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Health Science staff profile

 

Dr Gregory Gimenez

PositionSenior Research Fellow
DepartmentDepartment of Pathology (DSM)
Research summaryGenomics, bioinformatics

Research

My research interests are in genomics and bioinformatics, focused on Next Generation Sequencing (NGS) and their translational applications towards a better understanding of immunological and pathologic issues.

Publications

Rossi, L., Cassella, L., Iacopetti, P., Ghezzani, C., Tana, L., Gimenez, G., … Salvetti, A. (2018). Insight into stem cell regulation from sub-lethally irradiated worms. Gene, 662, 37-45. doi: 10.1016/j.gene.2018.04.009

Torre, C., Abnave, P., Tsoumtsa, L. L., Mottola, G., Lepolard, C., Trouplin, V., Gimenez, G., … Ghigo, E. (2017). Staphylococcus aureus promotes Smed-PGRP-2/Smed-setd8-1 Methyltransferase signalling in planarian neoblasts to sensitize anti-bacterial gene responses during re-infection. EBioMedicine, 20, 150-160. doi: 10.1016/j.ebiom.2017.04.031

Tsoumtsa, L. L., Torre, C., Trouplin, V., Coiffard, B., Gimenez, G., Mege, J.-L., & Ghigo, E. (2017). Antimicrobial capacity of the freshwater planarians against S.aureus is under the control of Timeless. Virulence, 8(7), 1160-1169. doi: 10.1080/21505594.2016.1276689

Mossadegh-Keller, N., Gentek, R., Gimenez, G., Bigot, S., Mailfert, S., & Sieweke, M. H. (2017). Developmental origin and maintenance of distinct testicular macrophage populations. Journal of Experimental Medicine, 214(10), 2829-2841. doi: 10.1084/jem.20170829

Lateef, Z., Gimenez, G., Baker, E. S., & Ward, V. K. (2017). Transcriptomic analysis of human norovirus NS1-2 protein highlights a multifunctional role in murine monocytes. BMC Genomics, 18, 39. doi: 10.1186/s12864-016-3417-4

Journal - Research Article

Rossi, L., Cassella, L., Iacopetti, P., Ghezzani, C., Tana, L., Gimenez, G., … Salvetti, A. (2018). Insight into stem cell regulation from sub-lethally irradiated worms. Gene, 662, 37-45. doi: 10.1016/j.gene.2018.04.009

Torre, C., Abnave, P., Tsoumtsa, L. L., Mottola, G., Lepolard, C., Trouplin, V., Gimenez, G., … Ghigo, E. (2017). Staphylococcus aureus promotes Smed-PGRP-2/Smed-setd8-1 Methyltransferase signalling in planarian neoblasts to sensitize anti-bacterial gene responses during re-infection. EBioMedicine, 20, 150-160. doi: 10.1016/j.ebiom.2017.04.031

Lateef, Z., Gimenez, G., Baker, E. S., & Ward, V. K. (2017). Transcriptomic analysis of human norovirus NS1-2 protein highlights a multifunctional role in murine monocytes. BMC Genomics, 18, 39. doi: 10.1186/s12864-016-3417-4

Mossadegh-Keller, N., Gentek, R., Gimenez, G., Bigot, S., Mailfert, S., & Sieweke, M. H. (2017). Developmental origin and maintenance of distinct testicular macrophage populations. Journal of Experimental Medicine, 214(10), 2829-2841. doi: 10.1084/jem.20170829

Tsoumtsa, L. L., Torre, C., Trouplin, V., Coiffard, B., Gimenez, G., Mege, J.-L., & Ghigo, E. (2017). Antimicrobial capacity of the freshwater planarians against S.aureus is under the control of Timeless. Virulence, 8(7), 1160-1169. doi: 10.1080/21505594.2016.1276689

Cassella, L., Salvetti, A., Iacopetti, P., Ippolito, C., Ghezzani, C., Gimenez, G., … Rossi, L. (2017). Putrescine independent wound response phenotype is produced by ODC-like RNAi in planarians. Scientific Reports, 7, 9736. doi: 10.1038/s41598-017-09567-6

Soucie, E. L., Weng, Z., Geirsdóttir, L., Molawi, K., Maurizio, J., Fenouil, R., … Gimenez, G., … Sieweke, M. H. (2016). Lineage-specific enhancers activate self-renewal genes in macrophages and embryonic stem cells. Science, 351(6274), aad5510. doi: 10.1126/science.aad5510

Gimenez, G., Metcalf, P., Paterson, N. G., & Sharpe, M. L. (2016). Mass spectrometry analysis and transcriptome sequencing reveal glowing squid crystal proteins are in the same superfamily as firefly luciferase. Scientific Reports, 6, 27638. doi: 10.1038/srep27638

Sharpe, M. L., Dearden, P. K., Gimenez, G., & Krause, K. L. (2015). Comparative RNA seq analysis of the New Zealand glowworm Arachnocampa luminosa reveals bioluminescence-related genes. BMC Genomics, 16, 825. doi: 10.1186/s12864-015-2006-2

Abnave, P., Mottola, G., Gimenez, G., Boucherit, N., Trouplin, V., Torre, C., … Ghigo, E. (2014). Screening in planarians identifies MORN2 as a key component in LC3-associated phagocytosis and resistance to bacterial infection. Cell Host & Microbe, 16(3), 338-350. doi: 10.1016/j.chom.2014.08.002

Rolain, J. M., Vayssier-Taussat, M., Saisongkorh, W., Merhej, V., Gimenez, G., Robert, C., … Raoult, D. (2013). Partial disruption of translational and posttranslational machinery reshapes growth rates of Bartonella birtlesii. mBio, 4(2), e00115-13. doi: 10.1128/mBio.00115-13

Colson, P., Fancello, L., Gimenez, G., Armougom, F., Desnues, C., Fournous, G., … Raoult, D. (2013). Evidence of the megavirome in humans. Journal of Clinical Virology, 57(3), 191-200. doi: 10.1016/j.jcv.2013.03.018

Clarke, M., Lohan, A. J., Liu, B., Lagkouvardos, I., Roy, S., Zafar, N., … Gimenez, G., … Loftus, B. J. (2013). Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling. Genome Biology, 14, R11. doi: 10.1186/gb-2013-14-2-r11

Pradel, N., Ji, B., Gimenez, G., Talla, E., Lenoble, P., Garel, M., … Dolla, A. (2013). The first genomic and proteomic characterization of a deep-sea sulfate reducer: Insights into the piezophilic lifestyle of Desulfovibrio piezophilus. PLoS ONE, 8(1), e55130. doi: 10.1371/journal.pone.0055130

De la Cruz, M. A., Zhao, W., Farenc, C., Gimenez, G., Raoult, D., Cambillau, C., … Méresse, S. (2013). A toxin-antitoxin module of Salmonella promotes virulence in mice. PLoS Pathogens, 9(12), e1003827. doi: 10.1371/journal.ppat.1003827

Ji, B., Gimenez, G., Barbe, V., Vacherie, B., Rouy, Z., Amrani, A., … Pradel, N. (2013). Complete genome sequence of the piezophilic, mesophilic, sulfate-reducing bacterium Desulfovibrio hydrothermalis AM13T. Genome Announcements, 1(1), e00226-12. doi: 10.1128/genomeA.00226-12

Elbir, H., Robert, C., Nguyen, T. T., Gimenez, G., El Sanousi, S. M., Flock, J.-I., … Drancourt, M. (2013). Staphylococcus aureus subsp. anaerobius strain ST1464 genome sequence. Standards in Genomic Sciences, 9, 1. doi: 10.4056/sigs.3748294

Rolain, J.-M., Diene, S. M., Kempf, M., Gimenez, G., Robert, C., & Raoult, D. (2013). Real-time sequencing to decipher the molecular mechanism of resistance of a clinical pan-drug-resistant Acinetobacter baumannii isolate from Marseille, France. Antimicrobial Agents & Chemotherapy, 57(1), 592-596. doi: 10.1128/AAC.01314-12

Lagier, J.-C., Gimenez, G., Robert, C., Raoult, D., & Fournier, P.-E. (2012). Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov. Standards in Genomic Sciences, 7(2), 200-209. doi: 10.4056/sigs.3086474

Lagier, J.-C., Armougom, F., Million, M., Hugon, P., Pagnier, I., Robert, C., … Gimenez, G., … Raoult, D. (2012). Microbial culturomics: Paradigm shift in the human gut microbiome study. Clinical Microbiology & Infection, 18(12), 1185-1193. doi: 10.1111/1469-0691.12023

Roux, V., Robert, C., Gimenez, G., & Raoult, D. (2012). Draft genome sequence of Staphylococcus massiliensis strain 5402776T. Journal of Bacteriology, 194(24), 6984-6985. doi: 10.1128/JB.01909-12

Gorlas, A., Gimenez, G., Raoult, D., & Roux, V. (2012). Draft genome sequences of Actinomyces timonensis strain 7400942T and its prophage. Journal of Bacteriology, 194(23), 6613-6614. doi: 10.1128/JB.01730-12

Rolain, J.-M., Vayssier-Taussat, M., Gimenez, G., Robert, C., Fournier, P.-E., & Raoult, D. (2012). Genome sequence of Bartonella birtlesii, a bacterium isolated from small rodents of the genus Apodemus. Journal of Bacteriology, 194(17), 4779. doi: 10.1128/JB.01044-12

Roux, V., Robert, C., Gimenez, G., Gharbi, R., & Raoult, D. (2012). Draft genome sequence of Actinomyces massiliensis strain 4401292T. Journal of Bacteriology, 194(18), 5121. doi: 10.1128/JB.01039-12

Mishra, A. K., Gimenez, G., Lagier, J.-C., Robert, C., Raoult, D., & Fournier, P.-E. (2012). Genome sequence and description of Alistipes senegalensis sp. nov. Standards in Genomic Sciences, 6(3), 304-314. doi: 10.4056/sigs.2625821

Sharma, P., Diene, S. M., & Gimenez, G. (2012). Genome sequence of Microbacterium yannicii, a bacterium isolated from a cystic fibrosis patient. Journal of Bacteriology, 194(17), 4785. doi: 10.1128/JB.01088-12

Gorlas, A., Robert, C., Gimenez, G., Drancourt, M., & Raoult, D. (2012). Complete genome sequence of Methanomassiliicoccus luminyensis, the largest genome of a human-associated Archaea species. Journal of Bacteriology, 194(17), 4745. doi: 10.1128/JB.00956-12

Oulmi, L., Gorlas, G., Gimenez, G., Robert, C., Boulahrouf, A., Raoult, D., & Roux, V. (2012). Draft genome sequence of Tsukamurella sp. strain 1534. Journal of Bacteriology, 194(19), 5482-5483. doi: 10.1128/JB.01279-12

Roux, V., Robert, C., Gimenez, G., & Raoult, D. (2012). Draft genome sequence of Brevibacterium massiliense strain 541308T. Journal of Bacteriology, 194(18), 5151-5152. doi: 10.1128/JB.01182-12

Haitham, E., Gimenez, G., Sokhna, C., Desalegn Bilcha, K., Ali, J., Barker, S. C., … Drancourt, M. (2012). Multispacer sequence typing relapsing fever borreliae in africa. PLoS Neglected Tropical Diseases, 6(6), e1652. doi: 10.1371/journal.pntd.0001652

Elbir, H., Gimenez, G., Robert, C., Bergström, S., Cutler, S., Raoult, D., & Drancourt, M. (2012). Complete genome sequence of Borrelia crocidurae. Journal of Bacteriology, 194(14), 3723-3724. doi: 10.1128/JB.00118-12

Gimenez, G., Bertelli, C., Moliner, C., Robert, C., Raoult, D., Fournier, P.-E., & Greub, G. (2011). Insight into cross-talk between intra-amoebal pathogens. BMC Genomics, 12, 542. doi: 10.1186/1471-2164-12-542

Colson, P., Gimenez, G., Boyer, M., Fournous, G., & Raoult, D. (2011). The giant Cafeteria roenbergensis virus that infects a widespread marine phagocytic protist is a new member of the fourth domain of life. PLoS ONE, 6(4), e18935. doi: 10.1371/journal.pone.0018935

Audoly, G., Vincentelli, R., Edouard, S., Georgiades, K., Mediannikov, O., Gimenez, G., … Raoult, D. (2011). Effect of rickettsial toxin vapC on its eukaryotic host. PLoS ONE, 6(10), e26528. doi: 10.1371/journal.pone.0026528

Boyer, M., Gimenez, G., Suzan-Monti, M., & Raoult, D. (2010). Classification and determination of possible origins of ORFans through analysis of nucleocytoplasmic large DNA viruses. Intervirology, 53(5), 310-320. doi: 10.1159/000312916

Li, W., Ortiz, G., Fournier, P.-E., Gimenez, G., Reed, D. L., Pittendrigh, B., & Raoult, D. (2010). Genotyping of human lice suggests multiple emergences of body lice from local head louse populations. PLoS Neglected Tropical Diseases, 4(3), e641. doi: 10.1371/journal.pntd.0000641

Boyer, M., Madoui, M.-A., Gimenez, G., La Scola, B., & Raoult, D. (2010). Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4th domain of life including giant viruses. PLoS ONE, 5(12), e15530. doi: 10.1371/journal.pone.0015530

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Journal - Research Other

Fournier, P.-E., Gouriet, F., Gimenez, G., Robert, C., & Raoult, D. (2013). Deciphering genomic virulence traits of a Staphylococcus epidermidis strain causing native-valve endocarditis. Journal of Clinical Microbiology, 51(5), 1617-1621. doi: 10.1128/JCM.02820-12

Salgado, D., Gimenez, G., Coulier, F., & Marcelle, C. (2008). COMPARE, a multi-organism system for cross-species data comparison and transfer of information. Bioinformatics, 24(3), 447-449. doi: 10.1093/bioinformatics/btm599

Deutsch, E. W., Ball, C. A., Berman, J. J., Bova, G. S., Brazma, A., Bumgarner, R. E., … Gimenez, G., … True, L. D. (2008). Minimum information specification for in situ hybridization and imminohistochemistry experiments (MISFISHIE). Nature Biotechnology, 26, 305-312. doi: 10.1038/nbt1391

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