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LRCstats, a tool for evaluating long reads correction methods.
La S, Haghshenas E, Chauve C. La S, et al. Among authors: chauve c. Bioinformatics. 2017 Nov 15;33(22):3652-3654. doi: 10.1093/bioinformatics/btx489. Bioinformatics. 2017. PMID: 29036421
A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.
Chauve C, Tannier E. Chauve C, et al. PLoS Comput Biol. 2008 Nov;4(11):e1000234. doi: 10.1371/journal.pcbi.1000234. Epub 2008 Nov 28. PLoS Comput Biol. 2008. PMID: 19043541 Free PMC article.
Reconstructing the architecture of the ancestral amniote genome.
Ouangraoua A, Tannier E, Chauve C. Ouangraoua A, et al. Among authors: chauve c. Bioinformatics. 2011 Oct 1;27(19):2664-71. doi: 10.1093/bioinformatics/btr461. Epub 2011 Aug 16. Bioinformatics. 2011. PMID: 21846735
This strategy offers a solid methodological base for the reconstruction of ancient vertebrate genomes. AVAILABILITY: Source code, in C++ and Python, is available at http://www.cecm.sfu.ca/~cchauve/SUPP/AMNIOTE2010/ CONTACT: cedric.chauve@sfu.ca SUPPLEMENTARY INFORMA …
This strategy offers a solid methodological base for the reconstruction of ancient vertebrate genomes. AVAILABILITY: Source code, in C
Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes.
Wittler R, Chauve C. Wittler R, et al. Among authors: chauve c. BMC Bioinformatics. 2011 Oct 5;12 Suppl 9(Suppl 9):S21. doi: 10.1186/1471-2105-12-S9-S21. BMC Bioinformatics. 2011. PMID: 22152084 Free PMC article.
ANGES: reconstructing ANcestral GEnomeS maps.
Jones BR, Rajaraman A, Tannier E, Chauve C. Jones BR, et al. Among authors: chauve c. Bioinformatics. 2012 Sep 15;28(18):2388-90. doi: 10.1093/bioinformatics/bts457. Epub 2012 Jul 20. Bioinformatics. 2012. PMID: 22820205
FPSAC: fast phylogenetic scaffolding of ancient contigs.
Rajaraman A, Tannier E, Chauve C. Rajaraman A, et al. Among authors: chauve c. Bioinformatics. 2013 Dec 1;29(23):2987-94. doi: 10.1093/bioinformatics/btt527. Epub 2013 Sep 24. Bioinformatics. 2013. PMID: 24068034
Polytomy refinement for the correction of dubious duplications in gene trees.
Lafond M, Chauve C, Dondi R, El-Mabrouk N. Lafond M, et al. Among authors: chauve c. Bioinformatics. 2014 Sep 1;30(17):i519-26. doi: 10.1093/bioinformatics/btu463. Bioinformatics. 2014. PMID: 25161242 Free PMC article.
The BRaliBase dent-a tale of benchmark design and interpretation.
Löwes B, Chauve C, Ponty Y, Giegerich R. Löwes B, et al. Among authors: chauve c. Brief Bioinform. 2017 Mar 1;18(2):306-311. doi: 10.1093/bib/bbw022. Brief Bioinform. 2017. PMID: 26984616 Free PMC article.
ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony.
Jacox E, Chauve C, Szöllősi GJ, Ponty Y, Scornavacca C. Jacox E, et al. Among authors: chauve c. Bioinformatics. 2016 Jul 1;32(13):2056-8. doi: 10.1093/bioinformatics/btw105. Epub 2016 Feb 26. Bioinformatics. 2016. PMID: 27153713
CoLoRMap: Correcting Long Reads by Mapping short reads.
Haghshenas E, Hach F, Sahinalp SC, Chauve C. Haghshenas E, et al. Among authors: chauve c. Bioinformatics. 2016 Sep 1;32(17):i545-i551. doi: 10.1093/bioinformatics/btw463. Bioinformatics. 2016. PMID: 27587673
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