Publication List

2023

  • Bintener T, Pacheco MP, Philippidou D, Margue C, Kishk A, Del Mistro G, Di Leo L, Moscardó Garcia M, Halder R, Sinkkonen L, De Zio D, Kreis S, Kulms D, Sauter T. Metabolic modelling-based in silico drug target prediction identifies six novel repurposable drugs for melanoma. Cell Death Dis. 2023 Jul 26;14(7):468. doi: 10.1038/s41419-023-05955-1. PMID: 37495601; PMCID: PMC10372000.
  • Pavlou MAS, Singh K, Ravichandran S, Halder R, Nicot N, Birck C, Grandbarbe L, Del Sol A, Michelucci A. Transcriptional and Chromatin Accessibility Profiling of Neural Stem Cells Differentiating into Astrocytes Reveal Dynamic Signatures Affected under Inflammatory Conditions. Cells. 2023 Mar 21;12(6):948. doi: 10.3390/cells12060948. PMID: 36980289; PMCID: PMC10047363.
  • de Nies L, Galata V, Martin-Gallausiaux C, Despotovic M, Busi SB, Snoeck CJ, Delacour L, Budagavi DP, Laczny CC, Habier J, Lupu PC, Halder R, Fritz JV, Marques T, Sandt E, O’Sullivan MP, Ghosh S, Satagopam V; CON-VINCE Consortium; Krüger R, Fagherazzi G, Ollert M, Hefeng FQ, May P, Wilmes P. Altered infective competence of the human gut microbiome in COVID-19. Microbiome. 2023 Mar 9;11(1):46. doi: 10.1186/s40168-023-01472-7. PMID: 36894986; PMCID: PMC9995755.

2022

  • Tranchevent LC, Halder R, Glaab E. Systems level analysis of sex-dependent gene expression changes in Parkinson’s disease. NPJ Parkinsons Dis. 2023 Jan 21;9(1):8. doi: 10.1038/s41531-023-00446-8. PMID: 36681675; PMCID: PMC9867746.
  • Balta MG, Schreurs O, Halder R, Küntziger TM, Saetre F, Blix IJS, Baekkevold ES, Glaab E, Schenck K. RvD1n-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. Int J Mol Sci. 2022 Nov 28;23(23):14878. doi: 10.3390/ijms232314878. PMID: 36499208; PMCID: PMC9737907.
  • Pires-Afonso Y, Muller A, Grzyb K, Oudin A, Yabo YA, Sousa C, Scafidi A, Poli A, Cosma A, Halder R, Coowar D, Golebiewska A, Skupin A, Niclou SP, Michelucci A. Elucidating tumour-associated microglia/macrophage diversity along glioblastoma progression and under ACOD1 deficiency. Mol Oncol. 2022 Sep;16(17):3167-3191. doi: 10.1002/1878-0261.13287. Epub 2022 Aug 15. PMID: 35838338; PMCID: PMC9441003.
  • Ali M, Huarte OU, Heurtaux T, Garcia P, Rodriguez BP, Grzyb K, Halder R, Skupin A, Buttini M, Glaab E. Single-Cell Transcriptional Profiling and Gene Regulatory Network Modeling in Tg2576 Mice Reveal Gender-Dependent Molecular Features Preceding Alzheimer-Like Pathologies. Mol Neurobiol. 2022 Aug 18. doi: 10.1007/s12035-022-02985-2. Epub ahead of print. PMID: 35980567.
  • de Nies L, Busi SB, Tsenkova M, Halder R, Letellier E, Wilmes P. Evolution of the murine gut resistome following broad-spectrum antibiotic treatment. Nat Commun. 2022 Apr 28;13(1):2296. doi: 10.1038/s41467-022-29919-9. PMID: 35484157; PMCID: PMC9051133.
  • Del Mistro G, Riemann S, Schindler S, Beissert S, Kontermann RE, Ginolhac A, Halder R, Presta L, Sinkkonen L, Sauter T, Kulms D. Focal adhesion kinase plays a dual role in TRAIL resistance and metastatic outgrowth of malignant melanoma. Cell Death Dis. 2022 Jan 12;13(1):54. doi: 10.1038/s41419-022-04502-8. PMID: 35022419; PMCID: PMC8755828.

2021

  • De Saedeleer B, Malabirade A, Ramiro-Garcia J, Habier J, Trezzi JP, Peters SL, Daujeumont A, Halder R, Jäger C, Busi SB, May P, Oertel W, Mollenhauer B, Laczny CC, Hettich RL, Wilmes P. Systematic characterization of human gut microbiome-secreted molecules by integrated multi-omics. ISME Commun. 2021 Dec 21;1:82. doi: 10.1038/s43705-021-00078-0. PMID: 35106519; PMCID: PMC7612290.
  • Van Den Bossche T, Kunath BJ, Schallert K, Schäpe SS, Abraham PE, Armengaud J, Arntzen MØ, Bassignani A, Benndorf D, Fuchs S, Giannone RJ, Griffin TJ, Hagen LH, Halder R, Henry C, Hettich RL, Heyer R, Jagtap P, Jehmlich N, Jensen M, Juste C, Kleiner M, Langella O, Lehmann T, Leith E, May P, Mesuere B, Miotello G, Peters SL, Pible O, Queiros PT, Reichl U, Renard BY, Schiebenhoefer H, Sczyrba A, Tanca A, Trappe K, Trezzi JP, Uzzau S, Verschaffelt P, von Bergen M, Wilmes P, Wolf M, Martens L, Muth T. Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nat Commun. 2021 Dec 15;12(1):7305. doi: 10.1038/s41467-021-27542-8. PMID: 34911965; PMCID: PMC8674281.
  • Galata V, Busi SB, Kunath BJ, de Nies L, Calusinska M, Halder R, May P, Wilmes P, Laczny CC. Functional meta-omics provide critical insights into long- and short-read assemblies. Brief Bioinform. 2021 Nov 5;22(6):bbab330. doi: 10.1093/bib/bbab330. PMID: 34453168; PMCID: PMC8575027.
  • Uriarte Huarte O, Kyriakis D, Heurtaux T, Pires-Afonso Y, Grzyb K, Halder R, Buttini M, Skupin A, Mittelbronn M, Michelucci A. Single-Cell Transcriptomics and In Situ Morphological Analyses Reveal Microglia Heterogeneity Across the Nigrostriatal Pathway. Front Immunol. 2021 Mar 29;12:639613. doi: 10.3389/fimmu.2021.639613. PMID: 33854507; PMCID: PMC8039119.
  • Busi SB, de Nies L, Habier J, Wampach L, Fritz JV, Heintz-Buschart A, May P, Halder R, de Beaufort C, Wilmes P. Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life. ISME Commun. 2021 Mar 26;1(1):8. doi: 10.1038/s43705-021-00003-5. PMID: 36717704; PMCID: PMC9723731.

2020

  • Hayoun K, Geersens E, Laczny CC, Halder R, Lázaro Sánchez C, Manna A, Bringel F, Ryckelynck M, Wilmes P, Muller EEL, Alpha-Bazin B, Armengaud J, Vuilleumier S. Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics. Microorganisms. 2020 Nov 27;8(12):1876. doi: 10.3390/microorganisms8121876. PMID: 33260855; PMCID: PMC7760279.
  • Busi SB, Pramateftaki P, Brandani J, Fodelianakis S, Peter H, Halder R, Wilmes P, Battin TJ. Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams. PeerJ. 2020 Oct 27;8:e9973. doi: 10.7717/peerj.9973. PMID: 33194372; PMCID: PMC7597623.
  • Gui Y, Thomas MH, Garcia P, Karout M, Halder R, Michelucci A, Kollmus H, Zhou C, Melmed S, Schughart K, Balling R, Mittelbronn M, Nadeau JH, Williams RW, Sauter T, Buttini M, Sinkkonen L. Pituitary Tumor Transforming Gene 1 Orchestrates Gene Regulatory Variation in Mouse Ventral Midbrain During Aging. Front Genet. 2020 Sep 23;11:566734. doi: 10.3389/fgene.2020.566734. PMID: 33173537; PMCID: PMC7538689.
  • Marynowska M, Goux X, Sillam-Dussès D, Rouland-Lefèvre C, Halder R, Wilmes P, Gawron P, Roisin Y, Delfosse P, Calusinska M. Compositional and functional characterisation of biomass-degrading microbial communities in guts of plant fibre- and soil-feeding higher termites. Microbiome. 2020 Jun 23;8(1):96. doi: 10.1186/s40168-020-00872-3. PMID: 32576253; PMCID: PMC7313118.
  • Calusinska M, Marynowska M, Bertucci M, Untereiner B, Klimek D, Goux X, Sillam-Dussès D, Gawron P, Halder R, Wilmes P, Ferrer P, Gerin P, Roisin Y, Delfosse P. Integrative omics analysis of the termite gut system adaptation to Miscanthus diet identifies lignocellulose degradation enzymes. Commun Biol. 2020 Jun 1;3(1):275. doi: 10.1038/s42003-020-1004-3. PMID: 32483294; PMCID: PMC7264248.
  • Kurniawan H, Franchina DG, Guerra L, Bonetti L, -Baguet LS, Grusdat M, Schlicker L, Hunewald O, Dostert C, Merz MP, Binsfeld C, Duncan GS, Farinelle S, Nonnenmacher Y, Haight J, Das Gupta D, Ewen A, Taskesen R, Halder R, Chen Y, Jäger C, Ollert M, Wilmes P, Vasiliou V, Harris IS, Knobbe-Thomsen CB, Turner JD, Mak TW, Lohoff M, Meiser J, Hiller K, Brenner D. Glutathione Restricts Serine Metabolism to Preserve Regulatory T Cell Function. Cell Metab. 2020 May 5;31(5):920-936.e7. doi: 10.1016/j.cmet.2020.03.004. Epub 2020 Mar 25. PMID: 32213345; PMCID: PMC7265172.

2019

  • Gomez-Giro G, Arias-Fuenzalida J, Jarazo J, Zeuschner D, Ali M, Possemis N, Bolognin S, Halder R, Jäger C, Kuper WFE, van Hasselt PM, Zaehres H, Del Sol A, van der Putten H, Schöler HR, Schwamborn JC. Synapse alterations precede neuronal damage and storage pathology in a human cerebral organoid model of CLN3-juvenile neuronal ceroid lipofuscinosis. Acta Neuropathol Commun. 2019 Dec 30;7(1):222. doi: 10.1186/s40478-019-0871-7. PMID: 31888773; PMCID: PMC6937812.
  • Bernatz S, Ilina EI, Devraj K, Harter PN, Mueller K, Kleber S, Braun Y, Penski C, Renner C, Halder R, Jennewein L, Solbach C, Thorsen F, Pestalozzi BC, Mischo A, Mittelbronn M. Impact of Docetaxel on blood-brain barrier function and formation of breast cancer brain metastases. J Exp Clin Cancer Res. 2019 Oct 29;38(1):434. doi: 10.1186/s13046-019-1427-1. PMID: 31665089; PMCID: PMC6819416.
  • Nickels SL, Walter J, Bolognin S, Gérard D, Jaeger C, Qing X, Tisserand J, Jarazo J, Hemmer K, Harms A, Halder R, Lucarelli P, Berger E, Antony PMA, Glaab E, Hankemeier T, Klein C, Sauter T, Sinkkonen L, Schwamborn JC. Impaired serine metabolism complements LRRK2-G2019S pathogenicity in PD patients. Parkinsonism Relat Disord. 2019 Oct;67:48-55. doi: 10.1016/j.parkreldis.2019.09.018. Epub 2019 Sep 19. PMID: 31621607.
  • Greenhalgh K, Ramiro-Garcia J, Heinken A, Ullmann P, Bintener T, Pacheco MP, Baginska J, Shah P, Frachet A, Halder R, Fritz JV, Sauter T, Thiele I, Haan S, Letellier E, Wilmes P. Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells. Cell Rep. 2019 Apr 30;27(5):1621-1632.e9. doi: 10.1016/j.celrep.2019.04.001. PMID: 31042485.
  • Linnartz-Gerlach B, Bodea LG, Klaus C, Ginolhac A, Halder R, Sinkkonen L, Walter J, Colonna M, Neumann H. TREM2 triggers microglial density and age- related neuronal loss. Glia. 2019 Mar;67(3):539-550. doi: 10.1002/glia.23563. Epub 2018 Dec 11. PMID: 30548312; PMCID: PMC6590266.
  • Gérard D, Schmidt F, Ginolhac A, Schmitz M, Halder R, Ebert P, Schulz MH, Sauter T, Sinkkonen L. Temporal enhancer profiling of parallel lineages identifies AHR and GLIS1 as regulators of mesenchymal multipotency. Nucleic Acids Res. 2019 Feb 20;47(3):1141-1163. doi: 10.1093/nar/gky1240. PMID: 30544251; PMCID: PMC6380961.

2018

  • Wampach L, Heintz-Buschart A, Fritz JV, Ramiro-Garcia J, Habier J, Herold M, Narayanasamy S, Kaysen A, Hogan AH, Bindl L, Bottu J, Halder R, Sjöqvist C, May P, Andersson AF, de Beaufort C, Wilmes P. Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential. Nat Commun. 2018 Nov 30;9(1):5091. doi: 10.1038/s41467-018-07631-x. PMID: 30504906; PMCID: PMC6269548.
  • Kirchmeyer M, Servais FA, Hamdorf M, Nazarov PV, Ginolhac A, Halder R, Vallar L, Glanemann M, Rubie C, Lammert F, Kreis S, Behrmann I. Cytokine- mediated modulation of the hepatic miRNome: miR-146b-5p is an IL-6-inducible miRNA with multiple targets. J Leukoc Biol. 2018 Nov;104(5):987-1002. doi: 10.1002/JLB.MA1217-499RR. Epub 2018 Aug 26. PMID: 30145833.
  • Malabirade A, Habier J, Heintz-Buschart A, May P, Godet J, Halder R, Etheridge A, Galas D, Wilmes P, Fritz JV. The RNA Complement of Outer Membrane Vesicles From Salmonella enterica Serovar Typhimurium Under Distinct Culture Conditions. Front Microbiol. 2018 Aug 30;9:2015. doi: 10.3389/fmicb.2018.02015. PMID: 30214435; PMCID: PMC6125333.