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Results: 1 to 20 of 59

1.

Orthology detection combining clustering and synteny for very large datasets.

Lechner M, Hernandez-Rosales M, Doerr D, Wieseke N, Thévenin A, Stoye J, Hartmann RK, Prohaska SJ, Stadler PF.

PLoS One. 2014 Aug 19;9(8):e105015. doi: 10.1371/journal.pone.0105015. eCollection 2014.

PMID:
25137074
[PubMed - in process]
Free PMC Article
2.

morFeus: a web-based program to detect remotely conserved orthologs using symmetrical best hits and orthology network scoring.

Wagner I, Volkmer M, Sharan M, Villaveces JM, Oswald F, Surendranath V, Habermann BH.

BMC Bioinformatics. 2014 Aug 6;15:263. doi: 10.1186/1471-2105-15-263.

PMID:
25096057
[PubMed - in process]
Free PMC Article
3.

Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification.

Pongor LS, Vera R, Ligeti B.

PLoS One. 2014 Jul 31;9(7):e103441. doi: 10.1371/journal.pone.0103441. eCollection 2014.

PMID:
25077800
[PubMed - in process]
Free PMC Article
4.

Coiled-coil proteins facilitated the functional expansion of the centrosome.

Kuhn M, Hyman AA, Beyer A.

PLoS Comput Biol. 2014 Jun 5;10(6):e1003657. doi: 10.1371/journal.pcbi.1003657. eCollection 2014 Jun.

PMID:
24901223
[PubMed - in process]
Free PMC Article
5.

Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score.

Chiba H, Uchiyama I.

BMC Bioinformatics. 2014 May 18;15:148. doi: 10.1186/1471-2105-15-148.

PMID:
24885064
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Genome sequence of Ensifer adhaerens OV14 provides insights into its ability as a novel vector for the genetic transformation of plant genomes.

Rudder S, Doohan F, Creevey CJ, Wendt T, Mullins E.

BMC Genomics. 2014 Apr 7;15:268. doi: 10.1186/1471-2164-15-268.

PMID:
24708309
[PubMed - in process]
Free PMC Article
7.

Abnormal fecal microbiota community and functions in patients with hepatitis B liver cirrhosis as revealed by a metagenomic approach.

Wei X, Yan X, Zou D, Yang Z, Wang X, Liu W, Wang S, Li X, Han J, Huang L, Yuan J.

BMC Gastroenterol. 2013 Dec 26;13:175. doi: 10.1186/1471-230X-13-175.

PMID:
24369878
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

eggNOG v4.0: nested orthology inference across 3686 organisms.

Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P.

Nucleic Acids Res. 2014 Jan;42(Database issue):D231-9. doi: 10.1093/nar/gkt1253. Epub 2013 Dec 1.

PMID:
24297252
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032.

Mentz A, Neshat A, Pfeifer-Sancar K, Pühler A, Rückert C, Kalinowski J.

BMC Genomics. 2013 Oct 19;14:714. doi: 10.1186/1471-2164-14-714.

PMID:
24138339
[PubMed - in process]
Free PMC Article
10.

A new method for extracting skin microbes allows metagenomic analysis of whole-deep skin.

Garcia-Garcerà M, Garcia-Etxebarria K, Coscollà M, Latorre A, Calafell F.

PLoS One. 2013 Sep 20;8(9):e74914. doi: 10.1371/journal.pone.0074914. eCollection 2013.

PMID:
24073227
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks.

Jin Y, Turaev D, Weinmaier T, Rattei T, Makse HA.

PLoS One. 2013;8(3):e58134. doi: 10.1371/journal.pone.0058134. Epub 2013 Mar 20.

PMID:
23526967
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer.

Wolf YI, Makarova KS, Yutin N, Koonin EV.

Biol Direct. 2012 Dec 14;7:46. doi: 10.1186/1745-6150-7-46.

PMID:
23241446
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis.

Whiteside MD, Winsor GL, Laird MR, Brinkman FS.

Nucleic Acids Res. 2013 Jan;41(Database issue):D366-76. doi: 10.1093/nar/gks1241. Epub 2012 Nov 29.

PMID:
23203876
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

The ac53, ac78, ac101, and ac103 genes are newly discovered core genes in the family Baculoviridae.

Garavaglia MJ, Miele SA, Iserte JA, Belaich MN, Ghiringhelli PD.

J Virol. 2012 Nov;86(22):12069-79. doi: 10.1128/JVI.01873-12. Epub 2012 Aug 29.

PMID:
22933288
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Millimeter-scale patterns of phylogenetic and trait diversity in a salt marsh microbial mat.

Armitage DW, Gallagher KL, Youngblut ND, Buckley DH, Zinder SH.

Front Microbiol. 2012 Aug 10;3:293. doi: 10.3389/fmicb.2012.00293. eCollection 2012.

PMID:
22908010
[PubMed]
Free PMC Article
16.

QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence.

Yu C, Desai V, Cheng L, Reifman J.

BMC Bioinformatics. 2012 Jun 22;13:143. doi: 10.1186/1471-2105-13-143.

PMID:
22726705
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Evolutionary patterns of carbohydrate transport and metabolism in Halomonas boliviensis as derived from its genome sequence: influences on polyester production.

Guzmán D, Balderrama-Subieta A, Cardona-Ortuño C, Guevara-Martínez M, Callisaya-Quispe N, Quillaguamán J.

Aquat Biosyst. 2012 Apr 17;8(1):9. doi: 10.1186/2046-9063-8-9.

PMID:
22510370
[PubMed]
Free PMC Article
18.

Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life.

Puigbò P, Wolf YI, Koonin EV.

Methods Mol Biol. 2012;856:53-79. doi: 10.1007/978-1-61779-585-5_3.

PMID:
22399455
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates.

Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CC, Troost FJ, Bork P, Wels M, de Vos WM, Kleerebezem M.

ISME J. 2012 Jul;6(7):1415-26. doi: 10.1038/ismej.2011.212. Epub 2012 Jan 19.

PMID:
22258098
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Dissecting plant genomes with the PLAZA comparative genomics platform.

Van Bel M, Proost S, Wischnitzki E, Movahedi S, Scheerlinck C, Van de Peer Y, Vandepoele K.

Plant Physiol. 2012 Feb;158(2):590-600. doi: 10.1104/pp.111.189514. Epub 2011 Dec 23.

PMID:
22198273
[PubMed - indexed for MEDLINE]
Free PMC Article

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