  | 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 |
 | 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 |
 | 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., Jaeger, 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., Gérard, 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). 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 |
 | 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 |
 | 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 |
