Publications

All publications made in the GenomMed doctoral program are open access.

2023

Region-wise loss for biomedical image segmentation
Authors: J.M. Valverde, J. Tohka
Published in: Pattern Recognition, 136, 2023
DOI: 10.1016/j.patcog.2022.109208

Liver saturated fat content associates with hepatic DNA methylation in obese individuals
Authors: Ratika Sehgal, Alexander Perfilyev, Ville Männistö, Jyrki Ågren, Emma Nilsson, Pirjo Käkelä, Charlotte Ling, Vanessa D. de Mello, Jussi Pihlajamäki
Published in: Clinical Epigenetics, 15, 2023
DOI: 10.1186/s13148-023-01431-x

2022

Convolutional Neural Networks Enable Robust Automatic Segmentation of the Rat Hippocampus in MRI After Traumatic Brain Injury
Authors: De Feo, Riccardo; Hämäläinen, Elina; Manninen, Eppu; Immonen, Riikka; Valverde, Juan Miguel; Ndode-Ekane, Xavier Ekolle; Gröhn, Olli; Pitkänen, Asla; Tohka, Jussi
Published in: Frontiers in Neurology, 13, 2022, Page 820267
DOI: 10.3389/fneur.2022.820267

Automatic Cerebral Hemisphere Segmentation in Rat MRI with Ischemic Lesions via Attention-based Convolutional Neural Networks
Authors: Juan Miguel Valverde, Artem Shatillo, Riccardo De Feo, and Jussi Tohka
Published in: Neuroinformatics, 2022
DOI: 10.1007/s12021-022-09607-1

PI3Kβ inhibition enhances ALK-inhibitor sensitivity in ALK-rearranged lung cancer
Authors: 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
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
Authors: Sehgal, R., de Mello, V. D., Männistö, V., Lindström, J., Tuomilehto, J., Pihlajamäki, J., Uusitupa, M
Published in: Nutrients, 14, 2022
DOI: 10.3390/nu14214695

Deficient neurotransmitter systems and synaptic function in frontotemporal lobar degeneration—Insights into disease mechanisms and current therapeutic approaches
Authors: Nadine Huber, Sonja Korhonen, Dorit Hoffmann, Stina Leskelä, Hannah Rostalski, Anne M. Remes, Paavo Honkakoski, Eino Solje, Annakaisa Haapasalo
Published in: Molecular Psychiatry, 27, 2022
DOI: 10.1038/s41380-021-01384-8

C9orf72 hexanucleotide repeat expansion leads to altered neuronal and dendritic spine morphology and synaptic dysfunction
Authors: 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, 162, 2022
DOI: 10.1016/j.nbd.2021.105584

Metabolite Signature in the Carriers of Pathogenic Genetic Variants for Cardiomyopathy: A Population-Based METSIM Study
Authors: Ravi R, Fernandes Silva L, Vangipurapu J, Maria M, Raivo J, Helisalmi S, Laakso M
Published in: Metabolites, 12, 2022
DOI: 10.3390/metabo12050437

2021

Indole-3-Propionic Acid, a Gut-Derived Tryptophan Metabolite, Associates with Hepatic Fibrosis
Authors: 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, 13, 2021
DOI: 10.3390/nu13103509

Transfer Learning in Magnetic Resonance Brain Imaging: A Systematic Review.
Authors: Juan Miguel Valverde; Vandad Imani; Ali Abdollahzadeh; Riccardo De Feo; Mithilesh Prakash; Robert Ciszek; Jussi Tohka
Published in: Journal of Imaging, 7, 2021,
DOI: 10.3390/jimaging7040066

Automated joint skull-stripping and segmentation with Multi-Task U-Net in large mouse brain MRI databases
Authors: Riccardo De Feo, Artem Shatillo, Alejandra Sierra, Juan Miguel Valverde, Olli Gröhn, Federico Giove, Jussi Tohka
Published in: NeuroImage, 229, 2021
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.
Authors: 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, 10, 2021
DOI: 10.3390/cells10040860

GFAP as a biomarker in frontotemporal dementia and primary psychiatric disorders: diagnostic and prognostic performance
Authors: 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, 92, 2021
DOI: 10.1136/jnnp-2021-326487

Characterization of a functional endothelial super-enhancer that regulates ADAMTS18 and angiogenesis
Authors: Isidore Mushimiyimana, Henri Niskanen, Mustafa Beter, Johanna P Laakkonen, Minna U Kaikkonen, Seppo Ylä-Herttuala, Nihay Laham-Karam
Published in: Nucleic Acids Research, 49, 2021
DOI: 10.1093/nar/gkab633

Light sedation with short habituation time for large-scale functional magnetic resonance imaging studies in rats
Authors: Lenka Dvořáková, Petteri Stenroos, Ekaterina Paasonen, Raimo A. Salo, Jaakko Paasonen, Olli Gröhn
Published in: NMR in Biomedicine, 35, 2021
DOI: 10.1002/nbm.4679

BMP6/TAZ-Hippo signaling modulates angiogenesis and endothelialcell response to VEGF
Authors: H. H. Pulkkinen, M. Kiema, J. P. Lappalainen, A. Toropainen, M. Beter, A. Tirronen, L. Holappa, H. Niskanen, M. U. Kaikkonen, S. Ylä-Herttuala & Johanna P. Laakkonen
Published in: Angiogenesis, 24, 2021
DOI: 10.1007/s10456-020-09748-4

A Novel Genetic Marker for the C9orf72 Repeat Expansion in the Finnish Population
Authors: 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, 83, 2021
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
Authors: 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, 1868, 2021
DOI: 10.1016/j.bbamcr.2021.119021

2020

RatLesNetv2: A Fully Convolutional Network for Rodent Brain Lesion Segmentation
Authors: Juan Miguel Valverde; Artem, Shatillo; De Feo, Riccardo; Olli, Gröhn; Alejandra, Sierra; Jussi, Tohka
Published in: Frontiers in Neuroscience, 14, 2020
DOI: 10.3389/fnins.2020.610239

The Alzheimer’s disease-associated protective Plcγ2-P522R variant promotes immune functions
Authors: 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, 15, 2020
DOI: 10.1186/s13024-020-00402-7

Hypoxia-Mediated Regulation of Histone Demethylases Affects Angiogenesis-Associated Functions in Endothelial Cells
Authors: Liu, O. H. F., Kiema, M., Beter, M., Ylä-Herttuala, S., Laakkonen, J. P., Kaikkonen, M. U.
Published in: Arteriosclerosis, Thrombosis, and Vascular Biology, 40, 2020
DOI: 10.1161/atvbaha.120.315214

BV-2 Microglial Cells Overexpressing C9orf72 Hexanucleotide Repeat Expansion Produce DPR Proteins and Show Normal Functionality but No RNA Foci
Authors: 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, 11, 2020
DOI: 10.3389/fneur.2020.550140

2019

C9orf72 proteins regulate autophagy and undergo autophagosomal or proteasomal degradation in a cell type-dependent manner
Authors: Leskelä; Huber; Rostalski; Natunen; Remes; Takalo; Hiltunen; Haapasalo
Published in: Cells, 84, 2019
DOI: 10.3390/cells8101233

Astrocytes and Microglia as Potential Contributors to the Pathogenesis of C9orf72 Repeat Expansion-Associated FTLD and ALS
Authors: 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, 13, 2019
DOI: 10.3389/fnins.2019.00486