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Health Sciences profile

Dr Gregory Gimenez

PositionSenior Research Fellow
DepartmentDepartment of Pathology (Dunedin)
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

Ahn, A., Rodger, E. J., Motwani, J., Gimenez, G., Stockwell, P. A., Parry, M., … Chatterjee, A., & Eccles, M. R. (2021). Transcriptional reprogramming and constitutive PD-L1 expression in melanoma are associated with dedifferentiation and activation of interferon and tumour necrosis factor signalling pathways. Cancers, 13, 4250. doi: 10.3390/cancers13174250

Wade, E. M., Jenkins, Z. A., Morgan, T., Gimenez, G., Gibson, H., Peng, H., … Robertson, S. P. (2021). Exon skip-inducing variants in FLNA in an attenuated form of frontometaphyseal dysplasia. American Journal of Medical Genetics Part A. Advance online publication. doi: 10.1002/ajmg.a.62424

Tran, K. B., Gimenez, G., Tsai, P., Kolekar, S., Rodger, E., Chatterjee, A., … Eccles, M. R., … Shepherd, P. R. (2021). Genomic and signalling pathway characterisation of the NZM panel of melanoma cell lines: A valuable model for studying the impact of genetic diversity in melanoma. Pigment Cell & Melanoma Research, 34(1), 136-143. doi: 10.1111/pcmr.12908

Chin, C. V., Antony, J., Ketharnathan, S., Labudina, A., Gimenez, G., Parsons, K. M., … Braithwaite, A., Guilford, P., … Horsfield, J. A. (2020). Cohesin mutations are synthetic lethal with stimulation of WNT signaling. eLIFE, 9, e61405. doi: 10.7554/eLife.61405

Antony, J., Gimenez, G., Taylor, T., Khatoon, U., Day, R., Morison, I. M., & Horsfield, J. A. (2020). BET inhibition prevents aberrant RUNX1 and ERG transcription in STAG2 mutant leukaemia cells. Journal of Molecular Cell Biology, 12(5), 397-399. doi: 10.1093/jmcb/mjz114

Ahn, A., Rodger, E. J., Motwani, J., Gimenez, G., Stockwell, P. A., Parry, M., … Chatterjee, A., & Eccles, M. R. (2021). Transcriptional reprogramming and constitutive PD-L1 expression in melanoma are associated with dedifferentiation and activation of interferon and tumour necrosis factor signalling pathways. Cancers, 13, 4250. doi: 10.3390/cancers13174250

Journal - Research Article

Wade, E. M., Jenkins, Z. A., Morgan, T., Gimenez, G., Gibson, H., Peng, H., … Robertson, S. P. (2021). Exon skip-inducing variants in FLNA in an attenuated form of frontometaphyseal dysplasia. American Journal of Medical Genetics Part A. Advance online publication. doi: 10.1002/ajmg.a.62424

Journal - Research Article

Chin, C. V., Antony, J., Ketharnathan, S., Labudina, A., Gimenez, G., Parsons, K. M., … Braithwaite, A., Guilford, P., … Horsfield, J. A. (2020). Cohesin mutations are synthetic lethal with stimulation of WNT signaling. eLIFE, 9, e61405. doi: 10.7554/eLife.61405

Journal - Research Article

Knapp, K. M., Sullivan, R., Murray, J., Gimenez, G., Arn, P., D'Souza, P., … Bicknell, L. S. (2020). Linked-read genome sequencing identifies biallelic pathogenic variants in DONSON as a novel cause of Meier-Gorlin syndrome. Journal of Medical Genetics, 57, 195-202. doi: 10.1136/jmedgenet-2019-106396

Journal - Research Article

Marsman, J., Gimenez, G., Day, R. C., Horsfield, J. A., & Jones, G. T. (2020). A non-coding genetic variant associated with abdominal aortic aneurysm alters ERG gene regulation. Human Molecular Genetics, 29(4), 554-565. doi: 10.1093/hmg/ddz256

Journal - Research Article

Kazantseva, M., Mehta, S., Eiholzer, R. A., Gimenez, G., Bowie, S., Campbell, H., Reily-Bell, A. L., … Ray, S., Drummond, C. J., Reid, G., … Wiles, A., Morrin, H. R., Reader, K. L., Hung, N. A., Baird, M. A., Slatter, T. L., & Braithwaite, A. W. (2019). The Δ133p53β isoform promotes an immunosuppressive environment leading to aggressive prostate cancer. Cell Death & Disease, 10, 631. doi: 10.1038/s41419-019-1861-1

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

Journal - Research Article

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

Journal - Research Article

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

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

Tran, K. B., Gimenez, G., Tsai, P., Kolekar, S., Rodger, E., Chatterjee, A., … Eccles, M. R., … Shepherd, P. R. (2021). Genomic and signalling pathway characterisation of the NZM panel of melanoma cell lines: A valuable model for studying the impact of genetic diversity in melanoma. Pigment Cell & Melanoma Research, 34(1), 136-143. doi: 10.1111/pcmr.12908

Journal - Research Other

Antony, J., Gimenez, G., Taylor, T., Khatoon, U., Day, R., Morison, I. M., & Horsfield, J. A. (2020). BET inhibition prevents aberrant RUNX1 and ERG transcription in STAG2 mutant leukaemia cells. Journal of Molecular Cell Biology, 12(5), 397-399. doi: 10.1093/jmcb/mjz114

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

Journal - Research Other

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

Journal - Research Other

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

Journal - Research Other

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