基于基因组的屎肠球菌进化和功能研究
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摘要
全基因组研究是分析细菌的遗传特性、菌株的亲缘关系和毒性特征的重要方法。本文主要基于屎肠球菌基因组信息，来系统的分析其相关特性。屎肠球菌在自然界通常扮演两种角色，共生于人肠道的细菌及重要的医院病原菌，后者常伴随有多种抗生素耐药性。然而，分离于不同环境的菌株，其基因组往往表现出很大的多样性。本文首先对28株来源不同的屎肠球菌进行比较基因组分析，揭示屎肠球菌基因组的开放特性及其亲缘关系。在分析这种亲缘关系时，分别采用了16SrRNA、MLST、核心基因组的方法。随后，针对一株医院病原屎肠球菌C309，我们以全基因组分析为研究手段，试图建立一套标准的医院病原菌的分析方法。为了获得较为完整的基因组，我们采用三种不同的新一代测序平台（Roche的454GS-FLX，Illumina公司GAIIx，ABI公司的SOLiD4.0）对C309进行全基因组测序。同时，我们建立了一套混合拼接的方法，相比单一平台的拼接结果，三种平台数据的混合拼接，能够得到更加完整的基因组。此外，通过评估不同测序平台之间的偏好性如覆盖深度的偏好、特定序列的偏好（GC含量，k-mer多样性）和平台特异性替换错误的偏好，给出了一些可以帮助细菌基因组拼接的指导建议。在C309全基因组功能分析中，基于KEGG、COG、ARDB和PAIDB数据库，对其基因功能模块的注释，分析基因富集的主要代谢通路,特异性蛋白的来源，耐药性和潜在毒性。我们的研究将对其他基于基因组病原微生物的研究工作，具有直接的指导意义。
论文的第四章为博士学习期间另一部分主要研究工作，该部分介绍了人类疾病相关基因的表达敏感特性，展示与不同疾病相关的基因，受到外界扰动时，基因的表达差异特性。我们发现癌症、衰老和药物基因组学相关基因都表现出非易扰性，而精神类，化学药物依赖类和生殖相关的基因都表现出易扰性。因此，研究疾病基因的表达敏感性，可能有助于疾病的病因查找和发病机制的阐述。
The Genome-based research is an important approach to analyze thegenetic characteristics of bacteria, relationships among close relatedpathogenic strains and toxicity. This article is primarily based on genomicinformation to investigate Enterococcus faecium systematically.Enterococcus faecium is a commensal bacterium inhabiting in thegastrointestinal tract of human, and an important nosocomial pathogenwhich is often accompanied with a variety of antibiotics resistance. Somestudies suggested strains isolated from different environments often hadhighly divergent genomes. To illustrate this feature, firstly, thecomparative genome study of28E. faecium strains was performed. Then,we analyzed the phylogenetic relationships with methods of16S rRNA,the MLST and core genome respectively. After that, we studied a hospitalpathogen Enterococcus faecium C309by whole genome analysis andtried to establish a standard set of research strategy for the hospitalpathogens studies. In order to obtain a more complete genome, we haveadopted three different NGS platform (Roche454GS-FLX, Illumina GAIIx and ABI SOLiD4.0) to perform whole-genome sequencing. Then,we established a hybrid assembly method to integrate data from threeplatforms and constructed a more complete genome in comparison withusing any single platform data. In addition, the biases of platforms wereassessed, including biases of coverage depth, specific sequence biases(GC content and the k-mer diversity) and the bias from platform-specificsubstitution errors, to provide valuable guidelines for the genomeassembly. After acquiring C309genome sequence, the whole genomefunctional analysis was performed to character the major metabolicpathway, the source of specific proteins, antibiotic resistance andpotential toxicity. In all, our study helped form some guidelines to directgenomic work on other microorganisms, thus have important practicalimplications.
The fourth chapter of the thesis described another major researchwork during the doctoral studies. In that section, we illustrated theexpression sensitivity of human disease-related genes. The genesassociated with distinct diseases reveals different expression perturbationsensitivities in various conditions. The diseases associated with robustgenes seem to be relatively lethal like cancer, aging andpharmacogenomic. On the other hand, the diseases associated withsensitive genes are apparently nonlethal like psych, chemdependency andreproduction diseases. Thus, this work may help to discover the etiologyand pathogenesis of common disease.
论文的第四章为博士学习期间另一部分主要研究工作，该部分介绍了人类疾病相关基因的表达敏感特性，展示与不同疾病相关的基因，受到外界扰动时，基因的表达差异特性。我们发现癌症、衰老和药物基因组学相关基因都表现出非易扰性，而精神类，化学药物依赖类和生殖相关的基因都表现出易扰性。因此，研究疾病基因的表达敏感性，可能有助于疾病的病因查找和发病机制的阐述。
The Genome-based research is an important approach to analyze thegenetic characteristics of bacteria, relationships among close relatedpathogenic strains and toxicity. This article is primarily based on genomicinformation to investigate Enterococcus faecium systematically.Enterococcus faecium is a commensal bacterium inhabiting in thegastrointestinal tract of human, and an important nosocomial pathogenwhich is often accompanied with a variety of antibiotics resistance. Somestudies suggested strains isolated from different environments often hadhighly divergent genomes. To illustrate this feature, firstly, thecomparative genome study of28E. faecium strains was performed. Then,we analyzed the phylogenetic relationships with methods of16S rRNA,the MLST and core genome respectively. After that, we studied a hospitalpathogen Enterococcus faecium C309by whole genome analysis andtried to establish a standard set of research strategy for the hospitalpathogens studies. In order to obtain a more complete genome, we haveadopted three different NGS platform (Roche454GS-FLX, Illumina GAIIx and ABI SOLiD4.0) to perform whole-genome sequencing. Then,we established a hybrid assembly method to integrate data from threeplatforms and constructed a more complete genome in comparison withusing any single platform data. In addition, the biases of platforms wereassessed, including biases of coverage depth, specific sequence biases(GC content and the k-mer diversity) and the bias from platform-specificsubstitution errors, to provide valuable guidelines for the genomeassembly. After acquiring C309genome sequence, the whole genomefunctional analysis was performed to character the major metabolicpathway, the source of specific proteins, antibiotic resistance andpotential toxicity. In all, our study helped form some guidelines to directgenomic work on other microorganisms, thus have important practicalimplications.
The fourth chapter of the thesis described another major researchwork during the doctoral studies. In that section, we illustrated theexpression sensitivity of human disease-related genes. The genesassociated with distinct diseases reveals different expression perturbationsensitivities in various conditions. The diseases associated with robustgenes seem to be relatively lethal like cancer, aging andpharmacogenomic. On the other hand, the diseases associated withsensitive genes are apparently nonlethal like psych, chemdependency andreproduction diseases. Thus, this work may help to discover the etiologyand pathogenesis of common disease.
引文
1. Euzéby J: List of prokaryotic names with standing in nomenclature-genus. In.:Mycobacterium;2008.
2. Naser S, Thompson F, Hoste B, Gevers D, Vandemeulebroecke K, Cleenwerck I,Thompson C, Vancanneyt M, Swings J: Phylogeny and identification of enterococciby atpA gene sequence analysis. Journal of clinical microbiology2005,43(5):2224.
3. Devriese L, Pot B:10The genus Enterococcus. Genera of Lactic Acid Bacteria1995,2:327.
4. Treitman AN, Yarnold PR, Warren J, Noskin GA: Emerging incidence ofEnterococcus faecium among hospital isolates (1993to2002). Journal of clinicalmicrobiology2005,43(1):462.
5. Top J, Willems R, Blok H, De Regt M, Jalink K, Troelstra A, Goorhuis B, BontenM: Ecological replacement of Enterococcus faecalis by multiresistant clonalcomplex17Enterococcus faecium. Clinical microbiology and infection2007,13(3):316-319.
6. Montero CI, Stock F, Murray PR: Mechanisms of resistance to daptomycin inEnterococcus faecium. Antimicrobial agents and chemotherapy2008,52(3):1167-1170.
7. Scheetz MH, Knechtel S, Malczynski M, Postelnick MJ, Qi C: IncreasingIncidence of Linezolid Intermediate or Resistant, Vancomycin-ResistantEnterococcus faecium (LIRVREF) Parallels Increasing Linezolid Consumption.Antimicrobial agents and chemotherapy2008:AAC.00070-00008v00071.
8. Hidron AI, Edwards JR, Patel J, Horan TC, Sievert DM, Pollock DA, Fridkin SK:Antimicrobial‐resistant pathogens associated with healthcare‐associatedinfections: annual summary of data reported to the National Healthcare SafetyNetwork at the Centers for Disease Control and Prevention,2006–2007. infectioncontrol and hospital epidemiology2008,29(11):996-1011.
9. Werner G, Coque T, Hammerum A, Hope R, Hryniewicz W, Johnson A, Klare I,Kristinsson K, Leclercq R, Lester C: Emergence and spread of vancomycinresistance among enterococci in Europe. Euro Surveill2008,13(47):1-11.
10. Arthur M, Depardieu F, Reynolds P, Courvalin P: Quantitative analysis of themetabolism of soluble cytoplasmic peptidoglycan precursors of glycopeptide‐resistant enterococci. Molecular microbiology1996,21(1):33-44.
11. Depardieu F, Reynolds PE, Courvalin P: VanD-type vancomycin-resistantEnterococcus faecium10/96A. Antimicrobial agents and chemotherapy2003,47(1):7-18.
12. Reynolds PE, Courvalin P: Vancomycin resistance in enterococci due tosynthesis of precursors terminating in D-alanyl-D-serine. Antimicrobial agentsand chemotherapy2005,49(1):21-25.
13. Leavis HL, Willems RJL, Van Wamel WJB, Schuren FH, Caspers MPM, BontenMJM: Insertion Sequence–Driven Diversification Creates a Globally DispersedEmerging Multiresistant Subspecies of E. faecium. PLoS pathogens2007,3(1):e7.
14. Homan WL, Tribe D, Poznanski S, Li M, Hogg G, Spalburg E, van Embden JDA,Willems RJL: Multilocus sequence typing scheme for Enterococcus faecium.Journal of clinical microbiology2002,40(6):1963.
15. Vancanneyt M, Lombardi A, Andrighetto C, Knijff E, Torriani S, Bjorkroth KJ,Franz CMAP, Foulquie Moreno MR, Revets H, De Vuyst L: Intraspecies genomicgroups in Enterococcus faecium and their correlation with origin andpathogenicity. Applied and environmental microbiology2002,68(3):1381.
16. Willems R, Top J, van Santen M, Robinson DA, Coque TM, Baquero F,Grundmann H, Bonten M: Global spread of vancomycin-resistant Enterococcusfaecium from distinct nosocomial genetic complex. Emerg Infect Dis2005,11(6):821-828.
17. Leavis HL, Bonten MJM, Willems RJL: Identification of high-riskenterococcal clonal complexes: global dispersion and antibiotic resistance.Current opinion in microbiology2006,9(5):454-460.
18. Heikens E, Bonten MJM, Willems RJL: Enterococcal surface protein Esp isimportant for biofilm formation of Enterococcus faecium E1162. Journal ofbacteriology2007,189(22):8233.
19. Leendertse M, Heikens E, Wijnands LM, van Luit-Asbroek M, Teske GJD,Roelofs JJTH, Bonten MJM, Van der Poll T, Willems RJL: Enterococcal SurfaceProtein Transiently Aggravates Enterococcus faecium–Induced Urinary TractInfection in Mice. Journal of Infectious Diseases2009,200(7):1162.
20. Nallapareddy SR, Weinstock GM, Murray BE: Clinical isolates of Enterococcusfaecium exhibit strain‐specific collagen binding mediated by Acm, a newmember of the MSCRAMM family. Molecular microbiology2003,47(6):1733-1747.
21. Nallapareddy SR, Singh KV, Murray BE: Contribution of the collagen adhesinAcm to pathogenesis of Enterococcus faecium in experimental endocarditis.Infection and immunity2008,76(9):4120.
22. Rice LB, Carias L, Rudin S, Vael C, Goossens H, Konstabel C, Klare I,Nallapareddy SR, Huang W, Murray BE: A potential virulence gene, hylEfm,predominates in Enterococcus faecium of clinical origin. Journal of InfectiousDiseases2003,187(3):508.
23. Eppinger M, Mammel MK, LeClerc JE, Ravel J, Cebula TA: Genome signaturesof Escherichia coli O157: H7isolates from the bovine host reservoir. Applied andenvironmental microbiology2011,77(9):2916-2925.
24. Van Schaik W, Top J, Riley D, Boekhorst J, Vrijenhoek J, Schapendonk C,Hendrickx A, Nijman I, Bonten M, Tettelin H: Pyrosequencing-based comparativegenome analysis of the nosocomial pathogen Enterococcus faecium andidentification of a large transferable pathogenicity island. Bmc Genomics2010,11(1):239.
25. Watson JD, Crick FHC: Molecular structure of nucleic acids. Nature1953,171(4356):737-738.
26. Whitfeld P: A method for the determination of nucleotide sequence inpolyribonucleotides. Biochemical Journal1954,58(3):390.
27. Davis BD: The human genome and other initiatives. Science1990,249(4967):342.
28. Mardis ER: The impact of next-generation sequencing technology on genetics.Trends in Genetics2008,24(3):133-141.
29. Morozova O, Marra MA: Applications of next-generation sequencingtechnologies in functional genomics. Genomics2008,92(5):255-264.
30. Strausberg RL, Levy S, Rogers YH: Emerging DNA sequencing technologiesfor human genomic medicine. Drug discovery today2008,13(13-14):569-577.
31. Pettersson E, Lundeberg J, Ahmadian A: Generations of sequencingtechnologies. Genomics2009,93(2):105-111.
32. Sanger F, Nicklen S, Coulson AR: DNA sequencing with chain-terminatinginhibitors. Proceedings of the National Academy of Sciences1977,74(12):5463.
33. http://my454.com/products/technology.asp.
34. Berka J, Chen YJ, Leamon JH, Lefkowitz S, Lohman KL, Makhijani VB,Rothberg JM, Sarkis GJ, Srinivasan M, Weiner MP: Bead emulsion nucleic acidamplification. In.: Google Patents;2011.
35. http://wwwpyrosequencingcom/DynPageaspx.
36. Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM: Accuracy andquality of massively parallel DNA pyrosequencing. Genome Biol2007,8(7):R143.
37.http://wwwappliedbiosystemscom/absite/us/en/home/applications-technologies/solid-next-generation-sequencinghtml.
38. http://wwwilluminacom/.
39. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P,Bettman B: Real-time DNA sequencing from single polymerase molecules. Science2009,323(5910):133.
40. Ewing B, Green P: Base-calling of automated sequencer traces usingPhred. II.error probabilities. Genome research1998,8(3):186-194.
41. Dohm JC, Lottaz C, Borodina T, Himmelbauer H: Substantial biases inultra-short read data sets from high-throughput DNA sequencing. Nucleic AcidsResearch2008,36(16):e105-e105.
42. Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY,Schork NJ, Murray SS, Topol EJ, Levy S: Evaluation of next generation sequencingplatforms for population targeted sequencing studies. Genome Biol2009,10(3):R32.
43. Siegel AF, van den Engh G, Hood L, Trask B, Roach JC: Modeling thefeasibility of whole genome shotgun sequencing using a pairwise end strategy.Genomics2000,68(3):237-246.
44. Phillippy AM, Schatz MC, Pop M: Genome assembly forensics: finding theelusive mis-assembly. Genome Biology2008,9(3):R55.
45. Miller JR, Koren S, Sutton G: Assembly algorithms for next-generationsequencing data. Genomics2010,95(6):315-327.
46. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol: ABySS: aparallel assembler for short read sequence data. Genome research2009,19(6):1117-1123.
47. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES,Nusbaum C, Jaffe DB: ALLPATHS: de novo assembly of whole-genome shotgunmicroreads. Genome research2008,18(5):810-820.
48. Denisov G, Walenz B, Halpern AL, Miller J, Axelrod N, Levy S, Sutton G:Consensus generation and variant detection by Celera Assembler. Bioinformatics2008,24(8):1035-1040.
49. Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G: De novo assembly andgenotyping of variants using colored de Bruijn graphs. Nature genetics2012.
50. Pevzner PA, Tang H, Waterman MS: An Eulerian path approach to DNAfragment assembly. Proceedings of the National Academy of Sciences2001,98(17):9748.
51. Hernandez D, Fran ois P, Farinelli L, ster s M, Schrenzel J: De novo bacterialgenome sequencing: millions of very short reads assembled on a desktopcomputer. Genome research2008,18(5):802-809.
52. DiGuistini S, Liao NY, Platt D, Robertson G, Seidel M, Chan SK, Docking TR,Birol I, Holt RA, Hirst M: De novo genome sequence assembly of a filamentousfungus using Sanger,454and Illumina sequence data. Genome Biol2009,10(9):R94.
53. Peng Y, Leung H, Yiu S, Chin F: IDBA–A Practical Iterative de Bruijn GraphDe Novo Assembler. In:2010: Springer;2010:426-440.
54. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WEG, Wetter T, Suhai S:Using the miraEST assembler for reliable and automated mRNA transcriptassembly and SNP detection in sequenced ESTs. Genome research2004,14(6):1147-1159.
55. Chaisson MJ, Pevzner PA: Short read fragment assembly of bacterial genomes.Genome research2008,18(2):324-330.
56. Boisvert S, Laviolette F, Corbeil J: Ray: Simultaneous assembly of reads froma mix of high-throughput sequencing technologies. Journal of ComputationalBiology2010,17(11):1519-1533.
57. Dohm JC, Lottaz C, Borodina T, Himmelbauer H: SHARCGS, a fast and highlyaccurate short-read assembly algorithm for de novo genomic sequencing.Genome research2007,17(11):1697-1706.
58. Dayarian A, Michael TP, Sengupta AM: SOPRA: Scaffolding algorithm forpaired reads via statistical optimization. BMC Bioinformatics2010,11(1):345.
59. Warren RL, Sutton GG, Jones SJM, Holt RA: Assembling millions of shortDNA sequences using SSAKE. Bioinformatics2007,23(4):500-501.
60. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K:De novo assembly of human genomes with massively parallel short readsequencing. Genome research2010,20(2):265-272.
61. Schmidt B, Sinha R, Beresford-Smith B, Puglisi SJ: A fast hybrid short readfragment assembly algorithm. Bioinformatics2009,25(17):2279-2280.
62. Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, Dangl JL: Denovo assembly using low-coverage short read sequence data from the ricepathogen Pseudomonas syringae pv. oryzae. Genome research2009,19(2):294-305.
63. Mullikin JC, Ning Z: The phusion assembler. Genome research2003,13(1):81-90.
64. Zerbino DR, Birney E: Velvet: algorithms for de novo short read assemblyusing de Bruijn graphs. Genome research2008,18(5):821-829.
65. MacLean D, Jones JDG, Studholme DJ: Applicationof'next-generation'sequencing technologies to microbial genetics. Nature ReviewsMicrobiology2009,7(4):287-296.
66. Tauch A, Schneider J, Szczepanowski R, Tilker A, Viehoever P, Gartemann KH,Arnold W, Blom J, Brinkrolf K, Brune I: Ultrafast pyrosequencing ofCorynebacterium kroppenstedtii DSM44385revealed insights into thephysiology of a lipophilic corynebacterium that lacks mycolic acids. Journal ofbiotechnology2008,136(1-2):22-30.
67. Smith MG, Gianoulis TA, Pukatzki S, Mekalanos JJ, Ornston LN, Gerstein M,Snyder M: New insights into Acinetobacter baumannii pathogenesis revealed byhigh-density pyrosequencing and transposon mutagenesis. Genes&development2007,21(5):601-614.
68. Alikhan NF, Petty NK, Zakour NLB, Beatson SA: BLAST Ring ImageGenerator (BRIG): simple prokaryote genome comparisons. Bmc Genomics2011,12(1):402.
69. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, AngiuoliSV, Crabtree J, Jones AL, Durkin AS: Genome analysis of multiple pathogenicisolates of Streptococcus agalactiae: implications for the microbial “pan-genome”.Proceedings of the National Academy of Sciences of the United States of America2005,102(39):13950.
70. Snipen L, Ussery DW: Standard operating procedure for computingpangenome trees. Standards in genomic sciences2010,2(1):135.
71. Snel B, Bork P, Huynen MA: Genome phylogeny based on gene content.Nature genetics1999,21:108-110.
72. Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ: Universal treesbased on large combined protein sequence data sets. Nature genetics2001,28(3):281-285.
73. Rokas A, Williams BL, King N, Carroll SB: Genome-scale approaches toresolving incongruence in molecular phylogenies. Nature2003,425(6960):798-804.
74. Wolf Y, Rogozin I, Grishin N, Tatusov R, Koonin E: Genome trees constructedusing five different approaches suggest new major bacterial clades. BMCEvolutionary Biology2001,1(1):8.
75. Gu X, Zhang H: Genome phylogenetic analysis based on extended genecontents. Molecular Biology and Evolution2004,21(7):1401-1408.
76. Lagesen K, Hallin P, R dland EA, St rfeldt HH, Rognes T, Ussery DW:RNAmmer: consistent and rapid annotation of ribosomal RNA genes. NucleicAcids Research2007,35(9):3100-3108.
77. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5:molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance, and maximum parsimony methods. Molecular Biology andEvolution2011,28(10):2731-2739.
78. Woo P, Lau S, Teng J, Tse H, Yuen KY: Then and now: use of16S rDNA genesequencing for bacterial identification and discovery of novel bacteria in clinicalmicrobiology laboratories. Clinical microbiology and infection2008,14(10):908-934.
79. Carias LL, Rudin SD, Donskey CJ, Rice LB: Genetic linkage and cotransfer ofa novel, vanB-containing transposon (Tn5382) and a low-affinitypenicillin-binding protein5gene in a clinical vancomycin-resistant Enterococcusfaecium isolate. Journal of bacteriology1998,180(17):4426-4434.
80. Rice LB, Lakti ova V, Carias LL, Rudin S, Hutton R, Marshall SH: Transferablecapacity for gastrointestinal colonization in Enterococcus faecium in a mousemodel. Journal of Infectious Diseases2009,199(3):342-349.
81. Fox J: DOE joint genome institute feat: one-day sequencing of E. faecium.ASM News2000,66(7).
82. Arduino R, Murray B, Rakita R: Roles of antibodies and complement inphagocytic killing of enterococci. Infection and immunity1994,62(3):987-993.
83. Palmer KL, Carniol K, Manson JM, Heiman D, Shea T, Young S, Zeng Q, GeversD, Feldgarden M, Birren B: High-quality draft genome sequences of28Enterococcus sp. isolates. Journal of bacteriology2010,192(9):2469-2470.
84. Arias CA, Torres HA, Singh KV, Panesso D, Moore J, Wanger A, Murray BE:Failure of daptomycin monotherapy for endocarditis caused by an Enterococcusfaecium strain with vancomycin-resistant and vancomycin-susceptiblesubpopulations and evidence of in vivo loss of the vanA gene cluster. Clinicalinfectious diseases2007,45(10):1343.
85. Nallapareddy SR, Singh KV, Murray BE: Construction of improvedtemperature-sensitive and mobilizable vectors and their use for constructingmutations in the adhesin-encoding acm gene of poorly transformable clinicalEnterococcus faecium strains. Applied and environmental microbiology2006,72(1):334-345.
86. Bedendo J, Pignatari A: Typing of Enterococcus faecium by polymerase chainreaction and pulsed field gel electrophoresis. Brazilian Journal of Medical andBiological Research2000,33(11):1269-1274.
87. Metzker ML: Sequencing technologies—the next generation. Nature ReviewsGenetics2009,11(1):31-46.
88. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J,Braverman MS, Chen YJ, Chen Z: Genome sequencing in microfabricatedhigh-density picolitre reactors. Nature2005,437(7057):376-380.
89. Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y: Thesequence and de novo assembly of the giant panda genome. Nature2009,463(7279):311-317.
90. Aury JM, Cruaud C, Barbe V, Rogier O, Mangenot S, Samson G, Poulain J,Anthouard V, Scarpelli C, Artiguenave F: High quality draft sequences forprokaryotic genomes using a mix of new sequencing technologies. Bmc Genomics2008,9(1):603.
91. Schmieder R, Edwards R: Quality control and preprocessing of metagenomicdatasets. Bioinformatics2011,27(6):863-864.
92. Altschul SF, Madden TL, Sch ffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ:Gapped BLAST and PSI-BLAST: a new generation of protein database searchprograms. Nucleic Acids Research1997,25(17):3389-3402.
93. Ewing B, Hillier LD, Wendl MC, Green P: Base-calling of automatedsequencer traces usingPhred. I. Accuracy assessment. Genome research1998,8(3):175-185.
94. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C,Salzberg SL: Versatile and open software for comparing large genomes. GenomeBiology2004,5(2):R12.
95. Li H, Durbin R: Fast and accurate short read alignment withBurrows–Wheeler transform. Bioinformatics2009,25(14):1754-1760.
96. Li R, Ye J, Li S, Wang J, Han Y, Ye C, Yang H, Yu J, Wong GKS: ReAS:Recovery of ancestral sequences for transposable elements from the unassembledreads of a whole genome shotgun. PLoS computational biology2005,1(4):e43.
97. Klare I, Konstabel C, Badstübner D, Werner G, Witte W: Occurrence andspread of antibiotic resistances in Enterococcus faecium. International journal offood microbiology2003,88(2-3):269-290.
98. Lin Y, Li J, Shen H, Zhang L, Papasian CJ, Deng H: Comparative studies of denovo assembly tools for next-generation sequencing technologies. Bioinformatics2011,27(15):2031-2037.
99. Zhang W, Chen J, Yang Y, Tang Y, Shang J, Shen B: A practical comparison ofde novo genome assembly software tools for next-generation sequencingtechnologies. PLoS One2011,6(3):e17915.
100. Broeckel U, Schork NJ: Identifying genes and genetic variationunderlying human diseases and complex phenotypes via recombination mapping.The Journal of physiology2004,554(1):40-45.
101. Hirschhorn JN, Daly MJ: Genome-wide association studies for commondiseases and complex traits. Nature Reviews Genetics2005,6(2):95-108.
102. Hardy J, Singleton A: Genomewide association studies and human disease.New England Journal of Medicine2009,360(17):1759-1768.
103. Jimenez-Sanchez G, Childs B, Valle D: Human disease genes. Nature2001,409(6822):853-855.
104. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS,Manolio TA: Potential etiologic and functional implications of genome-wideassociation loci for human diseases and traits. Proceedings of the NationalAcademy of Sciences2009,106(23):9362.
105. Becker KG, Barnes KC, Bright TJ, Wang SA: The genetic associationdatabase. Nature genetics2004,36(5):431-432.
106. Pei H, Siyuan Z, Jie P, Kang T, Christian G, Rui WS, Yang Z, Yixue L:Human gene expression sensitivity according to large scale meta-analysis. BMCBioinformatics2009,10.
107. Ohn JH, Kim J, Kim JH: Genomic characterization of perturbationsensitivity. Bioinformatics2007,23(13):i354-i358.
108. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, KimIF, Soboleva A, Tomashevsky M, Edgar R: NCBI GEO: mining tens of millions ofexpression profiles—database and tools update. Nucleic Acids Research2007,35(suppl1):D760-D765.
109. Wang GL, Jiang BH, Rue EA, Semenza GL: Hypoxia-inducible factor1isa basic-helix-loop-helix-PAS heterodimer regulated by cellular O2tension.Proceedings of the National Academy of Sciences1995,92(12):5510.
110.Fransén K, Fenech M, Fredrikson M, Dabrosin C, S derkvist P: Associationbetween ulcerative growth and hypoxia inducible factor‐1α polymorphisms incolorectal cancer patients. Molecular carcinogenesis2006,45(11):833-840.
111.Hong Y, Ho KS, Eu KW, Cheah PY: A susceptibility gene set for early onsetcolorectal cancer that integrates diverse signaling pathways: implication fortumorigenesis. Clinical cancer research2007,13(4):1107-1114.
112.Papadopoulos N, Nicolaides NC, Wei YF, Ruben SM, Carter KC, Rosen CA,Haseltine WA, Fleischmann RD, Fraser CM, Adams MD: Mutation of a mutLhomolog in hereditary colon cancer. Science1994,263(5153):1625-1629.
113.Liu T, Tannerg rd P, Hackman P, Rubio C, Lindmark G, Kressner U, Hellgren D,Lambert B, Lindblom A: Missense mutations in hMLH1associated with colorectalcancer. Human genetics1999,105(5):437-441.
114.Chan TL, Yuen ST, Ho J, Chan A, Kwan K, Chung LP, Lam P, Tse CW, Leung SY:A novel germline1.8-kb deletion of hMLH1mimicking alternative splicing: afounder mutation in the Chinese population. Oncogene2001,20(23):2976.
115.Nejda N, Iglesias D, Moreno Azcoita M, Medina Arana V, González-Aguilera JJ,Fernández-Peralta AM: A MLH1polymorphism that increases cancer risk isassociated with better outcome in sporadic colorectal cancer. Cancer genetics andcytogenetics2009,193(2):71-77.
116.S reide K, Janssen E, S iland H, K rner H, Baak J: Microsatellite instability incolorectal cancer. British journal of surgery2006,93(4):395-406.
117.Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A,Fridman WH, Pagès F, Trajanoski Z, Galon J: ClueGO: a Cytoscape plug-in todecipher functionally grouped gene ontology and pathway annotation networks.Bioinformatics2009,25(8):1091-1093.
118.Han JDJ, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D,Walhout AJM, Cusick ME, Roth FP: Evidence for dynamically organizedmodularity in the yeast protein–protein interaction network. Nature2004,430(6995):88-93.
119.Xu J, Li Y: Discovering disease-genes by topological features in humanprotein–protein interaction network. Bioinformatics2006,22(22):2800-2805.
120. Wang J, Zhang S, Wang Y, Chen L, Zhang XS: Disease-aging networkreveals significant roles of aging genes in connecting genetic diseases. PLoScomputational biology2009,5(9):e1000521.
2. Naser S, Thompson F, Hoste B, Gevers D, Vandemeulebroecke K, Cleenwerck I,Thompson C, Vancanneyt M, Swings J: Phylogeny and identification of enterococciby atpA gene sequence analysis. Journal of clinical microbiology2005,43(5):2224.
3. Devriese L, Pot B:10The genus Enterococcus. Genera of Lactic Acid Bacteria1995,2:327.
4. Treitman AN, Yarnold PR, Warren J, Noskin GA: Emerging incidence ofEnterococcus faecium among hospital isolates (1993to2002). Journal of clinicalmicrobiology2005,43(1):462.
5. Top J, Willems R, Blok H, De Regt M, Jalink K, Troelstra A, Goorhuis B, BontenM: Ecological replacement of Enterococcus faecalis by multiresistant clonalcomplex17Enterococcus faecium. Clinical microbiology and infection2007,13(3):316-319.
6. Montero CI, Stock F, Murray PR: Mechanisms of resistance to daptomycin inEnterococcus faecium. Antimicrobial agents and chemotherapy2008,52(3):1167-1170.
7. Scheetz MH, Knechtel S, Malczynski M, Postelnick MJ, Qi C: IncreasingIncidence of Linezolid Intermediate or Resistant, Vancomycin-ResistantEnterococcus faecium (LIRVREF) Parallels Increasing Linezolid Consumption.Antimicrobial agents and chemotherapy2008:AAC.00070-00008v00071.
8. Hidron AI, Edwards JR, Patel J, Horan TC, Sievert DM, Pollock DA, Fridkin SK:Antimicrobial‐resistant pathogens associated with healthcare‐associatedinfections: annual summary of data reported to the National Healthcare SafetyNetwork at the Centers for Disease Control and Prevention,2006–2007. infectioncontrol and hospital epidemiology2008,29(11):996-1011.
9. Werner G, Coque T, Hammerum A, Hope R, Hryniewicz W, Johnson A, Klare I,Kristinsson K, Leclercq R, Lester C: Emergence and spread of vancomycinresistance among enterococci in Europe. Euro Surveill2008,13(47):1-11.
10. Arthur M, Depardieu F, Reynolds P, Courvalin P: Quantitative analysis of themetabolism of soluble cytoplasmic peptidoglycan precursors of glycopeptide‐resistant enterococci. Molecular microbiology1996,21(1):33-44.
11. Depardieu F, Reynolds PE, Courvalin P: VanD-type vancomycin-resistantEnterococcus faecium10/96A. Antimicrobial agents and chemotherapy2003,47(1):7-18.
12. Reynolds PE, Courvalin P: Vancomycin resistance in enterococci due tosynthesis of precursors terminating in D-alanyl-D-serine. Antimicrobial agentsand chemotherapy2005,49(1):21-25.
13. Leavis HL, Willems RJL, Van Wamel WJB, Schuren FH, Caspers MPM, BontenMJM: Insertion Sequence–Driven Diversification Creates a Globally DispersedEmerging Multiresistant Subspecies of E. faecium. PLoS pathogens2007,3(1):e7.
14. Homan WL, Tribe D, Poznanski S, Li M, Hogg G, Spalburg E, van Embden JDA,Willems RJL: Multilocus sequence typing scheme for Enterococcus faecium.Journal of clinical microbiology2002,40(6):1963.
15. Vancanneyt M, Lombardi A, Andrighetto C, Knijff E, Torriani S, Bjorkroth KJ,Franz CMAP, Foulquie Moreno MR, Revets H, De Vuyst L: Intraspecies genomicgroups in Enterococcus faecium and their correlation with origin andpathogenicity. Applied and environmental microbiology2002,68(3):1381.
16. Willems R, Top J, van Santen M, Robinson DA, Coque TM, Baquero F,Grundmann H, Bonten M: Global spread of vancomycin-resistant Enterococcusfaecium from distinct nosocomial genetic complex. Emerg Infect Dis2005,11(6):821-828.
17. Leavis HL, Bonten MJM, Willems RJL: Identification of high-riskenterococcal clonal complexes: global dispersion and antibiotic resistance.Current opinion in microbiology2006,9(5):454-460.
18. Heikens E, Bonten MJM, Willems RJL: Enterococcal surface protein Esp isimportant for biofilm formation of Enterococcus faecium E1162. Journal ofbacteriology2007,189(22):8233.
19. Leendertse M, Heikens E, Wijnands LM, van Luit-Asbroek M, Teske GJD,Roelofs JJTH, Bonten MJM, Van der Poll T, Willems RJL: Enterococcal SurfaceProtein Transiently Aggravates Enterococcus faecium–Induced Urinary TractInfection in Mice. Journal of Infectious Diseases2009,200(7):1162.
20. Nallapareddy SR, Weinstock GM, Murray BE: Clinical isolates of Enterococcusfaecium exhibit strain‐specific collagen binding mediated by Acm, a newmember of the MSCRAMM family. Molecular microbiology2003,47(6):1733-1747.
21. Nallapareddy SR, Singh KV, Murray BE: Contribution of the collagen adhesinAcm to pathogenesis of Enterococcus faecium in experimental endocarditis.Infection and immunity2008,76(9):4120.
22. Rice LB, Carias L, Rudin S, Vael C, Goossens H, Konstabel C, Klare I,Nallapareddy SR, Huang W, Murray BE: A potential virulence gene, hylEfm,predominates in Enterococcus faecium of clinical origin. Journal of InfectiousDiseases2003,187(3):508.
23. Eppinger M, Mammel MK, LeClerc JE, Ravel J, Cebula TA: Genome signaturesof Escherichia coli O157: H7isolates from the bovine host reservoir. Applied andenvironmental microbiology2011,77(9):2916-2925.
24. Van Schaik W, Top J, Riley D, Boekhorst J, Vrijenhoek J, Schapendonk C,Hendrickx A, Nijman I, Bonten M, Tettelin H: Pyrosequencing-based comparativegenome analysis of the nosocomial pathogen Enterococcus faecium andidentification of a large transferable pathogenicity island. Bmc Genomics2010,11(1):239.
25. Watson JD, Crick FHC: Molecular structure of nucleic acids. Nature1953,171(4356):737-738.
26. Whitfeld P: A method for the determination of nucleotide sequence inpolyribonucleotides. Biochemical Journal1954,58(3):390.
27. Davis BD: The human genome and other initiatives. Science1990,249(4967):342.
28. Mardis ER: The impact of next-generation sequencing technology on genetics.Trends in Genetics2008,24(3):133-141.
29. Morozova O, Marra MA: Applications of next-generation sequencingtechnologies in functional genomics. Genomics2008,92(5):255-264.
30. Strausberg RL, Levy S, Rogers YH: Emerging DNA sequencing technologiesfor human genomic medicine. Drug discovery today2008,13(13-14):569-577.
31. Pettersson E, Lundeberg J, Ahmadian A: Generations of sequencingtechnologies. Genomics2009,93(2):105-111.
32. Sanger F, Nicklen S, Coulson AR: DNA sequencing with chain-terminatinginhibitors. Proceedings of the National Academy of Sciences1977,74(12):5463.
33. http://my454.com/products/technology.asp.
34. Berka J, Chen YJ, Leamon JH, Lefkowitz S, Lohman KL, Makhijani VB,Rothberg JM, Sarkis GJ, Srinivasan M, Weiner MP: Bead emulsion nucleic acidamplification. In.: Google Patents;2011.
35. http://wwwpyrosequencingcom/DynPageaspx.
36. Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM: Accuracy andquality of massively parallel DNA pyrosequencing. Genome Biol2007,8(7):R143.
37.http://wwwappliedbiosystemscom/absite/us/en/home/applications-technologies/solid-next-generation-sequencinghtml.
38. http://wwwilluminacom/.
39. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P,Bettman B: Real-time DNA sequencing from single polymerase molecules. Science2009,323(5910):133.
40. Ewing B, Green P: Base-calling of automated sequencer traces usingPhred. II.error probabilities. Genome research1998,8(3):186-194.
41. Dohm JC, Lottaz C, Borodina T, Himmelbauer H: Substantial biases inultra-short read data sets from high-throughput DNA sequencing. Nucleic AcidsResearch2008,36(16):e105-e105.
42. Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY,Schork NJ, Murray SS, Topol EJ, Levy S: Evaluation of next generation sequencingplatforms for population targeted sequencing studies. Genome Biol2009,10(3):R32.
43. Siegel AF, van den Engh G, Hood L, Trask B, Roach JC: Modeling thefeasibility of whole genome shotgun sequencing using a pairwise end strategy.Genomics2000,68(3):237-246.
44. Phillippy AM, Schatz MC, Pop M: Genome assembly forensics: finding theelusive mis-assembly. Genome Biology2008,9(3):R55.
45. Miller JR, Koren S, Sutton G: Assembly algorithms for next-generationsequencing data. Genomics2010,95(6):315-327.
46. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol: ABySS: aparallel assembler for short read sequence data. Genome research2009,19(6):1117-1123.
47. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES,Nusbaum C, Jaffe DB: ALLPATHS: de novo assembly of whole-genome shotgunmicroreads. Genome research2008,18(5):810-820.
48. Denisov G, Walenz B, Halpern AL, Miller J, Axelrod N, Levy S, Sutton G:Consensus generation and variant detection by Celera Assembler. Bioinformatics2008,24(8):1035-1040.
49. Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G: De novo assembly andgenotyping of variants using colored de Bruijn graphs. Nature genetics2012.
50. Pevzner PA, Tang H, Waterman MS: An Eulerian path approach to DNAfragment assembly. Proceedings of the National Academy of Sciences2001,98(17):9748.
51. Hernandez D, Fran ois P, Farinelli L, ster s M, Schrenzel J: De novo bacterialgenome sequencing: millions of very short reads assembled on a desktopcomputer. Genome research2008,18(5):802-809.
52. DiGuistini S, Liao NY, Platt D, Robertson G, Seidel M, Chan SK, Docking TR,Birol I, Holt RA, Hirst M: De novo genome sequence assembly of a filamentousfungus using Sanger,454and Illumina sequence data. Genome Biol2009,10(9):R94.
53. Peng Y, Leung H, Yiu S, Chin F: IDBA–A Practical Iterative de Bruijn GraphDe Novo Assembler. In:2010: Springer;2010:426-440.
54. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WEG, Wetter T, Suhai S:Using the miraEST assembler for reliable and automated mRNA transcriptassembly and SNP detection in sequenced ESTs. Genome research2004,14(6):1147-1159.
55. Chaisson MJ, Pevzner PA: Short read fragment assembly of bacterial genomes.Genome research2008,18(2):324-330.
56. Boisvert S, Laviolette F, Corbeil J: Ray: Simultaneous assembly of reads froma mix of high-throughput sequencing technologies. Journal of ComputationalBiology2010,17(11):1519-1533.
57. Dohm JC, Lottaz C, Borodina T, Himmelbauer H: SHARCGS, a fast and highlyaccurate short-read assembly algorithm for de novo genomic sequencing.Genome research2007,17(11):1697-1706.
58. Dayarian A, Michael TP, Sengupta AM: SOPRA: Scaffolding algorithm forpaired reads via statistical optimization. BMC Bioinformatics2010,11(1):345.
59. Warren RL, Sutton GG, Jones SJM, Holt RA: Assembling millions of shortDNA sequences using SSAKE. Bioinformatics2007,23(4):500-501.
60. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K:De novo assembly of human genomes with massively parallel short readsequencing. Genome research2010,20(2):265-272.
61. Schmidt B, Sinha R, Beresford-Smith B, Puglisi SJ: A fast hybrid short readfragment assembly algorithm. Bioinformatics2009,25(17):2279-2280.
62. Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, Dangl JL: Denovo assembly using low-coverage short read sequence data from the ricepathogen Pseudomonas syringae pv. oryzae. Genome research2009,19(2):294-305.
63. Mullikin JC, Ning Z: The phusion assembler. Genome research2003,13(1):81-90.
64. Zerbino DR, Birney E: Velvet: algorithms for de novo short read assemblyusing de Bruijn graphs. Genome research2008,18(5):821-829.
65. MacLean D, Jones JDG, Studholme DJ: Applicationof'next-generation'sequencing technologies to microbial genetics. Nature ReviewsMicrobiology2009,7(4):287-296.
66. Tauch A, Schneider J, Szczepanowski R, Tilker A, Viehoever P, Gartemann KH,Arnold W, Blom J, Brinkrolf K, Brune I: Ultrafast pyrosequencing ofCorynebacterium kroppenstedtii DSM44385revealed insights into thephysiology of a lipophilic corynebacterium that lacks mycolic acids. Journal ofbiotechnology2008,136(1-2):22-30.
67. Smith MG, Gianoulis TA, Pukatzki S, Mekalanos JJ, Ornston LN, Gerstein M,Snyder M: New insights into Acinetobacter baumannii pathogenesis revealed byhigh-density pyrosequencing and transposon mutagenesis. Genes&development2007,21(5):601-614.
68. Alikhan NF, Petty NK, Zakour NLB, Beatson SA: BLAST Ring ImageGenerator (BRIG): simple prokaryote genome comparisons. Bmc Genomics2011,12(1):402.
69. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, AngiuoliSV, Crabtree J, Jones AL, Durkin AS: Genome analysis of multiple pathogenicisolates of Streptococcus agalactiae: implications for the microbial “pan-genome”.Proceedings of the National Academy of Sciences of the United States of America2005,102(39):13950.
70. Snipen L, Ussery DW: Standard operating procedure for computingpangenome trees. Standards in genomic sciences2010,2(1):135.
71. Snel B, Bork P, Huynen MA: Genome phylogeny based on gene content.Nature genetics1999,21:108-110.
72. Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ: Universal treesbased on large combined protein sequence data sets. Nature genetics2001,28(3):281-285.
73. Rokas A, Williams BL, King N, Carroll SB: Genome-scale approaches toresolving incongruence in molecular phylogenies. Nature2003,425(6960):798-804.
74. Wolf Y, Rogozin I, Grishin N, Tatusov R, Koonin E: Genome trees constructedusing five different approaches suggest new major bacterial clades. BMCEvolutionary Biology2001,1(1):8.
75. Gu X, Zhang H: Genome phylogenetic analysis based on extended genecontents. Molecular Biology and Evolution2004,21(7):1401-1408.
76. Lagesen K, Hallin P, R dland EA, St rfeldt HH, Rognes T, Ussery DW:RNAmmer: consistent and rapid annotation of ribosomal RNA genes. NucleicAcids Research2007,35(9):3100-3108.
77. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5:molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance, and maximum parsimony methods. Molecular Biology andEvolution2011,28(10):2731-2739.
78. Woo P, Lau S, Teng J, Tse H, Yuen KY: Then and now: use of16S rDNA genesequencing for bacterial identification and discovery of novel bacteria in clinicalmicrobiology laboratories. Clinical microbiology and infection2008,14(10):908-934.
79. Carias LL, Rudin SD, Donskey CJ, Rice LB: Genetic linkage and cotransfer ofa novel, vanB-containing transposon (Tn5382) and a low-affinitypenicillin-binding protein5gene in a clinical vancomycin-resistant Enterococcusfaecium isolate. Journal of bacteriology1998,180(17):4426-4434.
80. Rice LB, Lakti ova V, Carias LL, Rudin S, Hutton R, Marshall SH: Transferablecapacity for gastrointestinal colonization in Enterococcus faecium in a mousemodel. Journal of Infectious Diseases2009,199(3):342-349.
81. Fox J: DOE joint genome institute feat: one-day sequencing of E. faecium.ASM News2000,66(7).
82. Arduino R, Murray B, Rakita R: Roles of antibodies and complement inphagocytic killing of enterococci. Infection and immunity1994,62(3):987-993.
83. Palmer KL, Carniol K, Manson JM, Heiman D, Shea T, Young S, Zeng Q, GeversD, Feldgarden M, Birren B: High-quality draft genome sequences of28Enterococcus sp. isolates. Journal of bacteriology2010,192(9):2469-2470.
84. Arias CA, Torres HA, Singh KV, Panesso D, Moore J, Wanger A, Murray BE:Failure of daptomycin monotherapy for endocarditis caused by an Enterococcusfaecium strain with vancomycin-resistant and vancomycin-susceptiblesubpopulations and evidence of in vivo loss of the vanA gene cluster. Clinicalinfectious diseases2007,45(10):1343.
85. Nallapareddy SR, Singh KV, Murray BE: Construction of improvedtemperature-sensitive and mobilizable vectors and their use for constructingmutations in the adhesin-encoding acm gene of poorly transformable clinicalEnterococcus faecium strains. Applied and environmental microbiology2006,72(1):334-345.
86. Bedendo J, Pignatari A: Typing of Enterococcus faecium by polymerase chainreaction and pulsed field gel electrophoresis. Brazilian Journal of Medical andBiological Research2000,33(11):1269-1274.
87. Metzker ML: Sequencing technologies—the next generation. Nature ReviewsGenetics2009,11(1):31-46.
88. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J,Braverman MS, Chen YJ, Chen Z: Genome sequencing in microfabricatedhigh-density picolitre reactors. Nature2005,437(7057):376-380.
89. Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y: Thesequence and de novo assembly of the giant panda genome. Nature2009,463(7279):311-317.
90. Aury JM, Cruaud C, Barbe V, Rogier O, Mangenot S, Samson G, Poulain J,Anthouard V, Scarpelli C, Artiguenave F: High quality draft sequences forprokaryotic genomes using a mix of new sequencing technologies. Bmc Genomics2008,9(1):603.
91. Schmieder R, Edwards R: Quality control and preprocessing of metagenomicdatasets. Bioinformatics2011,27(6):863-864.
92. Altschul SF, Madden TL, Sch ffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ:Gapped BLAST and PSI-BLAST: a new generation of protein database searchprograms. Nucleic Acids Research1997,25(17):3389-3402.
93. Ewing B, Hillier LD, Wendl MC, Green P: Base-calling of automatedsequencer traces usingPhred. I. Accuracy assessment. Genome research1998,8(3):175-185.
94. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C,Salzberg SL: Versatile and open software for comparing large genomes. GenomeBiology2004,5(2):R12.
95. Li H, Durbin R: Fast and accurate short read alignment withBurrows–Wheeler transform. Bioinformatics2009,25(14):1754-1760.
96. Li R, Ye J, Li S, Wang J, Han Y, Ye C, Yang H, Yu J, Wong GKS: ReAS:Recovery of ancestral sequences for transposable elements from the unassembledreads of a whole genome shotgun. PLoS computational biology2005,1(4):e43.
97. Klare I, Konstabel C, Badstübner D, Werner G, Witte W: Occurrence andspread of antibiotic resistances in Enterococcus faecium. International journal offood microbiology2003,88(2-3):269-290.
98. Lin Y, Li J, Shen H, Zhang L, Papasian CJ, Deng H: Comparative studies of denovo assembly tools for next-generation sequencing technologies. Bioinformatics2011,27(15):2031-2037.
99. Zhang W, Chen J, Yang Y, Tang Y, Shang J, Shen B: A practical comparison ofde novo genome assembly software tools for next-generation sequencingtechnologies. PLoS One2011,6(3):e17915.
100. Broeckel U, Schork NJ: Identifying genes and genetic variationunderlying human diseases and complex phenotypes via recombination mapping.The Journal of physiology2004,554(1):40-45.
101. Hirschhorn JN, Daly MJ: Genome-wide association studies for commondiseases and complex traits. Nature Reviews Genetics2005,6(2):95-108.
102. Hardy J, Singleton A: Genomewide association studies and human disease.New England Journal of Medicine2009,360(17):1759-1768.
103. Jimenez-Sanchez G, Childs B, Valle D: Human disease genes. Nature2001,409(6822):853-855.
104. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS,Manolio TA: Potential etiologic and functional implications of genome-wideassociation loci for human diseases and traits. Proceedings of the NationalAcademy of Sciences2009,106(23):9362.
105. Becker KG, Barnes KC, Bright TJ, Wang SA: The genetic associationdatabase. Nature genetics2004,36(5):431-432.
106. Pei H, Siyuan Z, Jie P, Kang T, Christian G, Rui WS, Yang Z, Yixue L:Human gene expression sensitivity according to large scale meta-analysis. BMCBioinformatics2009,10.
107. Ohn JH, Kim J, Kim JH: Genomic characterization of perturbationsensitivity. Bioinformatics2007,23(13):i354-i358.
108. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, KimIF, Soboleva A, Tomashevsky M, Edgar R: NCBI GEO: mining tens of millions ofexpression profiles—database and tools update. Nucleic Acids Research2007,35(suppl1):D760-D765.
109. Wang GL, Jiang BH, Rue EA, Semenza GL: Hypoxia-inducible factor1isa basic-helix-loop-helix-PAS heterodimer regulated by cellular O2tension.Proceedings of the National Academy of Sciences1995,92(12):5510.
110.Fransén K, Fenech M, Fredrikson M, Dabrosin C, S derkvist P: Associationbetween ulcerative growth and hypoxia inducible factor‐1α polymorphisms incolorectal cancer patients. Molecular carcinogenesis2006,45(11):833-840.
111.Hong Y, Ho KS, Eu KW, Cheah PY: A susceptibility gene set for early onsetcolorectal cancer that integrates diverse signaling pathways: implication fortumorigenesis. Clinical cancer research2007,13(4):1107-1114.
112.Papadopoulos N, Nicolaides NC, Wei YF, Ruben SM, Carter KC, Rosen CA,Haseltine WA, Fleischmann RD, Fraser CM, Adams MD: Mutation of a mutLhomolog in hereditary colon cancer. Science1994,263(5153):1625-1629.
113.Liu T, Tannerg rd P, Hackman P, Rubio C, Lindmark G, Kressner U, Hellgren D,Lambert B, Lindblom A: Missense mutations in hMLH1associated with colorectalcancer. Human genetics1999,105(5):437-441.
114.Chan TL, Yuen ST, Ho J, Chan A, Kwan K, Chung LP, Lam P, Tse CW, Leung SY:A novel germline1.8-kb deletion of hMLH1mimicking alternative splicing: afounder mutation in the Chinese population. Oncogene2001,20(23):2976.
115.Nejda N, Iglesias D, Moreno Azcoita M, Medina Arana V, González-Aguilera JJ,Fernández-Peralta AM: A MLH1polymorphism that increases cancer risk isassociated with better outcome in sporadic colorectal cancer. Cancer genetics andcytogenetics2009,193(2):71-77.
116.S reide K, Janssen E, S iland H, K rner H, Baak J: Microsatellite instability incolorectal cancer. British journal of surgery2006,93(4):395-406.
117.Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A,Fridman WH, Pagès F, Trajanoski Z, Galon J: ClueGO: a Cytoscape plug-in todecipher functionally grouped gene ontology and pathway annotation networks.Bioinformatics2009,25(8):1091-1093.
118.Han JDJ, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D,Walhout AJM, Cusick ME, Roth FP: Evidence for dynamically organizedmodularity in the yeast protein–protein interaction network. Nature2004,430(6995):88-93.
119.Xu J, Li Y: Discovering disease-genes by topological features in humanprotein–protein interaction network. Bioinformatics2006,22(22):2800-2805.
120. Wang J, Zhang S, Wang Y, Chen L, Zhang XS: Disease-aging networkreveals significant roles of aging genes in connecting genetic diseases. PLoScomputational biology2009,5(9):e1000521.