction

Autorzy: Huber N, Hoffmann D, Giniatullina R, Rostalski H, Leskelä S, Takalo M, Natunen T, Solje E, Remes AM, Giniatullin R, Hiltunen M, Haapasalo A
Opublikowane w: Neurobiology of Disease, Numer 162, 2022, Strona(/y) 105584, ISSN 0969-9961
Wydawca: Academic Press
DOI: 10.1016/j.nbd.2021.105584

Liver saturated fat content associates with hepatic DNA methylation in obese individuals

Autorzy: Ratika Sehgal, Alexander Perfilyev, Ville Männistö, Jyrki Ågren, Emma Nilsson, Pirjo Käkelä, Charlotte Ling, Vanessa D. de Mello, Jussi Pihlajamäki
Opublikowane w: Clinical Epigenetics, Numer 15, 2023, Strona(/y) 21, ISSN 1868-7083
Wydawca: BioMed Central Ltd
DOI: 10.1186/s13148-023-01431-x

BV-2 Microglial Cells Overexpressing C9orf72 Hexanucleotide Repeat Expansion Produce DPR Proteins and Show Normal Functionality but No RNA Foci

Autorzy: Hannah Rostalski, Tomi Hietanen, Stina Leskelä, Andrea Behánová, Ali Abdollahzadeh, Rebekka Wittrahm, Petra Mäkinen, Nadine Huber, Dorit Hoffmann, Eino Solje, Anne M. Remes, Teemu Natunen, Mari Takalo, Jussi Tohka, Mikko Hiltunen and Annakaisa Haapasalo
Opublikowane w: Frontiers in Neurology, Numer 11, 2020, Strona(/y) 1-21, ISSN 1664-2295
Wydawca: Frontiers Research Foundation
DOI: 10.3389/fneur.2020.550140

BMP6/TAZ-Hippo signaling modulates angiogenesis and endothelialcell response to VEGF

Autorzy: Pulkkinen, H. H., Kiema, M., Lappalainen, J. P., Toropainen, A., Beter, M., Tirronen, A., ... & Laakkonen, J. P
Opublikowane w: Angiogenesis, Numer 24, 2021, Strona(/y) 139-144, ISSN 0969-6970
Wydawca: Kluwer Academic Publishers
DOI: 10.1007/s10456-020-09748-4

A Novel Genetic Marker for the C9orf72 Repeat Expansion in the Finnish Population

Autorzy: Rostalski H, Korhonen V, Kuulasmaa T, Solje E, Krüger J, Gen F, Kaivola K, Eide PK, Lambert JC, Julkunen V, Tienari PJ, Remes AM, Leinonen V, Hiltunen M, Haapasalo A
Opublikowane w: Journal of Alzheimer's Disease, Numer vol. 83, no. 3, 2021, Strona(/y) 1325-1332, ISSN 1387-2877
Wydawca: IOS Press
DOI: 10.3233/jad-210599

Expression of C9orf72 hexanucleotide repeat expansion leads to formation of RNA foci and dipeptide repeat proteins but does not influence autophagy or proteasomal function in neuronal cells

Autorzy: Leskelä S, Huber N, Hoffmann D, Rostalski H, Remes AM, Takalo M, Hiltunen M, Haapasalo A
Opublikowane w: Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Numer vol. 1868, no. 7, 2021, Strona(/y) 119021, ISSN 0167-4889
Wydawca: Elsevier BV
DOI: 10.1016/j.bbamcr.2021.119021

Automatic Cerebral Hemisphere Segmentation in Rat MRI with Ischemic Lesions via Attention-based Convolutional Neural Networks

Autorzy: Juan Miguel Valverde, Artem Shatillo, Riccardo De Feo, and Jussi Tohka
Opublikowane w: Neuroinformatics, 2022, ISSN 1539-2791
Wydawca: Humana Press, Inc.
DOI: 10.1007/s12021-022-09607-1

Metabolite Signature in the Carriers of Pathogenic Genetic Variants for Cardiomyopathy: A Population-Based METSIM Study

Autorzy: Ravi R, Fernandes Silva L, Vangipurapu J, Maria M, Raivo J, Helisalmi S, Laakso M
Opublikowane w: Metabolites, Numer 12(5), 2022, Strona(/y) 437, ISSN 2218-1989
Wydawca: MDPI
DOI: 10.3390/metabo12050437

C9orf72 hexanucleotide repeat expansion in frontotemporal dementia special focus on genetics and microglia

Autorzy: Rostalski, Hannah
Opublikowane w: Dissertations in Health Sciences, Numer 688, 2022, ISBN 978-952-61-4570-9
Wydawca: PunaMusta Oy

Metabolomics and genomics approach in cardiovascular diseases

Autorzy: Rowmika Ravi
Opublikowane w: Dissertations in Health Sciences, Numer 742, 2023, ISBN 978-952-61-4821-2
Wydawca: PunaMusta Oy

MRI Segmentation With Deep Learning: Application in Rodent Brain Images with Lesions

Autorzy: Valverde, Juan Miguel
Opublikowane w: Dissertations in Health Sciences, Numer 700, 2022, ISBN 978-952-61-4623-2
Wydawca: PunaMusta Oy

Nutrient-related metabolites in non-alcoholic fatty liver disease: Association with molecular & clinical characteristics

Autorzy: Sehgal, Ratika
Opublikowane w: Dissertations in Health Sciences, Numer 703, 2022, ISBN 978-952-61-4639-3
Wydawca: PunaMusta Oy

Predicting intelligence based on cortical WM/GM contrast, cortical thickness and volumetry

Autorzy: Valverde, Juan Miguel; Imani, Vandad; Lewis, John D.; Tohka, Jussi
Opublikowane w: Lecture Notes in Computer Science, Numer 11791, 2019, Strona(/y) 57-65, ISBN 978-3-030-31901-4
Wydawca: Springer, Cham
DOI: 10.1007/978-3-030-31901-4_7

Automatic Rodent Brain MRI Lesion Segmentation with Fully Convolutional Networks

Autorzy: Valverde, Juan Miguel; Shatillo, Artem; de Feo, Riccardo; Gröhn, Olli; Sierra, Alejandra; Tohka, Jussi
Opublikowane w: Lecture Notes in Computer Science, Numer 11861, 2019, Strona(/y) 195-202, ISBN 978-3-030-32692-0
Wydawca: Springer, Cham
DOI: 10.48550/arxiv.1908.08746

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