Production scientifique de l'équipe Génomique/bioinformatique
2025
Rahmouni M, Clerc SL, Spadoni JL, Labib T, Tison M, Medina-Santos R, Bensussan A, Tamouza R, Deleuze JF, Zagury JF. Deep analysis of the major histocompatibility complex genetic associations using covariate analysis and haploblocks unravels new mechanisms for the molecular etiology of Elite Control in AIDS. BMC Immunol. 2025 Jan 6;26(1):1. doi: 10.1186/s12865-024-00680-6.
Gérardin P, Medina-Santos R, Le Clerc S, Bruneau L, Maillot A, Labib T, Rahmouni M, Spadoni JL, Meyniel JP, Cornet C, Lefebvre C, El Jahrani N, Savara J, Mathew MJ, Fontaine C, Payet C, Ah-You N, Chabert C, Mussard C, Porcherat S, Medjane S, Noirel J, Marimoutou C, Hocini H, Zagury JF. Transcriptomic analysis of chronic chikungunya in the Reunionese CHIKGene cohort uncovers a shift in gene expression more than 10 years after infection. Travel Med Infect Dis. 2025 Feb 23:102825. doi: 10.1016/j.tmaid.2025.102825.
Maxime Tison, Jean-François Zagury, Marion Leboyer, Ryad Tamouza. Chapitre : Facteurs de susceptibilité génétiques et suicide. Livre : approches biomédicales du suicide., Editeur : Philipe Courtet.
2024
Shi M, Evans CA, McQuillan JL, Noirel J, Pandhal J. LFQRatio: A Normalization Method to Decipher Quantitative Proteome Changes in Microbial Coculture Systems.J Proteome Res. 2024 Mar 1;23(3):999-1013. doi: 10.1021/acs.jproteome.3c00714. Epub 2024 Feb 14.
How-Kit A, Sahbatou M, Hardy LM, Tessier NP, Schiavon V, Le Buanec H, Sebaoun JM, Blanché H, Zagury JF, Deleuze JF. The CEPH aging cohort and biobank: a valuable collection of biological samples from exceptionally long-lived French individuals and their offspring for longevity studies. Geroscience. 2024 Apr;46(2):2681-2695. doi: 10.1007/s11357-023-01037-4.
Thiam F, Diop G, Coulonges C, Derbois C, Thiam A, Diouara AAM, Mbaye MN, Diop M, Nguer CM, Dieye Y, Mbengue B, Zagury JF, Deleuze JF, Dieye A. An elevated level of interleukin-17A in a Senegalese malaria cohort is associated with rs8193038 IL-17A genetic variant. BMC Infect Dis. 2024 Mar 4;24(1):275. doi: 10.1186/s12879-024-09149-8.
2023
Ndiaye M, Diop G, Derbois C, Spadoni JL, Noirel J, Medina-Santos R, Coulonges C, Torres M, Dieye A, Sembene M, Deleuze JF, Toledano A, Dem A, Le Clerc S*, Zagury JF*. Gene expression profiling of peripheral blood mononuclear cells from women with cervical lesions reveals new markers of cancer. Oncol Rep. 2023 Jun;49(6):118. doi: 10.3892/or.2023.8555. Epub 2023 Apr 28. *equal contribution
Vigan-Womas I, Spadoni JL, Poiret T, Taïeb F, Randrianarisaona F, Faye R, Mbow AA, Gaye A, Dia N, Loucoubar C, Ny Mioramalala DJ, Ratovoson R, Randremanana RV, Sall AA, Seydi M, Noirel J, Moreau G, Simon A, Holenya P, Meyniel JP, Schoenhals M*, Zagury JF*. Linear epitope mapping of the humoral response against SARS-CoV-2 in two independent African cohorts. Sci Rep. 2023 Jan 16;13(1):782. doi: 10.1038/s41598-023-27810-1.
Lombardi L, Le Clerc S, Wu CL, Bouassida J, Boukouaci W, Sugusabesan S, Richard JR, Lajnef M, Tison M, Le Corvoisier P, Barau C, Banaschewski T, Holt R, Durston S, Persico AM, Oakley B, Loth E, Buitelaar J, Murphy D, Leboyer M, Tamouza R*, Zagury JF*. A human leukocyte antigen imputation study uncovers possible genetic interplay between gut inflammatory processes and autism spectrum disorders. Transl Psychiatry. 2023 Jul 6;13(1):244. doi: 10.1038/s41398-023-02550-y.
McLaren PJ, Porreca I, Iaconis G, Mok HP, Mukhopadhyay S, Karakoc E, Cristinelli S, Pomilla C, Bartha I, Thorball CW, Tough RH, Angelino P, Kiar CS, Carstensen T, Fatumo S, Porter T, Jarvis I, Skarnes WC, Bassett A, DeGorter MK, Sathya Moorthy MP, Tuff JF, Kim EY, Walter M, Simons LM, Bashirova A, Buchbinder S, Carrington M, Cossarizza A, De Luca A, Goedert JJ, Goldstein DB, Haas DW, Herbeck JT, Johnson EO, Kaleebu P, Kilembe W, Kirk GD, Kootstra NA, Kral AH, Lambotte O, Luo M, Mallal S, Martinez-Picado J, Meyer L, Miro JM, Moodley P, Motala AA, Mullins JI, Nam K, Obel N, Pirie F, Plummer FA, Poli G, Price MA, Rauch A, Theodorou I, Trkola A, Walker BD, Winkler CA, Zagury JF, Montgomery SB, Ciuffi A, Hultquist JF, Wolinsky SM, Dougan G, Lever AML, Gurdasani D, Groom H, Sandhu MS, Fellay J. Africa-specific human genetic variation near CHD1L associates with HIV-1 load. Nature. 2023 Aug 2. doi: 10.1038/s41586-023-06370-4.
Rahmouni M, De Marco L, Spadoni JL, Tison M, Medina-Santos R, Labib T, Noirel J, Tamouza R, Limou S, Delaneau O, Fellay J, Bensussan A, Le Clerc S, McLaren PJ, Zagury JF. The HLA-B*57:01 allele corresponds to a very large MHC haploblock likely explaining its massive effect for HIV-1 elite control. Front Immunol. 2023 Dec 11;14:1305856. doi: 10.3389/fimmu.2023.1305856. eCollection 2023.
2022
Mazzolini J, Le Clerc S, Morisse G, Coulonges C, Zagury JF, Sieger D. Wasl is crucial to maintain microglial core activities during glioblastoma initiation stages. Glia. 2022 Feb 22. doi: 10.1002/glia.24154.
Mobuchon L, Derrien AC, Houy A, Verrier T, Pierron G, Cassoux N, Milder M, Deleuze JF, Boland A, Scelo G, Cancel-Tassin G, Cussenot O, Rodrigues M, Noirel J, Machiela MJ, Stern MH. Different Pigmentation Risk Loci for High-Risk Monosomy 3 and Low-Risk Disomy 3 Uveal Melanomas. J Natl Cancer Inst. 2022 Feb 7;114(2):302-309. doi: 10.1093/jnci/djab167.
Rahmouni M, Laville V, Spadoni JL, Jdid R, Eckhart L, Gruber F, Labib T, Coulonges C, Carpentier W, Latreille J, Morizot F, Tschachler E, Ezzedine K, Le Clerc S, Zagury JF. Identification of New Biological Pathways Involved in Skin Aging From the Analysis of French Women Genome-Wide Data. Front Genet. 2022 Mar 24;13:836581. doi: 10.3389/fgene.2022.836581.
Thiam F, Diop G, Coulonges C, Derbois C, Mbengue B, Thiam A, Nguer CM, Zagury JF, Deleuze JF, Dieye A. G6PD and HBB polymorphisms in the Senegalese population: prevalence, correlation with clinical malaria. PeerJ. 2022 Jul 5;10:e13487. doi: 10.7717/peerj.13487. eCollection 2022.
Derrien AC, Houy A, Ganier O, Dingli F, Ningarhari M, Mobuchon L, Espejo Díaz MI, Loew D, Cassoux N, Cussenot O, Cancel-Tassin G, Margueron R, Noirel J, Zucman-Rossi J, Rodrigues M, Stern MH. Functional characterization of 5p15.33 risk locus in uveal melanoma reveals rs452384 as a functional variant and NKX2.4 as an allele-specific interactor. Am J Hum Genet. 2022 Dec 1;109(12):2196-2209. doi: 10.1016/j.ajhg.2022.11.004.
2021
Mascret A, Mouhsine H, Attia G, Cabrera D, Benchekroun M, Gizzi P, Zerrouki C, Fourati N, Zagury JF, Veitía MS, Port M. New contributions to the drug profile of TNFα inhibitor SPD304: Affinity, selectivity and ADMET considerations. Eur J Pharmacol. 2021 Sep 15;907:174285. doi: 10.1016/j.ejphar.2021.174285. Epub 2021 Jun 26.
Le Clerc S, Lombardi L, Baune BT, …, Barrau C, Leboyer M*, Tamouza R*, Zagury JF*. HLA-DRB1 and HLA-DQB1 genetic diversity modulates response to lithium in bipolar affective disorders. Sci Rep. 2021 Sep 8;11(1):17823. doi: 10.1038/s41598-021-97140-7.
2019
Delaneau O, Zagury JF, Robinson MR, Marchini JL, Dermitzakis ET. Accurate, scalable and integrative haplotype estimation. Nat Commun. 2019 Nov 28;10(1):5436. doi: 10.1038/s41467-019-13225-y. PubMed PMID: 31780650; PubMed Central PMCID: PMC6882857.
Réau M, Lagarde N, Zagury JF, Montes M. Hits Discovery on the Androgen Receptor: In Silico Approaches to Identify Agonist Compounds. Cells. 2019 Nov 13;8(11). pii: E1431. doi: 10.3390/cells8111431. PubMed PMID: 31766271; PubMed Central PMCID: PMC6912550.
Le Clerc S, Limou S, Zagury JF. Large-Scale "OMICS" Studies to Explore the Physiopatholgy of HIV-1 Infection. Front Genet. 2019 Sep 13;10:799. doi: 10.3389/fgene.2019.00799. eCollection 2019. Review. PubMed PMID: 31572435; PubMed Central PMCID: PMC6754074.
Liu Y, Gao W, Koellmann C, Le Clerc S, Hüls A, Li B, Peng Q, Wu S, Ding A, Yang Y, Jin L, Krutmann J, Schikowski T, Zagury JF, Wang S. Genome-wide scan identified genetic variants associated with skin aging in a Chinese female population. J Dermatol Sci. 2019 Oct;96(1):42-49. doi: 10.1016/j.jdermsci.2019.08.010. Epub 2019 Sep 6. PubMed PMID: 31522824.
Mazzolini J, Le Clerc S, Morisse G, Coulonges C, Kuil LE, van Ham TJ, Zagury JF, Sieger D. Gene expression profiling reveals a conserved microglia signature in larval zebrafish. Glia. 2020 Feb;68(2):298-315. doi: 10.1002/glia.23717. Epub 2019 Sep 11. PubMed PMID: 31508850; PubMed Central PMCID: MC6916425.
Réau M, Lagarde N, Zagury JF, Montes M. Nuclear Receptors Database Including Negative Data (NR-DBIND): A Database Dedicated to Nuclear Receptors Binding Data Including Negative Data and Pharmacological Profile. J Med Chem. 2019 Mar 28;62(6):2894-2904. doi: 10.1021/acs.jmedchem.8b01105. Epub 2018 Nov 6. PubMed PMID: 30354114.
2018
Montagne L, Derhourhi M, Piton A, Toussaint B, Durand E, Vaillant E, Thuillier D, Gaget S, De Graeve F, Rabearivelo I, Lansiaux A, Lenne B, Sukno S, Desailloud R, Cnop M, Nicolescu R, Cohen L, Zagury JF, Amouyal M, Weill J, Muller J, Sand O, Delobel B, Froguel P, Bonnefond A. CoDE-seq, an augmented whole-exome sequencing, enables the accurate detection of CNVs and mutations in Mendelian obesity and intellectual disability. Mol Metab. 2018 Jul;13:1-9. doi: 10.1016/j.molmet.2018.05.005. Epub 2018 May 16. PubMed PMID: 29784605; PubMed Central PMCID: PMC6026315.
Laville V, Le Clerc S, Ezzedine K, Jdid R, Taing L, Labib T, Coulonges C, Ulveling D, Galan P, Guinot C, Fezeu L, Morizot F, Latreille J, Malvy D, Tschachler E, Zagury JF. A genome wide association study identifies new genes potentially associated with eyelid sagging. Exp Dermatol. 2019 Aug;28(8):892-898. doi: 10.1111/exd.13559. Epub 2018 Jun 28. PubMed PMID: 29654602.
Réau M, Langenfeld F, Zagury JF, Lagarde N, Montes M. Decoys Selection in Benchmarking Datasets: Overview and Perspectives. Front Pharmacol. 2018 Jan 24;9:11. doi: 10.3389/fphar.2018.00011. eCollection 2018. Review. PubMed PMID: 29416509; PubMed Central PMCID: PMC5787549.
Rayar AM, Lagarde N, Martin F, Blanchard F, Liagre B, Ferroud C, Zagury JF, Montes M, Sylla-Iyarreta Veitía M. New selective cyclooxygenase-2 inhibitors from cyclocoumarol: Synthesis, characterization, biological evaluation and molecular modeling. Eur J Med Chem. 2018 Feb 25;146:577-587. doi: 10.1016/j.ejmech.2018.01.054. Epub 2018 Jan 31. PubMed PMID: 29407982.
2017
Gérardin P, Coulonges C, Zagury JF. Genetic Associations with Spontaneous Preterm Birth. N Engl J Med. 2017 Dec 14;377(24):2401. doi: 10.1056/NEJMc1713902. PubMed PMID: 29239589.
Réau M, Langenfeld F, Zagury JF, Montes M. Predicting the affinity of Farnesoid X Receptor ligands through a hierarchical ranking protocol: a D3R Grand Challenge 2 case study. J Comput Aided Mol Des. 2018 Jan;32(1):231-238. doi: 10.1007/s10822-017-0063-0. Epub 2017 Sep 14. PubMed PMID: 28913743.
Rayar AM, Lagarde N, Ferroud C, Zagury JF, Montes M, Sylla-Iyarreta Veitia M. Update on COX-2 Selective Inhibitors: Chemical Classification, Side Effects and their Use in Cancers and Neuronal Diseases. Curr Top Med Chem. 2017;17(26):2935-2956. doi: 10.2174/1568026617666170821124947. Review. PubMed PMID: 28828990.
Jeanmougin M, Noirel J, Coulonges C, Zagury JF. HLA-check: evaluating HLA data from SNP information. BMC Bioinformatics. 2017 Jul 11;18(1):334. doi: 10.1186/s12859-017-1746-1. PubMed PMID: 28697761; PubMed Central PMCID: PMC5504728.
Lagarde N, Delahaye S, Jérémie A, Ben Nasr N, Guillemain H, Empereur-Mot C, Laville V, Labib T, Réau M, Langenfeld F, Zagury JF, Montes M. Discriminating Agonist from Antagonist Ligands of the Nuclear Receptors Using Different Chemoinformatics Approaches. Mol Inform. 2017 Oct;36(10). doi: 10.1002/minf.201700020. Epub 2017 Jul 3. PubMed PMID: 28671755.
Mouhsine H, Guillemain H, Moreau G, Fourati N, Zerrouki C, Baron B, Desallais L, Gizzi P, Ben Nasr N, Perrier J, Ratsimandresy R, Spadoni JL, Do H, England P, Montes M, Zagury JF. Identification of an in vivo orally active dual-binding protein-protein interaction inhibitor targeting TNFα through combined in
silico/in vitro/in vivo screening. Sci Rep. 2017 Jun 13;7(1):3424. doi: 10.1038/s41598-017-03427-z. PubMed PMID: 28611375; PubMed Central PMCID: PMC5469758.
Assier E, Bessis N, Zagury JF, Boissier MC. IL-1 Vaccination Is Suitable for Treating Inflammatory Diseases. Front Pharmacol. 2017 Jan 31;8:6. doi: 10.3389/fphar.2017.00006. eCollection 2017. PubMed PMID: 28197099; PubMed Central PMCID: PMC5281538.
Eckenfelder A, Ségéral E, Pinzón N, Ulveling D, Amadori C, Charpentier M, Nidelet S, Concordet JP, Zagury JF, Paillart JC, Berlioz-Torrent C, Seitz H, Emiliani S, Gallois-Montbrun S. Argonaute proteins regulate HIV-1 multiply spliced RNA and viral production in a Dicer independent manner. Nucleic Acids Res. 2017 Apr 20;45(7):4158-4173. doi: 10.1093/nar/gkw1289. PubMed PMID: 28003477; PubMed Central PMCID: PMC5397155.
Empereur-Mot C, Zagury JF, Montes M. Screening Explorer-An Interactive Tool for the Analysis of Screening Results. J Chem Inf Model. 2016 Dec 27;56(12):2281-2286. doi: 10.1021/acs.jcim.6b00283. Epub 2016 Nov 22. PubMed PMID: 27808512.
Laville V, Le Clerc S, Ezzedine K, Zagury JF. Response to the commentary on 'A genome-wide association study in Caucasian women suggests the involvement of HLA gene in the severity of facial solar lentigines'. Pigment Cell Melanoma Res. 2017 Jan;30(1):74-75. doi: 10.1111/pcmr.12552. Epub 2016 Nov 30. PubMed PMID: 27804239.
2016
Ulveling D, Le Clerc S, Cobat A, Labib T, Noirel J, Laville V, Coulonges C, Carpentier W, Nalpas B, Heim MH, Poynard T, Cerny A, Pol S, Bochud PY, Dabis F, Theodorou I, Lévy Y, Salmon D, Abel L, Dominguez S, Zagury JF; HEPAVIH ANRS CO13 Cohort Study Group; Swiss Hepatitis C Cohort Study Group; French ANRS HC EP 26 Genoscan Study Group. A new 3p25 locus is associated with liver fibrosis progression in human immunodeficiency virus/hepatitis C virus-coinfected patients. Hepatology. 2016 Nov;64(5):1462-1472. doi: 10.1002/hep.28695. Epub 2016 Jul 29. PubMed PMID: 27339598.
Lagarde N, Delahaye S, Zagury JF, Montes M. Discriminating agonist and antagonist ligands of the nuclear receptors using 3D-pharmacophores. J Cheminform. 2016 Sep 6;8(1):43. doi: 10.1186/s13321-016-0154-2. eCollection 2016. PubMed PMID: 27602059; PubMed Central PMCID: PMC5011875.
Laville V, Clerc SL, Ezzedine K, Jdid R, Taing L, Labib T, Coulonges C, Ulveling D, Carpentier W, Galan P, Hercberg S, Morizot F, Latreille J, Malvy D, Tschachler E, Zagury JF. A genome-wide association study in Caucasian women suggests the involvement of HLA genes in the severity of facial solar lentigines. Pigment Cell Melanoma Res. 2016 Sep;29(5):550-8. doi: 10.1111/pcmr.12502. Epub 2016 Aug 8. PubMed PMID: 27327535.
O'Connell J, Sharp K, Shrine N, Wain L, Hall I, Tobin M, Zagury JF, Delaneau O, Marchini J. Haplotype estimation for biobank-scale data sets. Nat Genet. 2016 Jul;48(7):817-20. doi: 10.1038/ng.3583. Epub 2016 Jun 6. PubMed PMID: 27270105; PubMed Central PMCID: PMC4926957.
Desallais L, Bouchez C, Mouhsine H, Moreau G, Ratsimandresy R, Montes M, Do H, Quintin-Colonna F, Zagury JF. Immunization against an IL-6 peptide induces anti-IL-6 antibodies and modulates the Delayed-Type Hypersensitivity reaction in cynomolgus monkeys. Sci Rep. 2016 Jan 19;6:19549. doi: 0.1038/srep19549. PubMed PMID: 26782790; PubMed Central PMCID: PMC4726013.
Cheng Y, Pardo M, Armini RS, Martinez A, Mouhsine H, Zagury JF, Jope RS, Beurel E. Stress-induced neuroinflammation is mediated by GSK3-dependent TLR4 signaling that promotes susceptibility to depression-like behavior. Brain Behav Immun. 2016 Mar;53:207-222. doi: 10.1016/j.bbi.2015.12.012. Epub 2016 Jan 6. PubMed PMID: 26772151; PubMed Central PMCID: PMC4783243.
2015
McLaren PJ, Coulonges C, Bartha I, Lenz TL, Deutsch AJ, Bashirova A, Buchbinder S, Carrington MN, Cossarizza A, Dalmau J, De Luca A, Goedert JJ, Gurdasani D, Haas DW, Herbeck JT, Johnson EO, Kirk GD, Lambotte O, Luo M, Mallal S, van Manen D, Martinez-Picado J, Meyer L, Miro JM, Mullins JI, Obel N, Poli G, Sandhu MS, Schuitemaker H, Shea PR, Theodorou I, Walker BD, Weintrob AC, Winkler CA, Wolinsky SM, Raychaudhuri S, Goldstein DB, Telenti A, de Bakker PI, Zagury JF, Fellay J. Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load. Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14658-63. doi: 10.1073/pnas.1514867112. Epub 2015 Nov 9. PubMed PMID: 26553974; PubMed Central PMCID: PMC4664299.
Empereur-Mot C, Guillemain H, Latouche A, Zagury JF, Viallon V, Montes M. Predictiveness curves in virtual screening. J Cheminform. 2015 Nov 4;7:52. doi: 10.1186/s13321-015-0100-8. eCollection 2015. PubMed PMID: 26539250; PubMed Central PMCID: PMC4631717.
Spadoni JL, Rucart P, Le Clerc S, van Manen D, Coulonges C, Ulveling D, Laville V, Labib T, Taing L, Delaneau O, Montes M, Schuitemaker H, Noirel J, Zagury JF. Identification of Genes Whose Expression Profile Is Associated with Non-Progression towards AIDS Using eQTLs. PLoS One. 2015 Sep 14;10(9):e0136989. doi: 10.1371/journal.pone.0136989. eCollection 2015. PubMed PMID: 26367535; PubMed Central PMCID: PMC4569262.
Le Clerc S, Taing L, Fond G, Meary A, Llorca PM, Blanc O, Beaune P, Rajagopal K, Jamain S, Tamouza R, Zagury JF, Leboyer M. A double amino-acid change in the HLA-A peptide-binding groove is associated with response to psychotropic treatment in patients with schizophrenia. Transl Psychiatry. 2015 Jul 28;5:e608. doi: 10.1038/tp.2015.97. PubMed PMID: 26218850; PubMed Central PMCID: PMC5068718.
Beauclair G, Bridier-Nahmias A, Zagury JF, Saïb A, Zamborlini A. JASSA: a comprehensive tool for prediction of SUMOylation sites and SIMs. Bioinformatics. 2015 Nov 1;31(21):3483-91. doi: 10.1093/bioinformatics/btv403. Epub 2015 Jul 2. PubMed PMID: 26142185.
Lagarde N, Zagury JF, Montes M. Benchmarking Data Sets for the Evaluation of Virtual Ligand Screening Methods: Review and Perspectives. J Chem Inf Model. 2015 Jul 27;55(7):1297-307. doi: 10.1021/acs.jcim.5b00090. Epub 2015 Jun 18. Review. PubMed PMID: 26038804.
Johnson RC, Nelson GW, Zagury JF, Winkler CA. ALDsuite: Dense marker MALD using principal components of ancestral linkage disequilibrium. BMC Genet. 2015 Mar 7;16:23. doi: 10.1186/s12863-015-0179-y. PubMed PMID: 25886794; PubMed Central PMCID: PMC4408589.
