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Protein Biomarker Discovery in Non-depleted Serum by Spectral Library-Based Data-Independent Acquisition Mass Spectrometry.

Kraut A, Louwagie M, Bruley C, Masselon C, Couté Y, Brun V, Hesse AM.

Methods Mol Biol. 2019;1959:129-150. doi: 10.1007/978-1-4939-9164-8_9.


AT_CHLORO: The First Step When Looking for Information About Subplastidial Localization of Proteins.

Salvi D, Bournais S, Moyet L, Bouchnak I, Kuntz M, Bruley C, Rolland N.

Methods Mol Biol. 2018;1829:395-406. doi: 10.1007/978-1-4939-8654-5_26.


Proteomic characterization of human exhaled breath condensate.

Lacombe M, Marie-Desvergne C, Combes F, Kraut A, Bruley C, Vandenbrouck Y, Chamel Mossuz V, Couté Y, Brun V.

J Breath Res. 2018 Feb 20;12(2):021001. doi: 10.1088/1752-7163/aa9e71.


Introducing plasma/serum glycodepletion for the targeted proteomics analysis of cytolysis biomarkers.

Maes P, Donadio-Andréi S, Louwagie M, Couté Y, Picard G, Lacoste C, Bruley C, Garin J, Ichai P, Faivre J, Jaquinod M, Brun V.

Talanta. 2017 Aug 1;170:473-480. doi: 10.1016/j.talanta.2017.04.042. Epub 2017 Apr 19.


ChloroKB: A Web Application for the Integration of Knowledge Related to Chloroplast Metabolic Network.

Gloaguen P, Bournais S, Alban C, Ravanel S, Seigneurin-Berny D, Matringe M, Tardif M, Kuntz M, Ferro M, Bruley C, Rolland N, Vandenbrouck Y, Curien G.

Plant Physiol. 2017 Jun;174(2):922-934. doi: 10.1104/pp.17.00242. Epub 2017 Apr 25.


MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones.

El Kennani S, Adrait A, Shaytan AK, Khochbin S, Bruley C, Panchenko AR, Landsman D, Pflieger D, Govin J.

Epigenetics Chromatin. 2017 Jan 10;10:2. doi: 10.1186/s13072-016-0109-x. eCollection 2017.


Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update.

Vandenbrouck Y, Lane L, Carapito C, Duek P, Rondel K, Bruley C, Macron C, Gonzalez de Peredo A, Couté Y, Chaoui K, Com E, Gateau A, Hesse AM, Marcellin M, Méar L, Mouton-Barbosa E, Robin T, Burlet-Schiltz O, Cianferani S, Ferro M, Fréour T, Lindskog C, Garin J, Pineau C.

J Proteome Res. 2016 Nov 4;15(11):3998-4019. Epub 2016 Aug 23.


DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics.

Wieczorek S, Combes F, Lazar C, Giai Gianetto Q, Gatto L, Dorffer A, Hesse AM, Couté Y, Ferro M, Bruley C, Burger T.

Bioinformatics. 2017 Jan 1;33(1):135-136. doi: 10.1093/bioinformatics/btw580. Epub 2016 Sep 6.


hEIDI: An Intuitive Application Tool To Organize and Treat Large-Scale Proteomics Data.

Hesse AM, Dupierris V, Adam C, Court M, Barthe D, Emadali A, Masselon C, Ferro M, Bruley C.

J Proteome Res. 2016 Oct 7;15(10):3896-3903. Epub 2016 Sep 12.


Uses and misuses of the fudge factor in quantitative discovery proteomics.

Giai Gianetto Q, Couté Y, Bruley C, Burger T.

Proteomics. 2016 Jul;16(14):1955-60. doi: 10.1002/pmic.201600132.


Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies.

Lazar C, Gatto L, Ferro M, Bruley C, Burger T.

J Proteome Res. 2016 Apr 1;15(4):1116-25. doi: 10.1021/acs.jproteome.5b00981. Epub 2016 Mar 1.


Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods.

Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssié D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianférani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O, Schaeffer C, Couté Y, Gonzalez de Peredo A.

Data Brief. 2015 Dec 17;6:286-94. doi: 10.1016/j.dib.2015.11.063. eCollection 2016 Mar.


Benchmarking quantitative label-free LC-MS data processing workflows using a complex spiked proteomic standard dataset.

Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssié D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianférani S, Ferro M, Van Dorssaeler A, Burlet-Schiltz O, Schaeffer C, Couté Y, Gonzalez de Peredo A.

J Proteomics. 2016 Jan 30;132:51-62. doi: 10.1016/j.jprot.2015.11.011. Epub 2015 Nov 14.


Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments.

Giai Gianetto Q, Combes F, Ramus C, Bruley C, Couté Y, Burger T.

Proteomics. 2016 Jan;16(1):29-32. doi: 10.1002/pmic.201500189. Erratum in: Proteomics. 2016 Apr;16(8):1309-10.


In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba.

Legendre M, Lartigue A, Bertaux L, Jeudy S, Bartoli J, Lescot M, Alempic JM, Ramus C, Bruley C, Labadie K, Shmakova L, Rivkina E, Couté Y, Abergel C, Claverie JM.

Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):E5327-35. doi: 10.1073/pnas.1510795112. Epub 2015 Sep 8.


Computational and Mass-Spectrometry-Based Workflow for the Discovery and Validation of Missing Human Proteins: Application to Chromosomes 2 and 14.

Carapito C, Lane L, Benama M, Opsomer A, Mouton-Barbosa E, Garrigues L, Gonzalez de Peredo A, Burel A, Bruley C, Gateau A, Bouyssié D, Jaquinod M, Cianferani S, Burlet-Schiltz O, Van Dorsselaer A, Garin J, Vandenbrouck Y.

J Proteome Res. 2015 Sep 4;14(9):3621-34. doi: 10.1021/pr5010345. Epub 2015 Jul 22.


Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology.

Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, Lescot M, Poirot O, Bertaux L, Bruley C, Couté Y, Rivkina E, Abergel C, Claverie JM.

Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):4274-9. doi: 10.1073/pnas.1320670111. Epub 2014 Mar 3.


Mass spectrometry-based workflow for accurate quantification of Escherichia coli enzymes: how proteomics can play a key role in metabolic engineering.

Trauchessec M, Jaquinod M, Bonvalot A, Brun V, Bruley C, Ropers D, de Jong H, Garin J, Bestel-Corre G, Ferro M.

Mol Cell Proteomics. 2014 Apr;13(4):954-68. doi: 10.1074/mcp.M113.032672. Epub 2014 Jan 29.


Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes.

Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C, Garin J, Claverie JM, Abergel C.

Science. 2013 Jul 19;341(6143):281-6. doi: 10.1126/science.1239181. Erratum in: Science. 2013 Sep 27;341(6153):1452.


Identification of a novel BET bromodomain inhibitor-sensitive, gene regulatory circuit that controls Rituximab response and tumour growth in aggressive lymphoid cancers.

Emadali A, Rousseaux S, Bruder-Costa J, Rome C, Duley S, Hamaidia S, Betton P, Debernardi A, Leroux D, Bernay B, Kieffer-Jaquinod S, Combes F, Ferri E, McKenna CE, Petosa C, Bruley C, Garin J, Ferro M, Gressin R, Callanan MB, Khochbin S.

EMBO Mol Med. 2013 Aug;5(8):1180-95. doi: 10.1002/emmm.201202034. Epub 2013 Jul 4.


A micro-silicon chip for in vivo cerebral imprint in monkey.

Zaccaria A, Bouamrani A, Selek L, El Atifi M, Hesse AM, Juhem A, Ratel D, Mathieu H, Coute Y, Bruley C, Garin J, Benabid AL, Chabardes S, Piallat B, Berger F.

ACS Chem Neurosci. 2013 Mar 20;4(3):385-92. doi: 10.1021/cn300116g. Epub 2013 Jan 15.


An extended proteome map of the lysosomal membrane reveals novel potential transporters.

Chapel A, Kieffer-Jaquinod S, Sagné C, Verdon Q, Ivaldi C, Mellal M, Thirion J, Jadot M, Bruley C, Garin J, Gasnier B, Journet A.

Mol Cell Proteomics. 2013 Jun;12(6):1572-88. doi: 10.1074/mcp.M112.021980. Epub 2013 Feb 24.


PSAQ™ standards for accurate MS-based quantification of proteins: from the concept to biomedical applications.

Picard G, Lebert D, Louwagie M, Adrait A, Huillet C, Vandenesch F, Bruley C, Garin J, Jaquinod M, Brun V.

J Mass Spectrom. 2012 Oct;47(10):1353-63. doi: 10.1002/jms.3106.


AT_CHLORO: A Chloroplast Protein Database Dedicated to Sub-Plastidial Localization.

Bruley C, Dupierris V, Salvi D, Rolland N, Ferro M.

Front Plant Sci. 2012 Sep 11;3:205. doi: 10.3389/fpls.2012.00205. eCollection 2012.


PredAlgo: a new subcellular localization prediction tool dedicated to green algae.

Tardif M, Atteia A, Specht M, Cogne G, Rolland N, Brugière S, Hippler M, Ferro M, Bruley C, Peltier G, Vallon O, Cournac L.

Mol Biol Evol. 2012 Dec;29(12):3625-39. doi: 10.1093/molbev/mss178. Epub 2012 Jul 23.


Introducing AAA-MS, a rapid and sensitive method for amino acid analysis using isotope dilution and high-resolution mass spectrometry.

Louwagie M, Kieffer-Jaquinod S, Dupierris V, Couté Y, Bruley C, Garin J, Dupuis A, Jaquinod M, Brun V.

J Proteome Res. 2012 Jul 6;11(7):3929-36. doi: 10.1021/pr3003326. Epub 2012 Jun 21.


Mass spectrometry-based absolute protein quantification: PSAQ™ strategy makes use of "noncanonical" proteotypic peptides.

Jaquinod M, Trauchessec M, Huillet C, Louwagie M, Lebert D, Picard G, Adrait A, Dupuis A, Garin J, Brun V, Bruley C.

Proteomics. 2012 Apr;12(8):1217-21. doi: 10.1002/pmic.201100538.


Development of a Protein Standard Absolute Quantification (PSAQ™) assay for the quantification of Staphylococcus aureus enterotoxin A in serum.

Adrait A, Lebert D, Trauchessec M, Dupuis A, Louwagie M, Masselon C, Jaquinod M, Chevalier B, Vandenesch F, Garin J, Bruley C, Brun V.

J Proteomics. 2012 Jun 6;75(10):3041-9. doi: 10.1016/j.jprot.2011.11.031. Epub 2011 Dec 6.


Investigating the macropinocytic proteome of Dictyostelium amoebae by high-resolution mass spectrometry.

Journet A, Klein G, Brugière S, Vandenbrouck Y, Chapel A, Kieffer S, Bruley C, Masselon C, Aubry L.

Proteomics. 2012 Jan;12(2):241-5. doi: 10.1002/pmic.201100313. Epub 2011 Dec 20.


Accurate quantification of cardiovascular biomarkers in serum using Protein Standard Absolute Quantification (PSAQ™) and selected reaction monitoring.

Huillet C, Adrait A, Lebert D, Picard G, Trauchessec M, Louwagie M, Dupuis A, Hittinger L, Ghaleh B, Le Corvoisier P, Jaquinod M, Garin J, Bruley C, Brun V.

Mol Cell Proteomics. 2012 Feb;11(2):M111.008235. doi: 10.1074/mcp.M111.008235. Epub 2011 Nov 11.


Proteomic profiling of oil bodies isolated from the unicellular green microalga Chlamydomonas reinhardtii: with focus on proteins involved in lipid metabolism.

Nguyen HM, Baudet M, Cuiné S, Adriano JM, Barthe D, Billon E, Bruley C, Beisson F, Peltier G, Ferro M, Li-Beisson Y.

Proteomics. 2011 Nov;11(21):4266-73. doi: 10.1002/pmic.201100114. Epub 2011 Sep 19.


Production and use of stable isotope-labeled proteins for absolute quantitative proteomics.

Lebert D, Dupuis A, Garin J, Bruley C, Brun V.

Methods Mol Biol. 2011;753:93-115. doi: 10.1007/978-1-61779-148-2_7.


MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data.

Joshi HJ, Hirsch-Hoffmann M, Baerenfaller K, Gruissem W, Baginsky S, Schmidt R, Schulze WX, Sun Q, van Wijk KJ, Egelhofer V, Wienkoop S, Weckwerth W, Bruley C, Rolland N, Toyoda T, Nakagami H, Jones AM, Briggs SP, Castleden I, Tanz SK, Millar AH, Heazlewood JL.

Plant Physiol. 2011 Jan;155(1):259-70. doi: 10.1104/pp.110.168195. Epub 2010 Nov 12.


AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins.

Ferro M, Brugière S, Salvi D, Seigneurin-Berny D, Court M, Moyet L, Ramus C, Miras S, Mellal M, Le Gall S, Kieffer-Jaquinod S, Bruley C, Garin J, Joyard J, Masselon C, Rolland N.

Mol Cell Proteomics. 2010 Jun;9(6):1063-84. doi: 10.1074/mcp.M900325-MCP200. Epub 2010 Jan 10.


A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa.

Dupierris V, Masselon C, Court M, Kieffer-Jaquinod S, Bruley C.

Bioinformatics. 2009 Aug 1;25(15):1980-1. doi: 10.1093/bioinformatics/btp301. Epub 2009 May 6.


Peptide storage: are you getting the best return on your investment? Defining optimal storage conditions for proteomics samples.

Kraut A, Marcellin M, Adrait A, Kuhn L, Louwagie M, Kieffer-Jaquinod S, Lebert D, Masselon CD, Dupuis A, Bruley C, Jaquinod M, Garin J, Gallagher-Gambarelli M.

J Proteome Res. 2009 Jul;8(7):3778-85. doi: 10.1021/pr900095u.


PepLine: a software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences.

Ferro M, Tardif M, Reguer E, Cahuzac R, Bruley C, Vermat T, Nugues E, Vigouroux M, Vandenbrouck Y, Garin J, Viari A.

J Proteome Res. 2008 May;7(5):1873-83. doi: 10.1021/pr070415k. Epub 2008 Mar 19.


A Proteomics Approach Highlights a Myriad of Transporters in the Arabidopsis thaliana Vacuolar Membrane.

Jaquinod M, Villiers F, Kieffer-Jaquinod S, Hugouvieux V, Bruley C, Garin J, Bourguignon J.

Plant Signal Behav. 2007 Sep;2(5):413-5.


A high content in lipid-modified peripheral proteins and integral receptor kinases features in the arabidopsis plasma membrane proteome.

Marmagne A, Ferro M, Meinnel T, Bruley C, Kuhn L, Garin J, Barbier-Brygoo H, Ephritikhine G.

Mol Cell Proteomics. 2007 Nov;6(11):1980-96. Epub 2007 Jul 20.


15N-metabolic labeling for comparative plasma membrane proteomics in Arabidopsis cells.

Lanquar V, Kuhn L, Lelièvre F, Khafif M, Espagne C, Bruley C, Barbier-Brygoo H, Garin J, Thomine S.

Proteomics. 2007 Mar;7(5):750-4.


A proteomics dissection of Arabidopsis thaliana vacuoles isolated from cell culture.

Jaquinod M, Villiers F, Kieffer-Jaquinod S, Hugouvieux V, Bruley C, Garin J, Bourguignon J.

Mol Cell Proteomics. 2007 Mar;6(3):394-412. Epub 2006 Dec 6.


A novel promoter for the 11beta-hydroxysteroid dehydrogenase type 1 gene is active in lung and is C/EBPalpha independent.

Bruley C, Lyons V, Worsley AG, Wilde MD, Darlington GD, Morton NM, Seckl JR, Chapman KE.

Endocrinology. 2006 Jun;147(6):2879-85. Epub 2006 Mar 16.


Growth selection in mice reveals conserved and redundant expression patterns of the insulin-like growth factor system.

Hoeflich A, Bünger L, Nedbal S, Renne U, Elmlinger MW, Blum WF, Bruley C, Kolb HJ, Wolf E.

Gen Comp Endocrinol. 2004 Apr;136(2):248-59.


Differences in gene density on chicken macrochromosomes and microchromosomes.

Smith J, Bruley CK, Paton IR, Dunn I, Jones CT, Windsor D, Morrice DR, Law AS, Masabanda J, Sazanov A, Waddington D, Fries R, Burt DW.

Anim Genet. 2000 Apr;31(2):96-103.


Integration of the genetic and physical maps of the chicken macrochromosomes.

Smith J, Paton IR, Bruley CK, Windsor D, Burke D, Ponce de Leon FA, Burt DW.

Anim Genet. 2000 Feb;31(1):20-7.


The dynamics of chromosome evolution in birds and mammals.

Burt DW, Bruley C, Dunn IC, Jones CT, Ramage A, Law AS, Morrice DR, Paton IR, Smith J, Windsor D, Sazanov A, Fries R, Waddington D.

Nature. 1999 Nov 25;402(6760):411-3.


Efficient high-resolution genetic mapping of mouse interspersed repetitive sequence PCR products, toward integrated genetic and physical mapping of the mouse genome.

McCarthy L, Hunter K, Schalkwyk L, Riba L, Anson S, Mott R, Newell W, Bruley C, Bar I, Ramu E, et al.

Proc Natl Acad Sci U S A. 1995 Jun 6;92(12):5302-6.


Photoaggravated allergic reaction to isotretinoin.

Auffret N, Bruley C, Brunetiere RA, Decot MC, Binet O.

J Am Acad Dermatol. 1990 Aug;23(2 Pt 1):321-2. No abstract available.


Photo-patch testing and patch testing with silver sulfadiazine cream.

Binet O, Bruley C, Robin J.

Photodermatol. 1987 Apr;4(2):102-3. No abstract available.


Allergy and photoallergy to frullania.

Bruley C, Beltzer-Garelly E, Kaufman P, Binet O, Robin J.

Photodermatol. 1986 Feb;3(1):49-50. No abstract available.


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