Publications

Articles, Books Chapters, Proceedings...

Articles

  1. Schvartz, M.; Saudrais, F.; Boulard, Y.; Renault, J.-P.; Henry, C.; Chédin, S.; Pin, S.; Aude, J.-C. «Dual Fractions Proteomic Analysis of Silica Nanoparticle Interactions with Protein Extracts» Materials. 2024. 17(19):4909.
  2. Nocente, M.C., Mesihovic Karamitsos, A., Drouineau, E., Soleil M., Albawardi W., Dulary C., Ribierre F., Picaud H., Alibert O., Acker J., Kervella M., Aude J.-C., Gilbert N., Ochsenbein F., Chantalat S., Gérard M. «cBAF generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers» Nat Struct Mol Biol 2024 Jul 02.
  3. Schvartz M, Saudrais F, Devineau S, Aude J-C, Chédin S, Henry C, Millán-Oropeza A, Perrault T, Pieri L, Pin S, Boulard Y, Brotons G, Renault J-P. « A proteome scale study reveals how plastic surfaces and agitation promote protein aggregation» Sci Rep. 2023 Jan 21. 13(1):1227.
  4. Marichal L, Degrouard J, Gatin A, Raffray N, Aude J-C, Boulard Y, Combet S, Cousin F, Hourdez S, Mary J, Pin S, Renault J-P. « From Protein Corona to Colloidal Self-Assembly: The Importance of Protein Size in Protein-Nanoparticle Interactions » Langmuir 2020. 36:8218–8230. hal
  5. Marichal L, Klein G, Armengaud J, Boulard Y, Chédin S, Labarre J, Pin S, Renault J-P, Aude J-C. « Protein Corona Composition of Silica Nanoparticles in Complex Media: Nanoparticle Size does not Matter » Nanomaterials (Basel). 2020 Jan 29;10(2). hal_icon
  6. Marichal L, Giraudon-Colas G, Cousin F, Thill A, Labarre J, Boulard Y, Aude J-C, Pin S, Renault J-P. « Protein-Nanoparticle Interactions: What Are the Protein-Corona Thickness and Organization? » Langmuir. 2019 Jul 23;35(33):10831–10837. hal_icon
  7. Godat E, Preiser J-C, Aude J-C, Kalfon P. « Dynamic properties of glucose complexity during the course of critical illness: a pilot study. » J Clin Monit Comput. 2019 Mar 19. hal_icon
  8. Petitalot A, Dardillac E, Jacquet E, Nhiri N, Guirouilh-Barbat J, Julien P, Bouazzaoui I, Bonte D, Feunteun J, Schnell J-A, Lafitte P, Aude J-C, Noguès C, Rouleau E, Lidereau R, Lopez BS, Zinn-Justin S, Caputo S-M; UNICANCER Genetic Group BRCA network « Combining Homologous Recombination and Phosphopeptide-binding Data to Predict the Impact of BRCA1 BRCT Variants on Cancer Risk. » Mol Cancer Res. 2019 Jan;17(1):54-69. hal_icon
  9. Marichal L, Renault J-P, Chédin S, Lagniel G, Klein G, Aude J-C, Tellier-Lebegue C, Armengaud J, Pin S, Labarre J, Boulard Y. « Importance of Post-translational Modifications in the Interaction of Proteins with Mineral Surfaces: The Case of Arginine Methylation and Silica surfaces. » Langmuir. 2018 May 8;34(18):5312-5322. hal_icon
  10. Klein G, Mathé C, Biola-Clier M, Devineau S, Drouineau E, Hatem E, Marichal L, Alonso B, Gaillard J-C, Lagniel G, Armengaud J, Carrière M, Chédin S, Boulard Y, Pin S, Renault J-P, Aude J-C, Labarre J « RNA binding proteins are a major target of silica nanoparticles in cell extracts. » Nanotoxicology 2016 Dec;10(10):1555-1564. hal_icon
  11. Dieuleveult M, Yen K, Hmitou I, Depaux A, Boussouar F, Bou Dargham D, Jounier S, Humbertclaude H, Ribierre F, Baulard C, Farrell N P, Park B, Keime C, Carrière L, Berlivet S, Gut M, Gut I, Werner M, Deleuze J-F, Olaso R, Aude J-C, Chantalat S, Pugh B-F, Gérard M « Genome-wide nucleosome specificity and function of chromatin remodellers in embryonic stem cells » Nature 2016 Feb 4;530(7588):113-6. hal_icon
  12. Klein G, Devineau S, Aude J-C, Boulard Y, Pasquier H, Labarre J, Pin S, Renault J-P « Interferences of Silica Nanoparticles in Green Fluorescent Protein Folding Processes » Langmuir 2016 Jan 12;32(1):195-202 hal_icon
  13. Mathé C, Devineau S, Aude J-C, Lagniel G, Chédin S, Legros V, Mathon M-H, Renault J-P, Pin S, Boulard Y, Labarre J « Structural determinants for protein adsorption/non-adsorption to silica surface. » PLoS ONE 2013, 8:e81346. hal_icon
  14. Leplat C, Champeimont R, Saenkham P, Cassier-Chauvat C, Aude J-C , Chauvat F « Genome-wide transcriptome analysis of hydrogen production in the cyanobacterium Synechocystis: Towards the identification of new players.» Int J of Hydrogen Energy 2013 38(4):1866-1872 hal_icon
  15. Carrière L, Graziani S, Alibert O, Ghavi-Helm Y, Boussouar F, Humbertclaude H, Jounier S, Aude J-C, Keime C, Murvai J, Foglio M, Gut M, Gut I, Lathrop M, Soutourina J, Gérard M, Werner M. « Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells. » Nucleic Acids Res. 2012 Jan;40(1):270-83.
  16. Gardarin A, Chédin S, Lagniel G, Aude J-C, Godat E, Catty P, Labarre J. «Endoplasmic reticulum is a major target of cadmium toxicity in yeast. » Mol Microbiol. 2010 May;76(4):1034-48 hal_icon
  17. Tavenet A, Suleau A, Dubreuil G, Ferrari R, Ducrot C, Michaut M, Aude J-C, Dieci G, Lefebvre O, Conesa C, Acker J. « Genome-wide location analysis reveals a role for Sub1 in RNA polymerase III transcription. » Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14265-70.
  18. Ghavi-Helm Y, Michaut M, Acker J, Aude JC, Thuriaux P, Werner M, Soutourina J. « Genome-wide location analysis reveals a role of TFIIS in RNA polymerase III transcription.» Genes Dev. 2008 Jul 15;22(14):1934-47.
  19. Michaut M, Kerrien S, Montecchi-Palazzi L, Chauvat F, Cassier-Chauvat C, Aude J-C, Legrain P, Hermjakob H. « InteroPORC: automated inference of highly conserved protein interaction networks. » Bioinformatics. 2008 Jul 15;24(14):1625-31.
  20. Houot L, Floutier M, Marteyn B, Michaut M, Picciocchi A, Legrain P, Aude J-C, Cassier-Chauvat C, Chauvat F. « Cadmium triggers an integrated reprogramming of the metabolism of Synechocystis PCC6803, under the control of the Slr1738 regulator. » BMC Genomics. 2007 Oct 2;8:350
  21. Mansour H, Cheval L, Elalouf J-M, Aude J-C, Alyanakian M-A, Mougenot B, Doucet A, Deschênes G. « T-cell transcriptome analysis points up a thymic disorder in idiopathic nephrotic syndrome. » Kidney Int. 2005 Jun;67(6):2168-77
  22. Lefebvre C, Aude J-C, Glémet E, Néri C. « Balancing protein similarity and gene co-expression reveals new links between genetic conservation and developmental diversity in invertebrates. » Bioinformatics. 2005 Apr 15;21(8):1550-8
  23. Desaint S, Luriau S, Aude J-C, Rousselet G, Toledano M B. « Mammalian antioxidant defenses are not inducible by H2O2. » J Biol Chem. 2004 Jul 23;279(30):31157-63
  24. Bastien O, Aude J-C, Roy S, Maréchal E. «Fundamentals of massive automatic pairwise alignments of protein sequences: theoretical significance of Z-value statistics.» Bioinformatics. 2004 Mar 1;20(4):534-7 hal_icon
  25. Chabardès-Garonne D, Mejéan A, Aude J-C, Cheval L, Di Stefano A, Gaillard M-C, Imbert-Teboul M, Wittner M, Balian C, Anthouard V, Robert C, Ségurens B, Wincker P, Weissenbach J, Doucet A, Elalouf J-M. «A panoramic view of gene expression in the human kidney.» Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13710-5 hal_icon
  26. Aude J-C, Louis A «An incremental algorithm for Z-values computations.» Comput Chem. 2002 Jul;26(5):403-11
  27. Fauchon M, Lagniel G, Aude J-C, Lombardia L, Soularue P, Petat C, Marguerie G, Sentenac A, Werner M, Labarre J «Sulfur-sparing in the yeast proteome in response to sulfur demand.» Mol Cell. 2002 Apr;9(4):713-23
  28. Elalouf J-M, Aude J-C, Billon E, Cheval L, Doucet A, Virlon B «Renal transcriptomes : segmental analysis of differential expression.» Exp. Nephrology, 2002 vol 10 pp. 75-81
  29. Cheval L, Virlon B, Billon E, Aude J-C, Elalouf J-M, Doucet A «Large-scale analysis of gene expression: methods & application to the kidney.» Journal of Nephrology, 2002 Mar-Apr;15 Suppl 5:S170-83 hal_icon
  30. Louis A, Ollivier E, Aude J-C, Risler J-L «Massive sequence comparisons as a help in annotating genomic sequences.» Genome Res. 2001 Jul;11(7):1296-303
  31. Aude J-C, Diaz-Lazcoz Y, Codani J-J, Risler J-L «Application of the pyramidal clustering method to biological objects.» Comput Chem. 1999 Jun 15;23(3-4):303-15.
  32. Comet J-P, Aude J-C, Glémet E, Risler J-L, Hénaut A, Slonimski P, Codani J-J «Significance of Z-value statistics of Smith & Waterman scores for protein alignments.» Comput Chem. 1999 Jun 15;23(3-4):317-31
  33. Diaz-Lazcoz Y, Aude J-C, Nitschké P, Chiapello H, Landès-Devauchelle C, Risler J-L «Evolution of genes, evolution of species: the case of amynoacyl-tRNA synthetases.» Mol Biol Evol. 1998 Nov;15(11):1548-61

Books Chapters

  1. Aude J-C In «bio-informatique : principes d’utilisation des outils.» Coll. Savoir faire (Eds Tagu D. and Risler J.L.), Quae 2010; pp. 85-115
  2. Polaillon G, Vescovo L, Michaut M, Aude J-C «Mining Biological Data Using Pyramids.» In Selected Contributions in Data Analysis and Classification (Eds Brito P, Bertrand P, Cucumel G, De Carvalho F), Springer-Verlag 2007; pp. 397-408
  3. Cheval L, Virlon B, Billon E, Aude J-C, Elalouf J-M, Doucet A «Analyse des transcriptomes : applications en physiologie et physiopathologie rénales.» Actualités Nephrologiques Jean Hamburger : Hopital Necker 2002 ; Medecine-Science Flammarion 2002 ; pp. 193-206
  4. Codani J-J, Comet J-P, Aude J-C, Glémet E, Wozniak A, Risler J-L, Hénaut A, Slonimski P «Automatic analysis of large scale pairwise alignments of protein sequences.» In Automation Genomic & Functional analyses: methods in microbiology serie (Eds Craig A.G. and Hoheisel J.D.), Academic Press 1999; pp. 229-244

Proceedings (international conferences)

  1. Champeimont R, Leplat C, Chauvat F, Aude J-C «SVGMapping: an R package to map omic datasets onto pathways templates.» Proceedings of the 8th International R User Conference (useR 2012) Vanderbilt University, USA 12th-15th June 2012
  2. Aude J-C «In-silico approaches to unravel Synechocystis sp. molecular processes.» International Conference on Biotechnology: A global scenario. Kakatiya University, Warangal India, 2010 November, 3.
  3. Aude J-C, Elalouf J-M, Bruat V «A SAGE data acquisition software.» Proceedings of the Sage conference, Baltimore USA 2000
  4. Aude J-C, Comet J-P «Construction of protein sequences families.» Proceedings of the 24th Aharon Katzir-Katchalsky conference, Jerusalem Israel 1996, November 17-21 Folding & Design supp. vol. 1, pp. S5-S6
  5. Slonimski P, Mossé M-O, Golik P, Hénaut A, Diaz Y, Risler J-L, Comet J-P, Aude J-C, Wozniak A, Glémet E, Codani J-J «The first laws of genomics.» Proceedings of microbial genomes II : sequencing, functional analysis and comparative genomics, Hilton Head US, 1998.
  6. Slonimski P, Risler J-L, Mossé M-O, Hénaut A, Diaz Y, Comet J-P, Aude J-C, Glémet E, Codani J-J «What can we learn about protein from complete sequences of microbial genomes.» Proceedings of the 2nd european symposium of the protein society, Cambridge UK, 12-16 April 1997, Protein science vol. 6 supp. 1

Proceedings (national conferences)

  1. Champeimont R, Leplat C, Chauvat F, Aude J-C «SVGMapping: an R package to map omic datasets onto pathways templates.» 1ères Rencontres R, Bordeaux 2012, pp. 44-45
  2. Michaut M, Kerrien S, Montecchi-Palazzi L, Chauvat F, Cassier-Chauvat C, Aude J-C, Legrain P, Hermjakob H «Inference of Synechocystis protein interaction network.» JOBIM, 2008, Lille, pp. 229-234
  3. Michaut M, Kerrien S, Montecchi-Palazzi L, Chauvat F, Cassier-Chauvat C, Aude J-C, Legrain P, Hermjakob H «Inference and validation of Synechocystis protein interaction network using orthology.» JOBIM, 2007, Marseille, pp. 229-234