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Items: 1 to 20 of 123

1.

HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers.

Zhu Q, Kosoy M, Dittmar K.

BMC Genomics. 2014 Aug 26;15:717. doi: 10.1186/1471-2164-15-717.

2.

An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales.

Le PT, Ramulu HG, Guijarro L, Paganini J, Gouret P, Chabrol O, Raoult D, Pontarotti P.

BMC Evol Biol. 2012 Dec 12;12:243. doi: 10.1186/1471-2148-12-243.

3.

A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm.

Podell S, Gaasterland T, Allen EE.

BMC Bioinformatics. 2008 Oct 7;9:419. doi: 10.1186/1471-2105-9-419.

4.

The cobweb of life revealed by genome-scale estimates of horizontal gene transfer.

Ge F, Wang LS, Kim J.

PLoS Biol. 2005 Oct;3(10):e316. Epub 2005 Aug 30.

5.

Inferring horizontal gene transfer.

Ravenhall M, Škunca N, Lassalle F, Dessimoz C.

PLoS Comput Biol. 2015 May 28;11(5):e1004095. doi: 10.1371/journal.pcbi.1004095. eCollection 2015 May.

6.

Estimating the extent of horizontal gene transfer in metagenomic sequences.

Tamames J, Moya A.

BMC Genomics. 2008 Mar 24;9:136. doi: 10.1186/1471-2164-9-136.

7.

To tree or not to tree? Genome-wide quantification of recombination and reticulate evolution during the diversification of strict intracellular bacteria.

Hernández-López A, Chabrol O, Royer-Carenzi M, Merhej V, Pontarotti P, Raoult D.

Genome Biol Evol. 2013;5(12):2305-17. doi: 10.1093/gbe/evt178.

8.

The impact of automated filtering of BLAST-determined homologs in the phylogenetic detection of horizontal gene transfer from a transcriptome assembly.

Wisecaver JH, Hackett JD.

Mol Phylogenet Evol. 2014 Feb;71:184-92. doi: 10.1016/j.ympev.2013.11.016. Epub 2013 Dec 7.

PMID:
24321593
9.

MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches.

Song W, Wemheuer B, Zhang S, Steensen K, Thomas T.

Microbiome. 2019 Mar 4;7(1):36. doi: 10.1186/s40168-019-0649-y.

10.

Comparison of genomic islands in cyanobacteria: Evidence of bacteriophage-mediated horizontal gene transfer from eukaryotes.

Godde JS, Baichoo S, Mungloo-Dilmohamud Z, Jaufeerally-Fakim Y.

Microbiol Res. 2018 Jun;211:31-46. doi: 10.1016/j.micres.2018.03.005. Epub 2018 Apr 11.

11.

Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates.

Stanhope MJ, Lupas A, Italia MJ, Koretke KK, Volker C, Brown JR.

Nature. 2001 Jun 21;411(6840):940-4.

PMID:
11418856
12.

Using the nucleotide substitution rate matrix to detect horizontal gene transfer.

Hamady M, Betterton MD, Knight R.

BMC Bioinformatics. 2006 Oct 26;7:476.

13.

Gene gain and loss events in Rickettsia and Orientia species.

Georgiades K, Merhej V, El Karkouri K, Raoult D, Pontarotti P.

Biol Direct. 2011 Feb 8;6:6. doi: 10.1186/1745-6150-6-6.

14.

Origin and Evolution of Rickettsial Plasmids.

El Karkouri K, Pontarotti P, Raoult D, Fournier PE.

PLoS One. 2016 Feb 11;11(2):e0147492. doi: 10.1371/journal.pone.0147492. eCollection 2016.

15.

Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss.

Zhang X, Liu X, Liang Y, Guo X, Xiao Y, Ma L, Miao B, Liu H, Peng D, Huang W, Zhang Y, Yin H.

Appl Environ Microbiol. 2017 Mar 17;83(7). pii: e03098-16. doi: 10.1128/AEM.03098-16. Print 2017 Apr 1.

16.

Untangling hybrid phylogenetic signals: horizontal gene transfer and artifacts of phylogenetic reconstruction.

Beiko RG, Ragan MA.

Methods Mol Biol. 2009;532:241-56. doi: 10.1007/978-1-60327-853-9_14.

PMID:
19271189
17.

The advantages and disadvantages of horizontal gene transfer and the emergence of the first species.

Vogan AA, Higgs PG.

Biol Direct. 2011 Jan 3;6:1. doi: 10.1186/1745-6150-6-1.

18.

A new computational method for the detection of horizontal gene transfer events.

Tsirigos A, Rigoutsos I.

Nucleic Acids Res. 2005 Feb 16;33(3):922-33. Print 2005.

19.

Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns.

Zaneveld JR, Nemergut DR, Knight R.

Microbiology. 2008 Jan;154(Pt 1):1-15. doi: 10.1099/mic.0.2007/011833-0. Review.

PMID:
18174121
20.

Horizontal gene transfer regulation in bacteria as a "spandrel" of DNA repair mechanisms.

Fall S, Mercier A, Bertolla F, Calteau A, Gueguen L, Perrière G, Vogel TM, Simonet P.

PLoS One. 2007 Oct 24;2(10):e1055.

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