[1] Muzzi A, Masignani V, Rappuoli R. The pan-genome: towards a knowledge-based discovery of novel targets for vaccines and antibacterials. Drug Discov Today, 2007, 12(11-12): 429-439.
[2] Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R. The microbial pan-genome. Curr Opin Genet Dev, 2005, 15(6): 589-594.
[3] Lefebure T, Stanhope MJ. Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol, 2007, 8(5): R71.
[4] Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarity Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Se-lengut J, Gwinn ML, Zhou LW, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O'Connor KJB, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM. Genome analysis of multiple pathogenic iso-lates of Streptococcus agalactiae: implications for the microbial pan-genome. Proc Natl Acad Sci, 2005, 102(39): 13950-13955.
[5] Bambini S, Rappuoli R. The use of genomics in microbial vaccine development. Drug Discov Today, 2009, 14(5-6): 252-260.
[6] Rasko DA, Rosovitz MJ, Myers GSA, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sebaihia M, Thomson NR, Chaudhuri R, Henderson IR, Sperandio V, Ravel J. The pangenome structure of Escherichia coli: com-parative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol, 2008, 190(20): 6881-6893.
[7] Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, Calteau A, Chiapello H, Clermont O, Cruveiller S, Dan-chin A, Diard M, Dossat C, Karoui ME, Frapy E, Garry L, Ghigo JM, Gilles AM, Johnson J, Le Bouguénec C, Lescat M, Mangenot S, Martinez-Jéhanne V, Matic I, Nassif X, Oztas S, Petit MA, Pichon C, Rouy Z, Ruf CS, Schneider D, Tourret J, Vacherie B, Vallenet D, Médigue C, Rocha EP, Denamur E. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet, 2009, 5(1): 1000344.
[8] Davids W, Zhang ZL. The impact of horizontal gene transfer in shaping operons and protein interaction networks--direct evidence of preferential attachment. BMC Evol Biol, 2008, 8: 23.
[9] Zhang R, Lin Y. DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res, 2009, 37(1): 455-458.
[10] Remm M, Storm CEV, Sonnhammer ELL. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol, 2001, 314(5): 1041-1052.
[11] Enright AJ, Dongen SV, Ouzounis CA. An efficient algo-rithm for large-scale detection of protein families. Nucleic Acids Res, 2002, 30(7): 1575-1584.
[12] Shi GQ, Zhang LQ, Jiang T. MSOAR 2.0: Incorporating tan-dem duplications into ortholog assignment based on genome rearrangement. BMC Bioinformatics, 2010, 11: 10.
[13] Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: A tool for genome-scale analysis of pro-tein functions and evolution. Nucleic Acids Res, 2000, 28(1): 33-36.
[14] Katoh K, Toh H. Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics, 2010, 26(15): 1899-1900.
[15] Hogg JS, Hu FZ, Janto B, Boissy R, Hayes J, Keefe R, Post JC, Ehrlich GD. Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains. Genome Biol, 2007, 8(6): R103.
[16] Hiller NL, Janto B, Hogg JS, Boissy R, Yu S, Powell E, Keefe R, Ehrlich NE, Shen K, Hayes J, Barbadora K, Klimke W, Dernovoy D
