  | 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. (2023). Multiomics analysis identifies novel facilitators of human dopaminergic neuron differentiation. EMBO Reports. doi:10.1038/s44319-023-00024-2  Peer Reviewed verified by ORBi |
 | DELOGU, F., Kunath, B. J., Queirós, P. M., HALDER, R., LEBRUN, L., Pope, P. B., MAY, P., Widder, S., MULLER, E., & WILMES, P. (2023). Forecasting the dynamics of a complex microbial community using integrated meta-omics. Nature Ecology and Evolution. doi:10.1038/s41559-023-02241-3 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 |
 | SCHMIT, K.* , GARCIA, P.* , SCIORTINO, A., AHO, V., Pardo Rodriguez, B., THOMAS, M., GERARDY, J.-J., Bastero Acha, I., HALDER, R., CIALINI, C., HEURTAUX, T., Ostahi, I., BUSI, S. B., Grandmougin, L., LOWNDES, T., Singh, Y., Martens, E. C., MITTELBRONN, M., BUTTINI, M.* , & WILMES, P. (26 September 2023). Fiber deprivation and microbiome-borne curli shift gut bacterial populations and accelerate disease in a mouse model of Parkinson's disease. Cell Reports, 42 (9), 113071. doi:10.1016/j.celrep.2023.113071 Peer Reviewed verified by ORBi* These authors have contributed equally to this work. |
 | 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 |
 | KONCINA, E., NURMIK, M., POZDEEV, V., GILSON, C., TSENKOVA, M., BEGAJ, R., Stang, S., GAIGNEAUX, A., Weindorfer, C., RODRIGUEZ, F., SCHMOETTEN, M., KLEIN, E., KARTA, J., Atanasova, V. S., GRZYB, K., ULLMANN, P., HALDER, R., Hengstschläger, M., Graas, J., ... LETELLIER, E. (17 July 2023). IL1R1+ cancer-associated fibroblasts drive tumor development and immunosuppression in colorectal cancer. Nature Communications, 14 (1), 4251. doi:10.1038/s41467-023-39953-w Peer Reviewed verified by ORBi |
ALI, M.* , GARCIA, P.* , Laetitia P. Lunkes, SCIORTINO, A., THOMAS, M., HEURTAUX, T., GRZYB, K., HALDER, R., SKUPIN, A., MITTELBRONN, M., BUTTINI, M., & GLAAB, E. (12 May 2023). Gene Regulatory Network Analysis of Single-Cell Transcriptomes from THY-Tau22 Mice Reveals Sex-Dependent Immune Dysregulation associated with Alzheimer-like pathology [Poster presentation]. The 7th Venusberg Meeting on Neuroinflammation, Belval, Luxembourg. * These authors have contributed equally to this work. |
 | de Nies, L., Galata, V., Martin-Gallausiaux, C., Despotovic, M., Busi, S. B., Snoeck, C. J., Delacour, L., Budagavi, D. P., Laczny, C. C., Habier, J., Lupu, P.-C., Halder, R., Fritz, J. V., Marques, T., Sandt, E., O'Sullivan, M. P., Ghosh, S., Satagopam, V., Consortium, C.-V., ... Wilmes, P. (09 March 2023). Altered infective competence of the human gut microbiome in COVID-19. Microbiome, 11 (1), 46. doi:10.1186/s40168-023-01472-7 Peer Reviewed verified by ORBi |
 | Tranchevent, L.-C., Halder, R., & Glaab, E. (2023). Systems level analysis of sex-dependent gene expression changes in Parkinson’s disease. NPJ Parkinson's Disease, 9 (8). doi:10.1038/s41531-023-00446-8 Peer Reviewed verified by ORBi |
 | Kunath, B., Hickl, O., Teixeira Queiros, P., Martin-Gallausiaux, C., Lebrun, L., Halder, R., Laczny, C. C., Schmidt, T. S., Hayward, M., Becher, D., Heintz-Buschart, A., de Beaufort, C., Bork, P., May, P., & Wilmes, P. (2022). Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses. Microbiome. doi:10.1186/s40168-022-01435-4 Peer Reviewed verified by ORBi |
 | Delogu, F., Kunath, B., Queirós, P. M., Halder, R., Lebrun, L., Pope, P. B., May, P., Widder, S., Muller, E. E. L., & Wilmes, P. (2022). Forecasting of a complex microbial community using meta-omics. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/52862. doi:10.1101/2022.10.19.512887 |
  | Pires-Afonso, Y., Muller, A., GRZYB, K., Oudin, A., Yabo, Y. A., SOUSA, C., Scafidi, A., Poli, A., COSMA, A., HALDER, R., COOWAR, D., GOLEBIEWSKA, A., SKUPIN, A., NICLOU, S. P., & MICHELUCCI, A. (September 2022). Elucidating tumour-associated microglia/macrophage diversity along glioblastoma progression and under ACOD1 deficiency. Molecular Oncology, 16 (17), 3167 - 3191. doi:10.1002/1878-0261.13287 Peer Reviewed verified by ORBi |
 | Ali, M., Huarte, O., Heurtaux, T., Garcia, P., Rodriguez, B. P., Grzyb, K., Halder, R., Skupin, A., Buttini, M., & Glaab, E. (2022). Single-cell transcriptional profiling and gene regulatory network modeling in Tg2576 mice reveal gender-dependent molecular features preceding Alzheimer-like pathologies. Molecular Neurobiology, in press (doi:10.1007/s12035-022-02985-2) (in press). doi:10.1007/s12035-022-02985-2 Peer Reviewed verified by ORBi |
 | Balta, M. G., Schreurs, O., Halder, R., Küntziger, T. M., Saetre, F., Blix, I. J. S., Baekkevold, E. S., Glaab, E., & Schenck, K. (2022). RvD1(n-3 DPA) Downregulates the Transcription of Pro-Inflammatory Genes in Oral Epithelial Cells and Reverses Nuclear Translocation of Transcription Factor p65 after TNF-α Stimulation. International Journal of Molecular Sciences, 23 (23). doi:10.3390/ijms232314878 Peer Reviewed verified by ORBi |
 | Trezzi, J.-P., Aho, V., Jäger, C., Schade, S., Janzen, A., Hickl, O., Kunath, B., Thomas, M., Schmit, K., Garcia, P., Sciortino, A., Martin-Gallausiaux, C., Halder, R., Huarte, O. U., Heurtaux, T., Heins-Marroquin, U., Gomez-Giro, G., Weidenbach, K., Delacour, L., ... Wilmes, P. (2022). An archaeal compound as a driver of Parkinson’s disease pathogenesis. (1). ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/51987. doi:10.21203/rs.3.rs-1827631/v1 |
 | de Nies, L., Busi, S. B., Tsenkova, M., Halder, R., Letellier, E., & Wilmes, P. (2022). Evolution of the murine gut resistome following broad-spectrum antibiotic treatment. Nature Communications, 13 (1), 2296. doi:10.1038/s41467-022-29919-9 Peer Reviewed verified by ORBi |
 | de Saedeleer, B., Malabirade, A., Ramiro Garcia, J., Habier, J., Trezzi, J.-P., Peters, S., Daujeumont, A., Halder, R., Jäger, C., Busi, S. B., May, P., Oertel, W., Mollenhauer, B., Laczny, C. C., Hettich, R., & Wilmes, P. (2021). Systematic characterization of human gut microbiome-secreted molecules by integrated multi-omics. ISME Communications. doi:10.1038/s43705-021-00078-0 Peer Reviewed verified by ORBi |
 | Galata, V., Busi, S. B., Kunath, B., de Nies, L., Calusinska, M., Halder, R., May, P., Wilmes, P., & Laczny, C. C. (2021). Functional meta-omics provide critical insights into long- and short-read assemblies. Briefings in Bioinformatics. doi:10.1093/bib/bbab330 Peer Reviewed verified by ORBi |
 | Uriarte Huarte, O., Kyriakis, D., Heurtaux, T., Pires-Afonso, Y., Grzyb, K., Halder, R., Buttini, M., Skupin, A., Mittelbronn, M., & Michelucci, A. (2021). Single-Cell Transcriptomics and In Situ Morphological Analyses Reveal Microglia Heterogeneity Across the Nigrostriatal Pathway. Frontiers in Immunology. doi:10.3389/fimmu.2021.639613 Peer Reviewed verified by ORBi |
 | Busi, S. B.* , de Nies, L.* , Habier, J., Wampach, L., Heintz-Buschart, A., Fritz, J., Halder, R., May, P., de Beaufort, C., & Wilmes, P. (2021). Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life. ISME Communications. doi:10.1038/s43705-021-00003-5 Peer reviewed* These authors have contributed equally to this work. |
 | Van Den Bossche, T., Kunath, B., Schallert, K., Schäpe, S. S., Abraham, P. E., Armengaud, J., Arntzen, M. Ø., Bassignani, A., Benndorf, D., Fuchs, S., Giannone, R. J., Griffin, T. J., Hagen, L. H., Halder, R., Henry, C., Hettich, R. L., Heyer, R., Jagtap, P., Jehmlich, N., ... Muth, T. (2021). Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nature Communications, 12 (1), 7305. doi:10.1038/s41467-021-27542-8 Peer Reviewed verified by ORBi |
 | Hayoun, K., Geersens, E., Laczny, C. C., Halder, R., Lázaro Sánchez, C., Manna, A., Bringel, F., Ryckelynck, M., Wilmes, P., Muller, E., Alpha-Bazin, A., & Vuilleumier, S. (2020). Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics. Microorganisms. doi:10.3390/microorganisms8121876 Peer reviewed |
 | Busi, S. B.* , Pramateftaki, P.* , Brandani, J., Fodelianakis, S., Peter, H., Halder, R., Wilmes, P., & Battin, T. (2020). Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams. PeerJ. doi:10.7717/peerj.9973 Peer Reviewed verified by ORBi* These authors have contributed equally to this work. |
 | 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 |
 | Zafeiriou, M.-P., Bao, G., Hudson, J., Halder, R., Blenkle, A., Schreiber, M.-K., Fischer, A., Schild, D., & Zimmermann, W.-H. (29 July 2020). Developmental GABA polarity switch and neuronal plasticity in Bioengineered Neuronal Organoids. Nature Communications, 11 (1), 3791. doi:10.1038/s41467-020-17521-w Peer Reviewed verified by ORBi |
 | Marynowska, M., Goux, X., Sillam-Dusses, D., Rouland-Lefevre, C., Halder, R., Wilmes, P., Gawron, P., Roisin, Y., Delfosse, P., & Calusinska, M. (2020). Compositional and functional characterisation of biomass-degrading microbial communities in guts of plant fibre- and soil-feeding higher termites. Microbiome. doi:10.1186/s40168-020-00872-3 Peer Reviewed verified by ORBi |
 | Calusinska, M., Marynowska, M., Bertucci, M., Untereiner, B., Klimek, D., Goux, X., Sillam-Dusses, D., Gawron, P., Halder, R., Wilmes, P., Ferrer, P., Gerin, P., Roisin, Y., & Delfosse, P. (2020). Integrative omics analysis of the termite gut system adaptation to Miscanthus diet identifies lignocellulose degradation enzymes. Communications Biology. doi:10.1038/s42003-020-1004-3 Peer Reviewed verified by ORBi |
 | Kurniawan, H., Franchina, D. G., Guerra, L., Bonetti, L., - Baguet, L. S., Grusdat, M., Schlicker, L., Hunewald, O., Dostert, C., Merz, M. P., Binsfeld, C., Duncan, G. S., Farinelle, S., Nonnenmacher, Y., Haight, J., Das Gupta, D., Ewen, A., Taskesen, R., Halder, R., ... Brenner, D. (05 May 2020). Glutathione Restricts Serine Metabolism to Preserve Regulatory T Cell Function. Cell Metabolism, 31 (5), 920--936.e7. doi:10.1016/j.cmet.2020.03.004 Peer reviewed |
 | Gomez Giro, G., Arias-Fuenzalida, J., Jarazo, J., Zeuschner, D., Ali, M., Possemis, N., Bolognin, S., Halder, R., Jäger, C., Kuper, W., van Hasselt, P., Zaehres, H., del Sol Mesa, A., van der Putten, H., Schoeler, H., & Schwamborn, J. C. (2020). Synapse alterations precede neuronal damage and storage pathology in a human cerebral organoid model of CLN3-juvenile neuronal ceroid lipofuscinosis. Acta Neuropathologica Communications. doi:10.1186/s40478-019-0871-7 Peer Reviewed verified by ORBi |
 | Greenhalgh, K., Ramiro Garcia, J., Heinken, Ullmann, P., Bintener, T. J. R., Pacheco, M., Baginska, J., Shah, P., Frachet Bour, A., Halder, R., Fritz, J., Sauter, T., Thiele, I., Haan, S., Letellier, E., & Wilmes, P. (30 April 2019). Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells. Cell Reports, 27, 1621–1632. doi:10.1016/j.celrep.2019.04.001 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 |
 | Trezzi, J.-P., Ramiro Garcia, J., Laczny, C. C., Daujeumont, A., Halder, R., Lebrun, L., Heintz, A., Oertel, W., Mollenhauer, B., & Wilmes, P. (October 2018). Microbiome-derived Multi-omicBiomarkers for Early-stage Detection and Stratification of Parkinson's Disease [Poster presentation]. 4th International Parkinson's Disease Symposium. |
 | Paiva, I., Jain, G., Lázaro, D. F., Gotovac Jerčić, K., Hentrich, T., Kerimoglu, C., Pinho, R., M. Szegő, E., Burkhardt, S., Capece, V., Halder, R., Islam, R., Xylaki, M., A. Caldi Gomes, L., Roser, A.-E., Lingor, P., M. Schulze-Hentrich, J., Borovečki, F., Fischer, A., & F. Outeiro, T. (2018). Alpha-synuclein deregulates the expression of COL4A2 and impairs ER-Golgi function. Neurobiology of Disease. doi:10.1016/j.nbd.2018.08.001 Peer reviewed |
 | Malabirade, A., Habier, J., Heintz-Buschart, A., May, P., Godet, J., Halder, R., Etheridge, A., Galas, D., Wilmes, P., & Fritz, J. (30 July 2018). The RNA Complement of Outer Membrane Vesicles From Salmonella enterica Serovar Typhimurium Under Distinct Culture Conditions. Frontiers in Microbiology, 9, 2015. doi:10.3389/fmicb.2018.02015 Peer Reviewed verified by ORBi |
 | Greenhalgh, K., Ramiro Garcia, J., Heinken, A. K., Baginska, J., Letellier, E., Halder, R., Frachet Bour, A., Ullmann, P., Thiele, I., Haan, S., & Wilmes, P. (16 February 2018). Cominatorial effect of dietary fibre and Lactobacillus rhamnosus in the context of colorectal cancer therapy [Poster presentation]. Cell Immunology symposium. |
 | Roser, A.-E., Caldi Gomes, L., Halder, R., Jain, G., Maass, F., Tönges, L., Tatenhorst, L., Bähr, M., Fischer, A., & Lingor, P. (2018). miR-182-5p and miR-183-5p Act as GDNF Mimics in Dopaminergic Midbrain Neurons. Molecular Therapy: Nucleic Acids. doi:10.1016/j.omtn.2018.01.005 Peer Reviewed verified by ORBi |
 | Kirchmeyer, M., Servais, F., Hamdorf, M., Nazarov, P. V., Ginolhac, A., Halder, R., Vallar, L., Glanemann, M., Rubie, C., Lammert, F., Kreis, S., & Behrmann, I. (2018). Cytokine-mediated modulation of the hepatic miRNome: miR-146b-5p is an IL-6-inducible miRNA with multiple targets. Journal of Leukocyte Biology. doi:10.1002/JLB.MA1217-499RR Peer Reviewed verified by ORBi |
 | Wampach, L., Heintz, A., Fritz, J., Ramiro Garcia, J., Habier, J., Herold, M., Narayanasamy, S., Kaysen, A., Hogan, A., Bindl, L., Bottu, J., Halder, R., Sjöqvist, C., May, P., Andersson, A., de Beaufort, C., & Wilmes, P. (2018). Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential. Nature Communications. doi:10.1038/s41467-018-07631-x Peer Reviewed verified by ORBi |
 | I. Hurtado-Zavala, J., Ramachandran, B., Ahmed, S., Halder, R., Bolleyer, C., Awasthi, A., A. Stahlberg, M., J. Wagener, R., Anderson, K., M. Drenan, R., A. Lester, H., M. Miwa, J., F. Staiger, J., Fischer, A., & Dean, C. (2017). TRPV1 regulates excitatory innervation of OLM neurons in the hippocampus. Nature Communications. doi:10.1038/ncomms15878 Peer Reviewed verified by ORBi |
 | Bahari-Javan, S., Varbanov, H., Halder, R., Benito, E., Kaurani, L., Burkhardt, S., Anderson-Schmidt, H., Anghelescu, I., Budde, M., Stilling, R., Costa, J., Juan, M., E. Dietrich, D., Figge, C., Folkerts, H., Gade, K., Heilbronner, U., Koller, M., Konrad, C., ... Fischer, A. (2017). HDAC1 links early life stress to schizophrenia-like phenotypes. Proceedings of the National Academy of Sciences of the United States of America. doi:10.1073/pnas.1613842114 Peer Reviewed verified by ORBi |
 | Kerimoglu, C., Sakib, M. S., Jain, G., Benito, E., Burkhardt, S., Capece, V., Kaurani, L., Halder, R., Carlos Agı´s-Balboa, R., Stilling, R., Urbanke, H., Kranz, A., Stewart, A. F., & Fiascher, A. (2017). KMT2A and KMT2B Mediate Memory Function by Affecting Distinct Genomic Regions. Cell Reports. doi:10.1016/j.celrep.2017.06.072 Peer Reviewed verified by ORBi |
Greenhalgh, K., Fritz, J., Letellier, E., Ramiro Garcia, J., Halder, R., Frachet Bour, A., Baginska, J., Ternes, D., Jäger, C., Haan, S., & Wilmes, P. (2017). A study of the molecular mechanisms underlying teh response of human colorectal adenomacarcinoma enterocytes to prebiotics and probiotics [Poster presentation]. ISAPP conference. |
 | Pena Centeno, T., Shomroni, O., Hennion, M., Halder, R., Vidal, R., Rahaman, R.-U., & Bonn, S. (2016). Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. Scientific Data. doi:10.1038/sdata.2016.90 Peer Reviewed verified by ORBi |
 | Halder, R., Hennion, M., Vidal, R., Shomroni, O., Rahaman, R.-U., Rajput, A., Pena Centeno, T., van Bebber, F., Capece, V., Garcia Vizcaino, J., Schuetz, A.-L., Burkhardt, S., Benito, E., Navarro Sala, M., Bahari Javan, S., Haass, C., Schmid, B., Fischer, A., & Bonn, S. (2015). DNA methylation changes in plasticity genes accompany the formation and maintenance of memory. Nature Neuroscience. doi:10.1038/nn.4194 Peer Reviewed verified by ORBi |