References

They used XEGEN technologies and expertise :

  • IHU « Méditerranée Infection » :
    • Definition of a specific bacterial genome assembly strategy  and automation of the process
    • Annotation of more than 400 bacterian genomes,
    • Research and study of toxin / antitoxin genes in a group of bacterial species.
  • UMR 7268 – ADES : Biocultural Anthropologie, Law, Ethics and Health

    • Variable region analysis of the HLA-G gene (coding and non-coding regions)
    • Development of a HLA-G allelic typing automation software (coding and non-coding regions)
    • Estimation of haplotypes of the HLA-G gene

    « UMR7268 is under the supervision of AMU, CNRS and the French Blood Establishment; one of the major challenges is to optimize transfusions, transplants and transplants.
    Our research team is investigating genetic polymorphisms of nonclassical class I HLA genes involved in immune tolerance mechanisms.
    Thanks to their expertise, members of XEGEN have successfully validated a custom analysis pipeline. We were able to apply the NGS sequencing tools to our research issues, in a very short time and with a high quality of results.
    This partnership has allowed us to make significant progress in understanding the regulation of these genes»

    J. Di Cristofaro, researcher EFS / UMR7268

  • AmiKana.BioLogics :
    • Analysis of cleavage sites within a polyprotein of viral origin,
    • Development of a software for the automation of reading and interpreting 96-well plates.

    « Our biotech company, Amikana.Biologics specializes in the design, development and commercialization of innovative tools for the analysis of resistances to therapeutic treatments. Partner of our research through the development of tailor-made IT tools, XEGEN has perfectly adapted to our problems and our technical and economic requirements. The professional rigor of the team and its mastery of bioinformatics tools have produced results that live up to our expectations.»
    P. Gluschankof CEO & CSO

     

« XEGEN has a strong experience in the field of health »

Publications

Xegen member as author

Xegen as subcontractor

Other publications

 

xegen as an author

1. Manel, S., Perrier, C., Pratlong, M., Abi‐Rached, L., Paganini, J., Pontarotti, P., & Aurelle, D. (2016). Genomic resources and their influence on the detection of the signal of positive selection in genome scans. Molecular ecology, 25(1), 170-184.
2. Poole, J. R. M., Paganini, J., & Pontarotti, P. (2017). Convergent evolution of the adaptive immune response in jawed vertebrates and cyclostomes: An evolutionary biology approach based study. Developmental & Comparative Immunology.

3. Camille Ribeyre, Federico Carlini, Céline René, François Jordier, Christophe Picard, Jacques Chiaroni, Laurent Abi-Rached, Philippe Gouret, Grégory Marin, Nicolas Molinari, Pascal Chanez, Julien Paganini, Delphine Gras, Julie Di Cristofaro, HLA-G haplotypes are differentially associated with asthmatic features. Front. Immunol.  doi: 10.3389/fimmu.2018.00278

submitted

4. Dr. Ramasamy Dhamodharan, Jaishriram Rathored , Philippe Gouret , Julien Paganini , Senthil Sankar, Laurent Abi-Rached, Didier Raoult, Pierre-Edouard Fournier, Pierre PONTAROTTI (corr-auth) A phylum level horizontal gene transfer in human gut bacterial and archaeal complete genomes (submitted)

5. Mohamed Slimane1, Christophe Picard2,3, Jacques Chiaroni2,3, Anderson Loundou4, Julien Paganini5, Pierre Tiberghien1,6, Jean-Michel Rebibou1,7, Julie Di Cristofaro HLA-G haplotype association with pregnancy alloimmunization: impact on transfusion and transplantation management of female recipients (submitted)

publications in which XEGEN is thanked for its NGS data analysis (subcontractor)

2018

  1. Leangapichart, T., Gautret, P., Nguyen, T. T., Armstrong, N., & Rolain, J. M. (2018). Genome sequence of “Leucobacter massiliensis” sp. nov. isolated from human pharynx after travel to the 2014 Hajj. New microbes and new infections21, 42-48.
  2. Jneid, J., Khalil, J. B., Aherfi, S., Blanc-Tailleur, C., Raoult, D., La Scola, B., & Pagnier, I. (2018). ‘Massilibacteroïdes vaginae’gen. nov., sp. nov., a new genus within the family of Bacteroïdaceae isolated from a patient with vaginosis. New microbes and new infections21, 1-8.
  3. Bilen, M., Cadoret, F., Richez, M., Tomei, E., Daoud, Z., Raoult, D., & Fournier, P. E. (2018). Libanicoccus massiliensis gen. nov., sp. nov., a new bacterium isolated from human stool. New microbes and new infections21, 63-71.

2017

  1. Loucif, L., Michelle, C., Terras, J., Rolain, J. M., Raoult, D., & Fournier, P. E. (2017). Draft Genome Sequence of Streptomyces specialis Type Strain GW41-1564 (DSM 41924). Genome announcements, 5(13), e00101-17
  2. Afouda, P., Dubourg, G., Labas, N., Raoult, D., & Fournier, P. E. (2017). Draft Genome Sequence of Agrococcus baldri Strain Marseille-P2731. Genome announcements, 5(10), e00015-17.
  3. Lo, C. I., Mailhe, M., Ricaboni, D., Vitton, V., Benezech, A., Michelle, C., … & Lagier, J. C. (2017). Massilioclostridium coli gen. nov., sp. nov., a new member of the Clostridiaceae family isolated from the left colon of a 27-year-old woman. New microbes and new infections, 16, 63-72.
  4. DIOP, Khoudia, ANDRIEU, Claudia, MICHELLE, Caroline, et al.Characterization of a New Ezakiella Isolated from the Human Vagina: Genome Sequence and Description of Ezakiella massiliensis sp. nov. Current microbiology, 2017, p. 1-8.
  5. El Houmami, N., Schrenzel, J., Yagupsky, P., Robert, C., Ceroni, D., Raoult, D., & Fournier, P. E. (2017). Draft Genome Sequence of Kingella negevensis SW7208426, the First European Strain of K. negevensis Isolated from a Healthy Child in Switzerland. Genome announcements5(26), e00571-17.
  6. BARDET, Lucie, CIMMINO, Teresa, BUFFET, Clémence, et al.Microbial Culturomics Application for Global Health: Noncontiguous Finished Genome Sequence and Description of Pseudomonas massiliensis Strain CB-1T sp. nov. in Brazil. Omics: a journal of integrative biology, 2017.
  7. Afouda, P., Ndongo, S., Khelaifia, S., Labas, N., Cadoret, F., Di Pinto, F., … & Million, M. (2017). Noncontiguous finished genome sequence and description of Prevotella phocaeensis sp. nov., a new anaerobic species isolated from human gut infected by Clostridium difficile. New microbes and new infections, 15, 117-127.
  8. TOGO, Amadou Hamidou, DURAND, Guillaume, KHELAIFIA, Saber, et al. Fournierella massiliensis gen. nov., sp. nov., a new human-associated member of the family Ruminococcaceae. International journal of systematic and evolutionary microbiology, 2017, vol. 67, no 5, p. 1393-1399.
  9. Dione, N., Rathored, J., Tomei, E., Lagier, J. C., Khelaifia, S., Robert, C., … & Fenollar, F. (2017). Dakarella massiliensis gen. nov., sp. nov., strain ND3 T: a new bacterial genus isolated from the female genital tract. New Microbes and New Infections, 18, 38-46.
  10. Elsawi, Z., Togo, A. H., Beye, M., Dubourg, G., Andrieu, C., Armsrtong, N., … & Fournier, P. E. (2017). Hugonella massiliensis gen. nov., sp. nov., genome sequence, and description of a new strictly anaerobic bacterium isolated from the human gut. MicrobiologyOpen.
  11. Abdallah, R. A., Cimmino, T., Baron, S., Cadoret, F., Michelle, C., Raoult, D., … & Bittar, F. (2017). Description of Chryseobacterium timonianum sp. nov., isolated from a patient with pneumonia. Antonie van Leeuwenhoek, 1-12.
  12. Alou, M. T., Rathored, J., Michelle, C., Dubourg, G., Andrieu, C., Armstrong, N., … & Fournier, P. E. (2017). Inediibacterium massiliense gen. nov., sp. nov., a new bacterial species isolated from the gut microbiota of a severely malnourished infant. Antonie Van Leeuwenhoek, 110(6), 737-750.
  13. NGOM, Issa Isaac, MAILHE, Morgane, RICABONI, Davide, et al.Noncontiguous finished genome sequence and description of Mediterranea massiliensis gen. nov., sp. nov., a new member of the Bacteroidaceae family isolated from the human colon. New Microbes and New Infections, 2017.
  14. Diop, K., Bretelle, F., Michelle, C., Richez, M., Rathored, J., Raoult, D., … & Fenollar, F. (2017). Taxonogenomics and description of Vaginella massiliensis gen. nov., sp. nov., strain Marseille P2517 T, a new bacterial genus isolated from the human vagina. New microbes and new infections, 15, 94-103.
  15. Alou, M. T., Rathored, J., Lagier, J. C., Khelaifia, S., Michelle, C., Sokhna, C., … & Edouard, S. (2017). Rubeoparvulum massiliense gen. nov., sp. nov., a new bacterial genus isolated from the human gut of a Senegalese infant with severe acute malnutrition. New microbes and new infections, 15, 49-60.
  16. Alou, M. T., Rathored, J., Nguyen, T. T., Andrieu, C., Couderc, C., Brah, S., … & Dubourg, G. (2017). Paenibacillus phocaensis sp. nov., isolated from the gut microbiota of a healthy infant. New microbes and new infections, 16, 13-24.
  17. Mailhe, M., Ricaboni, D., Vitton, V., Benezech, A., Dubourg, G., Michelle, C., … & Raoult, D. (2017). Noncontiguous finished genome sequence and description of Fusobacterium massiliense sp. nov. isolated from human duodenum. New microbes and new infections, 16, 3-12.
  18. Durand, G. A., Pham, T., Ndongo, S., Traore, S. I., Dubourg, G., Lagier, J. C., … & Million, M. (2017). Blautia massiliensis sp. nov., isolated from a fresh human fecal sample and emended description of the genus Blautia. Anaerobe, 43, 47-55.
  19. Guilhot, E., Alou, M. T., Lagier, J. C., Labas, N., Couderc, C., Delerce, J., … & Khelaifia, S. (2017). Genome sequence and description of Anaeromassilibacillus senegalensis gen. nov., sp. nov., isolated from the gut of patient with kwashiorkor. New Microbes and New Infections, 17, 54-64.
  20. Cadoret, F., Alou, M. T., Afouda, P., Traore, I. S., Bréchard, L., Michelle, C., … & Fournier, P. E. (2017). Non-contiguous finished genome sequences and description of Bacillus massiliglaciei, Bacillus mediterraneensis, Bacillus massilinigeriensis, Bacillus phocaeensis and Bacillus tuaregi, five new species identified by culturomics. New Microbes and New Infections.
  21. Ricaboni, D., Mailhe, M., Lagier, J. C., Michelle, C., Armstrong, N., Bittar, F., … & Million, M. (2017). Noncontiguous finished genome sequence and description of Streptococcus timonensis sp. nov. isolated from the human stomach. New microbes and new infections, 15, 77-88.
  22. BEYE, Mamadou, TRAORE, Sory Ibrahima, KHELAIFIA, Saber, et al. Bacillus kwashiorkori sp. nov., a new bacterial species isolated from a malnourished child using culturomics. MicrobiologyOpen, 2017.
  23. PHAM, T.-P.-T., ALOU, M. Tidjani, TRAORE, Sory Ibrahima, et al. Noncontiguous finished genome sequences and descriptions of ‘Paenibacillus bouchesdurhonensis,’‘Paenibacillus rubinfantis,’‘Paenibacillus senegalimassiliensis’ and ‘Paenibacillus tuaregi’identified by culturomics. New microbes and new infections, 2017, vol. 20, p. 1-13.
  24. Pinos, S., Pontarotti, P., Raoult, D., & Merhej, V. (2017). Identification of constraints influencing the bacterial genomes evolution in the PVC super-phylum. BMC evolutionary biology, 17(1), 75.
  25. Pratlong, M., Rancurel, C., Pontarotti, P., & Aurelle, D. (2017). Monophyly of Anthozoa (Cnidaria): why do nuclear and mitochondrial phylogenies disagree?. Zoologica Scripta, 46(3), 363-371.

2016

  1. Beye, M., Bakour, S., Labas, N., Raoult, D., & Fournier, P. E. (2016). Draft genome sequence of Actinobaculum massiliense strain FC3. Genome announcements, 4(1), e01537-15.
  2. Ricaboni, D., Mailhe, M., Labas, N., Vitton, V., Raoult, D., & Million, M. (2016). Draft genome sequence of Blautia faecis strain Marseille-P328, isolated from the human ascending colon. Genome announcements, 4(6), e01383-16.
  3. Le Page, S., Cimmino, T., Togo, A., Million, M., Michelle, C., Khelaifia, S., … & Rolain, J. M. (2016). Noncontiguous finished genome sequence and description of Enterococcus massiliensis sp. nov. New microbes and new infections, 12, 90-95.
  4. Togo, A. H., Khelaifia, S., Lagier, J. C., Caputo, A., Robert, C., Fournier, P. E., … & Million, M. (2016). Noncontiguous finished genome sequence and description of Paenibacillus ihumii sp. nov. strain AT5. New microbes and new infections, 10, 142-150.
  5. Cresci, M., Lo, C. I., Khelaifia, S., Mouelhi, D., Delerce, J., Di Pinto, F., … & Moal, V. (2016). Corynebacterium phoceense sp. nov., strain MC1 T a new bacterial species isolated from human urine. New microbes and new infections, 14, 73-82.
  6. Alou, M. T., Nguyen, T. T., Armstrong, N., Rathored, J., Khelaifia, S., Raoult, D., … & Lagier, J. C. (2016). Numidum massiliense gen. nov., sp. nov., a new member of the Bacillaceae family isolated from the human gut. New microbes and new infections, 12, 76-85.
  7. Alou, M. T., Rathored, J., Lagier, J. C., Khelaifia, S., Labas, N., Sokhna, C., … & Dubourg, G. (2016). Massilibacterium senegalense gen. nov., sp. nov., a new bacterial genus isolated from the human gut. New microbes and new infections, 10, 101-111.
  8. Togo, A. H., Diop, A., Dubourg, G., Nguyen, T. T., Andrieu, C., Caputo, A., … & Raoult, D. (2016). Butyricimonas phoceensis sp. nov., a new anaerobic species isolated from the human gut microbiota of a French morbidly obese patient. New microbes and new infections, 14, 38-48.
  9. Lo, C. I., Sankar, S. A., Ehounoud, C. B., Mediannikov, O., Labas, N., Caputo, A., … & Fenollar, F. (2016). High-quality genome sequencing and description of Dermabacter indicis sp. nov. New microbes and new infections, 11, 59-67.
  10. Lo, C. I., Sankar, S. A., Mediannikov, O., Ehounoud, C. B., Labas, N., Faye, N., … & Fenollar, F. (2016). High-quality genome sequence and description of Chryseobacterium senegalense sp. nov. New microbes and new infections, 10, 93-100.
  11. Hosny, M., Benamar, S., Durand, G., Armstrong, N., Michelle, C., Cadoret, F., … & Cassir, N. (2016). Description of Clostridium phoceensis sp. nov., a new species within the genus Clostridium. New microbes and new infections, 14, 85-92.
  12. Mourembou, G., Rathored, J., Lekana-Douki, J. B., Ndjoyi-Mbiguino, A., Fenollar, F., Michelle, C., … & Lagier, J. C. (2016). Noncontiguous finished genome sequence and description of Kallipyga gabonensis sp. nov. New microbes and new infections, 9, 15-23.
  13. Alou, M. T., Khelaifia, S., Michelle, C., Andrieu, C., Armstrong, N., Bittar, F., … & Million, M. (2016). Anaerococcus rubiinfantis sp. nov., isolated from the gut microbiota of a Senegalese infant with severe acute malnutrition. Anaerobe, 40, 85-94.
  14. Dione, N., Sankar, S. A., Lagier, J. C., Khelaifia, S., Michele, C., Armstrong, N., … & Fournier, P. E. (2016). Genome sequence and description of Anaerosalibacter massiliensis sp. nov. New microbes and new infections, 10, 66-76.
  15. Durand, G. A., Lagier, J. C., Khelaifia, S., Armstrong, N., Robert, C., Rathored, J., … & Raoult, D. (2016). Drancourtella massiliensis gen. nov., sp. nov. isolated from fresh healthy human faecal sample from South France. New microbes and new infections, 11, 34-42.
  16. Sokhna, C., Diallo, A., Fournier, P. E., Raoult, D., & Million, M. (2016). Anaerococcus rubiinfantis sp. nov., isolated from the gut microbiota of a Senegalese infant with severe acute malnutrition.

  17. Lo, C. I., Sankar, S. A., Fall, B., Sambe-Ba, B., Mediannikov, O., Robert, C., … & Fenollar, F. (2016). High-quality genome sequence and description of Paenibacillus dakarensis sp. nov. New microbes and new infections, 10, 132-141.
  18. Dubourg, G., Lagier, J. C., Robert, C., Armstrong, N., Couderc, C., Fournier, P. E., & Raoult, D. (2016). Risungbinella massiliensis sp. nov., a new member of Thermoactinomycetaceae isolated from human gut. Antonie van Leeuwenhoek, 109(6), 773-784.
  19. Bakour, S., Rathored, J., Lo, C. I., Mediannikov, O., Beye, M., Ehounoud, C. B., … & Fenollar, F. (2016). Non-contiguous finished genome sequence and description of Streptococcus varani sp. nov. New microbes and new infections, 11, 93-102.
  20. Seck, E., Traore, S. I., Khelaifia, S., Beye, M., Michelle, C., Couderc, C., … & Dubourg, G. (2016). Tessaracoccus massiliensis sp. nov., a new bacterial species isolated from the human gut. New microbes and new infections, 13, 3-12.
  21. Mourembou, G., Rathored, J., Ndjoyi-Mbiguino, A., Lekana-Douki, J. B., Fenollar, F., Robert, C., … & Lagier, J. C. (2016). Noncontiguous finished genome sequence and description of Gabonia massiliensis gen. nov., sp. nov. New microbes and new infections, 9, 35-44.
  22. Seck, E. H., Sankar, S. A., Khelaifia, S., Croce, O., Robert, C., Couderc, C., … & Lagier, J. C. (2016). Noncontiguous finished genome sequence and description of Planococcus massiliensis sp. nov., a moderately halophilic bacterium isolated from the human gut. New microbes and new infections, 10, 36-46.
  23. Moumene, M., Drissi, F., Croce, O., Djebbari, B., Robert, C., Angelakis, E., … & Merhej, V. (2016). Complete genome sequence and description of Lactococcus garvieae M14 isolated from Algerian fermented milk. New Microbes and New Infections, 10, 122-131.
  24. Mourembou, G., Rathored, J., Lekana-Douki, J. B., Ndjoyi-Mbiguino, A., Khelaifia, S., Robert, C., … & Fournier, P. E. (2016). Description of Gabonibacter massiliensis gen. nov., sp. nov., a New Member of the Family Porphyromonadaceae Isolated from the Human Gut Microbiota. Current microbiology, 73(6), 867-877.
  25. Dubourg, G., Sankar, S. A., Rathored, J., Lagier, J. C., Robert, C., Couderc, C., … & Fournier, P. E. (2016). Noncontiguous finished genome sequence and description of Nocardioides massiliensis sp. nov. GD13 T. New microbes and new infections, 10, 47-57.
  26. Caputo, A., Lagier, J. C., Azza, S., Robert, C., Mouelhi, D., Fournier, P. E., & Raoult, D. (2016). Microvirga massiliensis sp. nov., the human commensal with the largest genome. Microbiologyopen, 5(2), 307-322.
  27. Vicino, E., Traore, S. I., Cimmino, T., Dubourg, G., Labas, N., Andrieu, C., … & Rolain, J. M. (2016). Noncontiguous finished genome sequence and description of Murdochiella massiliensis strain SIT12 sp. nov. New microbes and new infections, 14, 31-35.
  28. Diop, A., Khelaifia, S., Armstrong, N., Labas, N., Fournier, P. E., Raoult, D., & Million, M. (2016). Microbial culturomics unravels the halophilic microbiota repertoire of table salt: description of Gracilibacillus massiliensis sp. nov. Microbial ecology in health and disease, 27(1), 32049.
  29. Hadjadj, L., Alou, M. T., Sokhna, C., Lagier, J. C., Raoult, D., & Rolain, J. M. (2016). Genome sequence and description of Desnuesiella massiliensis gen. nov., sp. nov. a new member of family Clostridiaceae. New microbes and new infections, 11, 84-90.
  30. Lo, C. I., Sankar, S. A., Fall, B., Sambe-Ba, B., Diawara, S., Gueye, M. W., … & Fournier, P. E. (2016). High-quality draft genome sequence and description of Haemophilus massiliensis sp. nov. Standards in genomic sciences, 11(1), 31.
  31. Keita, M. B., Padhmanabhan, R., Robert, C., Delaporte, E., Raoult, D., Fournier, P. E., & Bittar, F. (2016). Non-contiguous-Finished Genome Sequence and Description of Paenibacillus camerounensis sp. nov. Microbial ecology, 71(4), 990-998.
  32. Hadjadj, L., Rathored, J., Keita, M. B., Michelle, C., Levasseur, A., Raoult, D., … & Bittar, F. (2016). Non contiguous-finished genome sequence and description of Microbacterium gorillae sp. nov. Standards in genomic sciences, 11(1), 32.

2015

  1. Drissi, F., Merhej, V., Blanc-Tailleur, C., & Raoult, D. (2015). Draft genome sequence of the Lactobacillus mucosae strain Marseille. Genome announcements, 3(4), e00841-15.
  2. Drissi, F., Labas, N., Merhej, V., & Raoult, D. (2015). Draft genome sequence of the Lactobacillus agilis strain Marseille. Genome announcements, 3(4), e00840-15.
  3. Hadjadj, L., Bentorki, A. A., Michelle, C., Amoura, K., Djahoudi, A., & Rolain, J. M. (2015). Genome sequence and description of Mannheimia massilioguelmaensis sp. nov. New microbes and new infections, 8, 131-136.
  4. Alou, M. T., Rathored, J., Traore, S. I., Khelaifia, S., Michelle, C., Brah, S., … & Lagier, J. C. (2015). Bacillus niameyensis sp. nov., a new bacterial species isolated from human gut. New microbes and new infections, 8, 61-69.
  5. Alou, M. T., Rathored, J., Khelaifia, S., Michelle, C., Brah, S., Diallo, B. A., … & Lagier, J. C. (2015). Bacillus rubiinfantis sp. nov. strain mt2 T, a new bacterial species isolated from human gut. New microbes and new infections, 8, 51-60.
  6. Aghnatios, R., Cayrou, C., Garibal, M., Robert, C., Azza, S., Raoult, D., & Drancourt, M. (2015). Draft genome of Gemmata massiliana sp. nov, a water-borne Planctomycetes species exhibiting two variants. Standards in genomic sciences, 10(1), 120.
  7. Lo, C. I., Padhamanabhan, R., Fall, B., Sambe-Ba, B., Mediannikov, O., Nguyen, T. T., … & Fournier, P. E. (2015). Noncontiguous finished genome sequence and description of Necropsobacter massiliensis sp. nov. New microbes and new infections, 8, 41-50.
  8. Lo, C. I., Padhmanabhan, R., Mediannikov, O., Keita, A. K., Michelle, C., Terras, J., … & Fenollar, F. (2015). Noncontiguous finished genome sequence and description of Diaminobutyricimonas massiliensis strain FF2 T sp. nov. New Microbes and New Infections, 8, 31-40.
  9. Sankar, S. A., Lo, C. I., Fall, B., Sambe-Ba, B., Mediannikov, O., Diallo, I., … & Fournier, P. E. (2015). Noncontiguous finished genome sequence and description of Weeksella massiliensis sp. nov. New microbes and new infections, 8, 89-98.
  10. Seck, E., Rathored, J., Khelaifia, S., Croce, O., Robert, C., Couderc, C., … & Lagier, J. C. (2015). Virgibacillus senegalensis sp. nov., a new moderately halophilic bacterium isolated from human gut. New microbes and new infections, 8, 116-126.
  11. Dubourg, G., Cimmino, T., Senkar, S., Lagier, J. C., Robert, C., Flaudrops, C., … & Rolain, J. M. (2015). Noncontiguous finished genome sequence and description of Paenibacillus antibioticophila sp. nov. GD11 T, the type strain of Paenibacillus antibioticophila. New microbes and new infections, 8, 137-147.
  12. Sankar, S. A., Rathored, J., Metidji, S., Lagier, J. C., Khelaifia, S., Labas, N., … & Fournier, P. E. (2015). Clostridium polynesiense sp. nov., a new member of the human gut microbiota in French Polynesia. Anaerobe, 36, 79-87.
  13. Merhej, V., Pfleiderer, A., Ramasamy, D., Lagier, J. C., Michelle, C., Raoult, D., & Fournier, P. E. (2015). Non-contiguous finished genome sequence and description of Clostridium ihumii sp. nov. Standards in genomic sciences, 10(1), 63.

2014

  1. Roux, V., Robert, C., & Raoult, D. (2014). Non-contiguous finished genome sequence of Prevotella timonensis type strain 4401737 T. Standards in genomic sciences, 9(3), 1344.
  2. Roux, V., Robert, C., & Raoult, D. (2014). Non-contiguous finished genome sequence of Corynebacterium timonense type strain 5401744 T. Standards in genomic sciences, 9(3), 948.
  3. Edouard, S., Sankar, S., Dangui, N. P. M., Lagier, J. C., Michelle, C., Raoult, D., & Fournier, P. E. (2014). Genome sequence and description of Nesterenkonia massiliensis sp. nov. strain NP1 T. Standards in genomic sciences, 9(3), 866.
  4. Ikram, H. I., Catherine, R., Caroline, M., Didier, R., Hocine, H., & Christelle, D. (2014). Non-contiguous finished genome sequence and description of Halopiger goleamassiliensis sp. nov. Standards in genomic sciences, 9(3), 956.
  5. Lagier, J. C., Bibi, F., Ramasamy, D., Azhar, E. I., Robert, C., Yasir, M., … & Raoult, D. (2014). Non contiguous-finished genome sequence and description of Clostridium jeddahense sp. nov. Standards in genomic sciences, 9(3), 1003.
  6. Pfleiderer, A., Mishra, A. K., Lagier, J. C., Robert, C., Caputo, A., Raoult, D., & Fournier, P. E. (2014). Non-contiguous finished genome sequence and description of Alistipes ihumii sp. nov. Standards in genomic sciences, 9(3), 1221.
  7. Ramasamy, D., Lagier, J. C., Rossi-Tamisier, M., Pfleiderer, A., Michelle, C., Couderc, C., … & Fournier, P. E. (2014). Genome sequence and description of Bacteroides timonensis sp. nov. Standards in genomic sciences, 9(3), 1181.
  8. Angelakis, E., Bibi, F., Ramasamy, D., Azhar, E. I., Jiman-Fatani, A. A., Aboushoushah, S. M., … & Fournier, P. E. (2014). Non-contiguous finished genome sequence and description of Clostridium saudii sp. nov. Standards in genomic sciences, 9(1), 8.
  9. Roux, V., Lagier, J. C., Gorlas, A., Robert, C., & Raoult, D. (2014). Non-contiguous finished genome sequence and description of Kurthia senegalensis sp. nov. Standards in genomic sciences, 9(3), 1319.

  10. Roux, V., Lagier, J. C., Gorlas, A., Robert, C., & Raoult, D. (2014). Non-contiguous finished genome sequence and description of Kurthia senegalensis sp. nov. Standards in genomic sciences, 9(3), 1319.
  11. Keita, M. B., Padhmanabhan, R., Caputo, A., Robert, C., Delaporte, E., Raoult, D., … & Bittar, F. (2014). Non-contiguous finished genome sequence and description of Gorillibacterium massiliense gen. nov, sp. nov., a new member of the family Paenibacillaceae. Standards in genomic sciences, 9(3), 807.
  12. Ramasamy, D., Dubourg, G., Robert, C., Caputo, A., Papazian, L., Raoult, D., & Fournier, P. E. (2014). Non contiguous-finished genome sequence and description of Enorma timonensis sp. nov. Standards in genomic sciences, 9(3), 970.
  13. Keita, M. B., Padhmananabhan, R., Caputo, A., Robert, C., Delaporte, E., Raoult, D., … & Bittar, F. (2014). Non-contiguous finished genome sequence and description of Paenibacillus gorillae sp. nov. Standards in genomic sciences, 9(3), 1031.
  14. Edouard, S., Bibi, F., Dhamodharan, R., Lagier, J. C., Azhar, E. I., Robert, C., … & Fournier, P. E. (2014). Non-contiguous finished genome sequence and description of Corynebacterium jeddahense sp. nov. Standards in genomic sciences, 9(3), 987.
  15. Padmanabhan, R., Dubourg, G., Lagier, J. C., Couderc, C., Michelle, C., Raoult, D., & Fournier, P. E. (2014). Genome sequence and description of Corynebacterium ihumii sp. nov. Standards in genomic sciences, 9(3), 1128.
  16. Bendjama, E., Loucif, L., Diene, S. M., Michelle, C., Gacemi-Kirane, D., & Rolain, J. M. (2014). Non-contiguous finished genome sequence and description of Bacillus algeriensis sp. nov. Standards in genomic sciences, 9(3), 1046.
  17. Bendjama, E., Loucif, L., Diene, S. M., Michelle, C., Gacemi-Kirane, D., & Rolain, J. M. (2014). Non-contiguous finished genome sequence and description of Paucisalibacillus algeriensis sp. nov. Standards in genomic sciences, 9(3), 1352

2013

  1. 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.
  2. Roux, V., Robert, C., & Raoult, D. (2013). Non-contiguous finished genome sequence of Phocaeicola abscessus type strain 7401987 T. Standards in genomic sciences, 9(2), 351.
  3. Lagier, J. C., El Karkouri, K., Mishra, A. K., Robert, C., Raoult, D., & Fournier, P. E. (2013). Non contiguous-finished genome sequence and description of Enterobacter massiliensis sp. nov. Standards in genomic sciences, 7(3), 399.
  4. Hugon, P., Mishra, A. K., Lagier, J. C., Nguyen, T. T., Couderc, C., Raoult, D., & Fournier, P. E. (2013). Non-contiguous finished genome sequence and description of Brevibacillus massiliensis sp. nov. Standards in genomic sciences, 8(1), 1.
  5. Hugon, P., Ramasamy, D., Lagier, J. C., Rivet, R., Couderc, C., Raoult, D., & Fournier, P. E. (2013). Non contiguous-finished genome sequence and description of Alistipes obesi sp. nov. Standards in genomic sciences, 7(3), 427.
  6. Ramasamy, D., Lagier, J. C., Nguyen, T. T., Raoult, D., & Fournier, P. E. (2013). Non contiguous-finished genome sequence and description of Dielma fastidiosa gen. nov., sp. nov., a new member of the Family Erysipelotrichaceae. Standards in genomic sciences, 8(2), 336.
  7. Mishra, A. K., Pfleiderer, A., Lagier, J. C., Robert, C., Raoult, D., & Fournier, P. E. (2013). Non-contiguous finished genome sequence and description of Bacillus massilioanorexius sp. nov. Standards in genomic sciences, 8(3), 465.
  8. Mishra, A. K., Lagier, J. C., Pfleiderer, A., Nguyen, T. T., Caputo, A., Raoult, D., & Fournier, P. E. (2013). Non-contiguous finished genome sequence and description of Holdemania massiliensis sp. nov. Standards in genomic sciences, 9(2), 395.
  9. Padmanabhan, R., Lagier, J. C., Dangui, N. P. M., Michelle, C., Couderc, C., Raoult, D., & Fournier, P. E. (2013). Non-contiguous finished genome sequence and description of Megasphaera massiliensis sp. nov. Standards in genomic sciences, 8(3), 525.
  10. Mishra, A. K., Hugon, P., Lagier, J. C., Nguyen, T. T., Couderc, C., Raoult, D., & Fournier, P. E. (2013). Non contiguous-finished genome sequence and description of Enorma massiliensis gen. nov., sp. nov., a new member of the Family Coriobacteriaceae. Standards in genomic sciences, 8(2), 290.
  11. Hugon, P., Ramasamy, D., Robert, C., Couderc, C., Raoult, D., & Fournier, P. E. (2013). Non-contiguous finished genome sequence and description of Kallipyga massiliensis gen. nov., sp. nov., a new member of the family Clostridiales Incertae Sedis XI. Standards in genomic sciences, 8(3), 500.
  12. Lo, C. I., Mishra, A. K., Padhmanabhan, R., Ba, B. S., Sow, A. G., Robert, C., … & Fenollar, F. (2013). Non-contiguous finished genome sequence and description of Clostridium dakarense sp. nov. Standards in genomic sciences, 9(1), 14.
  13. Roux, V., Million, M., Robert, C., Magne, A., & Raoult, D. (2013). Non-contiguous finished genome sequence and description of Oceanobacillus massiliensis sp. nov. Standards in genomic sciences, 9(2), 370.
  14. Mishra, A. K., Lagier, J. C., Robert, C., Raoult, D., & Fournier, P. E. (2013). Genome sequence and description of Timonella senegalensis gen. nov., sp. nov., a new member of the suborder Micrococcinae. Standards in genomic sciences, 8(2), 318.
  15. Socolovschi, C., Audoly, G., & Raoult, D. (2013). Connection of toxin–antitoxin modules to inoculation eschar and arthropod vertical transmission in Rickettsiales. Comparative immunology, microbiology and infectious diseases, 36(2), 199-209.
  16. Lagier, J. C., Elkarkouri, K., Rivet, R., Couderc, C., Raoult, D., & Fournier, P. E. (2013). Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov. Standards in genomic sciences, 7(3), 343.
  17. Keita, M. B., Diene, S. M., Robert, C., Raoult, D., Fournier, P. E., & Bittar, F. (2013). Non-contiguous finished genome sequence and description of Bacillus massiliogorillae sp. nov. Standards in genomic sciences, 9(1), 93.
  18. Mishra, A. K., Edouard, S., Dangui, N. P. M., Lagier, J. C., Caputo, A., Blanc-Tailleur, C., … & Fournier, P. E. (2013). Non-contiguous finished genome sequence and description of Nosocomiicoccus massiliensis sp. nov. Standards in genomic sciences, 9(1), 205.

2012

  1. Ramasamy, D., Kokcha, S., Lagier, J. C., Nguyen, T. T., Raoult, D., & Fournier, P. E. (2012). Genome sequence and description of Aeromicrobium massiliense sp. nov. Standards in genomic sciences, 7(2), 246.
  2. Lagier, J. C., Ramasamy, D., Rivet, R., Raoult, D., & Fournier, P. E. (2012). Non contiguous-finished genome sequence and description of Cellulomonas massiliensis sp. nov. Standards in genomic sciences, 7(2), 258.

Some previous publications of the team members carried out during work directed by M.Pontarotti

1. »Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga », Nature 2013 DOI 10.1038/nature12326, Jean-François Flot et al,
2. »Contribution of Lateral Gene Transfers to the Genome Composition and Parasitic Ability of Root-Knot Nematodes », PLOS ONE 2012, 7(11): e50875. doi:10.1371/journal.pone.0050875, Paganini J., Campan-Fournier A., Da Rocha M., Gouret P., Pontarotti P., Wajnberg E., Abad P., Danchin E.
3. »An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales », BMC Evolutionary Biology 2012 dec 12, 12:243, Le P., Hemalatha G. R., Guijarro L., Paganini J., Gouret P., Chabrol O., Raoult D. and Pontarotti P.
4. »GLADX: An automated approach to analyze the lineage-specific orthologous gene loss and pseudogenization inMetazoans », PLoS ONE 2012, PLoS ONE 7(6): e38792. doi:10.1371/journal.pone.0038792, Dainat J, Paganini J, Pontarotti P, Gouret P.
5. »The rhizome of life: the sympatric Rickettsia felis paradigm demonstrates the random transfer of DNA sequences », MBE 2011; 28(11) 3213-3223, Merhej V , Notredame C, Royer-Carenzi M, Pontarotti P and Raoult D.
6. »Amphioxus FGF signaling predicts the acquisition of vertebrate morphological traits », PNAS 2011 108 (22) 9160-9165; published ahead of print May 12, 2011, doi:10.1073/pnas.1014235108, Stephanie Bertrand, Alain Camasses, Ildiko Somorjai, Mohamed R. Belgacem, Olivier Chabrol, Marie-Line Escande, Pierre Pontarotti, and Hector Escriva