, Proteogenomics. Proteomics, vol.14, pp.2631-2633, 2014.
Mass spectrometry at the interface of proteomics and genomics, Mol BioSyst, vol.7, issue.2, pp.284-91, 2011. ,
Proteogenomic mapping as a complementary method to perform genome annotation, Proteomics, vol.4, issue.1, pp.59-77, 2004. ,
Reannotation of genomes by means of proteomics data, Methods Enzymol, vol.585, pp.201-217, 2017. ,
Proteogenomic methods to improve genome annotation, Methods Mol Biol, vol.1410, pp.77-89, 2016. ,
Mass spectrometry allows direct identification of proteins in large genomes, Proteomics, vol.1, issue.5, pp.641-50, 2001. ,
Proteogenomics: concepts, applications and computational strategies, Nat Methods, vol.11, issue.11, pp.1114-1139, 2014. ,
Proteogenomics from a bioinformatics angle: a growing field, Mass Spectrom Rev, vol.36, issue.5, pp.584-99, 2017. ,
Methods, tools and current perspectives in proteogenomics, Mol Cell Proteomics, vol.16, issue.6, pp.959-81, 2017. ,
Error-tolerant identification of peptides in sequence databases by peptide sequence tags, Anal Chem, vol.66, issue.24, pp.4390-4399, 1994. ,
Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases, Anal Chem, vol.67, issue.18, pp.3202-3212, 1995. ,
Gene model detection using mass spectrometry, Methods Mol Biol, vol.604, pp.137-181, 2010. ,
Genome annotation of Anopheles gambiae using mass spectrometryderived data, BMC Genomics, vol.6, p.128, 2005. ,
Integrated transcriptomicproteomic analysis using a proteogenomic workflow refines rat genome annotation, Mol Cell Proteomics, vol.15, issue.1, pp.329-368, 2016. ,
Forty-four novel protein-coding loci discovered using a proteomics informed by transcriptomics (PIT) approach in rat male germ cells, Biol Reprod, vol.91, issue.5, p.123, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01121802
Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow, Nat Commun, vol.7, p.11778, 2016. ,
Plant proteogenomics: from protein extraction to improved gene predictions, Methods Mol Biol, vol.1002, pp.267-94, 2013. ,
PepLine: a software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences, J Proteome Res, vol.7, issue.5, pp.1873-83, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-02072530
Discovery and revision of Arabidopsis genes by proteogenomics, Proc Natl Acad Sci U S A, vol.105, issue.52, pp.21034-21042, 2008. ,
Proteogenomic analysis of mycobacterium smegmatis using high resolution mass spectrometry, Front Microbiol, vol.7, p.427, 2016. ,
Proteogenomics for environmental microbiology, Proteomics, vol.13, pp.2731-2773, 2013. ,
Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti, PLoS Genet, vol.5, issue.3, p.1000434, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00379051
Identification of new protein coding sequences and signal peptidase cleavage sites of helicobacter pylori strain 26695 by proteogenomics, J Proteome, vol.86, pp.27-42, 2013. ,
Proteogenomic analysis of bacteria and archaea: a 46 organism case study, PLoS One, vol.6, issue.11, p.27587, 2011. ,
Nonmodel organisms, a species endangered by proteogenomics, J Proteome, vol.105, pp.5-18, 2014. ,
PepNovo: de novo peptide sequencing via probabilistic network modeling, Anal Chem, vol.77, issue.4, pp.964-73, 2005. ,
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data, Bioinformatics, vol.28, issue.4, pp.464-473, 2012. ,
, BMC Genomics, vol.20, p.56, 2019.
Quantitative proteomic isotope-coded protein label (ICPL) analysis reveals alteration of several functional processes in the glioblastoma, J Proteome, vol.75, issue.13, pp.3898-913, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00877756
Direct iterative protein profiling (DIPP)-an innovative method for large-scale protein detection applied to budding yeast mitosis, Mol Cell Proteomics, vol.11, issue.2, pp.111-012682, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00682837
2016 update of the PRIDE database and its related tools, Nucleic Acids Res, vol.44, issue.D1, pp.447-56, 2016. ,
Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry, Anal Chem, vol.79, issue.4, pp.1393-400, 2007. ,
The Ectocarpus genome and the independent evolution of multicellularity in brown algae, Nature, vol.465, issue.7298, pp.617-638, 2010. ,
URL : https://hal.archives-ouvertes.fr/cea-00906990
Uncovering the genetic basis for early isogamete differentiation: a case study of Ectocarpus siliculosus, BMC Genomics, vol.14, p.909, 2013. ,
Towards deciphering dynamic changes and evolutionary mechanisms involved in the adaptation to low salinities in Ectocarpus (brown algae), Plant J, vol.71, issue.3, pp.366-77, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-01208656
Proposal of Ectocarpus siliculosus (Ectocarpales, Phaeophyceae) as a model organism for brown algal genetics and genomics, J Phycol, vol.40, pp.1079-88, 2004. ,
The Ectocarpus genome sequence: insights into brown algal biology and the evolutionary diversity of the eukaryotes, New Phytol, vol.188, issue.1, pp.1-4, 2010. ,
High-density genetic map and identification of QTLs for responses to temperature and salinity stresses in the model brown alga, Ectocarpus. Sci Rep, vol.7, p.43241, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01510346
A sequence-tagged genetic map for the brown alga Ectocarpus siliculosus provides large-scale assembly of the genome sequence, New Phytol, vol.188, issue.1, pp.42-51, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-01806415
OUROBOROS is a master regulator of the gametophyte to sporophyte life cycle transition in the brown alga Ectocarpus, Proc Natl Acad Sci, vol.108, issue.28, pp.11518-11541, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-01806390
Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress, Genome Biol, vol.10, issue.6, p.66, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-01806423
A haploid system of sex determination in the brown alga Ectocarpus sp, Curr Biol, vol.24, issue.17, pp.1945-57, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01132642
Development of PCR-based markers to determine the sex of kelps, PLoS One, vol.10, issue.10, p.140535, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01226462
Two-dimensional gel electrophoresis analysis of brown algal protein extracts(1), J Phycol, vol.44, issue.5, pp.1315-1336, 2008. ,
Copper stress proteomics highlights local adaptation of two strains of the model brown alga Ectocarpus siliculosus, Proteomics, vol.10, issue.11, pp.2074-88, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-01925564
HECTAR: a method to predict subcellular targeting in heterokonts, BMC Bioinformatics, vol.9, p.393, 2008. ,
DOI : 10.1186/1471-2105-9-393
URL : https://hal.archives-ouvertes.fr/hal-00359779
The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond, Plant J, vol.80, issue.2, pp.367-81, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01057153
Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching, Anal Chem, vol.73, issue.9, pp.1917-1943, 2001. ,
BioShaDock: a community driven bioinformatics shared Docker-based tools registry, vol.4, p.1443, 2015. ,
DOI : 10.12688/f1000research.7536.1
URL : https://hal.archives-ouvertes.fr/hal-01243520
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences, Genome Biol, vol.11, issue.8, p.86, 2010. ,
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update, Nucleic Acids Res, vol.46, issue.W1, pp.537-581, 2018. ,
DOI : 10.1093/nar/gky379
URL : https://academic.oup.com/nar/article-pdf/46/W1/W537/25110642/gky379.pdf
The proteogenomic mapping tool, BMC Bioinformatics, vol.12, p.115, 2011. ,
DOI : 10.1186/1471-2105-12-115
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-12-115
ProteoAnnotator-open source proteogenomics annotation software supporting PSI standards, Proteomics, vol.14, pp.2731-2772, 2014. ,
DOI : 10.1002/pmic.201400265
URL : http://eprints.keele.ac.uk/3464/1/J%20Wastling%20-%20ProteoAnnotator%20-%20Open%20Source%20proteogenomics%20annotation%20software%20supporting%20PSI%20standards.pdf
PGMiner reloaded, fully automated proteogenomic annotation tool linking genomes to proteomes, J Integr Bioinform, vol.13, issue.4, p.293, 2016. ,
DOI : 10.1515/jib-2016-293
URL : http://www.degruyter.com/downloadpdf/j/jib.2016.13.issue-4/jib-2016-293/jib-2016-293.xml
A hybrid, de novo based, genomewide database search approach applied to the sea urchin neuropeptidome, J Proteome Res, vol.9, issue.2, pp.990-996, 2010. ,
Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework, J Proteome Res, vol.13, issue.12, pp.5898-908, 2014. ,
Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations, BMC Genomics, vol.15, p.703, 2014. ,
Galaxy integrated omics: web-based standards-compliant workflows for proteomics informed by transcriptomics, Mol Cell Proteomics, vol.14, issue.11, pp.3087-93, 2015. ,
DOI : 10.1074/mcp.o115.048777
URL : http://europepmc.org/articles/pmc4638048?pdf=render
Bridging the chromosome-centric and biology/diseasedriven human proteome projects: accessible and automated tools for interpreting the biological and pathological impact of protein sequence variants detected via proteogenomics, J Proteome Res, 2018. ,
An accessible proteogenomics informatics resource for cancer researchers, Cancer Res, vol.77, issue.21, pp.43-49, 2017. ,
DOI : 10.1158/0008-5472.can-17-0331
URL : http://cancerres.aacrjournals.org/content/canres/77/21/e43.full.pdf
Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus, New Phytol, vol.214, issue.1, pp.219-251, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01402123
Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow, Nat Commun, vol.9, issue.1, p.903, 2018. ,
JUMPg: an integrative proteogenomics pipeline identifying unannotated proteins in human brain and Cancer cells, J Proteome Res, vol.15, issue.7, pp.2309-2329, 2016. ,
PGMiner reloaded, fully automated proteogenomic annotation tool linking genomes to proteomes, J Integr Bioinform, vol.13, issue.4, pp.16-23, 2016. ,
PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration, Nucleic Acids Res, vol.43, issue.5, p.29, 2015. ,
PGTools: a software suite for proteogenomic data analysis and visualization, J Proteome Res, vol.14, issue.5, pp.2255-66, 2015. ,
NextSearch: a search engine for mass spectrometry data against a compact nucleotide exon graph, J Proteome Res, vol.14, issue.7, pp.2784-91, 2015. ,
Peppy: proteogenomic search software, J Proteome Res, vol.12, issue.6, pp.3019-3044, 2013. ,