Production scientifique de l'équipe Génomique/bioinformatique
2019
1: 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.
2: 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.
3: 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.
4: 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.
5: 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.
6: 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
7: 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.
8: 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.
9: 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.
10: 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
11: 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.
12: 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.
13: 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.
14: 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.
15: 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.
16: 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.
17: 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.
18: 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.
19: 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.
20: 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
21: 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.
22: 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.
23: 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.
24: 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.
25: 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.
26: 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
27: 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.
28: 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.
29: 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.
30: 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.
31: 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.
32: 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.
33: 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.
