Home Publications

2015

  • Baeza, M., S. Viala, M. Heim, A. Dard, B. Hudry, M. Duffraisse, A. Rogulja-Ortmann, C. Brun and S. Merabet (2015). "Inhibitory activities of short linear motifs underlie Hox interactome specificity in vivo." Elife 4.
  • Bergon, A., R. Belzeaux, M. Comte, F. Pelletier, M. Herve, E. J. Gardiner, N. J. Beveridge, B. Liu, V. Carr, R. J. Scott, B. Kelly, M. J. Cairns, N. Kumarasinghe, U. Schall, O. Blin, J. Boucraut, P. A. Tooney, E. Fakra and C. Ibrahim el (2015). "CX3CR1 is dysregulated in blood and brain from schizophrenia patients." Schizophr Res 168(1-2): 434-443.
  • Bouchet, A., N. Sakakini, M. E. Atifi, C. Le Clec'h, E. Brauer-Krisch, L. Rogalev, J. A. Laissue, P. Rihet, G. Le Duc and L. Pelletier (2015). "Identification of AREG and PLK1 pathway modulation as a potential key of the response of intracranial 9L tumor to microbeam radiation therapy." Int J Cancer 136(11): 2705-2716.
  • Boudjarane, J., A. Essaydi, L. Farnault, C. Popovici, M. Lafage-Pochitaloff, N. Beaufils, Y. Berda-Haddad, R. Lacroix, C. Nicolino-Brunet, T. Le Treut, H. Zattara, J. Gabert, B. Kahn-Perles and R. Costello (2015). "Characterization of the novel Sezary lymphoma cell line BKP1." Exp Dermatol 24(1): 60-62.
  • Brisebarre, A., B. Kumulungui, S. Sawadogo, S. Afridi, F. Fumoux and P. Rihet (2015). "Genome-wide significant linkage to IgG subclass responses against Plasmodium falciparum antigens on chromosomes 8p22-p21, 9q34 and 20q13." Genes Immun 16(3): 187-192.
  • Cayrou, C., B. Ballester, I. Peiffer, R. Fenouil, P. Coulombe, J. C. Andrau, J. van Helden and M. Mechali (2015). "The chromatin environment shapes DNA replication origin organization and defines origin classes." Genome Res 25(12): 1873-1885.
  • Chapple, C. E. and C. Brun (2015). "Redefining protein moonlighting." Oncotarget 6(19): 16812-16813.
  • Chapple, C. E., C. Herrmann and C. Brun (2015). "PrOnto database : GO term functional dissimilarity inferred from biological data." Front Genet 6: 200.
  • Chapple, C. E., B. Robisson, L. Spinelli, C. Guien, E. Becker and C. Brun (2015). "Extreme multifunctional proteins identified from a human protein interaction network." Nat Commun 6: 7412.
  • Chetouhi, C., J. Panek, L. Bonhomme, H. ElAlaoui, C. Texier, T. Langin, C. de Bekker, S. Urbach, E. Demettre, D. Misse, P. Holzmuller, D. P. Hughes, A. Zanzoni, C. Brun and D. G. Biron (2015). "Cross-talk in host-parasite associations: What do past and recent proteomics approaches tell us?" Infect Genet Evol 33: 84-94.
  • Costello, R. T., A. Leclercq, T. L. Treut, C. Sanchez, D. Mercier and G. Sebahoun (2015). "Effects of 5-azacytidine on natural killer cell activating receptor expression in patients with refractory anemia with excess of blasts." Leuk Res Rep 4(1): 15-17.
  • Didier, G., C. Brun and A. Baudot (2015). "Identifying communities from multiplex biological networks." PeerJ 3: e1525.
  • Facchiano, A., C. Angelini, R. Bosotti, A. Guffanti, A. Marabotti, R. Marangoni, S. Pascarella, P. Romano, A. Zanzoni and M. Helmer-Citterich (2015). "Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics." BMC Bioinformatics 16 Suppl 9: S1.
  • Fanciullino, R., C. Mercier, C. Serdjebi, Y. Berda, F. Fina, L. Ouafik, B. Lacarelle, J. Ciccolini and R. Costello (2015). "Lethal toxicity after administration of azacytidine: implication of the cytidine deaminase-deficiency syndrome." Pharmacogenet Genomics 25(6): 317-321.
  • Feron, F., B. Gepner, E. Lacassagne, D. Stephan, B. Mesnage, M. P. Blanchard, N. Boulanger, C. Tardif, A. Deveze, S. Rousseau, K. Suzuki, J. C. Izpisua Belmonte, M. Khrestchatisky, E. Nivet and M. Erard-Garcia (2015). "Olfactory stem cells reveal MOCOS as a new player in autism spectrum disorders." Mol Psychiatry.
  • Griffon, A., Q. Barbier, J. Dalino, J. van Helden, S. Spicuglia and B. Ballester (2015). "Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape." Nucleic Acids Res 43(4): e27.
  • Medina-Rivera, A., M. Defrance, O. Sand, C. Herrmann, J. A. Castro-Mondragon, J. Delerce, S. Jaeger, C. Blanchet, P. Vincens, C. Caron, D. M. Staines, B. Contreras-Moreira, M. Artufel, L. Charbonnier-Khamvongsa, C. Hernandez, D. Thieffry, M. Thomas-Chollier and J. van Helden (2015). "RSAT 2015: Regulatory Sequence Analysis Tools." Nucleic Acids Res 43(W1): W50-56.
  • Metzler-Guillemain, C., G. Victorero, C. Lepoivre, A. Bergon, M. Yammine, J. Perrin, I. Sari-Minodier, N. Boulanger, P. Rihet and C. Nguyen (2015). "Sperm mRNAs and microRNAs as candidate markers for the impact of toxicants on human spermatogenesis: an application to tobacco smoking." Syst Biol Reprod Med 61(3): 139-149.
  • Nardacci, R., J. L. Perfettini, L. Grieco, D. Thieffry, G. Kroemer and M. Piacentini (2015). "Syncytial apoptosis signaling network induced by the HIV-1 envelope glycoprotein complex: an overview." Cell Death Dis 6: e1846.
  • Navarro, J. M., A. Touzart, L. C. Pradel, M. Loosveld, M. Koubi, R. Fenouil, S. Le Noir, M. A. Maqbool, E. Morgado, C. Gregoire, S. Jaeger, E. Mamessier, C. Pignon, S. Hacein-Bey-Abina, B. Malissen, M. Gut, I. G. Gut, H. Dombret, E. A. Macintyre, S. J. Howe, H. B. Gaspar, A. J. Thrasher, N. Ifrah, D. Payet-Bornet, E. Duprez, J. C. Andrau, V. Asnafi and B. Nadel (2015). "Site- and allele-specific polycomb dysregulation in T-cell leukaemia." Nat Commun 6: 6094.
  • Pradel, L. C., L. Vanhille and S. Spicuglia (2015). "[The European Blueprint project: towards a full epigenome characterization of the immune system]." Med Sci (Paris) 31(3): 236-238.
  • Rommelaere, S., V. Millet, P. Rihet, S. Atwell, E. Helfer, L. Chasson, C. Beaumont, G. Chimini, R. Sambo Mdo, A. Viallat, C. Penha-Goncalves, F. Galland and P. Naquet (2015). "Serum pantetheinase/vanin levels regulate erythrocyte homeostasis and severity of malaria." Am J Pathol 185(11): 3039-3052.
  • Sanchez, C., C. Baier, J. G. Colle, R. Chelbi, P. Rihet, T. Le Treut, J. Imbert, G. Sebahoun, G. Venton and R. T. Costello (2015). "Natural killer cells in patients with polycythemia vera." Hum Immunol 76(9): 644-650.
  • Sanchez, C., T. Le Treut, C. Baier, G. Sebahoun and R. T. Costello (2015). "Distribution of lymphocyte subpopulations in patients with polycythemia vera." Hum Immunol 76(6): 414-416.
  • Tiberi, G., A. Pekowska, C. Oudin, A. Ivey, A. Autret, T. Prebet, M. Koubi, F. Lembo, M. J. Mozziconacci, G. Bidaut, C. Chabannon, D. Grimwade, N. Vey, S. Spicuglia, B. Calmels and E. Duprez (2015). "PcG methylation of the HIST1 cluster defines an epigenetic marker of acute myeloid leukemia." Leukemia 29(5): 1202-1206.
  • van Oevelen, C., S. Collombet, G. Vicent, M. Hoogenkamp, C. Lepoivre, A. Badeaux, L. Bussmann, J. L. Sardina, D. Thieffry, M. Beato, Y. Shi, C. Bonifer and T. Graf (2015). "C/EBPalpha Activates Pre-existing and De Novo Macrophage Enhancers during Induced Pre-B Cell Transdifferentiation and Myelopoiesis." Stem Cell Reports 5(2): 232-247.
  • Vanhille, L., A. Griffon, M. A. Maqbool, J. Zacarias-Cabeza, L. T. Dao, N. Fernandez, B. Ballester, J. C. Andrau and S. Spicuglia (2015). "High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq." Nat Commun 6: 6905.
  • Via, A., B. Uyar, C. Brun and A. Zanzoni (2015). "How pathogens use linear motifs to perturb host cell networks." Trends Biochem.Sci. 40(1): 36-48.
  • Via, A. and A. Zanzoni (2015). "A prismatic view of protein phosphorylation in health and disease." Front Genet 6: 131.
  • Zacarias-Cabeza, J., M. Belhocine, L. Vanhille, P. Cauchy, F. Koch, A. Pekowska, R. Fenouil, A. Bergon, M. Gut, I. Gut, D. Eick, J. Imbert, P. Ferrier, J. C. Andrau and S. Spicuglia (2015). "Transcription-dependent generation of a specialized chromatin structure at the TCRbeta locus." J Immunol 194(7): 3432-3443.
  • Zanzoni, A., C. E. Chapple and C. Brun (2015). "Relationships between predicted moonlighting proteins, human diseases, and comorbidities from a network perspective." Front Physiol 6: 171.

2014

  • Alpern,D., Langer,D., Ballester,B., Le,G.S., Romier,C., Mengus,G., and Davidson,I. (2014). TAF4, a subunit of transcription factor II D, directs promoter occupancy of nuclear receptor HNF4A during post-natal hepatocyte differentiation. Elife. 3, e03613. PM:25209997
  • Amrani,A., Bergon,A., Holota,H., Tamburini,C., Garel,M., Ollivier,B., Imbert,J., Dolla,A., and Pradel,N. (2014). Transcriptomics Reveal Several Gene Expression Patterns in the Piezophile Desulfovibrio hydrothermalis in Response to Hydrostatic Pressure. PLoS ONE 9, e106831. PM:25215865
  • Ballester,B., Medina-Rivera,A., Schmidt,D., Gonzalez-Porta,M., Carlucci,M., Chen,X., Chessman,K., Faure,A.J., Funnell,A.P., Goncalves,A., Kutter,C., Lukk,M., Menon,S., McLaren,W.M., Stefflova,K., Watt,S., Weirauch,M.T., Crossley,M., Marioni,J.C., Odom,D.T., Flicek,P., and Wilson,M.D. (2014). Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways. Elife. 3, e02626. PM:25279814
  • Bond,J., Bergon,A., Durand,A., Tigaud,I., Thomas,X., Asnafi,V., Spicuglia,S., and Macintyre,E. (2014). Cryptic XPO1-MLLT10 translocation is associated with HOXA locus deregulation in T-ALL. Blood 124, 3023-3025. PM:25377562
  • Bouchet,A., Sakakini,N., Atifi,M.E., Le,C.C., Brauer-Krisch,E., Rogalev,L., Laissue,J.A., Rihet,P., Le,D.G., and Pelletier,L. (2014). Identification of AREG and PLK1 pathway modulation as a potential key of the response of intracranial 9L tumor to microbeam radiation therapy. Int. J. Cancer. PM:25382544
  • Brisebarre,A., Kumulungui,B., Sawadogo,S., Atkinson,A., Garnier,S., Fumoux,F., and Rihet,P. (2014). A genome scan for Plasmodium falciparum malaria identifies quantitative trait loci on chromosomes 5q31, 6p21.3, 17p12, and 19p13. Malar. J. 13, 198. PM:24884991
  • Brisebarre,A., Kumulungui,B., Sawadogo,S., Afridi,S., Fumoux,F., and Rihet,P. (2014). Genome-wide significant linkage to IgG subclass responses against Plasmodium falciparum antigens on chromosomes 8p22-p21, 9q34 and 20q13. Genes Immun. PM:25521226
  • Cieslak,A., Le,N.S., Trinquand,A., Lhermitte,L., Franchini,D.M., Villarese,P., Gon,S., Bond,J., Simonin,M., Vanhile,L., Reimann,C., Verhoeyen,E., Larghero,J., Six,E., Spicuglia,S., Andre-Schmutz,I., Langerak,A., Nadel,B., Macintyre,E., Payet-Bornet,D., and Asnafi,V. (2014). RUNX1-dependent RAG1 deposition instigates human TCR-delta locus rearrangement. J. Exp. Med. 211, 1821-1832. PM:25135298
  • Cornen,S., Guille,A., Adelaide,J., Addou-Klouche,L., Finetti,P., Saade,M.R., Manai,M., Carbuccia,N., Bekhouche,I., Letessier,A., Raynaud,S., Charafe-Jauffret,E., Jacquemier,J., Spicuglia,S., de,T.H., Viens,P., Bertucci,F., Birnbaum,D., and Chaffanet,M. (2014). Candidate luminal B breast cancer genes identified by genome, gene expression and DNA methylation profiling. PLoS ONE 9, e81843. PM:24416132
  • Defaye,A. and Perrin,L. (2014). Tissue specific RNA isolation in Drosophila embryos: a strategy to analyze context dependent transcriptome landscapes using FACS. Methods Mol. Biol. 1196, 183-195. PM:25151164
  • Di,G.E., Borroni,B., Giorgio,E., Lacerenza,D., Ferrero,M., Lo,B.N., Ragusa,N., Mancini,C., Gaussen,M., Calcia,A., Mitro,N., Hoxha,E., Mura,I., Coviello,D.A., Moon,Y.A., Tesson,C., Vaula,G., Couarch,P., Orsi,L., Duregon,E., Papotti,M.G., Deleuze,J.F., Imbert,J., Costanzi,C., Padovani,A., Giunti,P., Maillet-Vioud,M., Durr,A., Brice,A., Tempia,F., Funaro,A., Boccone,L., Caruso,D., Stevanin,G., and Brusco,A. (2014). ELOVL5 Mutations Cause Spinocerebellar Ataxia 38. Am. J Hum. Genet. 95, 209-217. PM:25065913
  • Erkosar,C.B., Defaye,A., Bozonnet,N., Puthier,D., Royet,J., and Leulier,F. (2014). Drosophila microbiota modulates host metabolic gene expression via IMD/NF-kappaB signaling. PLoS ONE 9, e94729. PM:24733183
  • Evangelista,A.F., Collares,C.V., Xavier,D.J., Macedo,C., Manoel-Caetano,F.S., Rassi,D.M., Foss-Freitas,M.C., Foss,M.C., Sakamoto-Hojo,E.T., Nguyen,C., Puthier,D., Passos,G.A., and Donadi,E.A. (2014). Integrative analysis of the transcriptome profiles observed in type 1, type 2 and gestational diabetes mellitus reveals the role of inflammation. BMC Med. Genomics 7, 28. PM:24885568
  • Farnault,L., Mercier,C., Berda-Haddad,Y., Sebahoun,G., and Costello,R. (2014). Is R-CHOP Therapy a Lymphoma Growth Factor? Am. J Ther. PM:24675549
  • Griffon,A., Barbier,Q., Dalino,J., van,H.J., Spicuglia,S., and Ballester,B. (2014). Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape. Nucleic Acids Res. PM:25477382
  • Hamidou Soumana,I., Tchicaya,B., Loriod,B., Rihet,P., and Geiger,A. (2014). Identification of overexpressed genes in Sodalis glossinidius inhabiting trypanosome-infected self-cured tsetse flies. Front Microbiol. 5, 255. PM:24904565
  • Hamidou Soumana,I., Loriod,B., Ravel,S., Tchicaya,B., Simo,G., Rihet,P., and Geiger,A. (2014). The transcriptional signatures of Sodalis glossinidius in the Glossina palpalis gambiensis flies negative for Trypanosoma brucei gambiense contrast with those of this symbiont in tsetse flies positive for the parasite: Possible involvement of a Sodalis-hosted prophage in fly Trypanosoma refractoriness? Infect. Genet. Evol. 24C, 41-56. PM:24637266
  • Hernandez-Valladares,M., Rihet,P., and Iraqi,F.A. (2014). Host susceptibility to malaria in human and mice: compatible approaches to identify potential resistant genes. Physiol Genomics 46, 1-16. PM:24170032
  • Katsogiannou,M., Andrieu,C., Baylot,V., Baudot,A., Dusetti,N.J., Gayet,O., Finetti,P., Garrido,C., Birnbaum,D., Bertucci,F., Brun,C., and Rocchi,P. (2014). The functional landscape of Hsp27 reveals new cellular processes such as DNA repair and alternative splicing and proposes novel anticancer targets. Mol. Cell Proteomics. 13, 3585-3601. PM:25277244
  • Landel,V., Baranger,K., Virard,I., Loriod,B., Khrestchatisky,M., Rivera,S., Benech,P., and Feron,F. (2014). Temporal gene profiling of the 5XFAD transgenic mouse model highlights the importance of microglial activation in Alzheimer's disease. Mol. Neurodegener. 9, 33. PM:25213090
  • Mathieu,E.L., Belhocine,M., Dao,L.T., Puthier,D., and Spicuglia,S. (2014). [Functions of lncRNA in development and diseases]. Med. Sci. (Paris) 30, 790-796. PM:25174757
  • Panek,J., El,A.H., Mone,A., Urbach,S., Demettre,E., Texier,C., Brun,C., Zanzoni,A., Peyretaillade,E., Parisot,N., Lerat,E., Peyret,P., Delbac,F., and Biron,D.G. (2014). Hijacking of host cellular functions by an intracellular parasite, the microsporidian Anncaliia algerae. PLoS ONE 9, e100791. PM:24967735
  • Potier,D., Seyres,D., Guichard,C., Iche-Torres,M., Aerts,S., Herrmann,C., and Perrin,L. (2014). Identification of cis-regulatory modules encoding temporal dynamics during development. BMC Genomics 15, 534. PM:24972496
  • Rommelaere,S., Millet,V., Vu Manh,T.P., Gensollen,T., Andreoletti,P., Cherkaoui-Malki,M., Bourges,C., Escaliere,B., Du,X., Xia,Y., Imbert,J., Beutler,B., Kanai,Y., Malissen,B., Malissen,M., Tailleux,A., Staels,B., Galland,F., and Naquet,P. (2014). Sox17 regulates liver lipid metabolism and adaptation to fasting. PLoS ONE 9, e104925. PM:25141153
  • Shimoyama,S., Kasai,S., Kahn-Perles,B., and Kikuchi,H. (2014). Dephosphorylation of Sp1 at Ser-59 by Protein Phosphatase 2A (PP2A) is required for induction of CYP1A1 transcription after treatment with 2,3,7,8-tetrachlorodibenzo-p-dioxin or omeprazole. Biochim. Biophys. Acta 1839, 107-115. PM:24382322
  • Souiai,O., Guerfali,F., Ben,M.S., Brun,C., and Benkahla,A. (2014). In silico prediction of protein-protein interactions in human macrophages. BMC. Res. Notes 7, 157. PM:24636261
  • Tevy,M.F., Seyres,D., Traina,C., Perrin,L., and Capovilla,M. (2014). Ndae1 expression and regulation in Drosophila embryos. PLoS ONE 9, e92956. PM:24676142
  • Tiberi,G., Pekowska,A., Oudin,C., Ivey,A., Autret,A., Prebet,T., Koubi,M., Lembo,F., Mozziconacci,M.J., Bidaut,G., Chabannon,C., Grimwade,D., Vey,N., Spicuglia,S., Calmels,B., and Duprez,E. (2014). PcG methylation of the HIST1 cluster defines an epigenetic marker of acute myeloid leukemia. Leukemia. PM:25482132

2013

  • Baier, C., A. Fino, C. Sanchez, L. Farnault, P. Rihet, B. Kahn-Perles, and R. T. Costello. 2013. Natural Killer Cells Modulation in Hematological Malignancies. Front Immunol. 4:459. doi:10.3389/fimmu.2013.00459 [doi].
  • Bouchet, A., N. Sakakini, A. M. El, C. C. Le, E. Brauer, A. Moisan, P. Deman, P. Rihet, D. G. Le, and L. Pelletier. 2013. Early Gene Expression Analysis in 9L Orthotopic Tumor-Bearing Rats Identifies Immune Modulation in Molecular Response to Synchrotron Microbeam Radiation Therapy. PLoS.ONE. 8:e81874. doi:10.1371/journal.pone.0081874 [doi];PONE-D-13-27200 [pii].
  • Chabas, J. F., D. Stephan, T. Marqueste, S. Garcia, M. N. Lavaut, C. Nguyen, R. Legre, M. Khrestchatisky, P. Decherchi, and F. Feron. 2013. Cholecalciferol (vitamin D(3)) improves myelination and recovery after nerve injury. PLoS.ONE. 8:e65034. doi:10.1371/journal.pone.0065034 [doi];PONE-D-13-01802 [pii].
  • Chebrek, S., K. Aissi, Y. Frances, C. Mercier, L. Farnault, G. Sebahoun, and R. Costello. 2013. Pulmonary hypertension in patients with chronic myeloproliferative neoplasms. Leuk.Lymphoma. doi:10.3109/10428194.2013.797083 [doi].
  • Collares, C. V., A. F. Evangelista, D. J. Xavier, D. M. Rassi, T. Arns, M. C. Foss-Freitas, M. C. Foss, D. Puthier, E. T. Sakamoto-Hojo, G. A. Passos, and E. A. Donadi. 2013. Identifying common and specific microRNAs expressed in peripheral blood mononuclear cell of type 1, type 2, and gestational diabetes mellitus patients. BMC.Res.Notes  6:491. doi:1756-0500-6-491 [pii];10.1186/1756-0500-6-491 [doi].
  • Costello, R. T., A. Boehrer, C. Sanchez, D. Mercier, C. Baier, T. LeTreut, and G. Sebahoun. 2013. Differential Expression of Natural Killer Cell Activating Receptors in Blood vs Bone Marrow in Patients with Monoclonal Gammopathy. Immunology. doi:10.1111/imm.12082 [doi].
  • Darbo, E., C. Herrmann, T. Lecuit, D. Thieffry, and J. van Helden. 2013. Transcriptional and epigenetic signatures of zygotic genome activation during early drosophila embryogenesis. BMC.Genomics 14:226. doi:1471-2164-14-226 [pii];10.1186/1471-2164-14-226 [doi].
  • Funnell, A. P., M. D. Wilson, B. Ballester, K. S. Mak, J. Burdach, N. Magan, R. C. Pearson, F. P. Lemaigre, K. M. Stowell, D. T. Odom, P. Flicek, and M. Crossley. 2013. A CpG mutational hotspot in a ONECUT binding site accounts for the prevalent variant of hemophilia B Leyden. Am.J Hum.Genet. 92:460-467. doi:S0002-9297(13)00074-8 [pii];10.1016/j.ajhg.2013.02.003 [doi].
  • Gensollen, T., C. Bourges, P. Rihet, A. Rostan, V. Millet, T. Noguchi, V. Bourdon, H. Sobol, L. Dubuquoy, B. Bertin, M. Fumery, P. Desreumaux, J. F. Colombel, X. Hebuterne, P. Hofman, P. Naquet, and F. Galland. 2013. Functional polymorphisms in the regulatory regions of the VNN1 gene are associated with susceptibility to inflammatory bowel diseases. Inflamm.Bowel.Dis. 19:2315-2325. doi:10.1097/MIB.0b013e3182a32b03 [doi].
  • Grange, M., G. Verdeil, F. Arnoux, A. Griffon, S. Spicuglia, J. Maurizio, M. Buferne, A. M. Schmitt-Verhulst, and N. Auphan-Anezin. 2013. Active STAT5 regulates T-bet and eomesodermin expression in CD8 T cells and imprints a T-bet-dependent Tc1 program with repressed IL-6/TGF-beta1 signaling. J Immunol. 191:3712-3724. doi:jimmunol.1300319 [pii];10.4049/jimmunol.1300319 [doi].
  • Grieco, L., L. Calzone, I. Bernard-Pierrot, F. Radvanyi, B. Kahn-Perles, and D. Thieffry. 2013. Integrative modelling of the influence of MAPK network on cancer cell fate decision. PLoS.Comput.Biol. 9:e1003286. doi:10.1371/journal.pcbi.1003286 [doi];PCOMPBIOL-D-13-00105 [pii].
  • Jia JS, Spicuglia S. [Hypermethylation of CpG island in promoter region of MEIS1 gene and its expression in HOX11(+) acute T lymphoblastic leukemia]. Zhonghua Yi Xue Za Zhi. 2013 Dec 24;93(48):3835-40.
  • Jia JS, Spicuglia S. [Methylation of CpG island in promoter region of RUNX2 gene and its expression in HOX11(+) acute T lymphoblastic leukemia]. Zhongguo Shi Yan Xue Ye Xue Za Zhi. 2013 Apr;21(2):273-8.
  • Lepoivre, C., M. Belhocine, A. Bergon, A. Griffon, M. Yammine, L. Vanhille, J. Zacarias-Cabeza, M. A. Garibal, F. Koch, M. A. Maqbool, R. Fenouil, B. Loriod, H. Holota, M. Gut, I. Gut, J. Imbert, J. C. Andrau, D. Puthier, and S. Spicuglia. 2013. Divergent transcription is associated with promoters of transcriptional regulators. BMC.Genomics 14:914. doi:1471-2164-14-914 [pii];10.1186/1471-2164-14-914 [doi].
  • Liang, Y., M. Cucchetti, R. Roncagalli, T. Yokosuka, A. Malzac, E. Bertosio, J. Imbert, I. J. Nijman, M. Suchanek, T. Saito, C. Wulfing, B. Malissen, and M. Malissen. 2013. The lymphoid lineage-specific actin-uncapping protein Rltpr is essential for costimulation via CD28 and the development of regulatory T cells. Nat.Immunol. 14:858-866. doi:ni.2634 [pii];10.1038/ni.2634 [doi].
  • Lortet, S., E. Lacombe, N. Boulanger, P. Rihet, C. Nguyen, L. K. Goff, and P. Salin. 2013. Striatal molecular signature of subchronic subthalamic nucleus high frequency stimulation in parkinsonian rat. PLoS.ONE. 8:e60447. doi:10.1371/journal.pone.0060447 [doi];PONE-D-12-36103 [pii].
  • Mamessier, E., L. C. Pradel, M. L. Thibult, C. Drevet, A. Zouine, J. Jacquemier, G. Houvenaeghel, F. Bertucci, D. Birnbaum, and D. Olive. 2013. Peripheral blood NK cells from breast cancer patients are tumor-induced composite subsets. J Immunol. 190 :2424-2436. doi:jimmunol.1200140 [pii];10.4049/jimmunol.1200140 [doi].
  • Mbodj, A., G. Junion, C. Brun, E. E. Furlong, and D. Thieffry. 2013. Logical modelling of Drosophila signalling pathways. Mol.Biosyst. 9:2248-2258. doi:10.1039/c3mb70187e [doi].
  • Mendes, N. D., F. Lang, Y. S. Le Cornec, R. Mateescu, G. Batt, and C. Chaouiya. 2013. Composition and abstraction of logical regulatory modules: application to multicellular systems. Bioinformatics 29:749-757. doi:btt033 [pii];10.1093/bioinformatics/btt033 [doi].
  • Montellier, E., F. Boussouar, S. Rousseaux, K. Zhang, T. Buchou, F. Fenaille, H. Shiota, A. Debernardi, P. Hery, S. Curtet, M. Jamshidikia, S. Barral, H. Holota, A. Bergon, F. Lopez, P. Guardiola, K. Pernet, J. Imbert, C. Petosa, M. Tan, Y. Zhao, M. Gerard, and S. Khochbin. 2013. Chromatin-to-nucleoprotamine transition is controlled by the histone H2B variant TH2B. Genes Dev. 27:1680-1692. doi:gad.220095.113 [pii];10.1101/gad.220095.113 [doi].
  • Paban, V., J. M. Billard, V. Bouet, T. Freret, M. Boulouard, C. Chambon, B. Loriod, and B. Alescio-Lautier. 2013. Genomic transcriptional profiling in LOU/C/Jall rats identifies genes for successful aging. Brain Struct.Funct. 218:1501-1512. doi:10.1007/s00429-012-0472-8 [doi].
  • Sawan, C., H. Hernandez-Vargas, R. Murr, F. Lopez, T. Vaissiere, A. Y. Ghantous, C. Cuenin, J. Imbert, Z. Q. Wang, B. Ren, and Z. Herceg. 2013. Histone acetyltransferase cofactor trrap maintains self-renewal and restricts differentiation of embryonic stem cells. Stem Cells 31:979-991. doi:10.1002/stem.1341 [doi].
  • Shimoyama, S., S. Kasai, B. Kahn-Perles, and H. Kikuchi. 2013. Dephosphorylation of Sp1 at Ser-59 by Protein Phosphatase 2A (PP2A) is required for induction of CYP1A1 transcription after treatment with 2,3,7,8-tetrachlorodibenzo-p-dioxin or omeprazole. Biochim.Biophys.Acta. doi:S1874-9399(13)00179-X [pii];10.1016/j.bbagrm.2013.12.004 [doi].
  • Spicuglia, S., M. A. Maqbool, D. Puthier, and J. C. Andrau. 2013. An update on recent methods applied for deciphering the diversity of the noncoding RNA genome structure and function. Methods. doi:S1046-2023(13)00107-2 [pii];10.1016/j.ymeth.2013.04.003 [doi].
  • Spinelli, L., P. Gambette, C. E. Chapple, B. Robisson, A. Baudot, H. Garreta, L. Tichit, A. Guenoche, and C. Brun. 2013. Clust&See: A Cytoscape plugin for the identification, visualization and manipulation of network clusters. Biosystems 113:91-95. doi:S0303-2647(13)00135-4 [pii];10.1016/j.biosystems.2013.05.010 [doi].
  • Sun, L., H. Li, J. Chen, V. Dehennaut, Y. Zhao, Y. Yang, Y. Iwasaki, B. Kahn-Perles, D. Leprince, Q. Chen, A. Shen, and Y. Xu. 2013. A SUMOylation-Dependent Pathway Regulates SIRT1 Transcription and Lung Cancer Metastasis. J Natl.Cancer Inst. 105:887-898. doi:djt118 [pii];10.1093/jnci/djt118 [doi].
  • Yammine, M., M. Saade, S. Chauvet, and C. Nguyen. 2013. Spatial gene's (Tbata) implication in neurite outgrowth and dendrite patterning in hippocampal neurons. Mol.Cell Neurosci. doi:S1044-7431(13)00121-8 [pii];10.1016/j.mcn.2013.12.007 [doi].

2012

  • Adams,D., Altucci,L., Antonarakis,S.E., Ballesteros,J., Beck,S., Bird,A., Bock,C., Boehm,B., Campo,E., Caricasole,A., Dahl,F., Dermitzakis,E.T., Enver,T., Esteller,M., Estivill,X., Ferguson-Smith,A., Fitzgibbon,J., Flicek,P., Giehl,C., Graf,T., Grosveld,F., Guigo,R., Gut,I., Helin,K., Jarvius,J., Kuppers,R., Lehrach,H., Lengauer,T., Lernmark,A., Leslie,D., Loeffler,M., Macintyre,E., Mai,A., Martens,J.H., Minucci,S., Ouwehand,W.H., Pelicci,P.G., Pendeville,H., Porse,B., Rakyan,V., Reik,W., Schrappe,M., Schubeler,D., Seifert,M., Siebert,R., Simmons,D., Soranzo,N., Spicuglia,S., Stratton,M., Stunnenberg,H.G., Tanay,A., Torrents,D., Valencia,A., Vellenga,E., Vingron,M., Walter,J., and Willcocks,S. (2012). BLUEPRINT to decode the epigenetic signature written in blood. Nat. Biotechnol. 30, 224-226. PM:22398613
  • Afridi,S., Atkinson,A., Garnier,S., Fumoux,F., and Rihet,P. (2012). Malaria resistance genes are associated with the levels of IgG subclasses directed against Plasmodium falciparum blood-stage antigens in Burkina Faso. Malar. J 11, 308. PM:22947458
  • Atkinson,A., Garnier,S., Afridi,S., Fumoux,F., and Rihet,P. (2012). Genetic variations in genes involved in heparan sulphate biosynthesis are associated with Plasmodium falciparum parasitaemia: a familial study in Burkina Faso. Malar. J. 11, 108. PM:22475533
  • Baudot,A., Souiai,O., and Brun,C. (2012). Network analysis and protein function prediction with the PRODISTIN Web site. Methods Mol. Biol. 804, 313-326. PM:22144161
  • Becker,E., Robisson,B., Chapple,C.E., Guenoche,A., and Brun,C. (2012). Multifunctional proteins revealed by overlapping clustering in protein interaction network. Bioinformatics. 28, 84-90. PM:22080466
  • Belzeaux,R., Bergon,A., Jeanjean,V., Loriod,B., Formisano-Treziny,C., Verrier,L., Loundou,A., Baumstarck-Barrau,K., Boyer,L., Gall,V., Gabert,J., Nguyen,C., Azorin,J.M., Naudin,J., and Ibrahim,E.C. (2012). Responder and nonresponder patients exhibit different peripheral transcriptional signatures during major depressive episode. Transl. Psychiatry 2, e185. PM:23149449
  • Boone,N., Bergon,A., Loriod,B., Deveze,A., Nguyen,C., Axelrod,F.B., and Ibrahim,E.C. (2012). Genome-wide analysis of familial dysautonomia and kinetin target genes with patient olfactory ecto-mesenchymal stem cells. Hum. Mutat. 33, 530-540. PM:22190446
  • Bouveret,E. and Brun,C. (2012). Bacterial interactomes: from interactions to networks. Methods Mol. Biol. 804, 15-33. PM:22144146
  • Chaouiya,C., Naldi,A., and Thieffry,D. (2012). Logical modelling of gene regulatory networks with GINsim. Methods Mol. Biol. 804, 463-479. PM:22144167
  • Costello,R., Huret,G., Sappa,E., and Bergoin-Costello,V. (2012). [Automated screening for transfusionnal hemochromatosis]. Transfus. Clin. Biol. 19, 57-59. PM:22503459
  • Costello,R.T., Knoblauch,B., Sanchez,C., Mercier,D., Le,T.T., and Sebahoun,G. (2012). Expression of natural killer cell activating receptors in patients with chronic lymphocytic leukaemia. Immunology 135, 151-157. PM:22044312
  • Dadi,S., Le Noir,S., Payet-Bornet,D., Lhermitte,L., Zacarias-Cabeza,J., Bergeron,J., Villarese,P., Vachez,E., Dik,W.A., Millien,C., Radford,I., Verhoeyen,E., Cosset,F.L., Petit,A., Ifrah,N., Dombret,H., Hermine,O., Spicuglia,S., Langerak,A.W., Macintyre,E.A., Nadel,B., Ferrier,P., and Asnafi,V. (2012). TLX homeodomain oncogenes mediate T cell maturation arrest in T-ALL via interaction with ETS1 and suppression of TCRalpha gene expression. Cancer Cell 21, 563-576. PM:22516263
  • de Bentzmann,S., Giraud,C., Bernard,C.S., Calderon,V., Ewald,F., Plesiat,P., Nguyen,C., Grunwald,D., Attree,I., Jeannot,K., Fauvarque,M.O., and Bordi,C. (2012). Unique Biofilm Signature, Drug Susceptibility and Decreased Virulence in Drosophila through the Pseudomonas aeruginosa Two-Component System PprAB. PLoS. Pathog. 8, e1003052. PM:23209420
  • Farnault,L., Sanchez,C., Baier,C., Le,T.T., and Costello,R.T. (2012). Hematological malignancies escape from NK cell innate immune surveillance: mechanisms and therapeutic implications. Clin. Dev. Immunol. 2012, 421702. PM:22899948
  • Farnault,L., Chebrek,S., Souteyrand,P., Sebahoun,G., and Costello,R. (2012). Recurrent superior vena cava syndrome caused by IgD multiple myeloma. Ann. Hematol. 91, 1977-1978. PM:22638757
  • Fauconnier,M., Palomo,J., Bourigault,M.L., Meme,S., Szeremeta,F., Beloeil,J.C., Danneels,A., Charron,S., Rihet,P., Ryffel,B., and Quesniaux,V.F. (2012). IL-12Rbeta2 Is Essential for the Development of Experimental Cerebral Malaria. J. Immunol. 188, 1905-1914. PM:22238458
  • Faust,K. and van Helden,J. (2012). Predicting metabolic pathways by sub-network extraction. Methods Mol. Biol. 804, 107-130. PM:22144151
  • Fenouil,R., Cauchy,P., Koch,F., Descostes,N., Cabeza,J.Z., Innocenti,C., Ferrier,P., Spicuglia,S., Gut,M., Gut,I., and Andrau,J.C. (2012). CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters. Genome Res. 22, 2399-2408. PM:23100115
  • Furlan,A., Lamballe,F., Stagni,V., Hussain,A., Richelme,S., Prodosmo,A., Moumen,A., Brun,C., Barrantes,I.D., Simon,C.A., Koleske,A.J., Nebreda,A.R., Barila,D., and Maina,F. (2012). Met acts through Abl to regulate p53 transcriptional outcomes and cell survival in the developing liver. J Hepatol. 57, 1292-1298. PM:22889954
  • Gaucher,J., Boussouar,F., Montellier,E., Curtet,S., Buchou,T., Bertrand,S., Hery,P., Jounier,S., Depaux,A., Vitte,A.L., Guardiola,P., Pernet,K., Debernardi,A., Lopez,F., Holota,H., Imbert,J., Wolgemuth,D.J., Gerard,M., Rousseaux,S., and Khochbin,S. (2012). Bromodomain-dependent stage-specific male genome programming by Brdt. EMBO J 31, 3809-3820. PM:22922464
  • Herrmann,C., Van de Sande,B., Potier,D., and Aerts,S. (2012). i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules. Nucleic Acids Res. 40, e114. PM:22718975
  • Le Noir,S., Ben,A.R., Lelorch,M., Bergeron,J., Sungalee,S., Payet-Bornet,D., Villarese,P., Petit,A., Callens,C., Lhermitte,L., Baranger,L., Radford-Weiss,I., Gregoire,M.J., Dombret,H., Ifrah,N., Spicuglia,S., Romana,S., Soulier,J., Nadel,B., Macintyre,E., and Asnafi,V. (2012). Extensive molecular mapping of TCRalpha/delta- and TCRbeta-involved chromosomal translocations reveals distinct mechanisms of oncogene activation in T-ALL. Blood 120, 3298-3309. PM:22948044
  • Lemaire,D., Barbosa,T., and Rihet,P. (2012). Coping with genetic diversity: the contribution of pathogen and human genomics to modern vaccinology. Braz. J. Med. Biol. Res. 45, 376-385. PM:22030866
  • Lepoivre,C., Bergon,A., Lopez,F., Perumal,N.B., Nguyen,C., Imbert,J., and Puthier,D. (2012). TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks. BMC. Bioinformatics. 13, 19. PM:22292669
  • Monnier V, Iché-Torres M, Rera M, Contremoulins V, Guichard C, Lalevée N, Tricoire H, Perrin L.(2012). dJun and Vri/dNFIL3 are major regulators of cardiac aging in Drosophil.PLoS Genet. 2012 Nov;8(11):e1003081. PM:23209438
  • Oliveira,E.H., Macedo,C., Donate,P.B., Almeida,R.S., Pezzi,N., Nguyen,C., Rossi,M.A., Sakamoto-Hojo,E.T., Donadi,E.A., and Passos,G.A. (2012). Expression profile of peripheral tissue antigen genes in medullary thymic epithelial cells (mTECs) is dependent on mRNA levels of autoimmune regulator (Aire). Immunobiology 218, 96-104. PM:22564670
  • Parvy,J.P., Napal,L., Rubin,T., Poidevin,M., Perrin,L., Wicker-Thomas,C., and Montagne,J. (2012). Drosophila melanogaster Acetyl-CoA-carboxylase sustains a fatty acid-dependent remote signal to waterproof the respiratory system. PLoS. Genet. 8, e1002925. PM:22956916
  • Pekowska,A., Zacarias-Cabeza,J., Jia,J., Ferrier,P., and Spicuglia,S. (2012). The Role of Epigenetics in Cancer: From Molecular Function to High-Throughput Assays. In Diagnostic, Prognostic and Therapeutic Value of Gene Signatures, A.Russo, S.Iacobelli, and J.Iovanna, eds. Humana Press), pp. 137-152.http://dx.doi.org/10.1007/978-1-61779-358-5_9
  • Potier,D., Atak,Z.K., Sanchez,M.N., Herrmann,C., and Aerts,S. (2012). Using cisTargetX to predict transcriptional targets and networks in Drosophila. Methods Mol. Biol. 786, 291-314. PM:21938634
  • Schmidt,D., Schwalie,P.C., Wilson,M.D., Ballester,B., Goncalves,A., Kutter,C., Brown,G.D., Marshall,A., Flicek,P., and Odom,D.T. (2012). Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell 148, 335-348. PM:22244452
  • Seyres,D., Roder,L., and Perrin,L. (2012). Genes and networks regulating cardiac development and function in flies: genetic and functional genomic approaches. Brief. Funct. Genomics 11, 366-374. PM:22908209
  • Spicuglia,S. and Vanhille,L. (2012). Chromatin signatures of active enhancers. Nucleus 3, 126-131. PM:22555596
  • Thomas-Chollier,M., Darbo,E., Herrmann,C., Defrance,M., Thieffry,D., and van,H.J. (2012). A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. Nat. Protoc. 7, 1551-1568. PM:22836136
  • Thomas-Chollier,M., Herrmann,C., Defrance,M., Sand,O., Thieffry,D., and van,H.J. (2012). RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res. 40, e31. PM:22156162
  • van Helden,J., Toussaint,A., and Thieffry,D. (2012). Bacterial molecular networks: bridging the gap between functional genomics and dynamical modelling. Methods Mol. Biol. 804, 1-11. PM:22144145

2011

  • Atkinson,A., Barbier,M., Afridi,S., Fumoux,F., and Rihet,P. (2011). Evidence for epistasis between hemoglobin C and immune genes in human P. falciparum malaria: a family study in Burkina Faso. Genes Immun. PM:21451558
  • Barbier,M., Faille,D., Loriod,B., Textoris,J., Camus,C., Puthier,D., Flori,L., Wassmer,S.C., Victorero,G., Alessi,M.C., Fusai,T., Nguyen,C., Grau,G.E., and Rihet,P. (2011). Platelets alter gene expression profile in human brain endothelial cells in an in vitro model of cerebral malaria. PLoS. ONE  6, e19651. PM:21603600
  • Blasco,V., Wiramus,S., Textoris,J., Antonini,F., Bechis,C., Albanese,J., Martin,C., and Leone,M. (2011). Monitoring of plasma creatinine and urinary gamma-glutamyl transpeptidase improves detection of acute kidney injury by more than 20%. Crit Care Med. 39, 52-56. PM:21178528
  • Brohee,S., Janky,R., Abdel-Sater,F., Vanderstocken,G., Andre,B., and van Helden,J. (2011). Unraveling networks of co-regulated genes on the sole basis of genome sequences. Nucleic Acids Res. 39, 6340-6358. PM:21572103
  • Delahaye,N.F., Rusakiewicz,S., Martins,I., Menard,C., Roux,S., Lyonnet,L., Paul,P., Sarabi,M., Chaput,N., Semeraro,M., Minard-Colin,V., Poirier-Colame,V., Chaba,K., Flament,C., Baud,V., Authier,H., Kerdine-Romer,S., Pallardy,M., Cremer,I., Peaudecerf,L., Rocha,B., Valteau-Couanet,D., Gutierrez,J.C., Nunes,J.A., Commo,F., Bonvalot,S., Ibrahim,N., Terrier,P., Opolon,P., Bottino,C., Moretta,A., Tavernier,J., Rihet,P., Coindre,J.M., Blay,J.Y., Isambert,N., Emile,J.F., Vivier,E., Lecesne,A., Kroemer,G., and Zitvogel,L. (2011). Alternatively spliced NKp30 isoforms affect the prognosis of gastrointestinal stromal tumors. Nat. Med. PM:21552268
  • Didier,G., Remy,E., and Chaouiya,C. (2011). Mapping multivalued onto Boolean dynamics. J. Theor. Biol. 270, 177-184. PM:20868697
  • Faust,K., Croes,D., and van Helden,J. (2011). Prediction of metabolic pathways from genome-scale metabolic networks. Biosystems 105, 109-121. PM:21645586
  • Koch,F., Fenouil,R., Gut,M., Cauchy,P., Albert,T.K., Zacarias-Cabeza,J., Spicuglia,S., de la Chapelle,A.L., Heidemann,M., Hintermair,C., Eick,D., Gut,I., Ferrier,P., and Andrau,J.C. (2011). Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Nat. Struct. Mol. Biol. 18, 956-963. PM:21765417
  • Liu,X., Wu,J., Yammine,M., Zhou,J., Posocco,P., Viel,S., Liu,C., Ziarelli,F., Fermeglia,M., Pricl,S., Victorero,G., Nguyen,C., Erbacher,P., Behr,J.P., and Peng,L. (2011). Structurally Flexible Triethanolamine Core PAMAM Dendrimers Are Effective Nanovectors for DNA Transfection in Vitro and in Vivo to the Mouse Thymus. Bioconjug. Chem. 22, 2461-2473. PM:22053932
  • Martens,G.A., Jiang,L., Hellemans,K.H., Stange,G., Heimberg,H., Nielsen,F.C., Sand,O., van Helden,J., Gorus,F.K., and Pipeleers,D.G. (2011). Clusters of conserved beta cell marker genes for assessment of beta cell phenotype. PLoS. ONE. 6, e24134. PM:21912665
  • Medina-Rivera,A., Abreu-Goodger,C., Thomas-Chollier,M., Salgado,H., Collado-Vides,J., and van Helden,J. (2011). Theoretical and empirical quality assessment of transcription factor-binding motifs. Nucleic Acids Res. 39, 808-824. PM:20923783
  • Merabet,S., Litim-Mecheri,I., Karlsson,D., Dixit,R., Saadaoui,M., Monier,B., Brun,C., Thor,S., Vijayraghavan,K., Perrin,L., Pradel,J., and Graba,Y. (2011). Insights into Hox protein function from a large scale combinatorial analysis of protein domains. PLoS. Genet. 7, e1002302. PM:22046139
  • Milani,P., Marilley,M., Sanchez-Sevilla,A., Imbert,J., Vaillant,C., Argoul,F., Egly,J.M., Rocca-Serra,J., and Arneodo,A. (2011). Mechanics of the IL2RA Gene Activation Revealed by Modeling and Atomic Force Microscopy. PLoS. ONE. 6, e18811. PM:21533205
  • Mokart,D., Textoris,J., Chow-Chine,L., Brun,J.P., Sannini,A., Turrini,O., Blache,J.L., Arnoulet,C., Sainty,D., and Leone,M. (2011). HLA-DR and B7-2 (CD86) monocyte expressions after major cancer surgery: profile in sepsis. Minerva Anestesiol. 77, 522-527. PM:21540807
  • Monier,B., Pelissier-Monier,A., and Sanson,B. (2011). Establishment and maintenance of compartmental boundaries: role of contractile actomyosin barriers. Cell Mol. Life Sci. 68, 1897-1910. PM:21437644
  • Pekowska,A., Benoukraf,T., Zacarias-Cabeza,J., Belhocine,M., Koch,F., Holota,H., Imbert,J., Andrau,J.C., Ferrier,P., and Spicuglia,S. (2011). H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J. PM:21847099
  • Sananmuang,T., Tharasanit,T., Nguyen,C., Phutikanit,N., and Techakumphu,M. (2011). Culture medium and embryo density influence on developmental competence and gene expression of cat embryos. Theriogenology 75, 1708-1719. PM:21396699
  • Sanchez,C.J., Le,T.T., Boehrer,A., Knoblauch,B., Imbert,J., Olive,D., and Costello,R.T. (2011). Natural killer cells and malignant haemopathies: a model for the interaction of cancer with innate immunity. Cancer Immunol. Immunother. 60, 1-13. PM:20697893
  • Souiai,O., Becker,E., Prieto,C., Benkahla,A., De las,R.J., and Brun,C. (2011). Functional integrative levels in the human interactome recapitulate organ organization. PLoS. ONE. 6, e22051. PM:21799769
  • Spicuglia,S., Vincent-Fabert,C., Benoukraf,T., Tiberi,G., Saurin,A.J., Zacarias-Cabeza,J., Grimwade,D., Mills,K., Calmels,B., Bertucci,F., Sieweke,M., Ferrier,P., and Duprez,E. (2011). Characterisation of genome-wide PLZF/RARA target genes. PLoS. ONE. 6, e24176. PM:21949697
  • Terrier,O., Josset,L., Textoris,J., Marcel,V., Cartet,G., Ferraris,O., N'guyen,C., Lina,B., Diaz,J.J., Bourdon,J.C., and Rosa-Calatrava,M. (2011). Cellular transcriptional profiling in human lung epithelial cells infected by different subtypes of influenza A viruses reveals an overall down-regulation of the host p53 pathway. Virol. J. 8, 285. PM:21651802
  • Textoris,J., Wiramus,S., Martin,C., and Leone,M. (2011). Overview of antimicrobial therapy in intensive care units. Expert. Rev. Anti. Infect. Ther. 9, 97-109. PM:21171881
  • Textoris,J., Wiramus,S., Martin,C., and Leone,M. (2011). Antibiotic therapy in patients with septic shock. Eur. J. Anaesthesiol. 28, 318-324. PM:21464717
  • Textoris,J., Loriod,B., Benayoun,L., Gourraud,P.A., Puthier,D., Albanese,J., Mantz,J., Martin,C., Nguyen,C., and Leone,M. (2011). An evaluation of the role of gene expression in the prediction and diagnosis of ventilator-associated pneumonia. Anesthesiology 115, 344-352. PM:21796056
  • Thomas-Chollier,M., Defrance,M., Medina-Rivera,A., Sand,O., Herrmann,C., Thieffry,D., and van,H.J. (2011). RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Res. 39, W86-W91. PM:21715389
  • Wurmser,F., Ogereau,D., Mary-Huard,T., Loriod,B., Joly,D., and Montchamp-Moreau,C. (2011). Population transcriptomics: insights from Drosophila simulans, Drosophila sechellia and their hybrids. Genetica 139, 465-477. PM:21424276

2010

  • Boone,N., Loriod,B., Bergon,A., Sbai,O., Formisano-Treziny,C., Gabert,J., Khrestchatisky,M., Nguyen,C., Feron,F., Axelrod,F.B., and Ibrahim,e.C. (2010). Olfactory stem cells, a new cellular model for studying molecular mechanisms underlying familial dysautonomia. PLoS ONE 5, e15590. PM:21187979
  • Borgel,J., Springer,S., Ghafoor,J., Arndt,D., Duchna,H.W., Barthel,A., Werner,S., van Helden,J., Hanefeld,C., Neubauer,H., Bulut,D., and Mugge,A. (2010). Unrecognized secondary causes of hypertension in patients with hypertensive urgency/emergency: prevalence and co-prevalence. Clin. Res. Cardiol. 99, 499-506. PM:20361196
  • Briolant,S., Almeras,L., Belghazi,M., Boucomont-Chapeaublanc,E., Wurtz,N., Fontaine,A., Granjeaud,S., Fusai,T., Rogier,C., and Pradines,B. (2010). Plasmodium falciparum proteome changes in response to doxycycline treatment. Malar. J. 9, 141. PM:20500856
  • Calzone,L., Tournier,L., Fourquet,S., Thieffry,D., Zhivotovsky,B., Barillot,E., and Zinovyev,A. (2010). Mathematical modelling of cell-fate decision in response to death receptor engagement. PLoS. Comput. Biol. 6, e1000702. PM:20221256
  • Costello,R. (2010). [Pulmonary arterial hypertension and malignant hematologic disorders.]. Rev. Med. Interne. PM:20674102
  • Costello,R., Sanchez,C., Le Treut,T., Rihet,P., Imbert,J., and Sebahoun,G. (2010). Peripheral T-cell lymphoma gene expression profiling and potential therapeutic exploitations. Br. J. Haematol. 150, 21-27.
  • Costello,R.T. and Sebahoun,G. (2010). Agranulocytosis occurring in a patient with chronic lymphocytic leukemia in complete remission; treatment by rituximab and cyclosporin. Leuk. Res. 34, e329-e330. PM:20723978
  • Devignot,S., Sapet,C., Duong,V., Bergon,A., Rihet,P., Ong,S., Lorn,P.T., Chroeung,N., Ngeav,S., Tolou,H.J., Buchy,P., and Couissinier-Paris,P. (2010). Genome-wide expression profiling deciphers host responses altered during dengue shock syndrome and reveals the role of innate immunity in severe dengue. PLoS. ONE. 5, e11671. PM:20652028
  • Donate,P.B., Fornari,T.A., Junta,C.M., Magalhaes,D.A., Macedo,C., Cunha,T.M., Nguyen,C., Cunha,F.Q., and Passos,G.A. (2010). Collagen induced arthritis (CIA) in mice features regulatory transcriptional network connecting major histocompatibility complex (MHC H2) with autoantigen genes in the thymus. Immunobiology. PM:21168240
  • Essaghir,A., Toffalini,F., Knoops,L., Kallin,A., van Helden,J., and Demoulin,J.B. (2010). Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data. Nucleic Acids Res. 38, e120. PM:20215436
  • Farcot,E., Bonnet,M., Jaeger,S., Spicuglia,S., Fernandez,B., and Ferrier,P. (2010). TCR beta allelic exclusion in dynamical models of V(D)J recombination based on allele independence. J. Immunol. 185, 1622-1632. PM:20585038
  • Faust,K., Dupont,P., Callut,J., and van Helden,J. (2010). Pathway discovery in metabolic networks by subgraph extraction. Bioinformatics 26, 1211-1218. PM:20228128
  • Jia,J., Pekowska,A., Jaeger,S., Benoukraf,T., Ferrier,P., and Spicuglia,S. (2010). Assessing the efficiency and significance of Methylated DNA Immunoprecipitation (MeDIP) assays in using in vitro methylated genomic DNA. BMC. Res. Notes 3, 240. PM:20846371
  • Josset,L., Textoris,J., Loriod,B., Ferraris,O., Moules,V., Lina,B., N'guyen,C., Diaz,J.J., and Rosa-Calatrava,M. (2010). Gene expression signature-based screening identifies new broadly effective influenza a antivirals. PLoS. ONE 5. PM:20957181
  • Leone,M., Textoris,J., Michel,F., Wiramus,S., and Martin,C. (2010). Emerging drugs in sepsis. Expert. Opin. Emerg. Drugs 15, 41-52. PM:20055688
  • Lesur,I., Textoris,J., Loriod,B., Courbon,C., Garcia,S., Leone,M., and Nguyen,C. (2010). Gene expression profiles characterize inflammation stages in the acute lung injury in mice. PLoS. ONE 5, e11485. PM:20628605
  • Medina-Rivera,A., breu-Goodger,C., Thomas-Chollier,M., Salgado,H., Collado-Vides,J., and van Helden,J. (2010). Theoretical and empirical quality assessment of transcription factor-binding motifs. Nucleic Acids Res. PM:20923783
  • Monier,B., Pelissier-Monier,A., Brand,A.H., and Sanson,B. (2010). An actomyosin-based barrier inhibits cell mixing at compartmental boundaries in Drosophila embryos. Nat. Cell Biol 12, 60-65. PM:19966783
  • Naldi,A., Carneiro,J., Chaouiya,C., and Thieffry,D. (2010). Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling. PLoS Comput Biol 6, e1000912. http://dx.doi.org/10.1371%2Fjournal.pcbi.1000912
  • Northern,J.H., Ritchie,G.A., Smakman,E.P., van Helden,J.H., Cockburn,J., and Duxbury,G. (2010). Rapid passage signals induced by chirped quantum cascade laser radiation: K state dependent-delay effects in the nu2 band of NH3. Opt. Lett. 35, 2750-2752. PM:20717445
  • Pekowska,A., Benoukraf,T., Ferrier,P., and Spicuglia,S. (2010). A unique H3K4me2 profile marks tissue-specific gene regulation. Genome Res. 20, 1493-1502. PM:20841431
  • Pilot-Storck,F., Chopin,E., Rual,J.F., Baudot,A., Dobrokhotov,P., Robinson-Rechavi,M., Brun,C., Cusick,M.E., Hill,D.E., Schaeffer,L., Vidal,M., and Goillot,E. (2010). Interactome mapping of the phosphatidylinositol 3-kinase-mammalian target of rapamycin pathway identifies deformed epidermal autoregulatory factor-1 as a new glycogen synthase kinase-3 interactor. Mol. Cell Proteomics. 9, 1578-1593. PM:20368287
  • Pumarola,T., Freeman,J., Saxton,E., Dillon,P., Bal,T., and van Helden,J. (2010). Performance evaluation of the ADVIA Centaur((R)) HIV Ag/Ab Combo assay. J. Virol. Methods 170, 16-20. PM:20723562
  • Punnamoottil,B., Herrmann,C., Pascual-Anaya,J., D'Aniello,S., Garcia-Fernandez,J., Akalin,A., Becker,T.S., and Rinkwitz,S. (2010). Cis-regulatory characterization of sequence conservation surrounding the Hox4 genes. Dev. Biol. 340, 269-282. PM:20144609
  • Saade,M., Irla,M., Yammine,M., Boulanger,N., Victorero,G., Vincentelli,R., Penninger,J.M., Hollander,G.A., Chauvet,S., and Nguyen,C. (2010). Spatial (Tbata) expression in mature medullary thymic epithelial cells. Eur. J. Immunol. 40, 530-538. PM:19918778
  • Schughart,K. (2010). SYSGENET: a meeting report from a new European network for systems genetics. Mamm. Genome. 21, 331-336.
  • Senatore,S., Rami,R., V, Semeriva,M., Perrin,L., and Lalevee,N. (2010). Response to mechanical stress is mediated by the TRPA channel painless in the Drosophila heart. PLoS. Genet. 6. PM:20824071
  • Spicuglia,S., Zacarias-Cabeza,J., Pekowska,A., and Ferrier,P. (2010). Epigenetic regulation of antigen receptor gene rearrangement. F1000. Biol. Rep. 2. PM:20948810
  • Spicuglia,S., Pekowska,A., Zacarias-Cabeza,J., and Ferrier,P. (2010). Epigenetic control of Tcrb gene rearrangement. Semin. Immunol. 22, 330-336. PM:20829066
  • Textoris,J., Ban,L.H., Capo,C., Raoult,D., Leone,M., and Mege,J.L. (2010). Sex-related differences in gene expression following Coxiella burnetii infection in mice: potential role of circadian rhythm. PLoS ONE 5, e12190. PM:20730052

2009

  • Barrey,E., Mucher,E., Jeansoule,N., Larcher,T., Guigand,L., Herszberg,B., Chaffaux,S., Guerin,G., Mata,X., Benech,P., Canale,M., Alibert,O., Maltere,P., and Gidrol,X. (2009). Gene expression profiling in equine polysaccharide storage myopathy revealed inflammation, glycogenesis inhibition, hypoxia and mitochondrial dysfunctions. BMC. Vet. Res. 5, 29. PM:19664222
  • Becker, E., Guenoche, A., and Brun, C. Systèmes de classes chevauchantes pour la recherche de protéines multifonctionnelles. JOBIM 2009. Actes des Journées Ouvertes Biologie Informatique Mathématiques , 49-54. 2009.
  • Belin,S., Beghin,A., Solano-Gonzalez,E., Bezin,L., Brunet-Manquat,S., Textoris,J., Prats,A.C., Mertani,H.C., Dumontet,C., and Diaz,J.J. (2009). Dysregulation of ribosome biogenesis and translational capacity is associated with tumor progression of human breast cancer cells. PLoS ONE 4, e7147. PM:19779612
  • Bell,C.L., Hancock,G., Peverall,R., Ritchie,G.A., van Helden,J.H., and van Leeuwen,N.J. (2009). Characterization of an external cavity diode laser based ring cavity NICE-OHMS system. Opt. Express 17, 9834-9839. PM:19506633
  • Benoukraf,T., Cauchy,P., Fenouil,R., Jeanniard,A., Koch,F., Jaeger,S., Thieffry,D., Imbert,J., Andrau,J.C., Spicuglia,S., and Ferrier,P. (2009). CoCAS: a ChIP-on-chip analysis suite. Bioinformatics 25, 954-955. PM:19193731
  • Birnbaum,D., Sircoulomb,F., and Imbert,J. (2009). A reason why the ERBB2 gene is amplified and not mutated in breast cancer. Cancer Cell Int. 9, 5. PM:19226453
  • Bonnet,M., Huang,F., Benoukraf,T., Cabaud,O., Verthuy,C., Boucher,A., Jaeger,S., Ferrier,P., and Spicuglia,S. (2009). Duality of enhancer functioning mode revealed in a reduced TCR beta gene enhancer knockin mouse model. J. Immunol. 183, 7939-7948. PM:19923469
  • Bonnet,M., Ferrier,P., and Spicuglia,S. (2009). Molecular genetics at the T-cell receptor beta locus: insights into the regulation of V(D)J recombination. Adv. Exp. Med. Biol. 650, 116-132. PM:19731806
  • Clarhaut,J., Gemmill,R.M., Potiron,V.A., it-Si-Ali,S., Imbert,J., Drabkin,H.A., and Roche,J. (2009). ZEB-1, a Repressor of the semaphorin 3F tumor suppressor gene in lung cancer cells. Neoplasia 11, 157-166. PM:19177200
  • Costello,R.T. (2009). Reversing the multidrug resistance in acute leukemia: until the leukemia initiating cell? Leuk. Res. 33, 749. PM:18977030
  • Costello,R.T. (2009). How to restore normal innate antitumor immunity in acute leukemia? Leuk. Res. 33, 613. PM:18952282
  • Defrance,M. and van Helden,J. (2009). info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling. Bioinformatics 25, 2715-2722. PM:19689955
  • Faure,A., Naldi,A., Lopez,F., Chaouiya,C., Ciliberto,A., and Thieffry,D. (2009). Modular logical modelling of the budding yeast cell cycle. Mol. Biosyst. PM:19763337
  • Faure,A. and Thieffry,D. (2009). Logical modelling of cell cycle control in eukaryotes: a comparative study. Mol. Biosyst. PM:19763341
  • Faust,K., Croes,D., and van Helden,J. (2009). Metabolic pathfinding using RPAIR annotation. J. Mol. Biol. 388, 390-414. PM:19281817
  • Faust,K., Croes,D., and van Helden,J. (2009). In response to 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'. Bioinformatics 25, 3202-3205. PM:19776213
  • Hermsen,D., Broecker-Preuss,M., Casati,M., Mas,J.C., Eckstein,A., Gassner,D., van Helden,J., Inomata,K., Jarausch,J., Kratzsch,J., Mann,K., Miyazaki,N., Navarro Moreno,M.A., Murakami,T., Roth,H.J., Noh,J.Y., Scherbaum,W.A., and Schott,M. (2009). Technical evaluation of the first fully automated assay for the detection of TSH receptor autoantibodies. Clin. Chim. Acta 401, 84-89. PM:19091299
  • Herrmann,C., Berard,S., and Tichit,L. (2009). SimCT: a generic tool to visualize ontology-based relationships for biological objects. Bioinformatics 25, 3197-3198. PM:19776214
  • Hua,G., Zhu,B., Rosa,F., Deblon,N., Adelaide,J., Kahn-Perles,B., Birnbaum,D., and Imbert,J. (2009). A Negative Feedback Regulatory Loop Associates the Tyrosine Kinase Receptor ERBB2 and the Transcription Factor GATA4 in Breast Cancer Cells. Mol. Cancer Res. 7, 402-414. PM:19276186
  • Lima-Mendez,G. and van Helden,J. (2009). The powerful law of the power law and other myths in network biology. Mol. Biosyst. 5, 1482-1493. PM:20023717
  • Medioni,C., Senatore,S., Salmand,P.A., Lalevee,N., Perrin,L., and Semeriva,M. (2009). The fabulous destiny of the Drosophila heart. Curr. Opin. Genet. Dev. 19, 518-525. PM:19717296
  • Naldi,A., Berenguier,D., Faure,A., Lopez,F., Thieffry,D., and Chaouiya,C. (2009). Logical modelling of regulatory networks with GINsim 2.3. Biosystems 97, 134-139. PM:19426782
  • Pasero,C., Barbarat,B., Just-Landi,S., Bernard,A., urran-Schleinitz,T., Rey,J., Eldering,E., Truneh,A., Costello,R.T., and Olive,D. (2009). A role for HVEM, but not lymphotoxin-beta receptor, in LIGHT-induced tumor cell death and chemokine production. Eur. J. Immunol. 39, 2502-2514. PM:19701890
  • Sahin,O., Frohlich,H., Lobke,C., Korf,U., Burmester,S., Majety,M., Mattern,J., Schupp,I., Chaouiya,C., Thieffry,D., Poustka,A., Wiemann,S., Beissbarth,T., and Arlt,D. (2009). Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. BMC Syst. Biol. 3, 1. PM:19118495
  • Sand,O., Thomas-Chollier,M., and van Helden,J. (2009). Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl. Bioinformatics 25, 2739-2740. PM:19720677
  • Schott,M., Hermsen,D., Broecker-Preuss,M., Casati,M., Mas,J.C., Eckstein,A., Gassner,D., Golla,R., Graeber,C., van Helden,J., Inomata,K., Jarausch,J., Kratzsch,J., Miyazaki,N., Moreno,M.A., Murakami,T., Roth,H.J., Stock,W., Noh,J.Y., Scherbaum,W.A., and Mann,K. (2009). Clinical value of the first automated TSH receptor autoantibody assay for the diagnosis of Graves' disease (GD): an international multicentre trial. Clin. Endocrinol. (Oxf) 71, 566-573. PM:19170704
  • Simoncini,S., Njock,M.S., Robert,S., Camoin-Jau,L., Sampol,J., Harle,J.R., Nguyen,C., Dignat-George,F., and Anfosso,F. (2009). TRAIL/Apo2l Mediates the Release of Procoagulant Endothelial Microparticles Induced by Thrombin In Vitro. A Potential Mechanism Linking Inflammation and Coagulation. Circ. Res. PM:19265041
  • Textoris,J., Davidson,J., Martin,C., and Leone,M. (2009). [Role of genetics in anaesthesia-related variability]. Ann. Fr. Anesth. Reanim. 28, 564-574. PM:19539443
  • Thieffry,D. (2009). [Systems biology: from molecular networks to personalized medicine]. Med. Sci. (Paris) 25, 547-548. PM:19602342
  • van Helden,J. (2009). Performance of Elecsys toxo IgG and IgM immunoassays. Clin. Lab 55, 267-273. PM:19894405
  • Vingron,M., Brazma,A., Coulson,R., van Helden,J., Manke,T., Palin,K., Sand,O., and Ukkonen,E. (2009). Integrating sequence, evolution and functional genomics in regulatory genomics. Genome Biol. 10, 202. PM:19226437

2008

  • Angelelli,J.B., Baudot,A., Brun,C., and Guenoche,A. (2008). Two local dissimilarity measures for weighted graphs with application to protein interaction networks. Advances in Data Analysis and Classification 2, 3-16.
  • Babcock,D.T., Brock,A.R., Fish,G.S., Wang,Y., Perrin,L., Krasnow,M.A., and Galko,M.J. (2008). Circulating blood cells function as a surveillance system for damaged tissue in Drosophila larvae. Proc. Natl. Acad. Sci. U. S. A 105, 10017-10022. PM:18632567
  • Barbier,M., Atkinson,A., Fumoux,F., and Rihet,P. (2008). IL12B polymorphisms are linked but not associated with Plasmodium falciparum parasitemia: a familial study in Burkina Faso. Genes Immun. 9, 405-411. PM:18449199
  • Barbier,M., Delahaye,N.F., Fumoux,F., and Rihet,P. (2008). Family-based association of a low producing lymphotoxin-alpha allele with reduced Plasmodium falciparum parasitemia. Microbes. Infect. 10, 673-679. PM:18457972
  • Baudot,A., Angelelli,J.B., Guenoche,A., Jacq,B., and Brun,C. (2008). Defining a modular signalling network from the fly interactome. BMC. Syst. Biol. 2, 45. PM:18489752
  • Baudot,A. and Brun,C. (2008). Outils bioinformatiques et ressources pour l'exploitation des données d'interactions protéine-protéine. Spectra Analyse 263, 40-45.
  • Blasco,V., Leone,M., Textoris,J., Visintini,P., Albanese,J., and Martin,C. (2008). [Venous oximetry: physiology and therapeutic implications]. Ann. Fr. Anesth. Reanim. 27, 74-82. PM:18079088
  • Brohee,S., Faust,K., Lima-Mendez,G., Sand,O., Janky,R., Vanderstocken,G., Deville,Y., and van Helden,J. (2008). NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways. Nucleic Acids Res. 36, W444-W451. PM:18524799
  • Brohee,S., Faust,K., Lima-Mendez,G., Vanderstocken,G., and van Helden,J. (2008). Network Analysis Tools: from biological networks to clusters and pathways. Nat. Protoc. 3, 1616-1629. PM:18802442
  • Defrance,M., Janky,R., Sand,O., and van Helden,J. (2008). Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences. Nat. Protoc. 3, 1589-1603. PM:18802440
  • Gonzalez,A., Chaouiya,C., and Thieffry,D. (2008). Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc. Bioinformatics. 24, i234-i240. PM:18689831
  • Haddad,L., El,H.H., bou-Merhi,R., Kfoury,Y., Mahieux,R., El-Sabban,M., and Bazarbachi,A. (2008). KSHV-transformed primary effusion lymphoma cells induce a VEGF-dependent angiogenesis and establish functional gap junctions with endothelial cells. Leukemia 22, 826-834. PM:18094712
  • Hingamp,P., Brochier,C., Talla,E., Gautheret,D., Thieffry,D., and Herrmann,C. (2008). Metagenome annotation using a distributed grid of undergraduate students. PLoS. Biol. 6, e296. PM:19067492
  • Irla,M., Saade,M., Kissenpfennig,A., Poulin,L.F., Leserman,L., Marche,P.N., Jouvin-Marche,E., Berger,F., and Nguyen,C. (2008). ZAP-70 restoration in mice by in vivo thymic electroporation. PLoS ONE 3, e2059. PM:18446234
  • Jaafari,N., Hua,G., Adelaide,J., Jule,Y., and Imbert,J. (2008). Expression of the tachykinin receptor mRNAs in healthy human colon. Eur. J. Pharmacol. 599, 121-125. PM:18835556
  • Janky,R. and van Helden,J. (2008). Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution. BMC Bioinformatics 9, 37. PM:18215291
  • Kontos,K., Godard,P., Andre,B., van Helden,J., and Bontempi,G. (2008). Machine learning techniques to identify putative genes involved in nitrogen catabolite repression in the yeast Saccharomyces cerevisiae. BMC Proc. 2 Suppl 4, S5. PM:19091052
  • Lima-Mendez,G., van Helden,J., Toussaint,A., and Leplae,R. (2008). Prophinder: a computational tool for prophage prediction in prokaryotic genomes. Bioinformatics 24, 863-865. PM:18238785
  • Lima-Mendez,G., van Helden,J., Toussaint,A., and Leplae,R. (2008). Reticulate representation of evolutionary and functional relationships between phage genomes. Mol. Biol. Evol. 25, 762-777. PM:18234706
  • Lopez,F., Textoris,J., Bergon,A., Didier,G., Remy,E., Granjeaud,S., Imbert,J., Nguyen,C., and Puthier,D. (2008). TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database. PLoS ONE 3 , e4001. PM:19104654
  • Martinez-Antonio,A., Janga,S.C., and Thieffry,D. (2008). Functional organisation of Escherichia coli transcriptional regulatory network. J. Mol. Biol. 381, 238-247. PM:18599074
  • Rihet,P. (2008). Innate immunity genes as candidate genes: searching for relevant natural polymorphisms in databases and assessing family-based association of polymorphisms with human diseases. Methods Mol. Biol. 415, 17-48. PM:18370146
  • Ritchie,W., Granjeaud,S., Puthier,D., and Gautheret,D. (2008). Entropy measures quantify global splicing disorders in cancer. PLoS Comput Biol 4, e1000011. PM:18369415
  • Ritchie,W., Theodule,F.X., and Gautheret,D. (2008). Mireval: a web tool for simple microRNA prediction in genome sequences. Bioinformatics 24, 1394-1396. PM:18453555
  • Sanchez,L., Chaouiya,C., and Thieffry,D. (2008). Segmenting the fly embryo: logical analysis of the role of the segment polarity cross-regulatory module. Int. J. Dev. Biol. 52, 1059-1075. PM:18956339
  • Sand,O., Thomas-Chollier,M., Vervisch,E., and van Helden,J. (2008). Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services: an example with ChIP-chip data. Nat. Protoc. 3, 1604-1615. PM:18802441
  • Schiano de Colella,J.M., Barbarat,B., Sweet,R., Gastaut,J.A., Olive,D., and Costello,R.T. (2008). Rank ligand stimulation induces a partial but functional maturation of human monocyte-derived dendritic cells. Eur. Cytokine Netw. 19, 81-88. PM:18632421
  • Serre,K., Mohr,E., Toellner,K.M., Cunningham,A.F., Granjeaud,S., Bird,R., and MacLennan,I.C. (2008). Molecular differences between the divergent responses of ovalbumin-specific CD4 T cells to alum-precipitated ovalbumin compared to ovalbumin expressed by Salmonella. Mol. Immunol. 45, 3558-3566. PM:18582945
  • Thomas-Chollier,M., Sand,O., Turatsinze,J.V., Janky,R., Defrance,M., Vervisch,E., Brohee,S., and van Helden,J. (2008). RSAT: regulatory sequence analysis tools. Nucleic Acids Res. 36, W119-W127. PM:18495751
  • Turatsinze,J.V., Thomas-Chollier,M., Defrance,M., and van Helden,J. (2008). Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat. Protoc. 3, 1578-1588. PM:18802439
  • van Helden,J., Cornely,C., Dati,F., Levy,H.R., Bal,T., Seeger,M., Wright,T., and Baker,L. (2008). Performance evaluation of the ADVIA Centaur anti-HBe and HBeAg assays. J. Clin. Virol. 43, 169-175. PM:18635392
  • Vendrell,J.A., Robertson,K.E., Ravel,P., Bray,S.E., Bajard,A., Purdie,C.A., Nguyen,C., Hadad,S.M., Bieche,I., Chabaud,S., Bachelot,T., Thompson,A.M., and Cohen,P.A. (2008). A candidate molecular signature associated with tamoxifen failure in primary breast cancer. Breast Cancer Res. 10, R88. PM:18928543