aminen

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Academic interests

I am a scientist interested in bioinformatics, microbial genomics and evolution. I obtained my doctoral degree in 2008. I was involved in several international projects. First, to understand the driven forces that shape the genome diversity of the tubercle bacilli, Mycobacterium tuberculosis. Second, to trace back the evolutionary history of outbreak clones with particular interest to multidrug resistance ones and third, to combine different omics data for tuberculosis drug discovery.

Since October 2016, I joined the Medplag (The medieval plagues: ecology, transmission modalities and routes of the infections) group at the Centre for Ecological and Evolutionary Synthesis. I will analyse genomic and metagenomics data from modern and ancient DNA samples of Yersinia pestis, the causative agent of plague. By combining genomics and phylogenomics, my main objective will be to reconstruct the evolutionary history of the Yersinia pestis isolates whose ancient DNAs were recovered from different archaeological sites through Europe.

Tags: Evolution, Genomics, Bioinformatics, Phylogenomics, Epidemiology

Publications

  • Bernard-Raichon, Lucie; Colom, André; Monard, Sarah C.; Namouchi, Amine; Cescato, Margaux & Garnier, Hugo [Show all 20 contributors for this article] (2021). A pulmonary lactobacillus murinus strain induces th17 and rorγt+ regulatory t cells and reduces lung inflammation in tuberculosis. Journal of Immunology. ISSN 0022-1767. 207(7), p. 1857–1870. doi: 10.4049/jimmunol.2001044.
  • Guellil, Meriam; Kersten, Oliver; Namouchi, Amine; Luciani, Stefania; Marota, Isolina & Arcini, Caroline [Show all 17 contributors for this article] (2020). A genomic and historical synthesis of plague in 18th century Eurasia. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 117(45), p. 28328–28335. doi: 10.1073/pnas.2009677117. Full text in Research Archive
  • Namouchi, Amine; Guellil, Meriam; Kersten, Oliver; Hänsch, Stephanie; Ottoni, Claudio & Schmid, Boris Valentijn [Show all 16 contributors for this article] (2018). Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 115(50), p. E11790–E11797. doi: 10.1073/pnas.1812865115. Full text in Research Archive
  • Guellil, Meriam; Kersten, Oliver; Namouchi, Amine; Bauer, Egil Lindhart; Derrick, Michael & Jensen, Anne Østergaard [Show all 8 contributors for this article] (2018). Genomic blueprint of a relapsing fever pathogen in 15th century Scandinavia. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 115(41), p. 10422–10427. doi: 10.1073/pnas.1807266115. Full text in Research Archive
  • Namouchi, Amine; Cimino, Mena; Favre-Rochex, Sandrine; Charles, Patricia & Gicquel, Brigitte (2017). Phenotypic and genomic comparison of Mycobacterium aurum and surrogate model species to Mycobacterium tuberculosis: Implications for drug discovery. BMC Genomics. ISSN 1471-2164. 18(1), p. 1–9. doi: 10.1186/s12864-017-3924-y.
  • Frye, Stephan Alfons; Beyene, Getachew Tesfaye; Namouchi, Amine; Munoz, Marta Gomez; Homberset, Håvard & Kalayou, Shewit [Show all 9 contributors for this article] (2017). The helicase DinG responds to stress due to DNA double strand breaks. PLOS ONE. ISSN 1932-6203. 12:e0187900(11), p. 1–23. doi: 10.1371/journal.pone.0187900.
  • Meftahi, Nedra; Namouchi, Amine; Mhenni, Besma; Brandis, Gerrit; Hughes, Diarmaid & Mardassi, Helmi (2016). Evidence for the critical role of a secondary site rpoB mutation in the compensatory evolution and successful transmission of an MDR tuberculosis outbreak strain. Journal of Antimicrobial Chemotherapy. ISSN 0305-7453. 71(2), p. 324–332. doi: 10.1093/jac/dkv345.
  • Beyene, Getachew Tesfaye; Balasingham, Seetha; Frye, Stephan Alfons; Namouchi, Amine; Homberset, Håvard & Kalayou, Shewit [Show all 8 contributors for this article] (2016). Characterization of the Neisseria meningitidis Helicase RecG. PLOS ONE. ISSN 1932-6203. 11:e0164588(10), p. 1–31. doi: 10.1371/journal.pone.0164588.
  • Namouchi, Amine; Gomez Munoz, Marta; Frye, Stephan Alfons; Moen, Line Victoria; Rognes, Torbjørn & Tonjum, Tone [Show all 7 contributors for this article] (2016). The Mycobacterium tuberculosis transcriptional landscape under genotoxic stress. BMC Genomics. ISSN 1471-2164. 17:791, p. 1–13. doi: 10.1186/s12864-016-3132-1. Full text in Research Archive
  • Yimer, Solomon Abebe; Namouchi, Amine; Zegeye, Ephrem Debebe; Holm-Hansen, Carol J C; Norheim, Gunnstein & Abebe, Markos [Show all 8 contributors for this article] (2016). Deciphering the recent phylogenetic expansion of the originally deeply rooted Mycobacterium tuberculosis lineage 7. BMC Evolutionary Biology. ISSN 1471-2148. 16:146, p. 1–10. doi: 10.1186/s12862-016-0715-z. Full text in Research Archive
  • Thabet, Sara; Namouchi, Amine & Mardassi, Helmi (2015). Evolutionary trends of the transposase-encoding open reading frames A and B (orfA and orfB) of the mycobacterial IS6110 insertion sequence. PLOS ONE. ISSN 1932-6203. 10:e0130161(6). doi: 10.1371/journal.pone.0130161.
  • Yimer, Solomon Abebe; Norheim, Gunnstein; Namouchi, Amine; Zegeye, Ephrem Debebe; Kinander, Wibeke & Tonjum, Tone [Show all 11 contributors for this article] (2015). Mycobacterium tuberculosis lineage 7 strains are associated with prolonged patient delay in seeking treatment for pulmonary tuberculosis in Amhara region, Ethiopia. Journal of Clinical Microbiology. ISSN 0095-1137. 53(4), p. 1301–1309. doi: 10.1128/JCM.03566-14.

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  • Namouchi, Amine; Guellil, Meriam; Kersten, Oliver Sven; Hänsch, Stephanie; Ottoni, Claudio & Schmid, Boris Valentijn [Show all 16 contributors for this article] (2020). Correction for Namouchi et al., Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 17(22). doi: 10.1073/pnas.2007983117.
  • Bramanti, Barbara; Namouchi, Amine; Schmid, Boris Valentijn; Dean, Katharine Rose & Stenseth, Nils Christian (2019). Reply to Barbieri et al.: Out of the Land of Darkness: Plague on the fur trade routes. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 116(16). doi: 10.1073/pnas.1902274116.
  • To, Thu-Hien; Grønvold, Lars; Nome, Torfinn; Namouchi, Amine; Våge, Dag Inge & Sandve, Simen Rød (2019). A salmonid ohnology pipeline.
  • Namouchi, Amine; Nome, Torfinn; To, Thu-Hien; Grønvold, Lars; Sandve, Simen Rød & Våge, Dag Inge (2019). SalmoBase2.0: An integrative genomic data resource for salmonids.
  • Bramanti, Barbara; Namouchi, Amine; Schmid, Boris Valentijn; Dean, Katharine Rose & Stenseth, Nils Christian (2019). Out of the land of darkness: Plague on the fur trade routes. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 116(16), p. 7622–7623. doi: 10.1073/pnas.1902274116.
  • Zegeye, Ephrem Debebe; Gómez-Muñoz, Marta; Namouchi, Amine; Balasingham, Seetha; Szpinda, Irena & Förstner, Konrad [Show all 8 contributors for this article] (2019). A nutrient supplement promotes the rapid detection and improved sensitivity of mycobacteria in clinical samples via the differential regulation of dormancy genes and noncoding RNAs.
  • Namouchi, Amine (2017). Revisiting the evolutionary history of Yersinia pestis: Zooming into the second pandemic with new ancient genomes.
  • Frye, Stephan Alfons; Balasingham, Seetha; Beyene, Getachew Tesfaye; Homberset, Håvard; Namouchi, Amine & Tonjum, Tone (2016). Meningococcal DNA binding and unwinding proteins.
  • Gomez Munoz, Marta; Namouchi, Amine; Balasingham, Seetha & Tonjum, Tone (2016). Identifiying ncRNAs expressed under genotoxic stress and dormancy in Mycobacterium tuberculosis.
  • Yimer, Solomon Abebe; Namouchi, Amine; Riaz, Tahira; Zegeye, Ephrem Debebe; Godana, Alemayehu & Holm-Hansen, Carol J C [Show all 9 contributors for this article] (2015). Genomic and proteomic analysis of Mycobacterium tuberculosis lineage 7 strains from Ethiopia. Oral presentation at the 46th Union World Conference on Lung Health Cape Town, South Africa: 2 December - 6 December 2015.
  • Yimer, Solomon Abebe; Norheim, Gunnstein; Namouchi, Amine; Zegeye, Ephrem Debebe; Kinander, Wibeke & Tonjum, Tone [Show all 9 contributors for this article] (2015). Lineage 7 Mycobacterium tuberculosis strains are associated with longer patient delay in pulmonary TB patients.
  • Tonjum, Tone; Balasingham, Seetha; Yimer, Solomon Abebe & Namouchi, Amine (2015). Outbreak of tuberculosis in a Norwegian dance academy delineated by whole genome sequencing and high end mass spectrometry.
  • Tonjum, Tone; Balasingham, Seetha; Namouchi, Amine & Yimer, Solomon Abebe (2015). Recent evolution in Mycobacterium tuberculosis: Genome dynamics, small RNAs and vesicles .
  • Namouchi, Amine (2015). Mycobacterium tuberculosis in the era of next generation sequencing.
  • Namouchi, Amine; Gómez-Muñoz, Marta; Debebe, Ephrem; Frye, Stephan Alfons; Tonjum, Tone & Balasingham, Seetha (2015). Global transcriptional responses to genotoxic stress in Mycobacterium tuberculosis .

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Published Dec. 8, 2016 1:31 PM - Last modified Dec. 8, 2016 2:52 PM

Projects

No ongoing projects