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Genomics and Mechanisms in Translational Medicine Doctoral Programme

Deliverables

Inform the Project Officer on publication of call

Inform for each call the Project Officer by sending the link to the Euraxess website where the Call has been published

Programme posters and flyers Media coverages

Media coverages, also done later in the Project when applicable

Publications

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

Author(s): 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
Published in: Molecular Neurobiology, Issue 58, 2021, Page(s) 5438-5458, ISSN 0893-7648
Publisher: Humana Press, Inc.
DOI: 10.1007/s12035-021-02475-x

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

Author(s): 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 
Published in: Molecular Neurodegeneration, Issue 15, 2020, Page(s) 52, ISSN 1750-1326
Publisher: BioMed Central
DOI: 10.1186/s13024-020-00402-7

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

Author(s): 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
Published in: Journal of Neurology, Neurosurgery and Psychiatry, Issue vol. 92, no. 12, 2021, Page(s) 1-8, ISSN 0022-3050
Publisher: 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

Author(s): Leskelä; Huber; Rostalski; Natunen; Remes; Takalo; Hiltunen; Haapasalo
Published in: Cells, Issue 84, 2019, Page(s) E1233, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells8101233

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

Author(s): 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
Published in: Molecular Oncology, 2022, ISSN 1574-7891
Publisher: 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

Author(s): Sehgal, R., de Mello, V. D., Männistö, V., Lindström, J., Tuomilehto, J., Pihlajamäki, J., Uusitupa, M
Published in: Nutrients, Issue 14(21), 2022, Page(s) 1-18, ISSN 2072-6643
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu14214695

A consensus protocol for functional connectivity analysis in the rat brain

Author(s): 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
Published in: Nature Neuroscience, 2023, ISSN 1097-6256
Publisher: 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

Author(s): "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"
Published in: Frontiers in Neurology, Issue 13, 2022, Page(s) 820267, ISSN 1664-2295
Publisher: Frontiers Research Foundation
DOI: 10.3389/fneur.2022.820267

Region-wise loss for biomedical image segmentation

Author(s): J.M. Valverde, J. Tohka
Published in: Pattern Recognition, Issue 136, 2023, Page(s) 109208, ISSN 0031-3203
Publisher: Pergamon Press
DOI: 10.1016/j.patcog.2022.109208

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

Author(s): Isidore Mushimiyimana, Henri Niskanen, Mustafa Beter, Johanna P Laakkonen, Minna U Kaikkonen, Seppo Ylä-Herttuala, Nihay Laham-Karam
Published in: Nucleic Acids Research, Issue vol. 49, no. 14, 2021, Page(s) 8078-8096, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab633

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

Author(s): 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.
Published in: Liver International, Issue 41, 2021, Page(s) 754-763, ISSN 1478-3231
Publisher: 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

Author(s): Nadine Huber, Sonja Korhonen, Dorit Hoffmann, Stina Leskelä, Hannah Rostalski, Anne M. Remes, Paavo Honkakoski, Eino Solje, Annakaisa Haapasalo
Published in: Molecular Psychiatry, Issue 27, 2022, Page(s) 1300-1309, ISSN 1359-4184
Publisher: 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

Author(s): Riccardo De Feo, Artem Shatillo, Alejandra Sierra, Juan Miguel Valverde, Olli Gröhn, Federico Giove, Jussi Tohka
Published in: NeuroImage, Issue 229, 2021, Page(s) 117734, ISSN 1053-8119
Publisher: 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.

Author(s): 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
Published in: Cells, Issue 10, 2021, Page(s) 860, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells10040860

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

Author(s): Liu, O. H. F., Kiema, M., Beter, M., Ylä-Herttuala, S., Laakkonen, J. P., & Kaikkonen, M. U.
Published in: Arteriosclerosis, Thrombosis, and Vascular Biology, Issue 40, 2020, Page(s) 2665-2667, ISSN 1079-5642
Publisher: Lippincott Williams & Wilkins Ltd.
DOI: 10.1161/atvbaha.120.315214

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

Author(s): Juan Miguel Valverde; Vandad Imani; Ali Abdollahzadeh; Riccardo De Feo; Mithilesh Prakash; Robert Ciszek; Jussi Tohka
Published in: Journal of Imaging, Issue 7, 2021, Page(s) 66, ISSN 2313-433X
Publisher: MDPI
DOI: 10.3390/jimaging7040066

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

Author(s): 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
Published in: Nutrients, Issue 13, 2021, Page(s) 3509, ISSN 2072-6643
Publisher: 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

Author(s): Lenka Dvořáková, Petteri Stenroos, Ekaterina Paasonen, Raimo A. Salo, Jaakko Paasonen, Olli Gröhn
Published in: NMR in Biomedicine, Issue vol. 35, no. 6, 2021, Page(s) 1-13, ISSN 0952-3480
Publisher: 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

Author(s): Hannah Rostalski, Stina Leskelä, Nadine Huber, Kasper Katisko, Antti Cajanus, Eino Solje, Mikael Marttinen, Teemu Natunen, Anne M. Remes, Mikko Hiltunen, Annakaisa Haapasalo
Published in: Frontiers in Neuroscience, Issue 13, 2019, ISSN 1662-453X
Publisher: Frontiers Media SA
DOI: 10.3389/fnins.2019.00486

RatLesNetv2: A Fully Convolutional Network for Rodent Brain Lesion Segmentation

Author(s): "Juan Miguel Valverde,; Artem, Shatillo; De Feo, Riccardo; Olli, Grö hn; Alejandra, Sierra; Jussi, Tohka"
Published in: Frontiers in Neuroscience, Issue 14, 2020, Page(s) 610239, ISSN 1662-453X
Publisher: 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

Author(s): Huber N, Hoffmann D, Giniatullina R, Rostalski H, Leskelä S, Takalo M, Natunen T, Solje E, Remes AM, Giniatullin R, Hiltunen M, Haapasalo A
Published in: Neurobiology of Disease, Issue 162, 2022, Page(s) 105584, ISSN 0969-9961
Publisher: Academic Press
DOI: 10.1016/j.nbd.2021.105584

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

Author(s): Ratika Sehgal, Alexander Perfilyev, Ville Männistö, Jyrki Ågren, Emma Nilsson, Pirjo Käkelä, Charlotte Ling, Vanessa D. de Mello, Jussi Pihlajamäki
Published in: Clinical Epigenetics, Issue 15, 2023, Page(s) 21, ISSN 1868-7083
Publisher: 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

Author(s): 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
Published in: Frontiers in Neurology, Issue 11, 2020, Page(s) 1-21, ISSN 1664-2295
Publisher: Frontiers Research Foundation
DOI: 10.3389/fneur.2020.550140

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

Author(s): Pulkkinen, H. H., Kiema, M., Lappalainen, J. P., Toropainen, A., Beter, M., Tirronen, A., ... & Laakkonen, J. P
Published in: Angiogenesis, Issue 24, 2021, Page(s) 139-144, ISSN 0969-6970
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10456-020-09748-4

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

Author(s): 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
Published in: Journal of Alzheimer's Disease, Issue vol. 83, no. 3, 2021, Page(s) 1325-1332, ISSN 1387-2877
Publisher: 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

Author(s): Leskelä S, Huber N, Hoffmann D, Rostalski H, Remes AM, Takalo M, Hiltunen M, Haapasalo A
Published in: Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Issue vol. 1868, no. 7, 2021, Page(s) 119021, ISSN 0167-4889
Publisher: 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

Author(s): Juan Miguel Valverde, Artem Shatillo, Riccardo De Feo, and Jussi Tohka
Published in: Neuroinformatics, 2022, ISSN 1539-2791
Publisher: 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

Author(s): Ravi R, Fernandes Silva L, Vangipurapu J, Maria M, Raivo J, Helisalmi S, Laakso M
Published in: Metabolites, Issue 12(5), 2022, Page(s) 437, ISSN 2218-1989
Publisher: MDPI
DOI: 10.3390/metabo12050437

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

Author(s): Rostalski, Hannah
Published in: Dissertations in Health Sciences, Issue 688, 2022, ISBN 978-952-61-4570-9
Publisher: PunaMusta Oy

Metabolomics and genomics approach in cardiovascular diseases

Author(s): Rowmika Ravi
Published in: Dissertations in Health Sciences, Issue 742, 2023, ISBN 978-952-61-4821-2
Publisher: PunaMusta Oy

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

Author(s): Valverde, Juan Miguel
Published in: Dissertations in Health Sciences, Issue 700, 2022, ISBN 978-952-61-4623-2
Publisher: PunaMusta Oy

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

Author(s): Sehgal, Ratika
Published in: Dissertations in Health Sciences, Issue 703, 2022, ISBN 978-952-61-4639-3
Publisher: PunaMusta Oy

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

Author(s): Valverde, Juan Miguel; Imani, Vandad; Lewis, John D.; Tohka, Jussi
Published in: Lecture Notes in Computer Science, Issue 11791, 2019, Page(s) 57-65, ISBN 978-3-030-31901-4
Publisher: Springer, Cham
DOI: 10.1007/978-3-030-31901-4_7

Automatic Rodent Brain MRI Lesion Segmentation with Fully Convolutional Networks

Author(s): Valverde, Juan Miguel; Shatillo, Artem; de Feo, Riccardo; Gröhn, Olli; Sierra, Alejandra; Tohka, Jussi
Published in: Lecture Notes in Computer Science, Issue 11861, 2019, Page(s) 195-202, ISBN 978-3-030-32692-0
Publisher: Springer, Cham
DOI: 10.48550/arxiv.1908.08746

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