Gimenez, G., Stockwell, P. A., Rodger, E. J., & Chatterjee, A. (2023). Strategy for RNA-seq experimental design and data analysis. In G. J. Seymour, M. P. Cullinan, N. C. K. Heng & P. R. Cooper (Eds.), Oral biology: Molecular techniques and applications: Methods in molecular biology (Vol. 2588). (3rd ed.) (pp. 249-278). New York, NY: Springer. doi: 10.1007/978-1-0716-2780-8_16

Chapter in Book - Research

Marsman, J., Day, R. C., & Gimenez, G. (2022). Circular chromosome conformation capture sequencing (4C-Seq ) in primary adherent cells. In J. Horsfield & J. Marsman (Eds.), Chromatin: Methods and protocols: Methods in molecular biology (Vol. 2458). (pp. 301-320). New York, NY: Springer. doi: 10.1007/978-1-0716-2140-0_16

Chapter in Book - Research

Hossain, S. M., Gimenez, G., Stockwell, P. A., Tsai, P., Print, C. G., Rys, J., … Jackson, C., Chatterjee, A., & Eccles, M. R. (2022). Innate immune checkpoint inhibitor resistance is associated with melanoma sub-types exhibiting invasive and de-differentiated gene expression signatures. Frontiers in Immunology, 13, 955063. doi: 10.3389/fimmu.2022.955063

Journal - Research Article

Mehta, P. M., Gimenez, G., Walker, R. J., & Slatter, T. L. (2022). Reduction of lithium induced interstitial fibrosis on co-administration with amiloride. Scientific Reports, 12(1), 14598. doi: 10.1038/s41598-022-18825-1

Journal - Research Article

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

Smith, J., Banerjee, R., Waly, R., Urbano, A., Gimenez, G., Day, R., Eccles, M. R., Weeks, R. J., & Chatterjee, A. (2021). Locus-specific DNA methylation editing in melanoma cell lines using a CRISPR-based system. Cancers, 13, 5433. doi: 10.3390/cancers13215433

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 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, 185A, 3675-3682. 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 AM13^T. 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 7400942^T 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 541308^T. 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 5402776^T. 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 4401292^T. 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 4^th 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

Mulholland, C. V., Gimenez, G., Williamson, A., Steele, M., Thorpe, D., Karalus, N., … Cook, G. M., … Aung, H. L. (2022). Complete genome sequence of a New Zealand Mycobacterium tuberculosis strain responsible for ongoing transmission over the past 30 years. Microbiology Resource Announcements. Advance online publication. doi: 10.1128/mra.00781-22

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