2018 

Abulfaraj AA, Mariappan K, Bigeard J, Manickam P, Blilou I, Guo X, Al-Babili S, Pflieger D, Hirt H and Rayapuram N
The Arabidopsis homolog of human G3BP1 is a key regulator of stomatal and apoplastic immunity.
Life Science Alliance, 2018, 1(2): e201800046

Adam C, Guerois R, Citarella A, Verardi L, Adolphe F, Beneut C, Sommermeyer V, Ramus C, Govin J, Coute Y and Borde V
The PHD finger protein Spp1 has distinct functions in the Set1 and the meiotic DSB formation complexes.
PLoS Genetics, 2018, 14(2): e1007223

Burger T
Gentle introduction to the statistical foundations of false discovery rate in quantitative proteomics.
Journal of Proteome Research, 2018, 17(1): 12-22

Dominguez-Medina S, Fostner S, Defoort M, Sansa M, Stark AK, Halim MA, Vernhes E, Gely M, Jourdan G, Alava T, Boulanger P, Masselon C and Hentz S
Neutral mass spectrometry of virus capsids above 100 megadaltons with nanomechanical resonators.
Science (New York, N.Y.), 2018, 362(6417): 918-22

El Kennani S, Adrait A, Permiakova O, Hesse AM, Ialy-Radio C, Ferro M, Brun V, Cocquet J, Govin J and Pflieger D
Systematic quantitative analysis of H2A and H2B variants by targeted proteomics.
Epigenetics and Chromatin, 2018, 11(1): Article number 2

El Kennani S, Crespo M, Govin J and Pflieger D
Proteomic analysis of histone variants and their PTMs: Strategies and pitfalls.
Proteomes, 2018, 6(3): Article number 29

Eymard-Vernain E, Coute Y, Adrait A, Rabilloud T, Sarret G and Lelong C
The poly-gamma-glutamate of Bacillus subtilis interacts specifically with silver nanoparticles.
PLoS One, 2018, 13(5): Article number e0197501

Fröhlich T, Hahn F, Belmudes L, Leidenberger M, Friedrich O, Kappes B, Couté Y, Marschall M and Tsogoeva SB
Synthesis of artemisinin-derived dimers, trimers and dendrimers: Investigation of their antimalarial and antiviral activities including putative mechanisms of action.
Chemistry - A European Journal, 2018, 24(32): 8103-8113

Garnaud C, Garcia-Oliver E, Wang Y, Maubon D, Bailly S, Despinasse Q, Champleboux M, Govin J and Cornet M
The Rim pathway mediates antifungal tolerance in Candida albicans through newly identified Rim101 transcriptional targets including Hsp90 and Ipt1.
Antimicrobial Agents and Chemotherapy, 2018, 62(3): article number e01785-17

Gerboth S, Frittoli E, Palamidessi A, Baltanas FC, Salek M, Rappsilber J, Giuliani C, Troglio F, Rolland Y, Pruneri G, Kreutmair S, Pallavicini I, Zobel M, Cinquanta M, Minucci S, Gomez C, Santos E, Illert AL and Scita G
Phosphorylation of SOS1 on tyrosine 1196 promotes its RAC GEF activity and contributes to BCR-ABL leukemogenesis.
Leukemia, 2018, 32(3): 820-827

Govin J, Barral S, Morozumi Y, Hoghoughi N, Buchou T, Rousseaux S and Khochbin S
Characterization of post-meiotic male germ cell genome organizational states.
Methods in Molecular Biology, 2018, 1832: 293-307

Hahn F, Hutterer C, Henry C, Hamilton ST, Strojan H, Kraut A, Schulte U, Schütz M, Kohrt S, Wangen C, Pfizer J, Couté Y, Rawlinson WD, Strobl S and Marschall M
Novel cytomegalovirus-inhibitory compounds of the class pyrrolopyridines show a complex pattern of target binding that suggests an unusual mechanism of antiviral activity.
Antiviral Research, 2018, 159: 84-94

He H, Brenier-Pinchart MP, Braun L, Kraut A, Touquet B, Coute Y, Tardieux I, Hakimi MA and Bougdour A
Characterization of a Toxoplasma effector uncovers an alternative GSK3/beta-catenin-regulatory pathway of inflammation.
eLife, 2018, 7: Article Number e39887

Jacob L, Combes F and Burger T
PEPA test: Fast and powerful differential analysis from relative quantitative proteomics data using shared peptides.
Biostatistics, 2018, kxy021

Jonckheere J, Deloulme JC, Dall'Igna G, Chauliac N, Pelluet A, Nguon AS, Lentini C, Brocard J, Denarier E, Brugiere S, Coute Y, Heinrich C, Porcher C, Holtzmann J, Andrieux A, Suaud-Chagny MF and Gory-Faure S
Short- and long-term efficacy of electroconvulsive stimulation in animal models of depression: The essential role of neuronal survival.
Brain Stimulation, 2018, 11(6): 1336-47

Lacombe M, Marie-Desvergne C, Combes F, Kraut A, Bruley C, Vandenbrouck Y, Chamel Mossuz V, Coute Y and Brun V
Proteomic characterization of human exhaled breath condensate.
Journal of Breath Research, 2018, 12(2): 021001

Legendre M, Fabre E, Poirot O, Jeudy S, Lartigue A, Alempic JM, Beucher L, Philippe N, Bertaux L, Christo-Foroux E, Labadie K, Couté Y, Abergel C and Claverie JM
Diversity and evolution of the emerging Pandoraviridae family.
Nature Communications, 2018, 9(1): Article number 2285

Mato JM, Elortza F, Lu SC, Brun V, Paradela A and Corrales FJ
Liver cancer-associated changes to the proteome: What deserves clinical focus?
Expert Review of Proteomics, 2018, 15(9): 749-56

De Muyt A, Pyatnitskaya A, Andreani J, Ranjha L, Ramus C, Laureau R, Fernandez-Vega A, Holoch D, Girard E, Govin J, Margueron R, Coute Y, Cejka P, Guerois R and Borde V
A meiotic XPF-ERCC1-like complex recognizes joint molecule recombination intermediates to promote crossover formation.
Genes & Developement, 2018, 32(3-4): 283-296

Petosa C, Govin J and Mietton F
[A new hope to fight invasive fungal infection].
Médecine Sciences, 2018, 34(2): 123-125

Picard MAL, Cosseau C, Ferre S, Quack T, Grevelding CG, Coute Y and Vicoso B
Evolution of gene dosage on the Z-chromosome of schistosome parasites.
eLife, 2018, 7: Article number e35684

Rayapuram N, Bigeard J, Alhoraibi H, Bonhomme L, Hesse AM, Vinh J, Hirt H and Pflieger D
Quantitative phosphoproteomic analysis reveals shared and specific targets of Arabidopsis mitogen-activated protein kinases (MAPKs) MPK3, MPK4, and MPK6.
Molecular & Cellular Proteomics, 2018, 17(1): 75-94

Salvi D, Bournais S, Moyet L, Bouchnak I, Kuntz M, Bruley C and Rolland N AT_CHLORO - The first step when looking for information about subplastidial localization of proteins. In: Plastids - Methods and Protocols. (E. Maréchal, Ed.), Humana Press, New-York, USA, Methods in Molecular Biology, 2018, 1829: 395-406

Shiota H, Barral S, Buchou T, Tan M, Couté Y, Charbonnier G, Reynoird N, Boussouar F, Gérard M, Zhu M, Bargier L, Puthier D, Chuffart F, Bourova-Flin E, Picaud S, Filippakopoulos P, Goudarzi A, Ibrahim Z, Panne D, Rousseaux S, Zhao Y and Khochbin S
Nut directs p300-dependent, genome-wide H4 hyperacetylation in male germ cells.
Cell Reports, 2018, 24(13): 3477-87.e6

Volz R, Kim SK, Mi JN, Mariappan KG, Guo XJ, Bigeard J, Alejandro S, Pflieger D, Rayapuram N, Al-Babili S and Hirt H
The Trihelix transcription factor GT2-like 1 (GTL1) promotes salicylic acid metabolism, and regulates bacterial-triggered immunity.
PLoS Genetics, 2018, 14(10): Article Number e1007708


2017 

Aillaud C, Bosc C, Peris L, Bosson A, Heemeryck P, Van Dijk J, Le Friec J, Boulan B, Vossier F, Sanman LE, Syed S, Amara N, Couté Y, Lafanechère L, Denarier E, Delphin C, Pelletier L, Humbert S, Bogyo M, Andrieux A, Rogowski K and Moutin MJ
Vasohibins/SVBP are tubulin carboxypeptidases (TCP) that regulate neuron differentiation.
Science, 2017, 358(6369): 1448-1453

Alfieri A, Sorokina O, Adrait A, Angelini C, Russo I, Morellato A, Matteoli M, Menna E, Erba EB, McLean C, Armstrong JD, Ala U, Buxbaum JD, Brusco A, Couté Y, De Rubeis S, Turco E and Defilippi P
Synaptic interactome mining reveals p140cap as a new hub for PSD proteins involved in psychiatric and neurological disorders.
Frontiers in Molecular Neuroscience, 2017, 10: Article number 212

Arvin-Berod M, Desroches-Castan A, Bonte S, Brugière S, Couté Y, Guyon L, Feige JJ, Baussanne I and Demeunynck M
Indolizine-based scaffolds as efficient and versatile tools: Application to the synthesis of biotin-tagged antiangiogenic drugs.
ACS Omega, 2017, 2(12): 9221-9230

Barral S, Morozumi Y, Tanaka H, Montellier E, Govin J, de Dieuleveult M, Charbonnier G, Couté Y, Puthier D, Buchou T, Boussouar F, Urahama T, Fenaille F, Curtet S, Héry P, Fernandez-Nunez N, Shiota H, Gérard M, Rousseaux S, Kurumizaka H and Khochbin S
Histone variant H2A.L.2 guides transition protein-dependent protamine assembly in male germ cells.
Molecular Cell, 2017, 66(1): 89-101

Bartoli J, My L, Belmudes L, Coute Y, Viala JP and Bouveret E
The long hunt for pssR-looking for a phospholipid synthesis transcriptional regulator, finding the ribosome.
Journal of Bacteriology, 2017, 199(14): Article number e00202-00217

Beaumel S, Picciocchi A, Debeurme F, Vives C, Hesse AM, Ferro M, Grunwald D, Stieglitz H, Thepchatri P, Smith SME, Fieschi F and José Stasia M
Down-regulation of NOX2 activity in phagocytes mediated by ATM-kinase dependent phosphorylation.
Free Radical Biology and Medicine, 2017, 113: 1-15

Boruc J, Weimer AK, Stoppin-Mellet V, Mylle E, Kosetsu K, Cedeno C, Jaquinod M, Njo M, De Milde L, Tompa P, Gonzalez N, Inze D, Beeckman T, Vantard M and Van Damme D
Phosphorylation of MAP65-1 by Arabidopsis aurora kinases is required for efficient cell cycle progression.
Plant Physiology, 2017, 173(1): 582-599

Carapito C, Duek P, Macron C, Seffals M, Rondel K, Delalande F, Lindskog C, Freour T, Vandenbrouck Y, Lane L and Pineau C
Validating missing proteins in human sperm cells by targeted mass-spectrometry- and antibody-based methods.
Journal of Proteome Research, 2017, 16(12): 4340-4351

Do LD, Chanson E, Desestret V, Joubert B, Ducray F, Brugière S, Couté Y, Formaglio M, Rogemond V, Thomas-Antérion C, Borrega L, Laurens B, Tison F, Curot J, De Brouker T, Lebrun-Frenay C, Delattre JY, Antoine JC and Honnorat J
Characteristics in limbic encephalitis with anti-adenylate kinase 5 autoantibodies.
Neurology, 2017, 88(6): 514-524

Duriez E, Masselon CD, Mesmin C, Court M, Demeure K, Allory Y, Malats N, Matondo M, Radvanyi F, Garin J and Domon B
Large-scale SRM screen of urothelial bladder cancer candidate biomarkers in urine.
Journal of Proteome Research, 2017, 16(4): 1617-1631

El Kennani S, Adrait A, Shaytan AK, Khochbin S, Bruley C, Panchenko AR, Landsman D, Pflieger D and Govin J
MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones.
Epigenetics & Chromatin, 2017, 10(1): article number 2

Erales J, Marchand V, Panthu B, Gillot S, Belin S, Ghayad SE, Garcia M, Laforêts F, Marcel V, Baudin-Baillieu A, Bertin P, Couté Y, Adrait A, Meyer M, Therizols G, Yusupov M, Namy O, Ohlmann T, Motorin Y, Catez F and Diaz JJ
Evidence for rRNA 2'-O-methylation plasticity: Control of intrinsic translational capabilities of human ribosomes.
Proceedings of the National Academy of Sciences, U S A, 2017, 114(49): 12934-12939

Fabre E, Jeudy S, Santini S, Legendre M, Trauchessec M, Coute Y, Claverie JM and Abergel C
Noumeavirus replication relies on a transient remote control of the host nucleus.
Nature Communications, 2017, 8: Article number 15087

Garcia-Oliver E, Ramus C, Perot J, Arlotto M, Champleboux M, Mietton F, Battail C, Boland A, Deleuze JF, Ferro M, Coute Y and Govin J
Bdf1 bromodomains are essential for meiosis and the expression of meiotic-specific genes.
PLoS Genetics, 2017, 13(1): e1006541

Gilquin B, Jaquinod M, Louwagie M, Kieffer-Jaquinod S, Kraut A, Ferro M, Becher F and Brun V
A proteomics assay to detect eight CBRN-relevant toxins in food.
Proteomics, 2017, 17: 1-2

Gilquin B, Louwagie M, Jaquinod M, Cez A, Picard G, El Kholy L, Surin B, Garin J, Ferro M, Kofman T, Barau C, Plaisier E, Ronco P and Brun V
Multiplex and accurate quantification of acute kidney injury biomarker candidates in urine using Protein Standard Absolute Quantification (PSAQ) and targeted proteomics.
Talanta, 2017, 164: 77-84

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 and Curien G
ChloroKB: A Web application for the integration of knowledge related to chloroplast metabolic network.
Plant Physiology, 2017, 174(2): 922-934

Maes P, Donadio-Andréi S, Louwagie M, Couté Y, Picard G, Lacoste C, Bruley C, Garin J, Ichai P, Faivre J, Jaquinod M and Brun V
Introducing plasma/serum glycodepletion for the targeted proteomics analysis of cytolysis biomarkers.
Talanta, 2017, 170: 473-480

Mietton F, Ferri E, Champleboux M, Zala N, Maubon D, Zhou Y, Harbut M, Spittler D, Garnaud C, Courçon M, Chauvel M, D'Enfert C, Kashemirov BA, Hull M, Cornet M, McKenna CE, Govin J and Petosa C
Selective BET bromodomain inhibition as an antifungal therapeutic strategy.
Nature Communications, 2017, 8: Article number 15482

Sage E, Sansa M, Fostner S, Defoort M, Gely M, Naik AK, Morel R, Duraffourg L, Roukes ML, Alava T, Jourdan G, Colinet E, Masselon C, Brenac A and Hentz S
Single-particle mass spectrometry with arrays of frequency-addressed nanomechanical resonators.
Nature Communications, 2018, 9(1): Article number 3283

Sindikubwabo F, Ding S, Hussain T, Ortet P, Barakat M, Baumgarten S, Cannella D, Palencia A, Bougdour A, Belmudes L, Coute Y, Tardieux I, Botte CY, Scherf A and Hakimi MA
Modifications at K31 on the lateral surface of histone H4 contribute to genome structure and expression in apicomplexan parasites.
eLife, 2017, 6: Article number e29391

Sonntag E, Milbradt J, Svrlanska A, Strojan H, Häge S, Kraut A, Hesse AM, Amin B, Sonnewald U, Couté Y and Marschall M
Protein kinases responsible for the phosphorylation of the nuclear egress core complex of human cytomegalovirus.
Journal of General Virology, 2017, 98(10): 2569-2581

Sorigue D, Legeret B, Cuine S, Blangy S, Moulin S, Billon E, Richaud P, Brugiere S, Couté Y, Nurizzo D, Muller P, Brettel K, Pignol D, Arnoux P, Li-Beisson Y, Peltier G and Beisson F
An algal photoenzyme converts fatty acids to hydrocarbons.
Science, 2017, 357(6354): 903-907

Tarasova IA, Masselon CD, Gorshkov AV and Gorshkov MV
Correction: Predictive chromatography of peptides and proteins as a complementary tool for proteomics (Analyst, 2016, 141: 4816, 2016).
Analyst, 2017, 142(11): 2054-2054

Tarasova IA, Masselon CD, Gorshkov AV and Gorshkov MV
Reply to 'Comparison of peptide retention prediction algorithm in reversed-phase chromatography. Comment on "Predictive chromatography of peptides and proteins as a complementary tool for proteomics"', by O. V. Krokhin, Analyst, 2017, 142, DOI: 10.1039/ c6an02510b.
Analyst, 2017, 142(11): 2052-2053

Van Lis R, Popek M, Couté Y, Kosta A, Drapier D, Nitschke W and Atteia A
Concerted up-regulation of aldehyde/alcohol dehydrogenase (ADHE) and starch in Chlamydomonas reinhardtii increases survival under dark anoxia.
Journal of Biological Chemistry, 2017, 292(6): 2395-2410

Vizcaino JA, Walzer M, Jimenez RC, Bittremieux W, Bouyssie D, Carapito C, Corrales F, Ferro M, Heck AJR, Horvatovich P, Hubalek M, Lane L, Laukens K, Levander F, Lisacek F, Novak P, Palmblad M, Piovesan D, Puhler A, Schwammle V, Valkenborg D, van Rijswijk M, Vondrasek J, Eisenacher M, Martens L and Kohlbacher O
A community proposal to integrate proteomics activities in ELIXIR.
F1000Research, 2017, 6(875)

Wieczorek S, Combes F, Lazar C, Giai Gianetto Q, Gatto L, Dorffer A, Hesse AM, Coute Y, Ferro M, Bruley C and Burger T
DAPAR & ProStaR: Software to perform statistical analyses in quantitative discovery proteomics.
Bioinformatics, 2017, 33(1): 135-136


2016 

Burger T
Geometric views on conflicting mass functions: From distances to angles.
International Journal of Approximate Reasoning, 2016, 70: 36-50

Cerveau D, Kraut A, Stotz HU, Mueller MJ, Couté Y and Rey P
Characterization of the Arabidopsis thaliana 2-Cys peroxiredoxin interactome.
Plant Science, 2016, 252: 30-41

Dell'Aglio E, Salvi D, Kraut A, Baudet M, Macherel D, Neveu M, Ferro M, Curien G and Rolland N
No plastidial Calmodulin-like proteins detected by two targeted mass-spectrometry approaches and GFP fusion proteins.
New Negatives in Plant Science, 2016, 3: 19–26

Deutsch EW, Overall CM, Van Eyk JE, Baker MS, Paik YK, Weintraub ST, Lane L, Martens L, Vandenbrouck Y, Kusebauch U, Hancock WS, Hermjakob H, Aebersold R, Moritz RL and Omenn GS
Human proteome project mass spectrometry data interpretation guidelines 2.1.
Journal of Proteome Research, 2016, 15(11): 3961-3970

Duek P, Bairoch A, Gateau A, Vandenbrouck Y and Lane L
Missing protein landscape of human chromosomes 2 and 14: Progress and current status.
Journal of Proteome Research, 2016, 15(11): 3971-3978

Farina F, Gaillard J, Guérin C, Couté Y, Sillibourne J, Blanchoin L and Théry M The centrosome is an actin-organizing centre. Nature Cell Biology, 2016, 18(1): 65-75

Garnaud C, Champleboux M, Maubon D, Cornet M and Govin J
Histone deacetylases and their Inhibition in Candida species.
Frontiers in Microbiology, 2016, 7: Article number 1238

Gay G, Braun L, Brenier-Pinchart MP, Vollaire J, Josserand V, Bertini RL, Varesano A, Touquet B, De Bock PJ, Coute Y, Tardieux I, Bougdour A and Hakimi MA
Toxoplasma gondii TgIST co-opts host chromatin repressors dampening STAT1-dependent gene regulation and IFN-γ-mediated host defenses.
Journal of Experimental Medecine, 2016, 213(9): 1779-1798

Gay O, Gilquin B, Assard N, Stuelsatz P, Delphin C, Lachuer J, Gidrol X and Baudier J
Refilins are short-lived Actin-bundling proteins that regulate lamellipodium protrusion dynamics.
Biology Open, 2016, 5(10): 1351-1361

Giai Gianetto Q, Combes F, Ramus C, Bruley C, Couté Y and Burger T
Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments.
Proteomics, 2016, 16(1): 29-32

Giai Gianetto Q, Couté Y, Bruley C and Burger T
Uses and misuses of the fudge factor in quantitative discovery proteomics.
Proteomics, 2016, 16(14): 1955-1960

Gilquin B, Louwagie M, Jaquinod M, Cez A, Picard G, El Kholy L, Surin B, Garin J, Ferro M, Kofman T, Barau C, Plaisier E, Ronco P and Brun V
Multiplex and accurate quantification of acute kidney injury biomarker candidates in urine using Protein Standard Absolute Quantification (PSAQ) and targeted proteomics.
Talanta, 2016, 164: 77-84

Goold HD, Cuiné S, Légeret B, Liang Y, Brugière S, Auroy P, Javot H, Tardif M, Jones B, Beisson F, Peltier G and Li-Beisson Y
Saturating light induces sustained accumulation of oil in plastidal lipid droplets in Chlamydomonas reinhardtii.
Plant Physiology, 2016, 171(4): 2406-2417

Hesse AM, Dupierris V, Adam C, Court M, Barthe D, Emadali A, Masselon C, Ferro M and Bruley C
hEIDI: An intuitive application tool to organize and treat large-scale proteomics data.
Journal of Proteome Research, 2016, 15(10): 3896-3903

Hodille E, Alekseeva L, Berkova N, Serrier A, Badiou C, Gilquin B, Brun V, Vandenesch F, Terman DS and Lina G
Staphylococcal enterotoxin O exhibits cell cycle modulating activity.
Frontiers in Microbiology, 2016, 7: 441

Lazar C, Gatto L, Ferro M, Bruley C and Burger T
Accounting for the multiple natures of missing values in label-free quantitative proteomics data sets to compare imputation strategies.
Journal of Proteome Research, 2016, 15(4): 1116-1125

Lee H, Mun DG, So JE, Bae J, Kim H, Masselon C and Lee SW
Efficient exploitation of separation space in two-dimensional liquid chromatography system for comprehensive and efficient proteomic analyses.
Analytical Chemistry, 2016, 88(23): 11734-11741

Ma S, Martin-Laffon J, Mininno M, Gigarel O, Brugiere S, Bastien O, Tardif M, Ravanel S and Alban C
Molecular evolution of the substrate specificity of chloroplastic aldolases/rubisco lysine methyltransferases in plants.
Molecular Plant, 2016, 9(4): 569-581

Michaud M, Gros V, Tardif M, Brugière S, Ferro M, Prinz W, Toulmay A, Mathur J, Wozny M, Falconet D, Maréchal E, Block M and Jouhet J
AtMic60 is involved in plant mitochondria lipid trafficking and is part of a large complex.
Current Biology, 2016, 26(5): 627-639

Monkkonen L, Edgar JS, Winters D, Heron SR, Mackay CL, Masselon CD, Stokes AA, Langridge-Smith PRR and Goodlett DR
Screen-printed digital microfluidics combined with surface acoustic wave nebulization for hydrogen-deuterium exchange measurements.
Journal of Chromatography A, 2016, 1439: 161-166

Osseni A, Sebastien M, Sarrault O, Baudet M, Coute Y, Faure J, Fourest-Lieuvin A and Marty I
Triadin and CLIMP-63 form a link between triads and microtubules in muscle cells.
Journal of Cell Science, 2016, 129(20): 3744-3755

Pinaud S, Portela J, Duval D, Nowacki FC, Olive MA, Allienne JF, Galinier R, Dheilly NM, Kieffer-Jaquinod S, Mitta G, Theron A and Gourbal B
A shift from cellular to humoral responses contributes to innate immune memory in the vector snail Biomphalaria glabrata.
PLoS Pathogens, 2016, 12(1): e1005361

Ramus C, Hovasse A, Marcellin M, Hesse A-M, 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 and Gonzalez de Peredo A
Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods.
Data in Brief, 2016, 6: 286-294

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 and Gonzalez de Peredo A
Benchmarking quantitative label-free LC-MS data processing workflows using a complex spiked proteomic standard dataset.
Journal of Proteomics, 2016, 132: 51-62

Sabra A, Leiba J, Mas L, Louwagie M, Couté Y, Journet A, Cosson P and Aubry L
Pycnosomes: Condensed endosomal structures secreted by dictyostelium amoebae.
PLoS One, 2016, 11(5): e0154875

Salvetti A, Couté Y, Epstein A, Arata L, Kraut A, Navratil V, Bouvet P and Greco A
Nuclear functions of nucleolin through global proteomics and interactomic approaches.
Journal of Proteome Research, 2016, 15(5): 1659-1669

Steingruber M, Kraut A, Socher E, Sticht H, Reichel A, Stamminger T, Amin B, Couté Y, Hutterer C and Marschall M
Proteomic interaction patterns between human cyclins, the cyclin-dependent kinase ortholog pUL97 and additional cytomegalovirus proteins.
Viruses, 2016, 8(8): Article number 219

Tarasova IA, Masselon CD, Gorshkov AV and Gorshkov MV
Predictive chromatography of peptides and proteins as a complementary tool for proteomics.
Analyst, 2016, 141(16): 4816-4832

Vandenbrouck Y, Lane L, Carapito C, Duek P, Rondel K, Bruley C, Macron C, Gonzalez de Peredo A, Coute Y, Chaoui K, Com E, Gateau A, Hesse AM, Marcellin M, Mear L, Mouton-Barbosa E, Robin T, Burlet-Schiltz O, Cianferani S, Ferro M, Freour T, Lindskog C, Garin J and Pineau C
Looking for missing proteins in the proteome of human spermatozoa: An update.
Journal of Proteome Research, 2016, 15(11): 3998-4019

Wagner R, von Sydow L, Aigner H, Netotea S, Brugiere S, Sjogren L, Ferro M, Clarke A and Funk C
Deletion of FtsH11 protease has impact on chloroplast structure and function in Arabidopsis thaliana when grown under continuous light.
Plant Cell and Environment, 2016, 39(11): 2530-2544

Zatylny-Gaudin C, Cornet V, Leduc A, Zanuttini B, Corre E, Le Corguillé G, Bernay B, Garderes J, Kraut A, Couté Y and Henry J
Neuropeptidome of the cephalopod Sepia officinalis: Identification, tissue mapping, and expression pattern of neuropeptides and neurohormones during egg laying.
Journal of Proteome Research, 2016, 15(1): 48-67


2015 

Carapito C, Lane L, Benama M, Opsomer A, Mouton-Barbosa E, Garrigues L, Gonzalez de Peredo A, Burel A, Bruley C, Gateau A, Bouyssie D, Jaquinod M, Cianferani S, Burlet-Schiltz O, Van Dorsselaer A, Garin J and Vandenbrouck Y
Computational and mass spectrometry-based workflow for the discovery and validation of missing human proteins: Application to chromosomes 2 and 14.
Journal of Proteome Research, 2015, 14(9): 3621-3634

Champleboux M and Govin J
Bromodomains shake the hegemony of pan-acetyl antibodies.
Proteomics, 2015, 15(9): 1457-1458

Chassefeyre R, Martinez-Hernandez J, Bertaso F, Bouquier N, Blot B, Laporte M, Fraboulet S, Couté Y, Devoy A, Isaacs AM, Pernet-Gallay K, Sadoul R, Fagni L and Goldberg Y
Regulation of postsynaptic function by the dementia-related ESCRT-III subunit CHMP2B.
Journal of Neuroscience, 2015, 35(7): 3155-3173

Couderc C, Bollard J, Coute Y, Massoma P, Poncet G, Lepinasse F, Hervieu V, Gadot N, Sanchez JC, Scoazec JY, Diaz JJ and Roche C
Mechanisms of local invasion in enteroendocrine tumors: Identification of novel candidate cytoskeleton-associated proteins in an experimental mouse model by a proteomic approach and validation in human tumors.
Molecular and Cellular Endocrinology, 2015, 399: 154-163

Court M, Garin J and Masselon CD Urine sample preparation and fractionation for global proteome profiling by LC-MS. Methods in Molecular Biology, 2015, 1243: 175-186

Dupre M, Gilquin B, Fenaille F, Feraudet-Tarisse C, Dano J, Ferro M, Simon S, Junot C, Brun V and Becher F
Multiplex quantification of protein toxins in human biofluids and food matrices using immunoextraction and high-resolution targeted mass spectrometry.
Analytical Chemistry, 2015, 87(16): 8473-8480

Hu J, Donahue G, Dorsey J, Govin J, Yuan Z, Garcia BA, Shah PP and Berger SL
H4K44 acetylation facilitates chromatin accessibility during meiosis.
Cell Reports, 2015, 13(9): 1772-1780

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 and Claverie JM
In-depth study of Mollivirus sibericum, a new 30,000-yold giant virus infecting Acanthamoeba.
Proceedings of the National Academy of Sciences of the USA, 2015, 112(38): E5327-E5335

Kessentini Y, Burger T and Paquet T
A Dempster-Shafer Theory based combination of handwriting recognition systems with multiple rejection strategies.
Pattern Recognition, 2015, 48(2): 534-544

Lebert D, Louwagie M, Goetze S, Picard G, Ossola R, Duquesne C, Basler K, Ferro M, Rinner O, Aebersold R, Garin J, Mouz N, Brunner E and Brun V
DIGESTIF: A universal quality standard for the control of bottom-up proteomics experiments.
Journal of Proteome Research, 2015, 14(2): 787-803

Lebert D, Picard G, Beau-Larvor C, Troncy L, Lacheny C, Maynadier B, Low W, Mouz N, Brun V, Klinguer-Hamour C, Jaquinod M and Beck A
Absolute and multiplex quantification of antibodies in serum using PSAQ™ standards and LC-MS/MS.
Bioanalysis, 2015, 7(10): 1237-1251

Le Roux C, Huet G, Jauneau A, Camborde L, Trémousaygue D, Kraut A, Zhou B, Levaillant M, Adachi H, Yoshioka H, Raffaele S, Berthomé R, Couté Y, Parker JE and Deslandes L
A receptor pair with an integrated decoy converts pathogen disabling of transcription factors to immunity.
Cell, 2015, 161(5): 1074-1088

Mazzoleni M, Figuet S, Martin-Laffon J, Mininno M, Gilgen A, Leroux M, Brugiere S, Tardif M, Alban C and Ravanel S
Dual-targeting of the protein methyltransferase PrmA contributes to both chloroplastic and mitochondrial ribosomal protein L11 methylation in Arabidopsis.
Plant & Cell Physiology, 2015, 56(9): 1697-1710

Mladenov P, Finazzi G, Bligny R, Moyankova D, Zasheva D, Boisson AM, Brugière S, Krasteva V, Alipieva K, Simova S, Tchorbadjieva M, Goltsev V, Ferro M, Rolland N and Djilianov D
In vivo spectroscopy and NMR metabolite fingerprinting approaches to connect the dynamics of photosynthetic and metabolic phenotypes in resurrection plant Haberlea rhodopensis during desiccation and recovery.
Frontiers Plant Science, 2015, 6: 564

Penzo M, Rocchi L, Brugiere S, Carnicelli D, Onofrillo C, Couté Y, Brigotti M and Montanaro L
Human ribosomes from cells with reduced dyskerin levels are intrinsically altered in translation.
FASEB Journal, 2015, 29(8): 3472-3482

Pichon F, Destercke S and Burger T
A consistency-specificity trade-off to select source behavior in information fusion.
Ieee Transactions on Cybernetics, 2015, 45(4): 598-609

Reichmann D, Couté Y and Ollagnier De Choudens S
Dual activity of quinolinate synthase: Triose phosphate isomerase and dehydration activities play together to form quinolinate.
Biochemistry, 2015, 54(42): 6443-6446

Sage E, Brenac A, Alava T, Morel R, Dupre C, Hanay MS, Roukes ML, Duraffourg L, Masselon C and Hentz S
Neutral particle mass spectrometry with nanomechanical systems.
Nature Communications, 2015, 6: 6482

Vanhove AS, Duperthuy M, Charriere GM, Le Roux F, Goudenege D, Gourbal B, Kieffer-Jaquinod S, Couté Y, Wai SN and Destoumieux-Garzon D
Outer membrane vesicles are vehicles for the delivery of Vibrio tasmaniensis virulence factors to oyster immune cells.
Environmental Microbiology, 2015, 17(4): 1152-1165

Vilmont V, Filhol O, Hesse AM, Couté Y, Hue C, Rémy-Tourneur L, Mistou S, Cochet C and Chiocchia G
Modulatory role of the anti-apoptotic protein kinase CK2 in the sub-cellular localization of Fas associated death domain protein (FADD).
Biochimica and Biophysica Acta, 2015, 1853(11 Pt A): 2885-2896


2014 

Alban C, Tardif M, Mininno M, Brugière S, Gilgen A, Ma S, Mazzoleni M, Gigarel O, Martin-Laffon J, Ferro M and Ravanel S
Uncovering the protein lysine and arginine methylation network in Arabidopsis chloroplasts.
PLoS One, 2014, 9(4): e95512

Biard D, Filhol O and Vandenbrouck Y Tame the expression of the genes with DSIR. Biofutur, 2014, (360): 52-55

Bounab Y, Hesse AM, Iannascoli B, Grieco L, Couté Y, Niarakis A, Roncagalli R, Lie E, Lam KP, Demangel C, Thieffry D, Garin J, Malissen B and Daëron M
Proteomic analysis of the SH2 domain-containing leukocyte protein of 76 kDa (SLP76) interactome in resting and activated primary mast cells.
Molecular and Cellular Proteomics, 2014, 13(2): 678

Chapel L, Burger T, Courty N and Lefevre S
PerTurbo manifold learning algorithm for weakly labeled hyperspectral image classification.
Ieee Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 2014, 7(4): 1070-1078

Chapman JD, Goodlett DR and Masselon CD
Multiplexed and data-independent tandem mass spectrometry for global proteome profiling.
Mass Spectrometry Reviews, 2014, 33(5): 452-470

Couderc C, Bollard J, Coute Y, Massoma P, Poncet G, Lepinasse F, Hervieu V, Gadot N, Sanchez JC, Scoazec JY, Diaz JJ and Roche C
Mechanisms of local invasion in enteroendocrine tumors: Identification of novel candidate cytoskeleton-associated proteins in an experimental mouse model by a proteomic approach and validation in human tumors.
Molecular and Cellular Endocrinology, 2014

Doustaly F, Combes F, Fiévet JB, Berthet S, Hugouvieux V, Bastien O, Aranjuelo I, Leonhardt N, Rivasseau C, Carrière M, Vavasseur A, Renou JP, Vandenbrouck Y and Bourguignon J
Uranium perturbs signaling and iron uptake response in Arabidopsis thaliana roots.
Metallomics, 2014, 6: 809-821

Elsen S, Huber P, Bouillot S, Couté Y, Fournier P, Dubois Y, Timsit JF, Maurin M and Attrée I
A Type III Secretion negative clinical strain of Pseudomonas aeruginosa employs a two-partner secreted Exolysin to induce hemorrhagic pneumonia.
Cell Host & Microbe, 2014, 15(2): 164-176

Engel E, Viargues P, Mortier M, Taillebourg E, Couté Y, Thevenon D and Fauvarque MO
Identifying USPs regulating immune signals in Drosophila: USP2 deubiquitinates Imd and promotes its degradation by interacting with the proteasome.
Cell Communication and Signaling, 2014, 12(1): 41

Estellon J, Ollagnier de Choudens S, Smadja M, Fontecave M and Vandenbrouck Y
An integrative computational model for large-scale identification of metalloproteins in microbial genomes: A focus on iron-sulfur cluster proteins.
Metallomics, 2014, 6(10): 1913-1930

Forterre A, Jalabert A, Berger E, Baudet M, Chikh K, Errazuriz E, De Larichaudy J, Chanon S, Weiss-Gayet M, Hesse AM, Record M, Geloen A, Lefai E, Vidal H, Couté Y and Rome S
Proteomic analysis of C2C12 myoblast and myotube exosome-like vesicles: A new paradigm for myoblast-myotube cross talk?
PLoS One, 2014, 9(1): e84153
Correction

Gatto L, Breckels LM, Burger T, Nightingale DJ, Groen AJ, Campbell C, Nikolovski N, Mulvey CM, Christoforou A, Ferro M and Lilley KS
A foundation for reliable spatial proteomics data analysis.
Molecular & Cellular Proteomics, 2014, 13(8): 1937-1952

Gatto L, Breckels LM, Wieczorek S, Burger T and Lilley KS
Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata.
Bioinformatics, 2014, 30(9): 1322-1324

Graindorge M, Giustini C, Kraut A, Moyet L, Curien G and Matringe M
Three different classes of aminotransferases evolved prephenate aminotransferase functionality in arogenate-competent microorganisms.
Journal of Biological Chemistry, 2014, 289(6): 3198-3208

Hardré H, Kuhn L, Albrieux C, Jouhet J, Michaud M, Seigneurin-Berny D, Falconet D, Block MA and Maréchal E
The selective biotin tagging and thermolysin proteolysis of chloroplast outer envelope proteins reveals information on protein topology and association into complexes.
Frontiers in Plant Science, 2014, 5: 203

Kessentini Y, Burger T and Paquet T
A Dempster–Shafer Theory based combination of handwriting recognition systems with multiple rejection strategies.
Pattern Recognition, 2014, 48(2): 534–544

Lafaye C, Barbier E, Miscioscia A, Saint-Pierre C, Kraut A, Couté Y, Plo I, Gasparutto D, Ravanat J-L and Breton J
DNA binding of the p21 repressor ZBTB2 is inhibited by cytosine hydroxymethylation.
Biochemical and Biophysical Research Communications, 2014, 446(1): 341-346

Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, Lescot M, Poirot O, Bertaux L, Bruley C, Coute Y, Rivkina E, Abergel C and Claverie JM
Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology.
Proceedings of the National Academy of Sciences USA, 2014, 111(11): 4274-4279

Legres LG, Janin A, Masselon C and Bertheau P
Beyond laser microdissection technology: Follow the yellow brick road for cancer research.
American Journal of Cancer Research, 2014, 4(1): 1-28

Milbradt J, Kraut A, Hutterer C, Sonntag E, Schmeiser C, Ferro M, Wagner S, Lenac T, Claus C, Pinkert S, Hamilton ST, Rawlinson WD, Sticht H, Coute Y and Marschall M
Proteomic analysis of the multimeric nuclear egress complex of human cytomegalovirus.
Molecular & Cellular Proteomics, 2014, 13(8): 2132-2146

Nguyen-Lefebvre AT, Leprun G, Morin V, Vinuelas J, Coute Y, Madjar JJ, Gandrillon O and Gonin-Giraud S
V-erbA generates ribosomes devoid of RPL11 and regulates translational activity in avian erythroid progenitors.
Oncogene, 2014, 33(12): 1581-1589

Niarakis A, Bounab Y, Grieco L, Roncagalli R, Hesse AM, Garin J, Malissen B, Daeron M and Thieffry D
Computational modeling of the main signaling pathways involved in mast cell activation In FC Receptors, Edited by Daeron M and Nimmerjahn F, Springer-Verlag Berlin, Current Topics in Microbiology and Immunology, 2014, 382: 69-93

Pasa-Tolié L and Masselon C
Shining a spotlight on intact proteins.
Proteomics, 2014, 14(10): 1125-1127

van Rooyen JM, Murat JB, Hammoudi PM, Kieffer-Jaquinod S, Coute Y, Sharma A, Pelloux H, Belrhali H and Hakimi MA
Assembly of the novel five-component apicomplexan multi-aminoacyl-tRNA synthetase complex is driven by the hybrid scaffold protein Tg-p43.
PLoS One, 2014, 9(2): e89487

Schild F, Kieffer-Jaquinod S, Palencia A, Cobessi D, Sarret G, Zubieta C, Jourdain A, Dumas R, Forge V, Testemale D, Bourguignon J and Hugouvieux V
Biochemical and biophysical characterization of the Selenium binding and reducing site in Arabidopsis thaliana homologue to mammals Selenium Binding Protein 1.
Journal of Biological Chemistry, 2014, 289(46): 31765-31776

Schvartz D, Coute Y and Sanchez JC
Quantitative proteomics reveals the link between minichromosome maintenance complex and glucose-induced proliferation of rat pancreatic INS-1E ß-cells.
Journal of Proteomics, 2014, 108: 163-170

Tomizioli M, Lazar C, Brugiere S, Burger T, Salvi D, Gatto L, Moyet L, Breckels LM, Hesse AM, Lilley KS, Seigneurin-Berny D, Finazzi G, Rolland N and Ferro M
Deciphering thylakoid sub-compartments using a mass spectrometry-based approach.
Molecular and Cellular Proteomics, 2014, 13(8): 2147-2167

Trauchessec M, Jaquinod M, Bonvalot A, Brun V, Bruley C, Ropers D, de Jong H, Garin J, Bestel-Corre G and Ferro M
Mass spectrometry-based workflow for accurate quantification of Escherichia coli enzymes: How proteomics can play a key role in metabolic engineering.
Molecular & Cellular Proteomics, 2014, 13(4): 954-968

Xiol J, Spinelli P, Laussmann MA, Homolka D, Yang Z, Cora E, Coute Y, Conn S, Kadlec J, Sachidanandam R, Kaksonen M, Cusack S, Ephrussi A and Pillai RS
RNA clamping by vasa assembles a piRNA amplifier complex on transposon transcripts.
Cell, 2014, 157(7): 1698-1711


2013 

Bougdour A, Durandau E, Brenier-Pinchart MP, Ortet P, Barakat M, Kieffer S, Curt-Varesano A, Curt-Bertini RL, Bastien O, Coute Y, Pelloux H and Hakimi MA
Host cell subversion by Toxoplasma GRA16, an exported dense granule protein that targets the host cell nucleus and alters gene expression.
Cell Host & Microbe, 2013, 13(4): 489-500

Bounab Y, Hesse AM, Iannascoli B, Grieco L, Coute Y, Niarakis A, Roncagalli R, Lie E, Lam KP, Demangel C, Thieffry D, Garin J, Malissen B and Daeron M
Proteomic analysis of the SLP76 interactome in resting and activated primary mast cells.
Molecular and Cellular Proteomics, 2013, 12(10): 2874-2889

Braun L, Brenier-Pinchart MP, Yogavel M, Curt-Varesano A, Curt-Bertini RL, Hussain T, Kieffer-Jaquinod S, Coute Y, Pelloux H, Tardieux I, Sharma A, Belrhali H, Bougdour A and Hakimi MA
A Toxoplasma dense granule protein, GRA24, modulates the early immune response to infection by promoting a direct and sustained host p38 MAPK activation.
Journal of Experimental Medicine, 2013, 210(10): 2071-2086

Burger T and Destercke S
How to randomly generate mass functions.
International Journal of Uncertainty Fuzziness and Knowledge-Based Systems, 2013, 21(5): 645-673

Casabona MG, Silverman JM, Sall KM, Boyer F, Coute Y, Poirel J, Grunwald D, Mougous JD, Elsen S and Attree I
An ABC transporter and an outer membrane lipoprotein participate in posttranslational activation of type VI secretion in Pseudomonas aeruginosa.
Environmental Microbiology, 2013, 15(2): 471-486

Casabona MG, Vandenbrouck Y, Attree I and Coute Y
Proteomic characterization of Pseudomonas aeruginosa PAO1 inner membrane.
Proteomics, 2013, 13(16): 2419-2423

Chapel A, Kieffer-Jaquinod S, Sagne C, Verdon Q, Ivaldi C, Mellal M, Thirion J, Jadot M, Bruley C, Garin J, Gasnier B and Journet A
An extended proteome map of the lysosomal membrane reveals novel potential transporters.
Molecular & Cellular Proteomics, 2013, 12(6): 1572-1588

Courty N and Burger T
A kernel view on manifold sub-sampling based on Karcher variance optimization.
Accepted to Geometric Sciences of Information (GSI 2013), LNCS 8085, pp. 751-758, Paris, France, July 2013

Dell'aglio E, Giustini C, Salvi D, Brugiere S, Delpierre F, Moyet L, Baudet M, Seigneurin-Berny D, Matringe M, Ferro M, Rolland N and Curien G
Complementary biochemical approaches applied to the identification of plastidial calmodulin-binding proteins.
Molecular BioSystems, 2013, 9(6): 1234-1248

Deshiere A, Duchemin-Pelletier E, Spreux E, Ciais D, Combes F, Vandenbrouck Y, Couté Y, Mikaelian I, Giusiano S, Charpin C, Cochet C and Filhol O
Unbalanced expression of CK2 kinase subunits is sufficient to drive epithelial-to-mesenchymal transition by Snail1 induction.
Oncogene, 2013, 32: 1373-1383

Destercke S and Burger T
Toward an axiomatic definition of conflict between belief functions.
IEEE Transactions on Cybernetics, 2013, 43(2): 585-596

Duan C, Adam V, Byrdin M, Ridard J, Kieffer-Jaquinod S, Morlot C, Arcizet D, Demachy I and Bourgeois D
Structural evidence for a two-regime photobleaching mechanism in a reversibly switchable fluorescent protein.
Journal of the American Chemical Society, 2013, 135(42): 15841-15850

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 and Khochbin S
Identification of a novel BET bromodomain inhibitor-sensitive, gene regulatory circuit that controls Rituximab response and tumour growth in aggressive lymphoid cancers.
EMBO Molecular Medicine, 2013, 5(8): 1180-1195

Forouhar F, Arragain S, Atta M, Gambarelli S, Mouesca JM, Hussain M, Xiao R, Kieffer-Jaquinod S, Seetharaman J, Acton TB, Montelione GT, Mulliez E, Hunt JF and Fontecave M
Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases.
Nature Chemical Biology, 2013, 9(5): 333-338

Govin J and Khochbin S
Histone variants and sensing of chromatin functional states.
Nucleus, 2013, 4(6)

Habif G, Grasset MF, Kieffer-Jaquinod S, Kuhn L, Mouchiroud G and Gobert-Gosse S
Phosphoproteome analyses reveal specific implications of Hcls1, p21-activated kinase 1 and Ezrin in proliferation of a myeloid progenitor cell line downstream of wild-type and ITD mutant Fms-like tyrosine kinase 3 receptors.
Journal of Proteomics, 2013, 78: 231-244

Hajj Chehade M, Loiseau L, Lombard M, Pecqueur L, Ismail A, Smadja M, Golinelli-Pimpaneau B, Mellot-Draznieks C, Hamelin O, Aussel L, Kieffer-Jaquinod S, Labessan N, Barras F, Fontecave M and Pierrel F
ubiI, a new gene in Escherichia coli Coenzyme Q biosynthesis, is involved in aerobic C5-hydroxylation.
Journal of Biological Chemistry, 2013, 288(27): 20085-20092

van Lis R, Baffert C, Coute Y, Nitschke W and Atteia A
Chlamydomonas reinhardtii chloroplasts contain a homodimeric pyruvate: Ferredoxin oxidoreductase that functions with FDX1.
Plant Physiology, 2013, 161(1): 57-71

Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C, Garin J, Claverie JM and Abergel C
Pandoraviruses: Amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes.
Science, 2013, 341(6143): 281-286

Pichon F, Destercke S and Burger T
Selecting source behavior in information fusion on the basis of consistency and specificity.
The Twelfth European Conference on Symbolic and Quantitative Approaches to Reasoning with Uncertainty (ECSQARU 2013), LNAI 7958, pp. 473–484, Utrecht, The Netherlands, July 2013

Robert-Genthon M, Casabona MG, Neves D, Couté Y, Cicéron F, Elsen S, Dessen A and Attrée I
Unique features of a Pseudomonas aeruginosa α2-macroglobulin homolog.
MBio, 2013, 4(4): e00309-13

Smith LM,  Kelleher NL & The Consortium for Top Down Proteomics
Proteoform: A single term describing protein complexity.
Nature Methods, 2013, 10: 186–187

Terman DS, Serier A, Dauwalder O, Badiou C, Dutour A, Thomas D, Brun V, Bienvenu J, Etienne J, Vandenesch F and Lina G
Staphylococcal enterotoxins of the enterotoxin gene cluster (egcSEs) induce nitrous oxide- and cytokine dependent tumor cell apoptosis in a broad panel of human tumor cells.
Frontiers in Cellular and Infection Microbiology, 2013, 3: 38

Zaccaria A, Bouamrani A, Selek L, El Atifi M, Hesse AM, Ratel D, Juhem A, Mathieu H, Couté Y, Bruley C, Garin J, Benabid AL, Chabardes S, Piallat B and Berger F
A micro silicon chip for in vivo cerebral imprint in monkey. 
ACS Chemical Neuroscience, 2013, 4(3): 385-392


2012 

Adrait A, Lebert D, Trauchessec M, Dupuis A, Louwagie M, Masselon C, Jaquinod M, Chevalier B, Vandenesch F, Garin J, Bruley C and Brun V
Development of a protein standard absolute quantification (PSAQ™) assay for the quantification of Staphylococcus aureus enterotoxin A in serum.
Journal of Proteomics, 2012, 75(10): 3041-3049

Bruley C, Dupierris V, Salvi D, Rolland N and Ferro M
AT_CHLORO - A chloroplast database dedicated to sub-plastidial localization.
Frontiers in Plant Science, 2012, 3: 205

Burger T and Destercke S
Random generation of mass functions: A short howto In Belief Functions: Theory and Applications, édité par Denoeux T and Masson MH. Advances in Intelligent and Soft Computing, 2012, vol.164, pp 145-152

Destercke S and Burger T
Revisiting the notion of conflicting belief functions In Belief Functions: Theory and Applications, édité par Denoeux T and Masson MH. Advances in Intelligent and Soft Computing, 2012, vol.164, pp 153-160

Filhol O, Ciais D, Lajaunie C, Charbonnier P, Foveau N, Vert JP and Vandenbrouck Y
DSIR: Assessing the design of highly potent siRNA by testing a set of cancer-relevant target genes.
PLoS One, 2012, 7(10): e48057

Forestier A, Sarrazy F, Caillat S, Vandenbrouck Y and Sauvaigo S
Functional DNA repair signature of cancer cell lines exposed to a set of cytotoxic anticancer drugs using a multiplexed enzymatic repair assay on biochip.
PLoS One, 2012, 7(12): e51754

Govin J, Gaucher J, Ferro M, Debernardi A, Garin J, Khochbin S and Rousseaux S
Proteomic strategy for the identification of critical actors in reorganization of the post-meiotic male genome.
Molecular Human Reproduction, 2012, 18(1): 1-13

Greco A, Arata L, Soler E, Gaume X, Couté Y, Hacot S, Callé A, Monier K, Epstein AL, Sanchez JC, Bouvet P and Diaz JJ
Nucleolin interacts with US11 protein of herpes simplex virus 1 and is involved in its trafficking.
Journal of Virology, 2012, 86(3): 1449-1457

Huang Y, Yoon SH, Heron SR, Masselon CD, Edgar JS, Turecek F and Goodlett DR
Surface acoustic wave nebulization produces ions with lower internal energy than electrospray ionization.
Journal of the American Society for Mass Spectrometry, 2012, 23(6): 1062-1070

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 and Brun V
Accurate quantification of cardiovascular biomarkers in serum using protein standard absolute quantification (PSAQ™) and selected reaction monitoring.
Molecular and Cellular Proteomics, 2012, 11(2): M111.008235

Ivaldi C, Martin BR, Kieffer-Jaquinod S, Chapel A, Levade T, Garin J and Journet A
Proteomic analysis of S-acylated proteins in human B cells reveals palmitoylation of the immune regulators CD20 and CD23.
PLoS One, 2012, 7(5): e37187

Jaquinod M, Trauchessec M, Huillet C, Louwagie M, Lebert D, Picard G, Adrait A, Dupuis A, Garin J, Brun V and Bruley C
Mass spectrometry-based absolute protein quantification: PSAQ™ strategy makes use of "noncanonical" proteotypic peptides.
Proteomics, 2012, 12(8): 1217-1221

Jézégou A, Llinares E, Anne C, Kieffer-Jaquinod S, O'Regan S, Aupetit J, Chabli A, Sagné C, Debacker C, Chadefaux-Vekemans B, Journet A, André B and Gasnier B
Heptahelical protein PQLC2 is a lysosomal cationic amino acid exporter underlying the action of cysteamine in cystinosis therapy.
Proceedings of the National Academy of Sciences, 2012, 109(50): E3434-3443

Journet A, Klein G, Brugiere S, Vandenbrouck Y, Chapel A, Kieffer S, Bruley C, Masselon C and Aubry L
Investigating the macropinocytic proteome of Dictyostelium amoebae by high-resolution mass spectrometry.
Proteomics, 2012, 12(2): 241-245

Kurowska M, Goudin N, Nehme NT, Court M, Garin J, Fischer A, de Saint Basile G and Ménasché G
Terminal transport of lytic granules to the immune synapse is mediated by the kinesin-1/Slp3/Rab27a complex. 
Blood, 2012, 119(17): 3879-3889

Louwagie M, Kieffer-Jaquinod S, Dupierris V, Coute Y, Bruley C, Garin J, Dupuis A, Jaquinod M and Brun V
Introducing AAA-MS, a rapid and sensitive method for amino acid analysis using isotope dilution and high-resolution mass spectrometry.
Journal of Proteome Research, 2012, 11(7): 3929-3936

Lupo J, Conti A, Sueur C, Coly P-A, Couté Y, Hunziker W, Burmeister WP, Germi R, Manet E, Gruffat H, Morand P and Boyer V
Identification of new interacting partners of the shuttling protein ubinuclein (Ubn-1).
Experimental Cell Research, 2012, 318(5): 509-520

Merle N, Féraud O, Gilquin B, Hubstenberger A, Kieffer-Jacquinot S, Assard N, Bennaceur-Griscelli A, Honnorat J and Baudier J
ATAD3B is a human embryonic stem cell specific mitochondrial protein, re-expressed in cancer cells, that functions as dominant negative for the ubiquitous ATAD3A.
Mitochondrion, 2012, 12(4): 441-448

Mininno M, Brugiere S, Pautre V, Gilgen A, Ma S, Ferro M, Tardif M, Alban C and Ravanel S
Characterization of chloroplastic fructose 1,6-bisphosphate aldolases as lysine-methylated proteins in plants.
Journal of Biological Chemistry, 2012, 287(25): 21034-21044

Ozeir M, Xie LX, Chehade MH, Tang JY, Chen JY, Kieffer-Jaquinod S, Fontecave M, Clarke CF and Pierrel F
In vivo accumulation of coenzyme Q biosynthetic intermediates and aminated analogs in the yeast Saccharomyces cerevisiae.
Biochimica et Biophysica Acta (BBA) - Bioenergetics, 2012, 1817, Supplement: S92

Paik YK, Omenn GS, Uhlen M, Hanash S, Marko-Varga G, Aebersold R, Bairoch A, Yamamoto T, Legrain P, Lee HJ, Na K, Jeong SK, He F, Binz PA, Nishimura T, Keown P, Baker MS, Yoo JS, Garin J, Archakov A, Bergeron J, Salekdeh GH and Hancock WS
Standard guidelines for the chromosome-centric human proteome project.
Journal of Proteome Research, 2012, 11(4): 2005-2013

Picard G, Lebert D, Louwagie M, Adrait A, Huillet C, Vandenesch F, Bruley C, Garin J, Jaquinod M and Brun V
PSAQ standards for accurate MS-based quantification of proteins: From the concept to biomedical applications.
Journal of Mass Spectrometry, 2012, 47(10): 1353-1363

Schvartz D, Couté Y, Brunner Y, Wollheim CB and Sanchez JC
Modulation of neuronal pentraxin 1 expression in rat pancreatic ß-cells submitted to chronic glucotoxic stress.
Molecular and Cellular Proteomics, 2012, 11(8): 244-254

Tarasova IA, Perlova TY, Pridatchenko ML, Goloborod’ko AA, Levitsky LI, Evreinov VV, Guryca V, Masselon CD, Gorshkov AV and Gorshkov MV
Inversion of chromatographic elution orders of peptides and its importance for proteomics.
Journal of Analytical Chemistry, 2012, 67(13): 1014–1025

Tardif M, Atteia A, Specht M, Cogne G, Rolland N, Brugiere S, Hippler M, Ferro M, Bruley C, Peltier G, Vallon O and Cournac L
PredAlgo, a new subcellular localization prediction tool dedicated to green algae.
Molecular Biology and Evolution, 2012, 29(12): 3625-3639

Tarrago L, Kieffer-Jaquinod S, Lamant T, Marcellin M, Garin J, Rouhier N and Rey P
Affinity chromatography: A valuable strategy to isolate substrates of methionine sulfoxide reductases?
Antioxidants & Redox Signaling, 2012, 16: 79-84

Wade A, Thomas C, Kalmar B, Terenzio M, Garin J, Greensmith L and Schiavo G
Activated leukocyte cell adhesion molecule modulates neurotrophin signaling.
Journal of Neurochemistry, 2012, 121(4): 575-586

Xie LX, Ozeir M, Tang JY, Chen JY, Kieffer-Jaquinod S, Fontecave M, Clarke CF and Pierrel F
Over-expression of the Coq8 kinase in Saccharomyces cerevisiae coq null mutants allows for accumulation of diagnostic intermediates of the Coenzyme Q6 biosynthetic pathway.
Journal of Biological Chemistry, 2012, 287(28): 23571-23581

Yoon SH, Huang Y, Edgar JS, Ting YS, Heron SR, Kao Y, Li Y, Masselon CD, Ernst RK, Goodlett DR 
Surface acoustic wave nebulization facilitating lipid mass spectrometric analysis.
Analytical Chemistry, 2012, 84(15): 6530-6537


2011 

Agrawal GK, Bourguignon J, Rolland N, Ephritikhine G, Ferro M, Jaquinod M, Alexiou KG, Chardot T, Chakraborty N, Jolivet P, Doonan JH and Rakwal R
Plant organelle proteomics: Collaborating for optimal cell function.
Mass Spectrometry Reviews, 2011, 211(30): 772-853

Beltran S, Gourbal B, Boissier J, Duval D, Kieffer-Jaquinod S, Pierce RJ, Grunau C, Theron A and Mitta G
Vertebrate host protective immunity drives genetic diversity and antigenic polymorphism in Schistosoma mansoni.
Journal of Evolutionary Biology, 2011, 24(3): 554-572

Baklouti F, Morinière M, Haj-Khélil A, Fénéant-Thibault M, Gruffat H, Couté Y, Ninot A, Guitton C and Delaunay J
Homozygous deletion of EPB41 genuine AUG-containing exons results in mRNA splicing defects, NMD activation and protein 4.1R complete deficiency in hereditary elliptocytosis.
Blood Cells, Molecules, and Diseases, 2011, 47(3): 158-165

Bounaix Morand du Puch C, Barbier E, Kraut A, Couté Y, Fuchs J, Buhot A, Livache T, Sève M, Favier A, Douki T, Gasparutto D, Sauvaigo S and Breton J
TOX4 and its binding partners recognize DNA adducts generated by platinum anticancer drugs.
Archives of Biochemistry and Biophysics, 2011, 507(2): 296-303

Court M, Selevsek N, Matondo M, Allory Y, Garin J, Masselon CD and Domon B
Toward a standardized urine proteome analysis methodology.
Proteomics, 2011, 11(6): 1160-1171

Crozat E, Hindre T, Kuhn L, Garin J, Lenski RE and Schneider D
Altered regulation of the OmpF porin by Fis in Escherichia coli during an evolution experiment and between B and K12 strains.
Journal of Bacteriology, 2011, 193(2): 429-440

Duperthuy M, Schmitt P, Garzón E, Caro A, Rosa RD, Le Roux F, Lautrédou-Audouy N, Got P, Romestand B, de Lorgeril J, Kieffer-Jaquinod S, Bachère E and Destoumieux-Garzón D
Use of OmpU for attachment and invasion of Crassostrea gigas immune cells by the oyster pathogen Vibrio splendidus.
Proceedings of the National Academy of Sciences USA, 2011, 108: 2993-2998

Guillaumond F, Boyer B, Becquet D, Guillen S, Kuhn L, Garin J, Belghazi M, Bosler O, Franc JL and François-Bellan AM
Chromatin remodeling as a mechanism for circadian prolactin transcription: Rhythmic NONO and SFPQ recruitment to HLTF.
FASEB J, 2011, 25: 2740-2756

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 and Heazlewood JL
MASCP Gator: An aggregation portal for the visualization of Arabidopsis proteomics data.
Plant Physiology, 2011, 155(1): 259-270

Lebert D, Dupuis A, Garin J, Bruley C and Brun V
Production and use of stable isotope-labeled proteins for absolute quantitative proteomics.
Methods in Molecular Biology, 2011, 753: 93-115

Nguyen HM, Baudet M, Cuiné S, Adriano JM, Barthe D, Billon E, Bruley C, Beisson F, Peltier G, Ferro M and Li-Beisson Y
Proteomic profiling of oil bodies isolated from the unicellular green microalga Chlamydomonas reinhardtii: With focus on proteins involved in lipid metabolism.
Proteomics, 2011, 11(21): 4266-4273

Nicolas E, Ramus C, Berthier S, Arlotto M, Bouamrani A, Lefebvre C, Morel F, Garin J, Ifrah N, Berger F, Cahn JY and Mossuz P
Expression of S100A8 in leukemic cells predicts poor survival in de novo AML patients.
Leukemia, 2011, 25: 57-65

Rolland D, Bouamrani A, Houlgatte R, Barbarat A, Ramus C, Arlotto M, Ballester B, Berger F, Felman P, Callet-Bauchu E, Baseggio L, Traverse-Glehen A, Brugière S, Garin J, Coiffier B, Berger F and Thieblemont C
Identification of proteomic signatures of mantle cell lymphoma, small lymphocytic lymphoma, and marginal zone lymphoma biopsies by surface enhanced laser desorption/ionization-time of flight mass spectrometry.
Leukemia & Lymphoma, 2011, 52: 648-658

Salvi D, Moyet L, Seigneurin-Berny D, Ferro M, Joyard J and Rolland N Preparation of envelope membrane fractions from Arabidopsis chloroplasts for proteomic analysis and other studies. Methods in Molecular Biology, 2011, 775: 189-206

Villiers F, Ducruix C, Hugouvieux V, Jarno N, Ezan E, Garin J, Junot C and Bourguignon J
Investigating the plant response to cadmium exposure by proteomic and metabolomic approaches.
Proteomics, 2011, 11(9): 1650-1663

Villiers F, Hugouvieux V, Leonhardt N, Vavasseur A, Junot C, Vandenbrouck Y and Bourguignon J Exploring the plant response to cadmium exposure by transcriptomic, proteomic and metabolomic approaches. Potentiality of high-throughput methods, promises of integrated biology In Metal Toxicity in Plants: Perception, Signaling and Remediation, Edited by Gupta DK and Sandalio LM, Springer, 2011, pp. 119-142

Wang J, Emadali A, Le Bescont A, Callanan M, Rousseaux S and Khochbin S
Induced malignant genome reprogramming in somatic cells by testis-specific factors.
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2011, 1809(4-6): 221-225


2010 

Bouamrani A, Ramus C, Gay E, Pelletier L, Cubizolles M, Brugiere S, Wion D, Berger F and Issartel JP
Increased phosphorylation of vimentin in noninfiltrative meningiomas.
PLoS One, 2010, 5(2): e9238

Braun L, Cannella D, Ortet P, Barakat M, Sautel CF, Kieffer S, Garin J, Bastien O, Voinnet O and Hakimi MA A complex small RNA repertoire is generated by a plant/fungal-like machinery and effected by a metazoan-like Argonaute in the single-cell human parasite Toxoplasma gondii. PLoS Pathogens, 2010, 6(5): e1000920

Dos Santos A, Court M, Thiers V, Sar S, Guettier C, Samuel D, Brechot C, Garin J, Demaugre F and Masselon CD
Identification of cellular targets in human intrahepatic cholangiocarcinoma using laser microdissection and AMT-tag proteomics.
Molecular and Cellular Proteomics, 2010, 9(9): 1991-2004

Ferro M, Brugiere 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 and Rolland N
AT_CHLORO: A comprehensive chloroplast proteome database with subplastidiallocalization and curated information on envelope proteins.
Molecular and Cellular Proteomics, 2010, 9(1): 1063-1084

Gilquin B, Cannon BR, Hubstenberger A, Moulouel B, Falk E, Merle N, Assard N, Kieffer S, Rousseau D, Wilder PT, Weber DJ and Baudier J
The calcium-dependent interaction between S100B and the mitochondrial AAA-ATPase ATAD3A and the role of this complex in the cytoplasmic processing of ATAD3A.
Molecular and Cellular Biology, 2010, 30(11): 2724-2736

Graindorge M, Giustini C, Jacomin AC, Kraut A, Curien G and Matringe M
Identification of a plant gene encoding glutamate/aspartate-prephenate aminotransferase: The last homeless enzyme of aromatic amino acids biosynthesis.
Febs Letters, 2010, 584(20): 4357-4360

Guillaumot P, Luquain C, Malek M, Huber AL, Brugière S, Garin J, Grunwald D, Régnier D, Pétrilli V, Lefai E and Manié SN
Pdro, a protein associated with late endosomes and lysosomes and implicated in cellular cholesterol homeostasis.
PLoS One, 2010, 5(6): 1-9

Hacot S, Coute Y, Belin S, Albaret MA, Mertani HC, Sanchez JC, Rosa-Calatrava M and Diaz JJ
Isolation of nucleoli.
Current Protocols in Cell Biology, 2010, (SUPPL. 47): 3.36.31-33.36.10

Jacquot JF, Le Bail JL, Bardet M and Tabony J
Exposure of biological preparations to radiofrequency electromagnetic fields under low gravity.
Review of Scientific Instruments, 2010, 81(11): 115103

Joyard J, Ferro M, Masselon C, Seigneurin-Berny D, Salvi D, Garin J and Rolland N
Chloroplast proteomics highlights the subcellular compartmentation of lipid metabolism.
Progress in Lipid Research, 2010, 49(2): 128-158

Legrès L, Varna M, Bouhidel F, Leboeuf C, Ratajczak P, Martin N, Plassa L-F, Soliman H, Turpin E, Lehmann-Che J, de Thé H, Court M, Masselon C, Garin J, Janin A and Bertheau P
Principe et applications de la microdissection laser en histopathologie.
Revue Francophone des Laboratoires, 2010, 2010(418): 57-66

Mischak H, Allmaier G, Apweiler R, Attwood T, Baumann M, Benigni A, Bennett SE, Bischoff R, Bongcam-Rudloff E, Capasso G, Coon JJ, D'Haese P, Dominiczak AF, Dakna M, Dihazi H, Ehrich JH, Fernandez-Llama P, Fliser D, Frokiaer J, Garin J, Girolami M, Hancock WS, Haubitz M, Hochstrasser D, Holman RR, Ioannidis JP, Jankowski J, Julian BA, Klein JB, Kolch W, Luider T, Massy Z, Mattes WB, Molina F, Monsarrat B, Novak J, Peter K, Rossing P, Sanchez-Carbayo M, Schanstra JP, Semmes OJ, Spasovski G, Theodorescu D, Thongboonkerd V, Vanholder R, Veenstra TD, Weissinger E, Yamamoto T and Vlahou A
Recommendations for biomarker identification and qualification in clinical proteomics.
Science Transational Medicine, 2010, 2(46): 46ps42

Mischak H, Kolch W, Aivaliotis M, Bouyssie D, Court M, Dihazi H, Dihazi GH, Franke J, Garin J, de Peredo AG, Iphofer A, Jansch L, Lacroix C, Makridakis M, Masselon C, Metzger J, Monsarrat B, Mrug M, Norling M, Novak J, Pich A, Pitt A, Bongcam-Rudloff E, Siwy J, Suzuki H, Thongboonkerd V, Wang LS, Zoidakis J, Zurbig P, Schanstra JP and Vlahou A
Comprehensive human urine standards for comparability and standardization in clinical proteome analysis.
Proteomics Clinical Applications, 2010, 4(4): 464-478

Mone Y, Gourbal B, Duval D, Du Pasquier L, Kieffer-Jaquinod S and Mitta G
A large repertoire of parasite epitopes matched by a large repertoire of host immune receptors in an invertebrate host/parasite model.
PLoS Neglected Tropical Diseases, 2010, 4(9): e813

Nicolas A, Alazard-Dany N, Biollay C, Arata L, Jolinon N, Kuhn L, Ferro M, Weller SK, Epstein AL, Salvetti A and Greco A
Identification of rep-associated factors in Hsv-1-induced aav-2 replication compartments.
Journal of Virology, 2010, 84(17): 8871-8887

Pierrel F, Hamelin O, Douki T, Kieffer-Jaquinod S, Mühlenhoff U, Ozeir M, Lill R and Fontecave M
Involvement of mitochondrial ferredoxin and para-aminobenzoic acid in yeast coenzyme Q biosynthesis.
Chemistry & Biology, 2010, 17(5): 449-459

Tasset C, Bernoux M, Jauneau A, Pouzet C, Briere C, Kieffer-Jacquinod S, Rivas S, Marco Y and Deslandes L
Autoacetylation of the Ralstonia solanacearum effector PopP2 targets a lysine residue essential for RRS1-R-mediated immunity in Arabidopsis.
PLoS Pathogens, 2010, 6(11): e1001202


2009 

Andreoletti P, Mouesca J-M, Gouet P, Jaquinod M, Capeillère-Blandin C and Jouve HM
Verdoheme formation in Proteus mirabilis catalase.
Biochimica et Biophysica Acta (BBA) - General Subjects, 2009, 1790(8): 741-753

Atteia A, Adrait A, Brugiere S, Tardif M, van Lis R, Deusch O, Dagan T, Kuhn L, Gontero B, Martin W, Garin J, Joyard J and Rolland N
A proteomic survey of Chlamydomonas reinhardtii mitochondria sheds new light on the metabolic plasticity of the organelle and on the nature of the {alpha}-proteobacterial mitochondrial ancestor.
Molecular Biology and Evolution, 2009, 26(7): 1533-1548

Bernay B, Gaillard MC, Guryca V, Emadali A, Kuhn L, Bertrand A, Detraz I, Carcenac C, Savasta M, Brouillet E, Garin J and Elalouf JM
Discovering new bioactive neuropeptides in the striatum secretome using in vivo microdialysis and versatile proteomics.
Molecular and Cellular Proteomics, 2009, 8(5): 946-958

Braun L, Cannella D, Pinheiro AM, Kieffer S, Belrhali H, Garin J and Hakimi MA
The small ubiquitin-like modifier (SUMO)-conjugating system of Toxoplasma gondii.
International Journal for Parasitology, 2009, 39(1): 81-90

Brun V, Masselon C, Garin J and Dupuis A
Isotope dilution strategies for absolute quantitative proteomics.
Journal of Proteomics, 2009, 72(5): 740-749

Chumpitazi BF, Bouillet L, Drouet MT, Kuhn L, Garin J, Zarski JP and Drouet C
Biological autoimmunity screening in hepatitis C patients by anti-HepG2 lysate and anti-heat shock protein 70.1 autoantibodies.
European Journal of Clinical Microbiology and Infectious Diseases, 2009, 28(2): 137-146

Dupierris V, Masselon C, Court M, Kieffer-Jaquinod S and Bruley C
A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa.
Bioinformatics, 2009, 25(15): 1980-1981

Emadali A and Gallagher-Gambarelli M
Quantitative proteomics by SILAC: Practicalities and perspectives for an evolving approach.
Medecine Sciences (Paris), 2009, 25(10): 835-842

Garin J and Jensen G
Techniques.
Current Opinion in Microbiology, 2009, 12(3): 282-284

Hennekinne JA, Brun V, De Buyser ML, Dupuis A, Ostyn A and Dragacci S
Innovative application of mass spectrometry for the characterization of staphylococcal enterotoxins involved in food poisoning outbreaks.
Applied and Environmental Microbiology, 2009, 75(3): 882-884

Joyard J, Ferro M, Masselon C, Seigneurin-Berny D, Salvi D, Garin J and Rolland N
Chloroplast proteomics and the compartmentation of plastidial isoprenoid biosynthetic pathways.
Molecular Plant, 2009, 2: 1154-1180

Kraut A, Marcellin M, Adrait A, Kieffer-Jaquinod S, Kuhn L, Louwagie M, Lebert D, Masselon CD, Dupuis A, Bruley C, Jaquinod M, Garin J and Gallagher-Gambarelli M
Peptide storage: Are you getting the best return on your investment? Defining optimal storage conditions for proteomics samples.
Journal of Proteome Research, 2009, 8(7): 3778-3785

Lehmann S, Roche S, Allory Y, Barthelaix A, Beaudeux JL, Berger F, Betsou F, Borg J, Dupuy A, Garin J, Quillard M, Lizard G, Peoc'H K, Riviere M and Ducoroy P
Preanalytical guidelines for clinical proteomics investigation of biological fluids.
Annales de Biologie Clinique, 2009, 67(6): 629-639

Li L, Sun CJ, Freeby S, Yee D, Kieffer-Jaquinod S, Guerrier L, Boschetti E and Lomas L
Protein sample treatment with peptide ligand library: Coverage and consistency.
Journal of Proteomics and Bioinformatics, 2009, 2.12: 485-494

Nicolau E, Kuhn L, Marchal R and Jouanneau Y
Proteomic investigation of enzymes involved in 2-ethylhexyl nitrate biodegradation in Mycobacterium austroafricanum IFP 2173.
Research in Microbiology, 2009, 160(10): 838-847

Polge C, Jaquinod M, Holzer F, Bourguignon J, Walling L and Brouquisse R
Evidence for the existence in Arabidopsis thaliana of the proteasome proteolytic pathway: Activation in response to cadmium.
Journal of Biological Chemistry, 2009, 284(51): 35412-35424

Rolland N, Atteia A, Decottignies P, Garin J, Hippler M, Kreimer G, Lemaire SD, Mittag M and Wagner V
Chlamydomonas proteomics.
Current Opinion in Microbiology, 2009, 12(3): 285-291

Rolland N, Ferro M, Seigneurin-Berny D, Garin J, Block MA and Joyard J
The Chloroplast envelope proteome and lipidome. In The Chloroplast - Interactions with the Environment (Anna-Stina Sandelius and Henrik Aronsson, eds.), Plant cell monograph series (David G Robinson, series editor). Springer Verlag, 2009, Vol.13 pp. 41-88

Sautel CF, Ortet P, Saksouk N, Kieffer S, Garin J, Bastien O and Hakimi MA
The histone methylase KMTox interacts with the redox-sensor peroxiredoxin-1 and targets genes involved in Toxoplasma gondii antioxidant defences.
Molecular Microbiology, 2009, 71(1): 212-226

Tarasova IA, Guryca V, Pridatchenko ML, Gorshkov AV, Kieffer-Jaquinod S, Evreinov VV, Masselon CD and Gorshkov MV
Standardization of retention time data for AMT tag proteomics database generation.
Journal of Chromatography B, 2009, 877(4): 433-440

Thomas D, Dauwalder O, Brun V, Badiou C, Ferry T, Etienne J, Vandenesch F and Lina G
Staphylococcus aureus superantigens elicit redundant and extensive human Vß patterns.
Infection Immunity, 2009, 77(5): 2043-2050

Trocme C, Marotte H, Baillet A, Pallot-Prades B, Garin J, Grange L, Miossec P, Tebib J, Berger F, Nissen MJ, Juvin R, Morel F and Gaudin P
Apolipoprotein A-I and platelet factor 4 are biomarkers for Infliximab response in rheumatoid arthritis.
Annals of the Rheumatic Diseases, 2009, 68(8): 1328-1333


2008 

Bennett N, Letourneur F, Ragno M and Louwagie M
Sorting of the v-SNARE VAMP7 in Dictyostelium discoideum: A role for more than one Adaptor Protein (AP) complex.
Experimental Cell Research, 2008, 314(15): 2822-2833

Bourguignon J and Jaquinod M An overview on Arabidopsis proteomics. In: Plant Proteomics: Technologies, strategies and applications. 2008, pp 143-164. Agrawal GK & Rakwal R (Eds), Wiley and Sons, NY

Braun L, Travier L, Kieffer S, Musset K, Garin J, Mercier C and Cesbron-Delauw MF
Purification of Toxoplasma dense granule proteins reveals that they are in complexes throughout the secretory pathway.
Molecular and Biochemical Parasitology, 2008, 157(1): 13-21

Dupuis A, Hennekinne JA, Garin J and Brun V
Protein Standard Absolute Quantification (PSAQ) for improved investigation of staphylococcal food poisoning outbreaks.
Proteomics, 2008, 8(22): 4633-4636

Ferro M, Tardif M, Reguer E, Cahuzac R, Bruley C, Vermat T, Nugues E, Vigouroux M, Vandenbrouck Y, Garin J and Viari A
PepLine: A software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences.
Journal of Proteome Research, 2008, 7(5): 1873-1883

Ghannam A, Hammache D, Matias C, Louwagie M, Garin J and Gerlier D
High-density rafts preferentially host the complement activator measles virus F glycoprotein but not the regulators of complement activation.
Molecular Immunology, 2008, 45(11): 3036-3044

Guryca V, Kieffer-Jaquinod S, Garin J and Masselon CD
Prospects for monolithic nano-LC columns in shotgun proteomics.
Analytical and Bioanalytical Chemistry, 2008, 392(7-8): 1291-1297

Kieffer-Jaquinod S, Chapel A, Garin J and Journet A
Affinity purification of soluble lysosomal proteins for mass spectrometric identification.
Methods in Molecular Biology, 2008, 432: 243-258

Lafourcade C, Sobo K, Kieffer-Jaquinod S, Garin J and van der Goot FG
Regulation of the V-ATPase along the endocytic pathway occurs through reversible subunit association and membrane localization.
PLoS ONE, 2008, 3(7): e2758

Mahul-Mellier AL, Strappazzon F, Petiot A, Chatellard-Causse C, Torch S, Blot B, Freeman K, Kuhn L, Garin J, Verna JM, Fraboulet S and Sadoul R
Alix and ALG-2 are involved in TNF-R1 induced cell death.
Journal of Biological Chemistry, 2008, 283(50): 34954-34965

Masselon CD, Kieffer-Jaquinod S, Brugière S, Dupierris V and Garin J
Influence of mass resolution on species matching in accurate mass and retention time (AMT) tag proteomics experiments.
Rapid Communication in Mass Spectrometry, 2008, 22(7): 986-992

Menasche G, Menager MM, Lefebvre JM, Deutsch E, Athman R, Lambert N, Mahlaoui N, Court M, Garin J, Fischer A and de Saint Basile G
A newly identified isoform of Slp2a associates with Rab27a in cytotoxic T cells and participates to cytotoxic granule secretion.
Blood, 2008, 112(13): 5052-5062

Salvi D, Rolland N, Joyard J and Ferro M
Purification and proteomic analysis of chloroplasts and their sub-organellar compartments.
Methods in Molecular Biology, 2008, 432: 19-36

Salvi D, Rolland N, Joyard J and Ferro M
Assessment of organelle purity using antibodies and specific assays: The example of the chloroplast envelope.
Methods in Molecular Biology, 2008, 432: 345-356

Wicker-Planquart C, Foucher AE, Louwagie M, Britton RA and Jault JM
Interactions of an essential Bacillus subtilis GTPase, YsxC, with ribosomes.
Journal of Bacteriology, 2008, 190(2): 681-690


2007 

Brun V, Dupuis A, Adrait A, Marcellin M, Thomas D, Court M, Vandenesch F and Garin J
Isotope-labeled protein standards: Toward absolute quantitative proteomics.
Molecular and Cellular Proteomics, 2007, 6(12): 2139-2149

Govin J, Escoffier E, Rousseaux S, Kuhn L, Ferro M, Thevenon J, Catena R, Davidson I, Garin J, Khochbin S and Caron C
Pericentric heterochromatin reprogramming by new histone variants during mouse spermiogenesis.
Journal of Cell Biology, 2007, 176(3): 283-294

Jaquinod M, Villiers F, Kieffer-Jaquinod S, Hugouvieux V, Bruley C, Garin J and Bourguignon J
A proteomics dissection of Arabidopsis thaliana vacuoles isolated from cell culture.
Molecular and Cellular Proteomics, 2007, 6(3): 394-412

Jaquinod M, Villiers F, Kieffer-Jaquinod S, Hugouvieux V, Bruley C, Garin J and Bourguignon J
A proteomics approach highlights a myriad of transporters in the Arabidopsis thaliana vacuolar membrane.
Plant Signaling & Behaviour, 2007, 2(5): 412-414

Jensen AG, Chemali M, Chapel A, Kieffer-Jaquinod S, Jadot M, Garin J and Journet A
Biochemical characterization and lysosomal localization of the mannose-6-phosphate protein p76 (hypothetical protein LOC196463).
Biochemical Journal, 2007, 402(3): 449-458

Lanquar V, Kuhn L, Lelievre F, Khafif M, Espagne C, Bruley C, Barbier-Brygoo H, Garin J and Thomine S
¹⁵N-Metabolic labeling for comparative plasma membrane proteomics in Arabidopsis cells.
Proteomics, 2007, 7(5):750-754

Lelong C, Aguiluz K, Luche S, Kuhn L, Garin J, Rabilloud T and Geiselmann J
The Crl-RpoS regulon of Escherichia coli.
Molecular and Cellular Proteomics, 2007, 6(4): 648-659

Lelong C, Rolland M, Louwagie M, Garin J and Geiselmann J
Mutual regulation of Crl and Fur in Escherichia coli W3110.
Molecular and Cellular Proteomics, 2007, 6(4): 660-668

Marmagne A, Ferro M, Meinnel T, Bruley C, Kuhn L, Garin J, Barbier-Brygoo H and Ephritikhine G
A high content in lipid-modified peripheral proteins and integral receptor kinases features the Arabidopsis plasma membrane proteome.
Molecular and Cellular Proteomics, 2007, 6(11): 1980-1996

Martelli A, Salin B, Dycke C, Louwagie M, Andrieu JP, Richaud P and Moulis JM
Folding and turnover of human iron regulatory protein 1 depend on its subcellular localization.
Febs Journal, 2007, 274(4): 1083-1092

Mossuz P, Bouamrani A, Brugière S, Arlotto M, Hermouet S, Lippert E, Laporte F, Girodon F, Dobo I, Praloran V, Garin J, Cahn JY and Berger F
Apolipoprotein A1: A new serum marker correlated to JAK2 V617F proportion at diagnosis in patients with polycythemia vera.
Proteomics. Clinical Applications, 2007, 1(12): 1605-1612

Paclet MH, Berthier S, Kuhn L, Garin J and Morel F
Regulation of phagocyte NADPH oxidase activity: Identification of two cytochrome b558 activation states.
FASEB Journal, 2007, 21(4): 1244-1255

Platel JC, Dupuis A, Boisseau S, Villaz M, Albrieux M and Brocard J
Synchrony of spontaneous calcium activity in mouse neocortex before synaptogenesis.
European Journal of Neuroscience, 2007, 25(4): 920-928

Sautel CF, Cannella D, Bastien O, Kieffer S, Aldebert D, Garin J, Tardieux I, Belrhali H and Hakimi MA
SET8-mediated methylations of histone H4 lysine 20 mark silent heterochromatic domains in apicomplexan genomes.
Molecular and Cellular Biology, 2007, 27(16): 5711-5724

Tolleter D, Jaquinod M, Mangavel C, Passirani C, Saulnier P, Manon S, Teyssier E, Payet N, Avelange-Macherel MH and Macherel D Structure and function of a mitochondrial late embryogenesis abundant protein are revealed by desiccation. Plant Cell, 2007, 19(5): 1580-1589

2006 

Albrieux M, Platel JC, Dupuis A, Brocard J, Savasta M and Villaz M
Neuronal activity before synaptogenesis: Na⁺ channels, Ca²⁺ signalling and glutamatergic secretion or how to play the part when some famous actors are missing in the scene?
Medecine Sciences (Paris), 22(4): 359-361

Atteia A, van Lis R, Gelius-Dietrich G, Adrait A, Garin J, Joyard J, Rolland N and Martin W
Pyruvate formate-lyase and a novel route of eukaryotic ATP-synthesis in Chlamydomonas mitochondria.
Journal of Biological Chemistry, 281(15): 9909-9918

Boonen M, Hamer I, Boussac M, Delsaute AF, Flamion B, Garin J and Jadot M
Intracellular localization of p40, a protein identified in a preparation of lysosomal membranes.
Biochemical Journal, 395(1): 39-47

Brosson D, Kuhn L, Delbac F, Garin J, Vivares CP and Texier C
Proteomic analysis of the eukaryotic parasite Encephalitozoon cuniculi (microsporidia): A reference map for proteins expressed in late sporogonial stages.
Proteomics, 6(12): 3625-3635

Burchak ON, Jaquinod M, Cottin C, Mugherli L, Iwai K, Chatelain F and Balakirev MY
Chemoenzymatic ubiquitination of artificial substrates.
Chembiochem, 7(11): 1667-1669

Chaput N, Flament C, Viaud S, Taieb J, Roux S, Spatz A, Andre F, LePecq JB, Boussac M, Garin J, Amigorena S, Thery C and Zitvogel L
Dendritic cell derived-exosomes: Biology and clinical implementations.
Journal of Leukocyte Biology, 80(3): 471-478

Decca MB, Bosc C, Luche S, Brugiere S, Job D, Rabilloud T, Garin J and Hallak ME
Protein arginylation in rat brain cytosol: A proteomic analysis.
Neurochemical Research, 31(3): 401-409

Faure J, Lachenal G, Court M, Hirrlinger J, Chatellard-Causse C, Blot B, Grange J, Schoehn G, Goldberg Y, Boyer V, Kirchhoff F, Raposo G, Garin J and Sadoul R
Exosomes are released by cultured cortical neurones.
Molecular and Cellular Neuroscience, 31(4): 642-648

Govin J, Caron C, Escoffier E, Ferro M, Kuhn L, Rousseaux S, Eddy EM, Garin J and Khochbin S
Post-meiotic shifts in HSPA2/HSP70.2 chaperone activity during mouse spermatogenesis.
Journal of Biological Chemistry, 281(49): 37888-37892

Hanano A, Burcklen M, Flenet M, Ivancich A, Louwagie M, Garin J and Blee E
Plant seed peroxygenase is an original heme-oxygenase with an EF-hand calcium binding motif.
Journal of Biological Chemistry, 281(44): 33140-33151

Le Lay P, Isaure MP, Sarry JE, Kuhn L, Fayard B, Le Bail JL, Bastien O, Garin J, Roby C and Bourguignon J
Metabolomic, proteomic and biophysical analyses of Arabidopsis thaliana cells exposed to a caesium stress. Influence of potassium supply.
Biochimie, 88: 1533-1547

Levine A, Vannier F, Absalon C, Kuhn L, Jackson P, Scrivener E, Labas V, Vinh J, Courtney P, Garin J and Seror S J
Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes.
Proteomics, 6(7): 2157-2173

Oficjalska-Pham D, Harismendy O, Smagowicz WJ, Gonzalez de Peredo A, Boguta M, Sentenac A and Lefebvre O
General repression of RNA polymerase III transcription is triggered by protein phosphatase type 2A-mediated dephosphorylation of Maf1.
Molecular Cell, 22(5): 623

Pelletier L, Guillaumot P, Frêche B, Luquain C, Christiansen D, Brugiere S, Garin J and Manié S
Gamma-secretase-dependent proteolysis of CD44 promotes neoplastic transformation of rat fibroblastic cells.
Cancer Research, 66(7): 3681-3687

Pelosi L, Kuhn L, Guetta D, Garin J, Geiselmann J, Lenski R and Schneider D
Parallel changes in global protein profiles during long-term evolution in Escherichia coli.
Genetics, 173(4): 1851-1869

Peuvel-Fanget I, Polonais V, Brosson D, Texier C, Kuhn L, Peyret P, Vivares C and Delbac F
EnP1 and EnP2, two proteins associated with the Encephalitozoon cuniculi endospore, the chitin-rich inner layer of the microsporidian spore wall.
International Journal of Parasitology, 36(3): 309-318

Ramus C, de Peredo AG, Dahout C, Gallagher M and Garin J
An optimized strategy for ICAT quantification of membrane proteins.
Molecular and Cellular Proteomics, 5(1): 68-78

Rolland N, Ferro M, Ephritikhine G, Marmagne A, Ramus C, Brugière S, Salvi D, Seigneurin-Berny D, Bourguignon J, Barbier-Brygoo H, Joyard J and Garin J
A versatile method for deciphering plant membrane proteomes.
Journal of Experimental Botany, 57: 1579-1589

Sarry JE, Kuhn L, Ducruix C, Lafaye A, Junot C, Hugouvieux V, Jourdain A, Bastien O, Fievet J, Vailhen D, Amekraz B, Moulin C, Ezan E, Garin J and Bourguignon J
The early responses of Arabidopsis thaliana cells to cadmium exposure explored by protein and metabolite profiling analyses.
Proteomics, 6(7): 2180-2198

Sarry JE, Kuhn L, Le Lay P, Garin J and Bourguignon J
Dynamics of Arabidopsis thaliana soluble proteome in response to different nutrient culture conditions.
Electrophoresis, 27(2): 495-507

Shen DK, Filopon D, Kuhn L, Polack B and Toussaint B
PsrA is a positive transcriptional regulator of the type III secretion system in Pseudomonas aeruginosa.
Infection Immunity, 74(2): 1121-1129


2005 

Brosson D, Kuhn L, Prensier G, Vivares CP and Texier C
The putative chitin deacetylase of Encephalitozoon cuniculi: A surface protein implicated in microsporidian spore-wall formation.
FEMS Microbiol Lett., 247(1): 81-90

Dahout-Gonzalez C, Ramus C, Dassa EP, Dianoux AC and Brandolin G
Conformation-dependent swinging of the matrix loop m2 of the mitochondrial Saccharomyces cerevisiae ADP/ATP carrier.
Biochemistry, 44(49): 16310-16320

Gache V, Louwagie M, Garin J, Caudron N, Lafanechère L and Valiron O
Identification of proteins binding the native tubulin dimer.
Biochem. Biophys. Res. Commun, 327(1): 35-42 Michaille, JJ, Tili E, Calin GA, Garin J, Louwagie M and Croce CM
Cloning and characterization of cDNAs expressed during chick development and encoding different isoforms of a putative zic finger transcriptional regulator.
Biochimie, 87(11): 939-949

Moscatelli A, Scali M, Prescianotto-Baschong C, Ferro M, Garin J, Vignani R, Ciampolini F and Cresti M
A methionine synthase homolog is associated with secretory vesicles in tobacco pollen tubes.
Planta, 221(6): 776-789

Pastor A, Chabert J, Louwagie M, Garin J and Attree I
PscF is a major component of the Pseudomonas aeruginosa type III secretion needle.
FEMS Microbiology Letters, 253(1): 95-101

Rey P, Cuiné S, Eymery F, Garin J, Court M, Jacquot JP, Rouhier N and Broin M
Analysis of the proteins targeted by CDSP32, a plastidic thioredoxin participating in oxidative stress responses.
Plant J., 41(1): 31-42

Rumeau D, Becuwe-Linka N, Louwagie M, Garin J and Peltier G
New subunits NDH-M, -N, and –O, encoded by nuclear genes, are essential for plastid Ndh complex functioning in higher plants.
Plant Cell, 17(1): 219-232

Saksouk N, Bhatti M, Kieffer S, Smith A, Musset K, Garin J, Sullivan W , Cesbron-Delauw MF and Hakimi M
Histone modifying complexes regulate gene expression pertinent to the differentiation of protozoan parasite Toxoplasma gondii.
Molecular and Cellular Biology, 25(23): 10301-10314

Sarrut N, Bouffet S, Mittler F, Constantin O, Combette P, Sudor J, Ricoul F, Vinet F, Garin J and Vauchier C
Enzymatic digestion and liquid chromatography in micro-pillar reactors. Hydrodynamic versus electroosmotic flow.
Proceeding of SPIE, 5718: 99-109

Vassilopoulos S, Thevenon D, Smida Rezgui S, Brocard J, Chapel A, Lacampagne A, Lunardi J, Dewaard M and Marty I
Triadins are not triad specific proteins: Two new skeletal muscle triadins possibly involved in the architecture of sarcoplasmic reticulum.
Journal of Biological Chemistry, 280(31): 28601-28609

Witkowska D, Mieszala M, Gamian A, Staniszewska M, Czarny A, Przondo-Mordarska A, Jaquinod M and Forest E
Major structural proteins of type 1 and type 3 Klebsiella fimbriae are effective protein carriers and immunogens in conjugates as revealed from their immunochemical characterization.
FEMS Immunology and Medical Microbiology, 45(2): 221-230


2004 

Benaud C, Gentil BJ, Assard N, Court M, Garin J, Delphin C and Baudier J
AHNAK interaction with the annexin 2/S100A10 complex regulates cell membrane cytoarchitecture.
J. Cell. Bio.l, 164(1): 133-144

Bourges I, Ramus C, Mousson de Camaret B, Beugnot R, Remacle C, Cardol P, Hofhaus G and Issartel JP
Structural organization of mitochondrial human complex I: Role of the ND4 and ND5 mitochondria-encoded subunits and interaction with prohibitin.
Biochem J., 383(Pt. 3): 491-499

Brugiere S, Kowalski S, Ferro M, Seigneurin-Berny D, Miras S, Salvi D, Ravanel S, d'Herin P, Garin J, Bourguignon J, Joyard J and Rolland N
The hydrophobic proteome of mitochondrial membranes from Arabidopsis cell suspensions.
Phytochemistry, 65(12): 1693-1707

Demaneche S, Meyer C, Micoud J, Louwagie M, Willison JC and Jouanneau Y
Identification and functional analysis of two aromatic-ring-hydroxylating dioxygenases from a sphingomonas strain that degrades various polycyclic aromatic hydrocarbons.
Appl. Environ. Microbiol., 70(11): 6714-6725

Ephritikhine G, Ferro M and Rolland N
Plant membrane proteomics.
Plant Physiol. Biochem., 42(12): 943-962

Journet A and Ferro M
The potentials of MS-based subproteomic approaches in medical science: The case of lysosomes and breast cancer.
Mass. Spectrom. Rev., 23(6): 393-442

Lemaitre G, Lamartine J, Pitaval A, Vaigot P, Garin J, Bouet S, Petat C, Soularue P, Gidrol X, Martin MT and Waksman G
Expression profiling of genes and proteins in HaCaT keratinocytes: Proliferating versus differentiated state.
J. Cell. Biochem., 93(5): 1048-1062

Marmagne A, Rouet MA, Ferro M, Rolland N, Alcon C, Joyard J, Garin J, Barbier-Brygoo H and Ephritikhine G
Identification of new intrinsic proteins in Arabidopsis plasma membrane proteome.
Mol. Cell Proteomics, 3(7): 675-691

Van Der Rest B, Rolland N, Boisson AM, Ferro M, Bligny R and Douce R
Identification and characterization of plant glycerophosphodiester phosphodiesterase.
Biochem. J., 379(Pt 3): 601-7


2003 

Berthier S, Paclet MH, Lerouge S, Roux F, Vergnaud S, Coleman AW and Morel F
Changing the conformation state of cytochrome b558 initiates NADPH oxidase activation: MRP8/MRP14 regulation.
J. Biol. Chem, 278(28): 25499-25508

Ferro M, Salvi D, Brugière S, Miras D, Kowalski S, Louwagie M, Garin J, Joyard J and Rolland N
Proteomics of the chloroplast envelope membranes from Arabidopsis thaliana.
Mol. Cell. Proteomics, 2(5): 325-345

Krivobok S, Kuony S, Meyer C, Louwagie M, Willison JC and Jouanneau Y
Identification of pyrene-induced proteins in Mycobacterium sp. strain 6PY1: Evidence for two ring-hydroxylating dioxygenases.
J. Bacteriol., 185(13): 3828-41 Lemercier C, Legube G, Caron C, Louwagie M, Garin J, Trouche D and Khochbin S
Tip60 acetyltransferase activity is controlled by phosphorylation.
J. Biol. Chem, 278(7): 4713-4718

Mollinari C, Reynaud C, Martineau-Thuillier S, Monier S, Kieffer S, Garin J, Andreassen PR, Boulet A, Goud B, Kleman JP and Margolis RL
The mammalian passenger protein TD-60 is an RCC1 family member with an essential role in prometaphase to metaphase progression.
Dev. Cell, 5(2): 295-307

Poinssot B, Vandelle E, Bentejac M, Adrian M, Levis C, Brygoo Y, Garin J, Sicilia F, Coutos-Thevenot P and Pugin A
The endopolygalacturonase 1 from Botrytis cinerea activates grapevine defense reactions unrelated to its enzymatic activity.
Mol. Plant Microbe Interact, 16(6): 553-564

Prevot D, Decimo D, Herbreteau CH, Roux F, Garin J, Darlix JL and Ohlmann T
Characterization of a novel RNA-binding region of eIF4GI critical for ribosomal scanning.
EMBO J, 22(8): 1909-1921

Rolland N, Ferro M, Seigneurin-Berny D, Garin J, Douce R and Joyard J
Proteomics of chloroplast envelope membranes.
Photosynthesis Res., 78(3): 205-230

Siaut M, Zaros C, Levivier E, Ferri ML, Court M, Werner M, Callebaut I, Thuriaux P, Sentenac A and Conesa C
An Rpb4/Rpb7-like complex in yeast RNA polymerase III contains the orthologue of mammalian CGRP-RCP.
Mol. Cell. Biol, 23(1): 195-205

Starita-Geribaldi M, Roux F, Garin J, Chevallier D, Fenichel P and Pointis G
Development of narrow immobilized pH gradients covering one pH unit for human seminal plasma proteomic analysis.
Proteomics, 3(8): 1611-1619

Van Niel G, Mallegol J, Bevilacqua C, Candalh C, Brugiere S, Tomaskovic-Crook E, Heath JK, Cerf-Bensussan N and Heyman M
Intestinal epithelial exosomes carry MHC class II/peptides able to inform the immune system in mice.
Gut, 52(12): 1690-1697


2002 

Bardel J, Louwagie M, Jaquinod M, Jourdain A, Luche S, Rabilloud T, Macherel D, Garin J and Bourguignon J
A survey of the plant mitochondrial proteome in relation to development.
Proteomics, 2: 880-898

Bebien M, Lagniel G, Garin J, Touati D, Vermeglio A and Labarre J
Involvment of superoxide dismutases in th response of Escherichia coli to selenium oxides.
J. Bacteriol., 184: 1556-1564

Bogdanovic A, Bennett N, Kieffer S, Louwagie M, Morio T, Garin J, Satre M and Bruckert F
Syntaxin 7, Syntaxin 8, Vti1 and VAMP7 form an active SNARE complex for early macropinocytic compartment fusion in Dictyostelium discoideum.
Biochem. J., 368(Pt 1): 29-39

Chapal N, Laplanche M, Ribes G, Pau B, Garin J and Petit P
Pharmaco-proteomic analysis: Application of proteomic analysis to the discovery and development of new drugs.
J. Soc. Biol., 196(4): 317-22

Ferro M, Salvi D, Rivière-Rolland H, Vermat T, Seigneurin-Berny D, Grunwald D, Garin J, Joyard J and Rolland N Integral membrane proteins of the chloroplast envelope: Identification and subcellular localization of new transporters. Proceedings of the National Academy of Sciences USA, 2002, 99: 11487-11492

Gauthier L, Rossi B, Roux F, Termine E and Schiff C
Galectin-1 is a stromal cell ligand of the pre-B cell receptor (BCR) implicated in synapse formation between pre-B and stromal cells and in pre-BCR triggering.
Proc. Natl. Acad. Sci. USA, 99: 13014-13019

Guzman-Verri C, Manterola L, Sola-Landa A, Parra A, Cloeckaert A, Garin J, Gorvel JP, Moriyon I, Moreno E and Lopez-Goni I
The two-component system BvrR/BvrS essential for Brucella abortus virulence regulates the expression of outer membrane proteins with counterparts in members of the Rhizobiaceae.
Proc. Natl. Acad. Sci. USA, 99(19): 12375-12380

Journet A, Chapel A, Kieffer S, Roux F and Garin J
Proteomic analysis of human lysosomes: Application to monocytic and breast cancer cells.
Proteomics, 2: 1026-1040

Magnard C, Bachelier R, Vincent A, Jaquinod M, Kieffer S, Lenoir GM and Venezia ND
BRCA1 interacts with acetyl-CoA carboxylase through its tandem of BRCT domains.
Oncogene, 21(44): 6729-6739

Mbele GO, Deloulme JC, Gentil BJ, Delphin C, Ferro M, Garin J, Takahashi M and Baudier J
The zinc- and calcium-binding S100B interacts and co-localizes with IQGAP1 during dynamic rearrangement of cell membranes.
J. Biol. Chem., 277(51): 49998-50007

Miras S, Salvi D, Ferro M, Grunwald D, Garin J, Joyard J and Rolland N
Non-canonical transit peptide for import into the chloroplast.
J. Biol. Chem., 277(49): 47770-47778

Ohlmann T, Prevot D, Decimo D, Roux F, Garin J, Morley SJ and Darlix JL
In vitro cleavage of eIF4GI but not eIFGII by HIV-1 protease and its effects on translation in the rabbit reticulocyte lysate system.
J. Mol. Biol., 318: 9-20

Pizzaro-Cerda J, Jonquieres R, Gouin E, Vandekerckove J, Garin J and Cossart P
Distinct protein patterns associated with Listeria monocytogenes InlA- or InlB- phagosomes.
Cell. Microbiol., 4: 101-115


2001 

Dermine J.F, Duclos S, Garin J, St-Louis F, Rea S, Parton R and Desjardins M
Flotillin-1-enriched lipid raft domains accumulate on maturing phagososmes.
J. Biol. Chem., 276: 18507-18512

Garin J, Diez R, Kieffer S, Dermine JF, Duclos S, Gagnon E, Sadoul R, Rondeau C and Desjardins M
The phagocyte proteome: Insight into phagocyte functions.
J. Cell Biol., 152: 165-180

Garin J, Ferro M, Rolland N and Joyard J
Stratégies en protéomique : outils, limites et développements. Génomique fonctionnelle chez les végétaux : du gène à la fonction. J. J. H. Barbier-Brygoo, Morot-Gaudry J.F. & Gaymard F, 2001, 39-48

Garin J, Ferro M, Rolland N, Riviere-Rolland H, Viari V and Joyard J
Méthodes de la protéomique, limites et développements technologiques. Exemple des protéines membranaires végétales.
C. R. Acad. Agric. Fr., 2001, 87: 9-20

Gentil B, Delphin C, Ouengue G, Deloulme J.C, Ferro M, Garin J and Baudier J
The giant protein AHNAK is a specific target for the calcium and zinc-binding S100B protein. Potential implication for Ca²⁺ homeostasis regulation by S100B.
J. Biol. Chem., 276: 23253-23261

Morris-Desbois C, Rety S, Ferro M, Garin J and Jalinot P
The human protein HSPC021 interacts with Int-6 and is associated with eukaryotic translation initiation factor 3.
J. Biol. Chem., 276: 45988-45995

Prouzet-Mauleon V, Monribot-Espagne C, Boucherie H, Lagniel G, Lopez S, Labarre J, Garin J and Lauquin GJ
Identification in S. cerevisiae of a new stable variant of alkyl hydroperoxide reductase 1 (Ahp1) induced by oxidative stress.
J. Biol. Chem., 277: 4823-4830

Rampazzo P, Biasiolo A, Garin J, Rosato A, Betterle C, Ruffatti A and Pengo V
Some patients with antiphospholipid syndrome express hitherto undescribed antibodies to cardiolipin-binding proteins.
Thromb. Haemost., 85: 57-62

Seigneurin-Berny D, Verdel A, Curtet S, Lemercier C, Garin J, Rousseaux S and Khochbin S
Identification of components of the murine histone deacetylase 6 complex: Link between acetylation and ubiquitination signaling pathways.
Mol. Cell. Biol., 23: 8035-8044

Starita-Geribaldi M, Poggioli S, Zucchini M, Garin J, Chevallier D, Fenichel P and Pointis G
Mapping of seminal plasma proteins by two-dimensional gel electrophoresis in men with normal and impaired spermatogenesis.
Mol. Hum. Reprod., 8: 715-722

Théry C, Boussac M, Véron P, Ricciardi-Castagnoli, P, Raposo G, Garin J and Amigorena S
Proteomic analysis of dendritic cell-derived exosomes, a secreted subcellular compartment distinct from apoptotic vesicles.
J. Immunol., 166: 7309-7318

Van Niel, G, Raposo, G, Candalh, C, Boussac, M, Hershberg, R, Cerf-bensussan, N and Heyman M
Intestinal epithelial cells secrete exosome-like vesicles.
Gastroenterology, 121: 337-349


2000 

Boutonnat J, Ducros V, Pinel C, Kieffer S, Favier A, Garin J and Seigneurin D
Identification of amylase crystalloids in cystic lesions of the parotid gland.
Acta Cytol., 44: 51-56

Boussac M and Garin J
Calcium-dependent secretion in human neutrophils: A proteomic approach.
Electrophoresis, 267: 2062-2070

Dianoux AC, Noel F, Fiore C, Trezeguet V, Kieffer S, Jaquinod M, Lauquin GJ and Brandolin G
Two distinct regions of the yeast mitochondrial ADP/ATP carrier are photolabeled by a new ADP analogue: 2-azido-3'-O-naphthoyl-[beta-³²P]ADP. Identification of the binding segments by mass spectrometry.
Biochemistry, 39: 11477-11487

Duclos S, Diez R, Garin J, Papadopoulou B, Descoteaux A, Stenmark H and Desjardins M
Rab5 regulates the kiss and run fusion between phagosomes and endosomes and the acquisition of phagosome leishmanicidal properties in RAW 264.7 macrophages.
J. Cell. Sci., 113: 3531-3541

Ferro M, Lorquin J, Ba S, Sanon K, Prome JC and Boivin C
Bradyrhizobium sp. strains that nodulate the leguminous tree Acacia albida produce fucosylated and partially sulfated nod factors.
Appl. Environ. Microbiol., 66: 5078-5082

Ferro M, Seigneurin D, Rolland N, Chapel A, Salvi D, Garin J and Joyard J
Organic solvent extraction as a versatile procedure to identify hydrophobic chloroplast proteins.
Electrophoresis, 21: 3517-3526

Gaudin P, Trocme C, Berthier S, Kieffer S, Boutonnat J, Lamy C, Surla A, Garin J and Morel F
TIMP-1/MMP-9 imbalance in an EBV-immortalized B lymphocyte cellular model: Evidence for multifunctional properties.
Biochim. Biophys. Acta, 1499: 19-33

Gueguen V, Macherel D, Jaquinod M, Douce R and Bourguignon J
Fatty acid and lipoic acid biosynthesis in high plant mitochondria.
Journal of Biological Chemistry, 2000, 275(7): 5016-5025

Journet A, Chapel A, Kieffer S, Louwagie M, Luche S and Garin J
Towards a human repertoire of monocytic lysosomal proteins.
Electrophoresis, 21: 3411-3419

Nosjean O, Ferro M, Coge F, Beauverger P, Henlin JM, Lefoulon F, Fauchere JL, Delagrange P, Canet E and Boutin JA
Identification of the melatonin-binding site MT3 as the quinone reductase 2.
J. Biol. Chem., 275: 31311-31317

Santoni V, Kieffer S, Desclaux D, Masson F and Rabilloud T
Membrane proteomics: Use of additive main effects with multiplicative interaction model to classify plasma membrane proteins according to their solubility and electrophoretic properties.
Electrophoresis, 21: 3329-3344

Weidenhaupt M, Bruckert F, Louwagie M, Garin J and Satre M
Functional and molecular identification of novel members of the ubiquitous membrane fusion proteins alpha and gamma SNAP families in Dictyostelium discoideum.
Eur. J. Biochem., 267: 2062-2070