  | HELGUETA ROMERO, S., HEURTAUX, T., SCIORTINO, A., GUI, Y., OHNMACHT, J., MENCKE, P., BOUSSAAD, I., HALDER, R., GARCIA, P., KRÜGER, R., MITTELBRONN, M., BUTTINI, M., SAUTER, T., & SINKKONEN, L. (04 January 2025). Park7 deletion leads to sex-specific transcriptome changes involving NRF2-CYP1B1 axis in mouse midbrain astrocytes. NPJ Parkinson's Disease, 11 (1), 8. doi:10.1038/s41531-024-00851-7  Peer Reviewed verified by ORBi |
 | Gomez Ramos, B., Ohnmacht, J., de Lange, N., VALCESCHINI, E., GINOLHAC, A., CATILLON, M., FERRANTE, D., Rakovic, A., HALDER, R., Massart, F., ARENA, G., ANTONY, P., BOLOGNIN, S., Klein, C., KRAUSE, R., Schulz, M. H., SAUTER, T., Krüger, R., & SINKKONEN, L. (19 December 2023). Multiomics analysis identifies novel facilitators of human dopaminergic neuron differentiation. EMBO Reports, 25 (1), 254-285. doi:10.1038/s44319-023-00024-2 Peer Reviewed verified by ORBi |
 | GAVRIIL, M., PROIETTO, M., PACZIA, N., GINOLHAC, A., HALDER, R., VALCESCHINI, E., SAUTER, T., LINSTER, C., & SINKKONEN, L. (November 2023). 2-Hydroxyglutarate modulates histone methylation at specific loci and alters gene expression via Rph1 inhibition. Life Science Alliance, 7 (2), 202302333. doi:10.26508/lsa.202302333 Peer Reviewed verified by ORBi |
 | de Sande, A. H., Turunen, T., Bouvy-Liivrand, M., Örd, T., Palani, S., Tundidor-Centeno, C., Liljenbäck, H., Virta, J., Smålander, O.-P., SINKKONEN, L., SAUTER, T., Roivainen, A., Lönnberg, T., Kaikkonen, M. U., & Heinäniemi, M. (2023). Cell-type-specific characterization of miRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/58864. doi:10.1101/2023.10.09.561173 |
 | Bintener, T., PIRES PACHECO, M. I., PHILIPPIDOU, D., MARGUE, C., KISHK, A., Del Mistro, G., Di Leo, L., MOSCARDO GARCIA, M., HALDER, R., SINKKONEN, L., De Zio, D., KREIS, S., Kulms, D., & SAUTER, T. (26 July 2023). Metabolic modelling-based in silico drug target prediction identifies six novel repurposable drugs for melanoma. Cell Death and Disease, 14 (468). doi:10.1038/s41419-023-05955-1 Peer Reviewed verified by ORBi |
 | Soriano-Baguet, L., Grusdat, M., Kurniawan, H., Benzarti, M., Binsfeld, C., Ewen, A., LONGWORTH, J., Bonetti, L., Guerra, L., Franchina, D. G., Kobayashi, T., Horkova, V., Verschueren, C., Helgueta, S., GERARD, D., More, T. H., Henne, A., Dostert, C., Farinelle, S., ... Brenner, D. (2023). Pyruvate dehydrogenase fuels a critical citrate pool that is essential for Th17 cell effector functions. Cell Reports. doi:10.1016/j.celrep.2023.112153 Peer Reviewed verified by ORBi |
 | HEURTAUX, T., Bouvier, D. S., Benani, A., Helgueta Romero, S., Frauenknecht, K. B. M., Mittelbronn, M., & SINKKONEN, L. (July 2022). Normal and Pathological NRF2 Signalling in the Central Nervous System. Antioxidants, 11 (8), 1426. doi:10.3390/antiox11081426 Peer reviewed |
 | Del Mistro, G., Riemann, S., Schindler, S., Beissert, S., Kontermann, R. E., GINOLHAC, A., Halder, R., PRESTA, L., SINKKONEN, L., SAUTER, T., & Kulms, D. (2022). Focal adhesion kinase plays a dual role in TRAIL resistance and metastatic outgrowth of malignant melanoma. Cell Death and Disease. doi:10.1038/s41419-022-04502-8 Peer Reviewed verified by ORBi |
 | KISHK, A., PIRES PACHECO, M. I., HEURTAUX, T., SINKKONEN, L., PANG, J., Fritah, S., NICLOU, S., & SAUTER, T. (2022). Review of Current Human Genome-Scale Metabolic Models for Brain Cancer and Neurodegenerative Diseases. Cells, 11 (16). doi:10.3390/cells11162486 Peer Reviewed verified by ORBi |
 | Lüth, T., WASNER, K., Klein, C., Schaake, S., Tse, R., Pereira, S. L., Laß, J., SINKKONEN, L., GRÜNEWALD, A., & Trinh, J. (2021). Nanopore Single-Molecule Sequencing for Mitochondrial DNA Methylation Analysis: Investigating Parkin-Associated Parkinsonism as a Proof of Concept. Frontiers in Aging Neuroscience. doi:10.3389/fnagi.2021.713084 Peer Reviewed verified by ORBi |
 | Gui, Y., GRZYB, K., THOMAS, M., OHNMACHT, J., GARCIA, P., BUTTINI, M., SKUPIN, A., SAUTER, T., & SINKKONEN, L. (2021). Single‑nuclei chromatin profiling of ventral midbrain reveals cell identity transcription factors and cell‑type‑specific gene regulatory variation. Epigenetics and Chromatin. doi:10.1186/s13072-021-00418-3 Peer Reviewed verified by ORBi |
  | Rufo, N., Korovesis, D., Van Eygen, S., Derua, R., Garg, A. D., Finotello, F., Vara-Perez, M., Rožanc, J., Dewaele, M., de Witte, P. A., Alexopoulos, L. G., Janssens, S., SINKKONEN, L., SAUTER, T., Verhelst, S. H. L., & Agostinis, P. (2021). Stress-induced inflammation evoked by immunogenic cell death is blunted by the IRE1α kinase inhibitor KIRA6 through HSP60 targeting. Cell Death and Differentiation. doi:10.1038/s41418-021-00853-5 Peer Reviewed verified by ORBi |
 | Frangez, Z., GERARD, D., He, Z., GAVRIIL, M., Fernández-Marrero, Y., Seyed Jafari, M., Hunger, R., LUCARELLI, P., Yousefi, S., SAUTER, T., SINKKONEN, L., & Simon, H.-U. (2021). ATG5 and ATG7 Expression Levels Are Reduced in Cutaneous Melanoma and Regulated by NRF1. Frontiers in Oncology. doi:10.3389/fonc.2021.721624 Peer Reviewed verified by ORBi |
 | THOMAS, M., Gui, Y., GARCIA, P., Karout, M., GOMEZ RAMOS, B., JÄGER, C., Michelucci, A., GAIGNEAUX, A., Kollmus, H., Centeno, A., Schughart, K., Balling, R., Mittelbronn, M., Nadeau, J. H., SAUTER, T., Williams, R. W., SINKKONEN, L., & BUTTINI, M. (2021). Quantitative trait locus mapping identifies a locus linked to striatal dopamine and points to collagen IV alpha-6 chain as a novel regulator of striatal axonal branching in mice. Genes, Brain, and Behavior. doi:10.1111/gbb.12769 Peer Reviewed verified by ORBi |
 | Walter, J., BOLOGNIN, S., Poovathingal, S., MAGNI, S., GERARD, D., ANTONY, P., NICKELS, S. L., Salamanca, L., Berger, E., SMITS, L., GRZYB, K., Perfeito, R., Hoel, F., Qing, X., OHNMACHT, J., Bertacchi, M., Jarazo, J., Ignac, T., Monzel, A., ... SCHWAMBORN, J. C. (2021). The Parkinson’s-disease-associated mutation LRRK2-G2019S alters dopaminergic differentiation dynamics via NR2F1. Cell Reports. doi:10.1016/j.celrep.2021.109864 Peer Reviewed verified by ORBi |
 | GUI, Y., Thomas, M. H., Garcia, P., Karout, M., HALDER, R., MICHELUCCI, A., Kollmus, H., Zhou, C., Melmed, S., Schughart, K., BALLING, R., MITTELBRONN, M., Nadeau, J. H., Williams, R. W., SAUTER, T., BUTTINI, M., & SINKKONEN, L. (2020). Pituitary Tumor Transforming Gene 1 Orchestrates Gene Regulatory Variation in Mouse Ventral Midbrain During Aging. Frontiers in Genetics. doi:10.3389/fgene.2020.566734 Peer Reviewed verified by ORBi |
 | Shahraz, A., Wißfeld, J., GINOLHAC, A., Matthews, M., SINKKONEN, L., & Neumann, H. (2020). Phagocytosis‐related NADPH oxidase 2 subunit gp91phox contributes to neurodegeneration after repeated systemic challenge with lipopolysaccharides. Glia. doi:10.1002/glia.23890 Peer Reviewed verified by ORBi |
 | OHNMACHT, J., MAY, P., SINKKONEN, L., & KRÜGER, R. (2020). Missing heritability in Parkinson’s disease: the emerging role of non‑coding genetic variation. Journal of Neural Transmission. doi:10.1007/s00702-020-02184-0 Peer Reviewed verified by ORBi |
 | Klaus, C., Hansen, J. N., GINOLHAC, A., GERARD, D., Gnanapragassam, V. S., Horstkorte, R., Rossdam, C., Buettner, F. F. R., SAUTER, T., SINKKONEN, L., Neumann, H., & Linnartz-Gerlach, B. (2020). Reduced sialylation triggers homeostatic synapse and neuronal loss in middle-aged mice. Neurobiology of Aging. doi:10.1016/j.neurobiolaging.2020.01.008 Peer Reviewed verified by ORBi |
 | BECKER, J. C., GERARD, D., GINOLHAC, A., SAUTER, T., & SINKKONEN, L. (2019). Identification of genes under dynamic post-transcriptional regulation from time-series epigenomic data. Epigenomics. doi:10.2217/epi-2018-0084 Peer Reviewed verified by ORBi |
 | NICKELS, S., Walter, J., BOLOGNIN, S., GERARD, D., Jäger, C., Qing, X., Tisserand, J., JARAZO, J., Hemmer, K., Harms, A., HALDER, R., Lucarelli, P., Berger, E., ANTONY, P., GLAAB, E., Hankemeier, T., Klein, C., SAUTER, T., SINKKONEN, L., & SCHWAMBORN, J. C. (2019). Impaired serine metabolism complements LRRK2-G2019S pathogenicity in PD patients. Parkinsonism and Related Disorders. doi:10.1016/j.parkreldis.2019.09.018 Peer Reviewed verified by ORBi |
 | GERARD, D., Schmidt, F., GINOLHAC, A., SCHMITZ, M., HALDER, R., Ebert, P., Schulz, M., SAUTER, T., & SINKKONEN, L. (2018). Temporal enhancer profiling of parallel lineages identifies AHR and GLIS1 as regulators of mesenchymal multipotency. Nucleic Acids Research. doi:10.1093/nar/gky1240 Peer Reviewed verified by ORBi |
 | Linnartz-Gerlach, B., Bodea, L.-G., Klaus, C., GINOLHAC, A., HALDER, R., SINKKONEN, L., Walter, J., Colonna, M., & Neumann, H. (2018). TREM2 triggers microglial density and age‐related neuronal loss. Glia. doi:10.1002/glia.23563 Peer Reviewed verified by ORBi |
 | Bouvy-Liivrand, M.* , Hernandez de Sande, A.* , Pölönen, P., Mehtonen, J., Vuorenmaa, T., Niskanen, H., SINKKONEN, L., Kaikkonen, M., & Heinäniemi, M. (2017). Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture. Nucleic Acids Research. doi:10.1093/nar/gkx680 Peer Reviewed verified by ORBi* These authors have contributed equally to this work. |
 | PACHECO, M., JOHN, E.* , Kaoma, T., Heinäniemi, M., Nicot, N., Vallar, L., BUEB, J.-L., SINKKONEN, L., & SAUTER, T. (19 October 2015). Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network. BMC Genomics, 16 (809). doi:10.1186/s12864-015-1984-4 Peer Reviewed verified by ORBi* These authors have contributed equally to this work. |
 | GALHARDO, M. S., Berninger, P., NGUYEN, T.-P., SAUTER, T., & SINKKONEN, L. (03 September 2015). Cell type-selective disease-association of genes under high regulatory load. Nucleic Acids Research, 43 (18), 8839-8855. doi:10.1093/nar/gkv863 Peer Reviewed verified by ORBi |
 | GALHARDO, M. S., SINKKONEN, L., Berninger, P., LIN, J., SAUTER, T., & HEINÄNIEMI, M. (December 2014). Transcriptomics profiling of human SGBS adipogenesis. Genomics Data, 2, 246-248. doi:10.1016/j.gdata.2014.07.004 Peer Reviewed verified by ORBi |
 | GALHARDO, M. S., SINKKONEN, L., Berninger, P., LIN, J., SAUTER, T., & Heinäniemi, M. (December 2014). ChIP-seq profiling of the active chromatin marker H3K4me3 and PPARγ, CEBPα and LXR target genes in human SGBS adipocytes. Genomics Data, 2, 230-236. doi:10.1016/j.gdata.2014.07.002 Peer reviewed |
 | Bodea, L.-G., Wang, Y., Linnartz-Gerlach, B., Kopatz, J., SINKKONEN, L., Musgrove, R., Kaoma, T., Muller, A., Vallar, L., Di Monte, D., BALLING, R., & Neumann, H. (18 June 2014). Neurodegeneration by Activation of the Microglial Complement–Phagosome Pathway. Journal of Neuroscience, 34 (25), 8546-8556. doi:10.1523/JNEUROSCI.5002-13.2014 Peer Reviewed verified by ORBi |
 | LIIVRAND, M., HEINÄNIEMI, M., JOHN, E., SCHNEIDER, J., SAUTER, T., & SINKKONEN, L. (16 January 2014). Combinatorial regulation of lipoprotein lipase by microRNAs during mouse adipogenesis. RNA Biology, 11 (1), 76-91. doi:10.4161/rna.27655 Peer Reviewed verified by ORBi |
 | GALHARDO, M. S.* , SINKKONEN, L.* , Berninger, P., LIN, J., SAUTER, T., & HEINÄNIEMI, M. (2013). Integrated analysis of transcript-level regulation of metabolism reveals disease-relevant nodes of the human metabolic network. Nucleic Acids Research. doi:10.1093/nar/gkt989 Peer Reviewed verified by ORBi* These authors have contributed equally to this work. |
 | HEINÄNIEMI, M., Nykter, M., Kramer, R., WIENECKE, A., SINKKONEN, L., Zhou, J. X., Kreisberg, R., Kauffman, S. A., Huang, S., & Shmulevich, I. (2013). Gene-pair expression signatures reveal lineage control. Nature Methods. doi:10.1038/nmeth.2445 Peer Reviewed verified by ORBi |
 | JOHN, E., WIENECKE-BALDACCHINO, A., LIIVRAND, M., HEINÄNIEMI, M., CARLBERG, C., & SINKKONEN, L. (07 February 2012). Dataset integration identifies transcriptional regulation of microRNA genes by PPARgamma in differentiating mouse 3T3-L1 adipocytes. Nucleic Acids Research, 40 (10), 4446-4460. doi:10.1093/nar/gks025 Peer Reviewed verified by ORBi |
 | Lahnalampi, M., HEINÄNIEMI, M., SINKKONEN, L., Wabitsch, M., & Carlberg, C. (27 September 2010). Time-Resolved Expression Profiling of the Nuclear Receptor Superfamily in Human Adipogenesis. PLoS ONE, 5 (9). doi:10.1371/journal.pone.0012991 Peer Reviewed verified by ORBi |
 | SINKKONEN, L., Hugenschmidt, T., Filipowicz, W., & Svoboda, P. (13 August 2010). Dicer is associated with ribosomal DNA chromatin in mammalian cells. PLoS ONE, 5 (8), 1-2. doi:10.1371/journal.pone.0012175 Peer Reviewed verified by ORBi |
 | SINKKONEN, L., Hugenschmidt, T., Berninger, P., Gaidatzis, D., Mohn, F., Artus-Revel, C. G., Zavolan, M., Svoboda, P., & Filipowicz, W. (March 2008). MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nature Structural and Molecular Biology, 15 (3), 259-67. doi:10.1038/nsmb.1391 Peer Reviewed verified by ORBi |
Väisänen, S., Dunlop, T. W., SINKKONEN, L., Frank, C., & CARLBERG, C. (01 July 2005). Spatio-temporal activation of chromatin on the human CYP24 gene promoter in the presence of 1alpha,25-Dihydroxyvitamin D3. Journal of Molecular Biology, 350 (1), 65-77. doi:10.1016/j.jmb.2005.04.057 Peer Reviewed verified by ORBi |
 | SINKKONEN, L., Malinen, M., Saavalainen, K., Väisänen, S., & CARLBERG, C. (29 April 2005). Regulation of the human cyclin C gene via multiple vitamin D3-responsive regions in its promoter. Nucleic Acids Research, 33 (8), 2440-51. doi:10.1093/nar/gki502 Peer Reviewed verified by ORBi |
Dataset: