Initiation of translation in prokaryotes and eukaryotes, Gene, vol.234, pp.187-208, 1999. ,
Direct detection of alternative open reading frames translation products in human significantly expands the proteome, PLoS One, vol.8, p.70698, 2013. ,
Death of a dogma: eukaryotic mRNAs can code for more than one protein, Nucleic Acids Res, vol.44, pp.14-23, 2016. ,
Extensive translation of small open reading frames revealed by Poly-Ribo-Seq, Elife, vol.3, p.3528, 2014. ,
Many lncRNAs, 5 UTRs, and pseudogenes are translated and some are likely to express functional proteins, 2015. ,
Peptidomic discovery of short open reading frame-encoded peptides in human cells, Nat. Chem. Biol, vol.9, pp.59-64, 2013. ,
UniProt: the universal protein knowledgebase, Nucleic Acids Res, vol.45, pp.158-169, 2017. ,
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation, Nucleic Acids Res, vol.44, pp.733-745, 2016. ,
OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes, Nucleic Acids Res, vol.47, pp.403-410, 2019. ,
Small proteins encoded by unannotated ORFs are rising stars of the proteome, confirming shortcomings in genome annotations and current vision of an mRNA, Proteomics, vol.18, p.1700058, 2018. ,
A rescue factor abolishing neuronal cell death by a wide spectrum of familial Alzheimer's disease genes and Abeta, Proc. Natl Acad. Sci. U.S.A, vol.98, pp.6336-6341, 2001. ,
Combined mass spectrometry imaging and top-down microproteomics reveals evidence of a hidden proteome in ovarian cancer, EBioMedicine, vol.21, pp.55-64, 2017. ,
Spatially-resolved top-down proteomics bridged to MALDI MS imaging reveals the molecular physiome of brain regions, Mol. Cell. Proteomics, vol.17, pp.357-372, 2018. ,
Viral infection identifies micropeptides differentially regulated in smORF-containing lncRNAs, Genes, vol.8, p.206, 2017. ,
The mitochondrial-derived peptide MOTS-c: a player in exceptional longevity?, Aging Cell, vol.14, pp.921-923, 2015. ,
Classification and function of small open reading frames, Nat. Rev. Mol. Cell Biol, vol.18, pp.575-589, 2017. ,
Mass spectrometry-based proteomics and network biology, Annu. Rev. Biochem, vol.81, pp.379-405, 2012. ,
Affinity-purification coupled to mass spectrometry: basic principles and strategies, Proteomics, vol.12, pp.1576-1590, 2012. ,
Functional organization of the yeast proteome by systematic analysis of protein complexes, Nature, vol.415, pp.141-147, 2002. ,
A generic protocol for the purification and characterization of water-soluble complexes of affinity-tagged proteins and lipids, Nat. Protoc, vol.9, pp.2256-2266, 2014. ,
Proximity labeling of interacting proteins: application of BioID as a discovery tool, Proteomics, vol.17, p.1700002, 2017. ,
Directed evolution of APEX2 for electron microscopy and proximity labeling, Nat. Methods, vol.12, pp.51-54, 2014. ,
A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells, J. Cell Biol, vol.196, pp.801-810, 2012. ,
BioID: a proximity-dependent labeling approach in proteomics study, Methods Mol. Biol, vol.1871, pp.143-151, 2019. ,
BioID: a screen for protein-protein interactions, Curr. Protoc. Protein Sci, vol.91, 2018. ,
Trapping mammalian protein complexes in viral particles, Nat. Commun, vol.7, p.11416, 2016. ,
Mass spectrometry: an emerging technology for interactomics and structural biology, Anal. Chem, vol.90, pp.144-165, 2018. ,
Chemical cross-linking with mass spectrometry: a tool for systems structural biology, Curr. Opin. Chem. Biol, vol.48, pp.8-18, 2019. ,
Development of a novel cross-linking strategy for fast and accurate identification of cross-linked peptides of protein complexes, Mol. Cell. Proteomics, vol.10, 2011. ,
Cleavable cross-linker for protein structure analysis: reliable identification of cross-linking products by tandem MS, Anal. Chem, vol.82, pp.6958-6968, 2010. ,
Optimizing the enrichment of cross-linked products for mass spectrometric protein analysis, Rapid Commun. Mass Spectrom, vol.26, pp.653-658, 2012. ,
EXL-MS: an enhanced cross-linking mass spectrometry workflow to study protein complexes, Anal. Chem, vol.90, pp.10707-10714, 2018. ,
URL : https://hal.archives-ouvertes.fr/pasteur-02331078
A novel bio-orthogonal cross-linker for improved protein/protein interaction analysis, Anal. Chem, vol.87, pp.1853-1860, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01144840
Synthesis of two new enrichable and MS-cleavable cross-linkers to define protein-protein interactions by mass spectrometry, Org. Biomol. Chem, vol.13, pp.5030-5037, 2015. ,
ProXL (protein cross-linking database): a platform for analysis, visualization, and sharing of protein cross-linking mass spectrometry data, J. Proteome Res, vol.15, pp.2863-2870, 2016. ,
StavroX: a software for analyzing crosslinked products in protein interaction studies, J. Am. Soc. Mass Spectrom, vol.23, pp.76-87, 2012. ,
On the reproducibility of label-free quantitative cross-linking/mass spectrometry, J. Am. Soc. Mass Spectrom, vol.29, pp.405-412, 2018. ,
Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline, Nat. Protoc, vol.9, pp.120-137, 2014. ,
XTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry, Nat. Methods, vol.12, pp.1185-1190, 2015. ,
xiNET: cross-link network maps with residue resolution, Mol. Cell. Proteomics, vol.14, pp.1137-1147, 2015. ,
To be or not to be? Five guidelines to avoid misassignments in cross-linking/mass spectrometry, Anal. Chem, vol.89, pp.7832-7835, 2017. ,
Xlink-Identifier: an automated data analysis platform for confident identifications of chemically cross-linked peptides using tandem mass spectrometry, J. Proteome Res, vol.10, pp.923-931, 2011. ,
Crosslinking and mass spectrometry: an integrated technology to understand the structure and function of molecular machines, Trends Biochem. Sci, vol.41, pp.20-32, 2016. ,
Efficient and robust proteome-wide approaches for cross-linking mass spectrometry, Nat. Protoc, vol.13, pp.2964-2990, 2018. ,
The advancement of chemical cross-linking and mass spectrometry for structural proteomics: from single proteins to protein interaction networks, Expert Rev. Proteomics, vol.11, pp.733-743, 2014. ,
Quantitative cross-linking/mass spectrometry to elucidate structural changes in proteins and their complexes, Nat. Protoc, vol.14, pp.171-201, 2019. ,
A new in vivo cross-linking mass spectrometry platform to define protein-protein interactions in living cells, Mol. Cell. Proteomics, vol.13, pp.3533-3543, 2014. ,
Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry, Nat. Methods, vol.12, pp.1179-1184, 2015. ,
Nuclei of HeLa cells interactomes unravel a network of ghost proteins involved in proteins translation, Biochim. Biophys. Acta: Gen. Subj, vol.1863, pp.1458-1470, 2019. ,
URL : https://hal.archives-ouvertes.fr/inserm-02941645
Activation of PKA leads to mesenchymal-to-epithelial transition and loss of tumor-initiating ability, Science, p.3680, 2016. ,
The anti-Warburg effect elicited by the cAMP-PGC1? pathway drives differentiation of glioblastoma cells into astrocytes, Cell Rep, vol.18, pp.468-481, 2017. ,
) miR-33a promotes glioma-initiating cell self-renewal via PKA and NOTCH pathways, J. Clin. Invest, vol.124, pp.4489-4502, 2014. ,
Universal sample preparation method for proteome analysis, Nat. Methods, vol.6, pp.359-362, 2009. ,
ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks, Bioinformatics, vol.25, pp.1091-1093, 2009. ,
Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res, vol.13, pp.2498-2504, 2003. ,
I-TASSER: a unified platform for automated protein structure and function prediction, Nat. Protoc, vol.5, pp.725-738, 2010. ,
ClusPro: a fully automated algorithm for protein-protein docking, Nucleic Acids Res, vol.32, pp.96-99, 2004. ,
UCSF Chimera: a visualization system for exploratory research and analysis, J. Comput. Chem, vol.25, pp.1605-1612, 2004. ,
Medicinal leech CNS as a model for exosome studies in the crosstalk between microglia and neurons, Int. J. Mol. Sci, vol.19, p.4124, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02183492
The death-inducer obliterator 1 (Dido1) gene regulates embryonic stem cell self-renewal, J. Biol. Chem, vol.289, pp.4778-4786, 2014. ,
Potential application of cell reprogramming techniques for cancer research, Cell. Mol. Life Sci, vol.76, pp.45-65, 2019. ,
Physiological substrates of cAMP-dependent protein kinase, Chem. Rev, vol.101, pp.2381-2411, 2001. ,
STRING v10: protein-protein interaction networks, integrated over the tree of life, Nucleic Acids Res, vol.43, pp.447-452, 2015. ,
Cytoskeletal dynamics and nerve growth, Neuron, vol.1, pp.761-772, 1988. ,
Stem cell pluripotency: a cellular trait that depends on transcription factors, chromatin state and a checkpoint deficient cell cycle, J. Cell. Physiol, vol.221, pp.10-17, 2009. ,
Inhibition of oncogenic transformation by mammalian Lin-9, a pRB-associated protein, EMBO J, vol.23, pp.4627-4638, 2004. ,
Interrogating the architecture of protein assemblies and protein interaction networks by cross-linking mass spectrometry, Curr. Opin. Struct. Biol, vol.35, pp.100-108, 2015. ,
Overlapping genes, Annu. Rev. Genet, vol.17, pp.499-525, 2003. ,
Utilization of an alternative open reading frame of a normal gene in generating a novel human cancer antigen, J. Exp. Med, vol.183, pp.1137-1140, 1996. ,
Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events, Mol. Cell. Proteomics, vol.12, pp.1780-1790, 2013. ,
Function of myosin-V in filopodial extension of neuronal growth cones, Science, vol.273, pp.660-663, 1996. ,
Myosin-X is an unconventional myosin that undergoes intrafilopodial motility, Nat. Cell Biol, vol.4, pp.246-250, 2002. ,
The multiverse nature of epithelial to mesenchymal transition, Semin. Cancer Biol, vol.58, pp.1-10, 2018. ,
Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins, p.27860, 2017. ,