DarkHorse: một phương pháp dự đoán chuyển gene ngang trên toàn bộ bộ gen

Koonin EV, Makarova KS, Aravind L: Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol. 2001, 55: 709-742. 10.1146/annurev.micro.55.1.709.

Lawrence JG, Ochman H: Reconciling the many faces of lateral gene transfer. Trends Microbiol. 2002, 10: 1-4. 10.1016/S0966-842X(01)02282-X.

Andersson JO: Lateral gene transfer in eukaryotes. Cell Mol Life Sci. 2005, 62: 1182-1197. 10.1007/s00018-005-4539-z.

Gogarten JP, Townsend JP: Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol. 2005, 3: 679-687. 10.1038/nrmicro1204.

Bapteste E, Susko E, Leigh J, MacLeod D, Charlebois RL, Doolittle WF: Do orthologous gene phylogenies really support tree-thinking?. BMC Evol Biol. 2005, 5: 33-10.1186/1471-2148-5-33.

Embley TM, Martin W: Eukaryotic evolution, changes and challenges. Nature. 2006, 440: 623-630. 10.1038/nature04546.

Ochman H, Lerat E, Daubin V: Examining bacterial species under the specter of gene transfer and exchange. Proc Natl Acad Sci USA. 2005, 102 (Suppl 1): 6595-6599. 10.1073/pnas.0502035102.

Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, Van de Peer Y, Vandamme P, Thompson FL, Swings J: Opinion: re-evaluating prokaryotic species. Nat Rev Microbiol. 2005, 3: 733-739. 10.1038/nrmicro1236.

Ge F, Wang LS, Kim J: The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol. 2005, 3: e316-10.1371/journal.pbio.0030316.

Gophna U, Charlebois RL, Doolittle WF: Have archaeal genes contributed to bacterial virulence?. Trends Microbiol. 2004, 12: 213-219. 10.1016/j.tim.2004.03.002.

Faguy DM: Lateral gene transfer (LGT) between Archaea and Escherichia coli is a contributor to the emergence of novel infectious disease. BMC Infect Dis. 2003, 3: 13-10.1186/1471-2334-3-13.

Ragan MA, Harlow TJ, Beiko RG: Do different surrogate methods detect lateral genetic transfer events of different relative ages?. Trends Microbiol. 2006, 14: 4-8. 10.1016/j.tim.2005.11.004.

Sharp PM, Li WH: The codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987, 15: 1281-1295. 10.1093/nar/15.3.1281.

Lawrence JG, Ochman H: Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol. 1997, 44: 383-397. 10.1007/PL00006158.

Garcia-Vallve S, Guzman E, Montero MA, Romeu A: HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res. 2003, 31: 187-189. 10.1093/nar/gkg004.

Dalevi D, Dubhashi D, Hermansson M: Bayesian classifiers for detecting HGT using fixed and variable order Markov models of genomic signatures. Bioinformatics. 2006, 22: 517-522. 10.1093/bioinformatics/btk029.

Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, Surovcik K, Meinicke P, Merkl R: Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics. 2006, 7: 142-10.1186/1471-2105-7-142.

Saunders NJ, Boonmee P, Peden JF, Jarvis SA: Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori. BMC Genomics. 2005, 6: 9-10.1186/1471-2164-6-9.

Tsirigos A, Rigoutsos I: A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes. Nucleic Acids Res. 2005, 33: 3699-3707. 10.1093/nar/gki660.

Koski LB, Morton RA, Golding GB: Codon bias and base composition are poor indicators of horizontally transferred genes. Mol Biol Evol. 2001, 18: 404-412.

Wang B: Limitations of compositional approach to identifying horizontally transferred genes. J Mol Evol. 2001, 53: 244-250. 10.1007/s002390010214.

Gophna U, Charlebois RL, Doolittle WF: Ancient lateral gene transfer in the evolution of Bdellovibrio bacteriovorus. Trends Microbiol. 2006, 14: 64-69. 10.1016/j.tim.2005.12.008.

Ortutay C, Gaspari Z, Toth G, Jager E, Vida G, Orosz L, Vellai T: Speciation in Chlamydia : genomewide phylogenetic analyses identified a reliable set of acquired genes. J Mol Evol. 2003, 57: 672-680. 10.1007/s00239-003-2517-3.

Guindon S, Perriere G: Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes. Mol Biol Evol. 2001, 18: 1838-1840.

Tsirigos A, Rigoutsos I: A new computational method for the detection of horizontal gene transfer events. Nucleic Acids Res. 2005, 33: 922-933. 10.1093/nar/gki187.

Martin W: Gene transfer from organelles to the nucleus: frequent and in big chunks. Proc Natl Acad Sci USA. 2003, 100: 8612-8614. 10.1073/pnas.1633606100.

Santos SR, Ochman H: Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ Microbiol. 2004, 6: 754-759. 10.1111/j.1462-2920.2004.00617.x.

Clarke GD, Beiko RG, Ragan MA, Charlebois RL: Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J Bacteriol. 2002, 184: 2072-2080. 10.1128/JB.184.8.2072-2080.2002.

Lyubetsky VA, V'Yugin VV: Methods of horizontal gene transfer determination using phylogenetic data. In Silico Biol. 2003, 3: 17-31.

MacLeod D, Charlebois RL, Doolittle F, Bapteste E: Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. BMC Evol Biol. 2005, 5: 27-10.1186/1471-2148-5-27.

Zhaxybayeva O, Gogarten JP: An improved probability mapping approach to assess genome mosaicism. BMC Genomics. 2003, 4: 37-10.1186/1471-2164-4-37.

Daubin V, Ochman H: Quartet mapping and the extent of lateral transfer in bacterial genomes. Mol Biol Evol. 2004, 21: 86-89. 10.1093/molbev/msg234.

Sicheritz-Ponten T, Andersson SG: A phylogenomic approach to microbial evolution. Nucleic Acids Res. 2001, 29: 545-552. 10.1093/nar/29.2.545.

Frickey T, Lupas AN: PhyloGenie: automated phylome generation and analysis. Nucleic Acids Res. 2004, 32: 5231-5238. 10.1093/nar/gkh867.

Huang J, Mullapudi N, Sicheritz-Ponten T, Kissinger JC: A first glimpse into the pattern and scale of gene transfer in Apicomplexa. Int J Parasitol. 2004, 34: 265-274. 10.1016/j.ijpara.2003.11.025.

Koski LB, Golding GB: The closest BLAST hit is often not the nearest neighbor. J Mol Evol. 2001, 52: 540-542.

Eisen JA: Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr Opin Genet Dev. 2000, 10: 606-611. 10.1016/S0959-437X(00)00143-X.

Pariasca JAT, Sunaga A, Miyazaki T, Hisaka H, Sonoda M, Nakagawa H, Sato T: Cloning of cDNAs encoding senescence-associated genes, ACC synthase and ACC oxidase from stored snow pea pods (Pisum sativum L. var saccharatum) and their expression during pod storage. Postharvest Biol Technol. 2001, 22: 191-290. 10.1016/S0925-5214(01)00094-1.

Ruepp A, Graml W, Santos-Martinez ML, Koretke KK, Volker C, Mewes HW, Frishman D, Stocker S, Lupas AN, Baumeister W: The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature. 2000, 407: 508-513. 10.1038/35035069.

Mongodin EF, Hance IR, Deboy RT, Gill SR, Daugherty S, Huber R, Fraser CM, Stetter K, Nelson KE: Gene transfer and genome plasticity in Thermotoga maritima, a model hyperthermophilic species. J Bacteriol. 2005, 187: 4935-4944. 10.1128/JB.187.14.4935-4944.2005.

Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, et al: Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature. 1999, 399: 323-329. 10.1038/20601.

Nesbo CL, L'Haridon S, Stetter KO, Doolittle WF: Phylogenetic analyses of two 'archaeal' genes in thermotoga maritima reveal multiple transfers between archaea and bacteria. Mol Biol Evol. 2001, 18: 362-375.

Loftus B, Anderson I, Davies R, Alsmark UC, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP, Mann BJ, et al: The genome of the protist parasite Entamoeba histolytica. Nature. 2005, 433: 865-868. 10.1038/nature03291.

Sharma A, Sojar HT, Glurich I, Honma K, Kuramitsu HK, Genco RJ: Cloning, expression, and sequencing of a cell surface antigen containing a leucine-rich repeat motif from Bacteroides forsythus ATCC 43037. Infect Immun. 1998, 66: 5703-5710.

NCBI GenBank Genomes. [ftp://ftp.ncbi.nih.gov/genbank/genomes/]

dictyBase. [http://dictybase.org/db/cgi-bin/dictyBase/download/blast_databases.pl]

The TIGR Arabidopsis thaliana Database. [http://www.tigr.org/tdb/e2k1/ath1/]

NCBI BLAST Database. [ftp://ftp.ncbi.nih.gov/blast/db/]

NCBI Taxonomy Database. [ftp://ftp.ncbi.nih.gov/pub/taxonomy]