@article{RN1273,

title = {The Safety Limits Of An Extended Fast: Lessons from a Non-Model Organism.},

author = {F. Bertile and L. Fouillen and T. Wasselin and P. Maes and Y. Le Maho and A. Van Dorsselaer and T. Raclot},

year  = {2017},

date = {2017-01-01},

journal = {Sci Rep.},

volume = {in press, doi: 10.1038/srep39008.},

note = {2007/08},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1298,

title = {MS-DECODER: Milliseconds Sequencing of Coded Polymers.},

author = {A Burel and C Carapito and J F Lutz and L Charles},

doi = {10.1021/acs.macromol.7b01737},

year  = {2017},

date = {2017-01-01},

journal = {Macromolecules},

volume = {50},

number = {20},

pages = {8290-8296},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1263,

title = {An evolutionary conserved zinc finger protein is involved in Toxoplasma gondii mRNA nuclear export.},

author = {M Gissot and A Hovasse and L Chaloin and C Schaeffer-Reiss and A Van Dorsselaer and S Tomavo},

year  = {2017},

date = {2017-01-01},

journal = {Cell Microbiol.},

volume = {19},

number = {2},

pages = {doi: 10.1111/cmi.12644.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1279,

title = {Proteomics towards the understanding of elicitor induced resistance of grapevine against downy mildew},

author = {C Lemaître-Guillier and A Hovasse and C Schaeffer-Reiss and G Recorbet and B Poinssot and S Trouvelot and X Daire and M Adrian and M -C Héloir},

year  = {2017},

date = {2017-01-01},

journal = {Journal of Proteomics},

volume = {156},

pages = {113–125},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{boruc_phosphorylation_2017,

title = {Phosphorylation of MAP65-1 by Arabidopsis Aurora Kinases Is Required for Efficient Cell Cycle Progression},

author = {Joanna Boruc and Annika K Weimer and Virginie Stoppin-Mellet and Evelien Mylle and Ken Kosetsu and Cesyen Cedeño and Michel Jaquinod and Maria Njo and Liesbeth De Milde and Peter Tompa and Nathalie Gonzalez and Dirk Inzé and Tom Beeckman and Marylin Vantard and Daniël Van Damme},

doi = {10.1104/pp.16.01602},

year  = {2017},

date = {2017-01-01},

journal = {Plant Physiology},

volume = {173},

number = {1},

pages = {582--599},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{garcia-oliver_bdf1_2017,

title = {Bdf1 Bromodomains Are Essential for Meiosis and the Expression of Meiotic-Specific Genes},

author = {Encar García-Oliver and Claire Ramus and Jonathan Perot and Marie Arlotto and Morgane Champleboux and Flore Mietton and Christophe Battail and Anne Boland and Jean-François Deleuze and Myriam Ferro and Yohann Couté and Jérôme Govin},

doi = {10.1371/journal.pgen.1006541},

year  = {2017},

date = {2017-01-01},

journal = {PLoS genetics},

volume = {13},

number = {1},

pages = {e1006541},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{el_kennani_ms_histonedb_2017,

title = {MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones},

author = {Sara El Kennani and Annie Adrait and Alexey K Shaytan and Saadi Khochbin and Christophe Bruley and Anna R Panchenko and David Landsman and Delphine Pflieger and Jérôme Govin},

doi = {10.1186/s13072-016-0109-x},

year  = {2017},

date = {2017-01-01},

journal = {Epigenetics & Chromatin},

volume = {10},

pages = {2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1470,

title = {VISLISI trial, a prospective clinical study allowing identification of a new metalloprotease and putative virulence factor from Staphylococcus lugdunensis},

author = {X. Argemi and G. Prevost and P. Riegel and D. Keller and N. Meyer and M. Baldeyrou and N. Douiri and N. Lefebvre and K. Meghit and C. R. Oustau and D. Christmann and S. Cianferani and J. M. Strub and Y. Hansmann},

url = {<Go to ISI>://WOS:000404469900015},

doi = {ARTN 334.e1 

10.1016/j.cmi.2016.12.018},

issn = {1198-743x},

year  = {2017},

date = {2017-01-01},

journal = {Clinical Microbiology and Infection},

volume = {23},

number = {5},

abstract = {Objective: Staphylococcus lugdunensis is a coagulase-negative staphylococcus that displays an unusually high virulence rate close to that of Staphylococcus aureus. It also shares phenotypic properties with S. aureus and several studies found putative virulence factors. The objective of the study was to describe the clinical manifestations of S. lugdunensis infections and investigate putative virulence factors. 

Method: We conducted a prospective study from November 2013 to March 2016 at the University Hospital of Strasbourg. Putative virulence factors were investigated by clumping factor detection, screening for proteolytic activity, and sequence analysis using tandem nano-liquid chromatography-mass spectrometry. Results: In total, 347 positive samples for S. lugdunensis were collected, of which 129 (37.2%) were from confirmed cases of S. lugdunensis infection. Eighty-one of these 129 patients were included in the study. Bone and prosthetic joints (PJI) were the most frequent sites of infection (n = 28; 34.6%) followed by skin and soft tissues (n = 23; 28.4%). We identified and purified a novel protease secreted by 50 samples (61.7%), most frequently associated with samples from deep infections and PJI (pr 0.97 and pr 0.91, respectively). Protease peptide sequencing by nano-liquid chromatography-mass spectrometry revealed a novel protease bearing 62.42% identity with ShpI, a metalloprotease secreted by Staphylococcus hyicus. 

Conclusion: This study confirms the pathogenicity of S. lugdunensis, particularly in bone and PJI. We also identified a novel metalloprotease called lugdulysin that may contribute to virulence. (C) 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.},

note = {2015/01},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1488,

title = {MS-DECODER: Milliseconds Sequencing of Coded Polymers},

author = {A. Burel and C. Carapito and J. F. Lutz and L. Charles},

url = {<Go to ISI>://WOS:000413885100050},

doi = {10.1021/acs.macromol.7b01737},

issn = {0024-9297},

year  = {2017},

date = {2017-01-01},

journal = {Macromolecules},

volume = {50},

number = {20},

pages = {8290-8296},

note = {pas de numéro de projet},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1479,

title = {Validating Missing Proteins in Human Sperm Cells by Targeted Mass-Spectrometry- and Antibody-based Methods},

author = {C. Carapito and P. Duek and C. Macron and M. Seffals and K. Rondel and F. Delalande and C. Lindskog and T. Freour and Y. Vandenbrouck and L. Lane and C. Pineau},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28891297},

doi = {10.1021/acs.jproteome.7b00374},

issn = {1535-3907 (Electronic) 

1535-3893 (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {J Proteome Res},

volume = {16},

number = {12},

pages = {4340-4351},

abstract = {The present study is a contribution to the "neXt50 challenge", a coordinated effort across C-HPP teams to identify the 50 most tractable missing proteins (MPs) on each chromosome. We report the targeted search of 38 theoretically detectable MPs from chromosomes 2 and 14 in Triton X-100 soluble and insoluble sperm fractions from a total of 15 healthy donors. A targeted mass-spectrometry-based strategy consisting of the development of LC-PRM assays (with heavy labeled synthetic peptides) targeting 92 proteotypic peptides of the 38 selected MPs was used. Out of the 38 selected MPs, 12 were identified with two or more peptides and 3 with one peptide after extensive SDS-PAGE fractionation of the two samples and with overall low-intensity signals. The PRM data are available via ProteomeXchange in PASSEL (PASS01013). Further validation by immunohistochemistry on human testes sections and cytochemistry on sperm smears was performed for eight MPs with antibodies available from the Human Protein Atlas. Deep analysis of human sperm still allows the validation of MPs and therefore contributes to the C-HPP worldwide effort. We anticipate that our results will be of interest to the reproductive biology community because an in-depth analysis of these MPs may identify potential new candidates in the context of human idiopathic infertilities.},

note = {pas de numéro de projet},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1483,

title = {The siRNA suppressor RTL1 is redox-regulated through glutathionylation of a conserved cysteine in the double-stranded-RNA-binding domain},

author = {C. Charbonnel and A. K. Niazi and E. Elvira-Matelot and E. Nowak and M. Zytnicki and A. Bures and E. Jobet and A. Opsomer and N. Shamandi and M. Nowotny and C. Carapito and J. P. Reichheld and H. Vaucheret and J. Saez-Vasquez},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28981840},

doi = {10.1093/nar/gkx820},

issn = {1362-4962 (Electronic) 

0305-1048 (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {Nucleic Acids Res},

volume = {45},

number = {20},

pages = {11891-11907},

abstract = {RNase III enzymes cleave double stranded (ds)RNA. This is an essential step for regulating the processing of mRNA, rRNA, snoRNA and other small RNAs, including siRNA and miRNA. Arabidopsis thaliana encodes nine RNase III: four DICER-LIKE (DCL) and five RNASE THREE LIKE (RTL). To better understand the molecular functions of RNase III in plants we developed a biochemical assay using RTL1 as a model. We show that RTL1 does not degrade dsRNA randomly, but recognizes specific duplex sequences to direct accurate cleavage. Furthermore, we demonstrate that RNase III and dsRNA binding domains (dsRBD) are both required for dsRNA cleavage. Interestingly, the four DCL and the three RTL that carry dsRBD share a conserved cysteine (C230 in Arabidopsis RTL1) in their dsRBD. C230 is essential for RTL1 and DCL1 activities and is subjected to post-transcriptional modification. Indeed, under oxidizing conditions, glutathionylation of C230 inhibits RTL1 cleavage activity in a reversible manner involving glutaredoxins. We conclude that the redox state of the dsRBD ensures a fine-tune regulation of dsRNA processing by plant RNase III.},

note = {2012/45},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1471,

title = {Structural studies of protein arginine methyltransferase 2 reveal its interactions with potential substrates and inhibitors},

author = {V. Cura and N. Marechal and N. Troffer-Charlier and J. M. Strub and M. J. Haren and N. I. Martin and S. Cianferani and L. Bonnefond and J. Cavarelli},

url = {<Go to ISI>://WOS:000393601200007},

doi = {10.1111/febs.13953},

issn = {1742-464x},

year  = {2017},

date = {2017-01-01},

journal = {Febs Journal},

volume = {284},

number = {1},

pages = {77-96},

abstract = {PRMT2 is the less-characterized member of the protein arginine methyltransferase family in terms of structure, activity, and cellular functions. PRMT2 is a modular protein containing a catalytic Ado-Met-binding domain and unique Src homology 3 domain that binds proteins with proline-rich motifs. PRMT2 is involved in a variety of cellular processes and has diverse roles in transcriptional regulation through different mechanisms depending on its binding partners. PRMT2 has been demonstrated to have weak methyltransferase activity on a histone H4 substrate, but its optimal substrates have not yet been identified. To obtain insights into the function and activity of PRMT2, we solve several crystal structures of PRMT2 from two homologs (zebrafish and mouse) in complex with either the methylation product S-adenosyl-L-homocysteine or other compounds including the first synthetic PRMT2 inhibitor (Cp1) studied so far. We reveal that the N-terminal-containing SH3 module is disordered in the full-length crystal structures, and highlights idiosyncratic features of the PRMT2 active site. We identify a new nonhistone protein substrate belonging to the serine-/arginine-rich protein family which interacts with PRMT2 and we characterize six methylation sites by mass spectrometry. To better understand structural basis for Cp1 binding, we also solve the structure of the complex PRMT4: Cp1. We compare the inhibitor-protein interactions occurring in the PRMT2 and PRMT4 complex crystal structures and show that this compound inhibits efficiently PRMT2. These results are a first step toward a better understanding of PRMT2 substrate recognition and may accelerate the development of structure-based drug design of PRMT2 inhibitors.},

note = {2014/05},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1485,

title = {Nucleolar Proteome Analysis and Proteasomal Activity Assays Reveal a Link between Nucleolus and 26S Proteasome in A. thaliana},

author = {C. Montacie and N. Durut and A. Opsomer and D. Palm and P. Comella and C. Picart and M. C. Carpentier and F. Pontvianne and C. Carapito and E. Schleiff and J. Saez-Vasquez},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29104584},

doi = {10.3389/fpls.2017.01815},

issn = {1664-462X (Print) 

1664-462X (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {Front Plant Sci},

volume = {8},

pages = {1815},

abstract = {In all eukaryotic cells, the nucleolus is functionally and structurally linked to rRNA synthesis and ribosome biogenesis. This compartment contains as well factors involved in other cellular activities, but the functional interconnection between non-ribosomal activities and the nucleolus (structure and function) still remains an open question. Here, we report a novel mass spectrometry analysis of isolated nucleoli from Arabidopsis thaliana plants using the FANoS (Fluorescence Assisted Nucleolus Sorting) strategy. We identified many ribosome biogenesis factors (RBF) and proteins non-related with ribosome biogenesis, in agreement with the recognized multi-functionality of the nucleolus. Interestingly, we found that 26S proteasome subunits localize in the nucleolus and demonstrated that proteasome activity and nucleolus organization are intimately linked to each other. Proteasome subunits form discrete foci in the disorganized nucleolus of nuc1.2 plants. Nuc1.2 protein extracts display reduced proteasome activity in vitro compared to WT protein extracts. Remarkably, proteasome activity in nuc1.2 is similar to proteasome activity in WT plants treated with proteasome inhibitors (MG132 or ALLN). Finally, we show that MG132 treatment induces disruption of nucleolar structures in WT but not in nuc1.2 plants. Altogether, our data suggest a functional interconnection between nucleolus structure and proteasome activity.},

note = {2012/45},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1433,

title = {Bifunctional bispidine derivatives for copper-64 labelling and positron emission tomography},

author = {A. Roux and R. Gillet and S. Huclier-Markai and L. Ehret-Sabatier and L. J. Charbonniere and A. M. Nonat},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28116378},

doi = {10.1039/c6ob02712a},

issn = {1477-0539 (Electronic) 

1477-0520 (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {Org Biomol Chem},

volume = {15},

number = {6},

pages = {1475-1483},

abstract = {The first radiolabelling studies of a bispidine (3,7-diazabicyclo[3.3.1]nonane) derivative substituted by a glycinate pendant arm (L1) with (64)Cu are reported. Labelling was fast and easily performed at room temperature and in a wide range of pH values. Under these conditions, radiochemical yields over 90% were achieved within 5 minutes at micromolar concentration of the ligand. A bifunctional analogue of L1 (L2) has been obtained by introducing an l-lysine amino acid on the bispidine skeleton. Ligand L2 demonstrates good radiolabelling capacities at room temperature and in water (pH 4 to pH 6). This new bispidine is a versatile platform which can easily react with NHS esters and can be subsequently coupled to a recognition unit in order to perform targeted Positron Emission Tomography (PET) imaging. As a proof of concept, two new bifunctional chelators (BFCs) with a biotin (L3) or a maleimide functional group (L4) have been synthesized. The biotinylated BFC is very valuable for pretargeting strategies using streptavidin-conjugated antibodies. The reactivity of the maleimide derivative L4 has been studied with the model peptide GP120. Quantitative coupling has been achieved under physiological conditions, showing a good regioselectivity towards cysteine residues versus lysine amino acids.},

note = {2011/18},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1303,

title = {A community proposal to integrate proteomics activities in ELIXIR},

author = {J. A. Vizcaino and M. Walzer and R. C. Jimenez and W. Bittremieux and D. Bouyssie and C. Carapito and F. Corrales and M. Ferro and A. J. R. Heck and P. Horvatovich and M. Hubalek and L. Lane and K. Laukens and F. Levander and F. Lisacek and P. Novak and M. Palmblad and D. Piovesan and A. Puhler and V. Schwammle and D. Valkenborg and M. Rijswijk and J. Vondrasek and M. Eisenacher and L. Martens and O. Kohlbacher},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28713550},

doi = {10.12688/f1000research.11751.1},

issn = {2046-1402 (Print) 

2046-1402 (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {F1000Res},

volume = {6},

abstract = {Computational approaches have been major drivers behind the progress of proteomics in recent years. The aim of this white paper is to provide a framework for integrating computational proteomics into ELIXIR in the near future, and thus to broaden the portfolio of omics technologies supported by this European distributed infrastructure. This white paper is the direct result of a strategy meeting on 'The Future of Proteomics in ELIXIR' that took place in March 2017 in Tubingen (Germany), and involved representatives of eleven ELIXIR nodes. These discussions led to a list of priority areas in computational proteomics that would complement existing activities and close gaps in the portfolio of tools and services offered by ELIXIR so far. We provide some suggestions on how these activities could be integrated into ELIXIR's existing platforms, and how it could lead to a new ELIXIR use case in proteomics. We also highlight connections to the related field of metabolomics, where similar activities are ongoing. This white paper could thus serve as a starting point for the integration of computational proteomics into ELIXIR. Over the next few months we will be working closely with all stakeholders involved, and in particular with other representatives of the proteomics community, to further refine this paper.},

note = {pas de numéro de projet},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1442,

title = {Developing a reference system for the IFCC standardization of HbA2},

author = {R. Paleari and D. Caruso and P. Kaiser and C. G. Arsene and C. Schaeffer-Reiss and A. Van Dorsselaer and E. Bisse and M. Ospina and V. R. De Jesus and B. Wild and A. Mosca and Ifcc Working Group on Standardisation of Hemoglobin A},

url = {https://www.ncbi.nlm.nih.gov/pubmed/27238872},

doi = {10.1016/j.cca.2016.05.023},

issn = {1873-3492 (Electronic) 

0009-8981 (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {Clin Chim Acta},

volume = {467},

pages = {21-26},

abstract = {The importance of hemoglobin A2 (HbA2) as an indicator of the presence of beta-thalassemia was established many years ago. However, clinical application of recommended HbA2 cut off values is often hampered due to poor equivalence of HbA2 results among methods and laboratories. Thus, the IFCC standardization program for HbA2 was initiated in 2004 with the goal of achieving a complete reference system for this measurand. HbA2 standardization efforts are still in progress, including the development of a higher-order HbA2 reference measurement procedure and the preparation of a certified reference material in collaboration with the IRMM. Here, we review the past, present and future of HbA2 standardization and describe the current status of HbA2 testing.},

note = {2004/06},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1480,

title = {A ruthenium anticancer compound interacts with histones and impacts differently on epigenetic and death pathways compared to cisplatin},

author = {C. Licona and M. E. Spaety and A. Capuozzo and M. Ali and R. Santamaria and O. Armant and F. Delalande and A. Van Dorsselaer and S. Cianferani and J. Spencer and M. Pfeffer and G. Mellitzer and C. Gaiddon},

url = {https://www.ncbi.nlm.nih.gov/pubmed/27935863},

doi = {10.18632/oncotarget.13711},

issn = {1949-2553 (Electronic) 

1949-2553 (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {Oncotarget},

volume = {8},

number = {2},

pages = {2568-2584},

abstract = {Ruthenium complexes are considered as potential replacements for platinum compounds in oncotherapy. Their clinical development is handicapped by a lack of consensus on their mode of action. In this study, we identify three histones (H3.1, H2A, H2B) as possible targets for an anticancer redox organoruthenium compound (RDC11). Using purified histones, we confirmed an interaction between the ruthenium complex and histones that impacted on histone complex formation. A comparative study of the ruthenium complex versus cisplatin showed differential epigenetic modifications on histone H3 that correlated with differential expression of histone deacetylase (HDAC) genes. We then characterized the impact of these epigenetic modifications on signaling pathways employing a transcriptomic approach. Clustering analyses showed gene expression signatures specific for cisplatin (42%) and for the ruthenium complex (30%). Signaling pathway analyses pointed to specificities distinguishing the ruthenium complex from cisplatin. For instance, cisplatin triggered preferentially p53 and folate biosynthesis while the ruthenium complex induced endoplasmic reticulum stress and trans-sulfuration pathways. To further understand the role of HDACs in these regulations, we used suberanilohydroxamic acid (SAHA) and showed that it synergized with cisplatin cytotoxicity while antagonizing the ruthenium complex activity. This study provides critical information for the characterization of signaling pathways differentiating both compounds, in particular, by the identification of a non-DNA direct target for an organoruthenium complex.},

note = {2011/15},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1295,

title = {Development and evaluation of β-galactosidase-sensitive antibody-drug conjugates.},

author = {S. Kolodych and C. Michel and S. Delacroix and O. Koniev and A. Ehkirch and J. Eberova and S. Cianférani and B. Renoux and W. Krezel and P. Poinot and CD. Muller and S. Papot and A. Wagner},

doi = {10.1016/j.ejmech.2017.08.008},

year  = {2017},

date = {2017-01-01},

journal = {Eur J Med Chem.},

volume = {pii: S0223-5234(17)30611-6},

note = {2016/19},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1274,

title = {Step by Step Assembly of Polynuclear Lanthanide Complexes with a Phosphonated Bipyridine Ligand},

author = {N Souri and P Tian and A Lecointre and Z Lemaire and S Chafaa and JM. Strub and S Cianférani and M Elhabiri and C Platas-Iglesias and LJ. Charbonnière},

doi = {10.1021/acs.inorgchem.6b02414},

year  = {2016},

date = {2016-12-19},

journal = {Inorg Chem.},

volume = {55},

number = {24},

pages = {12962-12974},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{lee_efficient_2016,

title = {Efficient Exploitation of Separation Space in Two-Dimensional Liquid Chromatography System for Comprehensive and Efficient Proteomic Analyses},

author = {Hangyeore Lee and Dong-Gi Mun and Jeong Eun So and Jingi Bae and Hokeun Kim and Christophe Masselon and Sang-Won Lee},

doi = {10.1021/acs.analchem.6b03366},

year  = {2016},

date = {2016-12-01},

journal = {Analytical Chemistry},

volume = {88},

number = {23},

pages = {11734-11741},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Vandenbrouck2016,

title = {Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update},

author = {Yves Vandenbrouck and Lydie Lane and Christine Carapito and Paula Duek and Karine Rondel and Christophe Bruley and Charlotte Macron and Anne Gonzalez De Peredo and Yohann Couté and Karima Chaoui and Emmanuelle Com and Alain Gateau and Anne Marie Hesse and Marlène Marcellin and Loren Méar and Emmanuelle Mouton-Barbosa and Thibault Robin and Odile Burlet-Schiltz and Sarah Cianférani and Myriam Ferro and Thomas Fréour and Cecilia Lindskog and Jérôme Garin and Charles Pineau},

doi = {10.1021/acs.jproteome.6b00400},

year  = {2016},

date = {2016-11-04},

journal = {Journal of Proteome Research},

volume = {15},

number = {11},

pages = {3998-4019},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Socoro-Yuste2016,

title = {Ph(-) myeloproliferative neoplasm red blood cells display deregulation of IQGAP1-Rho GTPase signaling depending on CALR/JAK2 status},

author = {Nuria Socoro-Yuste and Marie-Claire Dagher and Anne Gonzalez De Peredo and Julie Mondet and Affif Zaccaria and Florence Roux Dalvai and Isabelle Plo and Jean Yves Cahn and Pascal Mossuz},

doi = {10.1016/j.bbamcr.2016.08.012},

year  = {2016},

date = {2016-11-01},

journal = {Biochimica et biophysica acta},

volume = {1863},

number = {11},

pages = {2758-2765},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cerveau_characterization_2016,

title = {Characterization of the Arabidopsis thaliana 2-Cys peroxiredoxin interactome},

author = {Delphine Cerveau and Alexandra Kraut and Henrik U Stotz and Martin J Mueller and Yohann Couté and Pascal Rey},

doi = {10.1016/j.plantsci.2016.07.003},

year  = {2016},

date = {2016-11-01},

journal = {Plant Science: An International Journal of Experimental Plant Biology},

volume = {252},

pages = {30--41},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{wagner_deletion_2016,

title = {Deletion of FtsH11 protease has impact on chloroplast structure and function in Arabidopsis thaliana when grown under continuous light},

author = {Raik Wagner and Lotta Sydow and Harald Aigner and Sergiu Netotea and Sabine Brugière and Lars Sjögren and Myriam Ferro and Adrian Clarke and Christiane Funk},

doi = {10.1111/pce.12808},

year  = {2016},

date = {2016-11-01},

journal = {Plant, Cell & Environment},

volume = {39},

number = {11},

pages = {2530--2544},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{deutsch_human_2016,

title = {Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1},

author = {Eric W Deutsch and Christopher M Overall and Jennifer E Van Eyk and Mark S Baker and Young-Ki Paik and Susan T Weintraub and Lydie Lane and Lennart Martens and Yves Vandenbrouck and Ulrike Kusebauch and William S Hancock and Henning Hermjakob and Ruedi Aebersold and Robert L Moritz and Gilbert S Omenn},

doi = {10.1021/acs.jproteome.6b00392},

year  = {2016},

date = {2016-11-01},

journal = {Journal of Proteome Research},

volume = {15},

number = {11},

pages = {3961--3970},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{duek_missing_2016,

title = {Missing Protein Landscape of Human Chromosomes 2 and 14: Progress and Current Status},

author = {Paula Duek and Amos Bairoch and Alain Gateau and Yves Vandenbrouck and Lydie Lane},

doi = {10.1021/acs.jproteome.6b00443},

year  = {2016},

date = {2016-11-01},

journal = {Journal of Proteome Research},

volume = {15},

number = {11},

pages = {3971-3978},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gilquin_proteomics_2016,

title = {A proteomics assay to detect eight CBRN-relevant toxins in food},

author = {Benoit Gilquin and Michel Jaquinod and Mathilde Louwagie and Sylvie Kieffer-Jaquinod and Alexandra Kraut and Myriam Ferro and François Becher and Virginie Brun},

doi = {10.1002/pmic.201600357},

year  = {2016},

date = {2016-11-01},

journal = {Proteomics},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1267,

title = {Benchmarking sample preparation/digestion protocols reveals tube-gel being a fast and repeatable method for quantitative proteomics},

author = {L Muller and L Fornecker and A Van Dorsselaer and S Cianférani and C Carapito},

doi = {10.1002/pmic.201600288},

year  = {2016},

date = {2016-10-17},

journal = {Proteomics},

volume = {16},

number = {23},

pages = {2953-2961},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gautier2016,

title = {Extracellular IL-33 cytokine, but not endogenous nuclear IL-33, regulates protein expression in endothelial cells},

author = {Violette Gautier and Corinne Cayrol and Dorian Farache and Stéphane Roga and Bernard Monsarrat and Odile Burlet-Schiltz and Anne Gonzalez De Peredo and Jean Philippe Girard},

doi = {10.1038/srep34255},

year  = {2016},

date = {2016-10-01},

journal = {Scientific Reports},

volume = {6},

number = {1},

pages = {34255},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Le2016,

title = {Ser/Thr phosphorylation regulates the fatty Acyl-AMP ligase activity of FadD32, an essential enzyme in mycolic acid biosynthesis},

author = {Nguyen Hung Le and Virginie Molle and Nathalie Eynard and Mathieu Miras and Alexandre Stella and Fabienne Bardou and Ségolène Galandrin and Valérie Guillet and Gwenaëlle André-Leroux and Marco Bellinzoni and Pedro Alzari and Lionel Mourey and Odile Burlet-Schiltz and Mamadou Daffé and Hedia Marrakchi},

doi = {10.1074/jbc.M116.748053},

year  = {2016},

date = {2016-10-01},

journal = {Journal of Biological Chemistry},

volume = {291},

number = {43},

pages = {22793--22805},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mazzolini2016,

title = {Phosphorylation of CDC25A on SER283 in late S/G2 by CDK/cyclin complexes accelerates mitotic entry},

author = {Laurent Mazzolini and Anaïs Broban and Carine Froment and Odile Burlet-Schiltz and Arnaud Besson and Stéphane Manenti and Christine Dozier},

doi = {10.1080/15384101.2016.1220455},

year  = {2016},

date = {2016-10-01},

journal = {Cell Cycle},

volume = {15},

number = {20},

pages = {2742-2752},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Testard2016,

title = {Calcium- and Nitric Oxide-Dependent Nuclear Accumulation of Cytosolic Glyceraldehyde-3-Phosphate Dehydrogenase in Response to Long Chain Bases in Tobacco BY-2 Cells},

author = {Ambroise Testard and Daniel Da Silva and Mélanie Ormancey and Carole Pichereaux and Cécile Pouzet and Alain Jauneau and Sabine Grat and Eugénie Robe and Christian Brière and Valérie Cotelle and Christian Mazars and Patrice Thuleau},

doi = {10.1093/pcp/pcw137},

year  = {2016},

date = {2016-10-01},

journal = {Plant & cell physiology},

volume = {57},

number = {10},

pages = {2221-2231},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{osseni_triadin_2016,

title = {Triadin and CLIMP-63 form a link between triads and microtubules in muscle cells},

author = {Alexis Osseni and Muriel Sébastien and Oriana Sarrault and Mathieu Baudet and Yohann Couté and Julien Fauré and Anne Fourest-Lieuvin and Isabelle Marty},

doi = {10.1242/jcs.188862},

year  = {2016},

date = {2016-10-01},

journal = {Journal of Cell Science},

volume = {129},

number = {20},

pages = {3744-3755},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hesse_heidi:_2016,

title = {hEIDI: An Intuitive Application Tool To Organize and Treat Large-Scale Proteomics Data},

author = {Anne-Marie Hesse and Véronique Dupierris and Claire Adam and Magali Court and Damien Barthe and Anouk Emadali and Christophe Masselon and Myriam Ferro and Christophe Bruley},

doi = {10.1021/acs.jproteome.5b00853},

year  = {2016},

date = {2016-10-01},

journal = {Journal of Proteome Research},

volume = {15},

number = {10},

pages = {3896-3903},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1259,

title = {MetAP1 and MetAP2 drive cell selectivity for a potent anti-cancer agent in synergy, by controlling glutathione redox state},

author = {F Frottin and WV. Bienvenut and J Bignon and E Jacquet and AS. Vaca Jacome and A Van Dorsselaer and S Cianférani and C Carapito and T Meinnel and C Giglione},

doi = {10.18632/oncotarget.11216},

year  = {2016},

date = {2016-09-27},

journal = {Oncotarget},

volume = {7},

number = {39},

pages = {63306-63323},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jungas2016,

title = {Eph-mediated tyrosine phosphorylation of citron kinase controls abscission},

author = {Thomas Jungas and Renaud T Perchey and Mohamad Fawal and Caroline Callot and Carine Froment and Odile Burlet-Schiltz and Arnaud Besson and Alice Davy},

doi = {10.1083/jcb.201602057},

year  = {2016},

date = {2016-08-01},

journal = {Journal of Cell Biology},

volume = {214},

number = {5},

pages = {555-569},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{steingruber_proteomic_2016,

title = {Proteomic Interaction Patterns between Human Cyclins, the Cyclin-Dependent Kinase Ortholog pUL97 and Additional Cytomegalovirus Proteins},

author = {Mirjam Steingruber and Alexandra Kraut and Eileen Socher and Heinrich Sticht and Anna Reichel and Thomas Stamminger and Bushra Amin and Yohann Couté and Corina Hutterer and Manfred Marschall},

doi = {10.3390/v8080219},

year  = {2016},

date = {2016-08-01},

journal = {Viruses},

volume = {8},

number = {8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gay_toxoplasma_2016,

title = {Toxoplasma gondii TgIST co-opts host chromatin repressors dampening STAT1-dependent gene regulation and IFN-γ-mediated host defenses},

author = {Gabrielle Gay and Laurence Braun and Marie-Pierre Brenier-Pinchart and Julien Vollaire and Véronique Josserand and Rose-Laurence Bertini and Aurélie Varesano and Bastien Touquet and Pieter-Jan De Bock and Yohann Couté and Isabelle Tardieux and Alexandre Bougdour and Mohamed-Ali Hakimi},

doi = {10.1084/jem.20160340},

year  = {2016},

date = {2016-08-01},

journal = {The Journal of Experimental Medicine},

volume = {213},

number = {9},

pages = {1779-1798},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{goold_saturating_2016,

title = {Saturating Light Induces Sustained Accumulation of Oil in Plastidal Lipid Droplets in Chlamydomonas reinhardtii},

author = {Hugh Douglas Goold and Stéphan Cuiné and Bertrand Légeret and Yuanxue Liang and Sabine Brugière and Pascaline Auroy and Hélène Javot and Marianne Tardif and Brian Jones and Fred Beisson and Gilles Peltier and Yonghua Li-Beisson},

doi = {10.1104/pp.16.00718},

year  = {2016},

date = {2016-08-01},

journal = {Plant Physiology},

volume = {171},

number = {4},

pages = {2406-2417},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{tarasova_predictive_2016,

title = {Predictive chromatography of peptides and proteins as a complementary tool for proteomics},

author = {Irina A Tarasova and Christophe D Masselon and Alexander V Gorshkov and Mikhail V Gorshkov},

doi = {10.1039/c6an00919k},

year  = {2016},

date = {2016-08-01},

journal = {The Analyst},

volume = {141},

number = {16},

pages = {4816-4832},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lazar2016,

title = {Adipocyte Exosomes Promote Melanoma Aggressiveness through Fatty Acid Oxidation: A Novel Mechanism Linking Obesity and Cancer},

author = {Ikrame Lazar and Emily Clement and Stéphanie Dauvillier and Delphine Milhas and Manuelle Ducoux-Petit and Sophie LeGonidec and Coédric Moro and Vanessa Soldan and Stephane Dalle and Stéphanie Balor and Muriel Golzio and Odile Burlet-Schiltz and Philippe Valet and Catherine Muller and Laurence Nieto},

doi = {10.1158/0008-5472.CAN-16-0651},

year  = {2016},

date = {2016-07-01},

journal = {Cancer Research},

volume = {76},

number = {14},

pages = {4051-4057},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{giai_gianetto_uses_2016,

title = {Uses and misuses of the fudge factor in quantitative discovery proteomics},

author = {Quentin Giai Gianetto and Yohann Couté and Christophe Bruley and Thomas Burger},

doi = {10.1002/pmic.201600132},

year  = {2016},

date = {2016-07-01},

journal = {Proteomics},

volume = {16},

number = {14},

pages = {1955-1960},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Pichereaux2016,

title = {Comparative shotgun proteomic analysis of wild and domesticated Opuntia spp. species shows a metabolic adaptation through domestication},

author = {Carole Pichereaux and Eric E Hernández-Domínguez and Maria Del Socorro Santos-Diaz and Antonio Reyes-Agüero and Marizel Astello-García and Françoise Guéraud and Anne Negre-Salvayre and Odile Schiltz and Michel Rossignol and Ana Paulina Barba Rosa},

doi = {10.1016/j.jprot.2016.04.003},

year  = {2016},

date = {2016-06-01},

journal = {Journal of proteomics},

volume = {143},

pages = {353--364},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{petropoulos_roles_2016,

title = {Roles of paxillin family members in adhesion and ECM degradation coupling at invadosomes},

author = {Christos Petropoulos and Christiane Oddou and Anouk Emadali and Edwige Hiriart-Bryant and Cyril Boyault and Eva Faurobert and Scott Vande Pol and Joo-Ri Kim-Kaneyama and Alexandra Kraut and Yohann Couté and Marc Block and Corinne Albiges-Rizo and Olivier Destaing},

doi = {10.1083/jcb.201510036},

year  = {2016},

date = {2016-06-01},

journal = {The Journal of Cell Biology},

volume = {213},

number = {5},

pages = {585--599},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1253,

title = {Developing a reference system for the IFCC standardization of HbA2},

author = {R Paleari and D Caruso and P Kaiser and C G Arsene and C Schaeffer-Reiss and A Van Dorsselaer and E Bissé and M Ospina and VR. De Jesús and B Wild and A Mosca},

doi = {10.1016/j.cca.2016.05.023},

year  = {2016},

date = {2016-05-27},

journal = {Clin Chim Acta},

volume = {467},

pages = {21–26},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Fliegmann2016,

title = {LYR3, a high-affinity LCO-binding protein of Medicago truncatula, interacts with LYK3, a key symbiotic receptor},

author = {Judith Fliegmann and Alain Jauneau and Carole Pichereaux and Charles Rosenberg and Virginie Gasciolli and Antonius C J Timmers and Odile Burlet-Schiltz and Julie Cullimore and Jean Jacques Bono},

doi = {10.1002/1873-3468.12191},

year  = {2016},

date = {2016-05-01},

journal = {FEBS Letters},

volume = {590},

number = {10},

pages = {1477--1487},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zvezdova2016,

title = {Themis1 enhances T cell receptor signaling during thymocyte development by promoting Vav1 activity and Grb2 stability},

author = {Ekaterina Zvezdova and Judith Mikolajczak and Anne Garreau and Marlène Marcellin and Lise Rigal and Jan Lee and Seeyoung Choi and Gaëtan Blaize and Jérémy Argenty and Julien Familiades and Liqi Li and Anne Gonzalez De Peredo and Odile Burlet-Schiltz and Paul E Love and Renaud Lesourne},

doi = {10.1126/scisignal.aad1576},

year  = {2016},

date = {2016-05-01},

journal = {Science Signaling},

volume = {9},

number = {428},

pages = {ra51},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{salvetti_nuclear_2016,

title = {Nuclear Functions of Nucleolin through Global Proteomics and Interactomic Approaches},

author = {Anna Salvetti and Yohann Couté and Alberto Epstein and Loredana Arata and Alexandra Kraut and Vincent Navratil and Philippe Bouvet and Anna Greco},

doi = {10.1021/acs.jproteome.6b00126},

year  = {2016},

date = {2016-05-01},

journal = {Journal of Proteome Research},

volume = {15},

number = {5},

pages = {1659--1669},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{lazar_accounting_2016,

title = {Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies},

author = {Cosmin Lazar and Laurent Gatto and Myriam Ferro and Christophe Bruley and Thomas Burger},

doi = {10.1021/acs.jproteome.5b00981},

year  = {2016},

date = {2016-04-01},

journal = {Journal of Proteome Research},

volume = {15},

number = {4},

pages = {1116-1125},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ma_molecular_2016,

title = {Molecular Evolution of the Substrate Specificity of Chloroplastic Aldolases/Rubisco Lysine Methyltransferases in Plants},

author = {Sheng Ma and Jacqueline Martin-Laffon and Morgane Mininno and Océane Gigarel and Sabine Brugière and Olivier Bastien and Marianne Tardif and Stéphane Ravanel and Claude Alban},

doi = {10.1016/j.molp.2016.01.003},

year  = {2016},

date = {2016-04-01},

journal = {Molecular Plant},

volume = {9},

number = {4},

pages = {569-581},

keywords = {},

pubstate = {published},

tppubtype = {article}

}