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Results: 1 to 20 of 34

1.

The comparison of tree-sibling time consistent phylogenetic networks is graph isomorphism-complete.

Cardona G, Llabrés M, Rosselló F, Valiente G.

ScientificWorldJournal. 2014;2014:254279. doi: 10.1155/2014/254279. Epub 2014 Apr 2.

PMID:
24982934
[PubMed - in process]
Free PMC Article
2.

Further steps in TANGO: improved taxonomic assignment in metagenomics.

Alonso-Alemany D, Barré A, Beretta S, Bonizzoni P, Nikolski M, Valiente G.

Bioinformatics. 2014 Jan 1;30(1):17-23. doi: 10.1093/bioinformatics/btt256. Epub 2013 May 3.

PMID:
23645816
[PubMed - indexed for MEDLINE]
3.

Bioinformatics approaches and tools for metagenomic analysis. Editorial.

Valiente G, Pesole G.

Brief Bioinform. 2012 Nov;13(6):645. doi: 10.1093/bib/bbs079. No abstract available.

PMID:
23175747
[PubMed - indexed for MEDLINE]
4.

Reference databases for taxonomic assignment in metagenomics.

Santamaria M, Fosso B, Consiglio A, De Caro G, Grillo G, Licciulli F, Liuni S, Marzano M, Alonso-Alemany D, Valiente G, Pesole G.

Brief Bioinform. 2012 Nov;13(6):682-95. doi: 10.1093/bib/bbs036. Epub 2012 Jul 10. Review.

PMID:
22786784
[PubMed - indexed for MEDLINE]
5.

Computational challenges of sequence classification in microbiomic data.

Ribeca P, Valiente G.

Brief Bioinform. 2011 Nov;12(6):614-25. doi: 10.1093/bib/bbr019. Epub 2011 Apr 18.

PMID:
21504986
[PubMed - indexed for MEDLINE]
Free Article
6.

Flexible taxonomic assignment of ambiguous sequencing reads.

Clemente JC, Jansson J, Valiente G.

BMC Bioinformatics. 2011 Jan 7;12:8. doi: 10.1186/1471-2105-12-8.

PMID:
21211059
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Comparison of galled trees.

Cardona G, Llabrés M, Rosselló F, Valiente G.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Mar-Apr;8(2):410-27. doi: 10.1109/TCBB.2010.60.

PMID:
20660951
[PubMed - indexed for MEDLINE]
8.

Characterization of phylogenetic networks with NetTest.

Arenas M, Patricio M, Posada D, Valiente G.

BMC Bioinformatics. 2010 May 20;11:268. doi: 10.1186/1471-2105-11-268.

PMID:
20487540
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

An optimized TOPS+ comparison method for enhanced TOPS models.

Veeramalai M, Gilbert D, Valiente G.

BMC Bioinformatics. 2010 Mar 17;11:138. doi: 10.1186/1471-2105-11-138.

PMID:
20236520
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Accurate taxonomic assignment of short pyrosequencing reads.

Clemente JC, Jansson J, Valiente G.

Pac Symp Biocomput. 2010:3-9.

PMID:
19908352
[PubMed - indexed for MEDLINE]
Free Article
11.

On Nakhleh's metric for reduced phylogenetic networks.

Cardona G, Llabrés M, Rosselló F, Valiente G.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Oct-Dec;6(4):629-38. doi: 10.1109/TCBB.2009.33.

PMID:
19875861
[PubMed - indexed for MEDLINE]
12.

Comparison of tree-child phylogenetic networks.

Cardona G, Rosselló F, Valiente G.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Oct-Dec;6(4):552-69. doi: 10.1109/TCBB.2007.70270.

PMID:
19875855
[PubMed - indexed for MEDLINE]
13.

Nodal distances for rooted phylogenetic trees.

Cardona G, Llabrés M, Rosselló F, Valiente G.

J Math Biol. 2010 Aug;61(2):253-76. doi: 10.1007/s00285-009-0295-2. Epub 2009 Sep 16.

PMID:
19760227
[PubMed - indexed for MEDLINE]
14.

Metrics for phylogenetic networks II: nodal and triplets metrics.

Cardona G, Llabrés M, Rosselló F, Valiente G.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Jul-Sep;6(3):454-69. doi: 10.1109/TCBB.2008.127.

PMID:
19644173
[PubMed - indexed for MEDLINE]
15.

All that glisters is not galled.

Rosselló F, Valiente G.

Math Biosci. 2009 Sep;221(1):54-9. doi: 10.1016/j.mbs.2009.06.007. Epub 2009 Jul 2.

PMID:
19576908
[PubMed - indexed for MEDLINE]
16.

Optimized ancestral state reconstruction using Sankoff parsimony.

Clemente JC, Ikeo K, Valiente G, Gojobori T.

BMC Bioinformatics. 2009 Feb 7;10:51. doi: 10.1186/1471-2105-10-51.

PMID:
19200389
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Metrics for phylogenetic networks I: generalizations of the Robinson-Foulds metric.

Cardona G, Llabrés M, Rosselló F, Valiente G.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Jan-Mar;6(1):46-61. doi: 10.1109/TCBB.2008.70.

PMID:
19179698
[PubMed - indexed for MEDLINE]
18.

Efficient reconstruction of metabolic pathways by bidirectional chemical search.

Félix L, Rosselló F, Valiente G.

Bull Math Biol. 2009 Apr;71(3):750-69. doi: 10.1007/s11538-008-9380-8. Epub 2008 Dec 20.

PMID:
19101770
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Extended Newick: it is time for a standard representation of phylogenetic networks.

Cardona G, Rosselló F, Valiente G.

BMC Bioinformatics. 2008 Dec 15;9:532. doi: 10.1186/1471-2105-9-532.

PMID:
19077301
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Seeded tree alignment.

Lozano A, Pinter RY, Rokhlenko O, Valiente G, Ziv-Ukelson M.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Oct-Dec;5(4):503-13. doi: 10.1109/TCBB.2008.59.

PMID:
18989038
[PubMed - indexed for MEDLINE]

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