Genomics and Mechanisms in Translational Medicine Doctoral Programme

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

Autori: 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
Pubblicato in: Molecular Neurobiology, Numero 58, 2021, Pagina/e 5438-5458, ISSN 0893-7648
Editore: Humana Press, Inc.
DOI: 10.1007/s12035-021-02475-x

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

Autori: 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
Pubblicato in: Molecular Neurodegeneration, Numero 15, 2020, Pagina/e 52, ISSN 1750-1326
Editore: BioMed Central
DOI: 10.1186/s13024-020-00402-7

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

Autori: 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
Pubblicato in: Journal of Neurology, Neurosurgery and Psychiatry, Numero vol. 92, no. 12, 2021, Pagina/e 1-8, ISSN 0022-3050
Editore: 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

Autori: Leskelä; Huber; Rostalski; Natunen; Remes; Takalo; Hiltunen; Haapasalo
Pubblicato in: Cells, Numero 84, 2019, Pagina/e E1233, ISSN 2073-4409
Editore: MDPI
DOI: 10.3390/cells8101233

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

Autori: 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
Pubblicato in: Molecular Oncology, 2022, ISSN 1574-7891
Editore: 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

Autori: Sehgal, R., de Mello, V. D., Männistö, V., Lindström, J., Tuomilehto, J., Pihlajamäki, J., Uusitupa, M
Pubblicato in: Nutrients, Numero 14(21), 2022, Pagina/e 1-18, ISSN 2072-6643
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu14214695

A consensus protocol for functional connectivity analysis in the rat brain

Autori: 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
Pubblicato in: Nature Neuroscience, 2023, ISSN 1097-6256
Editore: 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

Autori: "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"
Pubblicato in: Frontiers in Neurology, Numero 13, 2022, Pagina/e 820267, ISSN 1664-2295
Editore: Frontiers Research Foundation
DOI: 10.3389/fneur.2022.820267

Region-wise loss for biomedical image segmentation

Autori: J.M. Valverde, J. Tohka
Pubblicato in: Pattern Recognition, Numero 136, 2023, Pagina/e 109208, ISSN 0031-3203
Editore: Pergamon Press
DOI: 10.1016/j.patcog.2022.109208

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

Autori: Isidore Mushimiyimana, Henri Niskanen, Mustafa Beter, Johanna P Laakkonen, Minna U Kaikkonen, Seppo Ylä-Herttuala, Nihay Laham-Karam
Pubblicato in: Nucleic Acids Research, Numero vol. 49, no. 14, 2021, Pagina/e 8078-8096, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkab633

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

Autori: 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.
Pubblicato in: Liver International, Numero 41, 2021, Pagina/e 754-763, ISSN 1478-3231
Editore: 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

Autori: Nadine Huber, Sonja Korhonen, Dorit Hoffmann, Stina Leskelä, Hannah Rostalski, Anne M. Remes, Paavo Honkakoski, Eino Solje, Annakaisa Haapasalo
Pubblicato in: Molecular Psychiatry, Numero 27, 2022, Pagina/e 1300-1309, ISSN 1359-4184
Editore: 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

Autori: Riccardo De Feo, Artem Shatillo, Alejandra Sierra, Juan Miguel Valverde, Olli Gröhn, Federico Giove, Jussi Tohka
Pubblicato in: NeuroImage, Numero 229, 2021, Pagina/e 117734, ISSN 1053-8119
Editore: 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.

Autori: 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
Pubblicato in: Cells, Numero 10, 2021, Pagina/e 860, ISSN 2073-4409
Editore: MDPI
DOI: 10.3390/cells10040860

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

Autori: Liu, O. H. F., Kiema, M., Beter, M., Ylä-Herttuala, S., Laakkonen, J. P., & Kaikkonen, M. U.
Pubblicato in: Arteriosclerosis, Thrombosis, and Vascular Biology, Numero 40, 2020, Pagina/e 2665-2667, ISSN 1079-5642
Editore: Lippincott Williams & Wilkins Ltd.
DOI: 10.1161/atvbaha.120.315214

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

Autori: Juan Miguel Valverde; Vandad Imani; Ali Abdollahzadeh; Riccardo De Feo; Mithilesh Prakash; Robert Ciszek; Jussi Tohka
Pubblicato in: Journal of Imaging, Numero 7, 2021, Pagina/e 66, ISSN 2313-433X
Editore: MDPI
DOI: 10.3390/jimaging7040066

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

Autori: 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
Pubblicato in: Nutrients, Numero 13, 2021, Pagina/e 3509, ISSN 2072-6643
Editore: 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

Autori: Lenka Dvořáková, Petteri Stenroos, Ekaterina Paasonen, Raimo A. Salo, Jaakko Paasonen, Olli Gröhn
Pubblicato in: NMR in Biomedicine, Numero vol. 35, no. 6, 2021, Pagina/e 1-13, ISSN 0952-3480
Editore: 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

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

RatLesNetv2: A Fully Convolutional Network for Rodent Brain Lesion Segmentation

Autori: "Juan Miguel Valverde,; Artem, Shatillo; De Feo, Riccardo; Olli, Grö hn; Alejandra, Sierra; Jussi, Tohka"
Pubblicato in: Frontiers in Neuroscience, Numero 14, 2020, Pagina/e 610239, ISSN 1662-453X
Editore: 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

Autori: Huber N, Hoffmann D, Giniatullina R, Rostalski H, Leskelä S, Takalo M, Natunen T, Solje E, Remes AM, Giniatullin R, Hiltunen M, Haapasalo A
Pubblicato in: Neurobiology of Disease, Numero 162, 2022, Pagina/e 105584, ISSN 0969-9961
Editore: Academic Press
DOI: 10.1016/j.nbd.2021.105584

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

Autori: Ratika Sehgal, Alexander Perfilyev, Ville Männistö, Jyrki Ågren, Emma Nilsson, Pirjo Käkelä, Charlotte Ling, Vanessa D. de Mello, Jussi Pihlajamäki
Pubblicato in: Clinical Epigenetics, Numero 15, 2023, Pagina/e 21, ISSN 1868-7083
Editore: 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

Autori: 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
Pubblicato in: Frontiers in Neurology, Numero 11, 2020, Pagina/e 1-21, ISSN 1664-2295
Editore: Frontiers Research Foundation
DOI: 10.3389/fneur.2020.550140

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

Autori: Pulkkinen, H. H., Kiema, M., Lappalainen, J. P., Toropainen, A., Beter, M., Tirronen, A., ... & Laakkonen, J. P
Pubblicato in: Angiogenesis, Numero 24, 2021, Pagina/e 139-144, ISSN 0969-6970
Editore: Kluwer Academic Publishers
DOI: 10.1007/s10456-020-09748-4

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

Autori: 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
Pubblicato in: Journal of Alzheimer's Disease, Numero vol. 83, no. 3, 2021, Pagina/e 1325-1332, ISSN 1387-2877
Editore: 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

Autori: Leskelä S, Huber N, Hoffmann D, Rostalski H, Remes AM, Takalo M, Hiltunen M, Haapasalo A
Pubblicato in: Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Numero vol. 1868, no. 7, 2021, Pagina/e 119021, ISSN 0167-4889
Editore: 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

Autori: Juan Miguel Valverde, Artem Shatillo, Riccardo De Feo, and Jussi Tohka
Pubblicato in: Neuroinformatics, 2022, ISSN 1539-2791
Editore: 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

Autori: Ravi R, Fernandes Silva L, Vangipurapu J, Maria M, Raivo J, Helisalmi S, Laakso M
Pubblicato in: Metabolites, Numero 12(5), 2022, Pagina/e 437, ISSN 2218-1989
Editore: MDPI
DOI: 10.3390/metabo12050437

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

Autori: Rostalski, Hannah
Pubblicato in: Dissertations in Health Sciences, Numero 688, 2022, ISBN 978-952-61-4570-9
Editore: PunaMusta Oy

Metabolomics and genomics approach in cardiovascular diseases

Autori: Rowmika Ravi
Pubblicato in: Dissertations in Health Sciences, Numero 742, 2023, ISBN 978-952-61-4821-2
Editore: PunaMusta Oy

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

Autori: Valverde, Juan Miguel
Pubblicato in: Dissertations in Health Sciences, Numero 700, 2022, ISBN 978-952-61-4623-2
Editore: PunaMusta Oy

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

Autori: Sehgal, Ratika
Pubblicato in: Dissertations in Health Sciences, Numero 703, 2022, ISBN 978-952-61-4639-3
Editore: PunaMusta Oy

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

Autori: Valverde, Juan Miguel; Imani, Vandad; Lewis, John D.; Tohka, Jussi
Pubblicato in: Lecture Notes in Computer Science, Numero 11791, 2019, Pagina/e 57-65, ISBN 978-3-030-31901-4
Editore: Springer, Cham
DOI: 10.1007/978-3-030-31901-4_7

Automatic Rodent Brain MRI Lesion Segmentation with Fully Convolutional Networks

Autori: Valverde, Juan Miguel; Shatillo, Artem; de Feo, Riccardo; Gröhn, Olli; Sierra, Alejandra; Tohka, Jussi
Pubblicato in: Lecture Notes in Computer Science, Numero 11861, 2019, Pagina/e 195-202, ISBN 978-3-030-32692-0
Editore: Springer, Cham
DOI: 10.48550/arxiv.1908.08746

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