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A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data.
Coil D, Jospin G, Darling AE. Coil D, et al. Bioinformatics. 2015 Feb 15;31(4):587-9. doi: 10.1093/bioinformatics/btu661. Epub 2014 Oct 22. Bioinformatics. 2015. PMID: 25338718
Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource.
Sharpton TJ, Jospin G, Wu D, Langille MG, Pollard KS, Eisen JA. Sharpton TJ, et al. BMC Bioinformatics. 2012 Oct 13;13:264. doi: 10.1186/1471-2105-13-264. BMC Bioinformatics. 2012. PMID: 23061897 Free PMC article.
Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups.
Wu D, Jospin G, Eisen JA. Wu D, et al. PLoS One. 2013 Oct 17;8(10):e77033. doi: 10.1371/journal.pone.0077033. eCollection 2013. PLoS One. 2013. PMID: 24146954 Free PMC article.
We are particularly interested in identifying and using such marker genes for phylogenetic and phylogeny-driven ecological studies of microbes and their communities (e.g., construction of species trees, phylogenetic based assignment of metagenomic sequence reads to taxonom …
We are particularly interested in identifying and using such marker genes for phylogenetic and phylogeny-driven ecological studies of microb …
PhyloSift: phylogenetic analysis of genomes and metagenomes.
Darling AE, Jospin G, Lowe E, Matsen FA 4th, Bik HM, Eisen JA. Darling AE, et al. PeerJ. 2014 Jan 9;2:e243. doi: 10.7717/peerj.243. eCollection 2014. PeerJ. 2014. PMID: 24482762 Free PMC article.
As a pipeline, PhyloSift incorporates several other programs including LAST, HMMER, and pplacer to automate phylogenetic analysis of protein coding and RNA sequences in metagenomic datasets generated by modern sequencing platforms (e.g., Illumina, 454)....
As a pipeline, PhyloSift incorporates several other programs including LAST, HMMER, and pplacer to automate phylogenetic analysis of protein …
Whole genome sequencing of extended-spectrum β-lactamase producing Klebsiella pneumoniae isolated from a patient in Lebanon.
Tokajian S, Eisen JA, Jospin G, Farra A, Coil DA. Tokajian S, et al. Front Cell Infect Microbiol. 2015 Apr 8;5:32. doi: 10.3389/fcimb.2015.00032. eCollection 2015. Front Cell Infect Microbiol. 2015. PMID: 25905047 Free PMC article.
The final draft genome sequence consists of a combined 5,632,663 bases with 57% G+C content. Automated annotation was performed using the RAST annotation server. ...
The final draft genome sequence consists of a combined 5,632,663 bases with 57% G+C content. Automated annotation was performed using …
Swabs to genomes: a comprehensive workflow.
Dunitz MI, Lang JM, Jospin G, Darling AE, Eisen JA, Coil DA. Dunitz MI, et al. PeerJ. 2015 May 14;3:e960. doi: 10.7717/peerj.960. eCollection 2015. PeerJ. 2015. PMID: 26020012 Free PMC article.
Draft Genome Sequence of Planomicrobium glaciei UCD-HAM (Phylum Firmicutes).
Betts MN, Jospin G, Eisen JA, Coil DA. Betts MN, et al. Genome Announc. 2015 Oct 15;3(5):e01209-15. doi: 10.1128/genomeA.01209-15. Genome Announc. 2015. PMID: 26472846 Free PMC article.
The assembly consists of 3,925,122 bp, contained in 109 contigs, with a G+C content of 46.7%....
The assembly consists of 3,925,122 bp, contained in 109 contigs, with a G+C content of 46.7%....
Genomic attributes of extended-spectrum β-lactamase-producing Escherichia coli isolated from patients in Lebanon.
Tokajian S, Salloum T, Eisen JA, Jospin G, Farra A, Mokhbat JE, Coil DA. Tokajian S, et al. Future Microbiol. 2017 Mar;12:213-226. doi: 10.2217/fmb-2017-0171. Epub 2017 Feb 27. Future Microbiol. 2017. PMID: 28262042
Bacterial communities associated with cell phones and shoes.
Coil DA, Neches RY, Lang JM, Jospin G, Brown WE, Cavalier D, Hampton-Marcell J, Gilbert JA, Eisen JA. Coil DA, et al. Among authors: jospin g. PeerJ. 2020 Jun 9;8:e9235. doi: 10.7717/peerj.9235. eCollection 2020. PeerJ. 2020. PMID: 32551196 Free PMC article.
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