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Journal of Pathogens
Volume 2011, Article ID 310135, 11 pages
http://dx.doi.org/10.4061/2011/310135
Review Article

Recent Advances in Molecular Technologies and Their Application in Pathogen Detection in Foods with Particular Reference to Yersinia

1College of Management and Technology, Walden University, 155 Fifth Avenue South, Minneapolis, MN 55401, USA
2Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, MOD 1 Facility, Laurel, MD 20708, USA

Received 22 June 2011; Accepted 8 September 2011

Academic Editor: Latiful Bari

Copyright © 2011 Jin Gui and Isha R. Patel. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. B. Swaminathan, M. C. Harmon, and I. J. Mehlman, “A review: Yersinia enterocolitia,” Journal of Applied Bacteriology, vol. 52, no. 2, pp. 151–183, 1982. View at Google Scholar · View at Scopus
  2. E. J. Bottone, “Yersinia enterocolitica: overview and epidemiologic correlates,” Microbes and Infection, vol. 1, no. 4, pp. 323–333, 1999. View at Publisher · View at Google Scholar · View at Scopus
  3. C. Pujol and J. B. Bliska, “Turning Yersinia pathogenesis outside in: subversion of macrophage function by intracellular yersiniae,” Clinical Immunology, vol. 114, no. 3, pp. 216–226, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  4. D. M. Hunter and D. V. Lim, “Rapid detection and identification of bacterial pathogens by using an ATP bioluminescence immunoassay,” Journal of Food Protection, vol. 73, no. 4, pp. 739–746, 2010. View at Google Scholar · View at Scopus
  5. D.-H. Kim, B.-K. Lee, Y.-D. Kim, S.-K. Rhee, and Y.-C. Kim, “Detection of representative enteropathogenic bacteria, Vibrio spp., pathogenic Escherichia coli, Salmonella spp., Shigella spp., and Yersinia enterocolitica, using a virulence factor gene-based oligonucleotide microarray,” Journal of Microbiology, vol. 48, no. 5, pp. 682–688, 2010. View at Publisher · View at Google Scholar · View at PubMed
  6. E. C. D. Todd, J. D. Greig, C. A. Bartleson, and B. S. Michaels, “Outbreaks where food workers have been implicated in the spread of foodborne disease. Part 4. Infective doses and pathogen carriage,” Journal of Food Protection, vol. 71, no. 11, pp. 2339–2373, 2008. View at Google Scholar · View at Scopus
  7. E. R. Rocha, C. D. Herren, D. J. Smalley, and C. J. Smith, “The complex oxidative stress response of Bacteroides fragilis: the role of OxyR in control of gene expression,” Anaerobe, vol. 9, no. 4, pp. 165–173, 2003. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  8. A. S. Waage, T. Vardund, V. Lund, and G. Kapperud, “Detection of low numbers of pathogenic Yersinia enterocolitica in environmental water and sewage samples by nested polymerase chain reaction,” Journal of Applied Microbiology, vol. 87, no. 6, pp. 814–821, 1999. View at Publisher · View at Google Scholar · View at Scopus
  9. V. Thibodeau, E. H. Frost, S. Chénier, and S. Quessy, “Presence of Yersinia enterocolitica in tissues of orally-inoculated pigs and the tonsils and feces of pigs at slaughter,” Canadian Journal of Veterinary Research, vol. 63, no. 2, pp. 96–100, 1999. View at Google Scholar · View at Scopus
  10. S. C. A. Chen and D. P. Kontoyiannis, “New molecular and surrogate biomarker-based tests in the diagnosis of bacterial and fungal infection in febrile neutropenic patients,” Current Opinion in Infectious Diseases, vol. 23, no. 6, pp. 567–577, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  11. R. Girones, M. A. Ferrús, J. L. Alonso et al., “Molecular detection of pathogens in water—the pros and cons of molecular techniques,” Water Research, vol. 44, no. 15, pp. 4325–4339, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  12. J. Shendure and H. Ji, “Next-generation DNA sequencing,” Nature Biotechnology, vol. 26, no. 10, pp. 1135–1145, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  13. S. M. Yoo and S. Y. Lee, “Diagnosis of pathogens using DNA microarray,” Recent Patents on Biotechnology, vol. 2, no. 2, pp. 124–129, 2008. View at Publisher · View at Google Scholar · View at Scopus
  14. L. Cerqueira, N. F. Azevedo, C. Almeida, T. Jardim, C. W. Keevil, and M. J. Vieira, “DNA mimics for the rapid identification of microorganisms by fluorescence in situ hybridization (FISH),” International Journal of Molecular Sciences, vol. 9, no. 10, pp. 1944–1960, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  15. H. P. Dwivedi and L. A. Jaykus, “Detection of pathogens in foods: the current state-of-art and future directions,” Critical Review in Microbiology, vol. 37, no. 1, pp. 40–63, 2011. View at Google Scholar
  16. A. Tsourkas and G. Bao, “Shedding light on health and disease using molecular beacons,” Brief Funct Genomic Proteomic, vol. 1, no. 4, pp. 372–384, 2003. View at Google Scholar · View at Scopus
  17. J. J. Adamczyk, L. C. Adams, and D. D. Hardee, “Field efficacy and seasonal expression profiles for terminal leaves of single and double Bacillus thuringiensis toxin cotton genotypes,” Journal of Economic Entomology, vol. 94, no. 6, pp. 1589–1593, 2001. View at Google Scholar · View at Scopus
  18. Z. Li, Y. Wang, J. Wang, Z. Tang, J. G. Pounds, and Y. Lin, “Rapid and sensitive detection of protein biomarker using a portable fluorescence biosensor based on quantum dots and a lateral flow test strip,” Analytical Chemistry, vol. 82, no. 16, pp. 7008–7014, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  19. N. R. Thomson, S. Howard, B. W. Wren et al., “The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081,” PLoS Genetics, vol. 2, no. 12, pp. 2039–2051, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  20. J. Parkhill, B. W. Wren, N. R. Thomson et al., “Genome sequence of Yersinia pestis, the causative agent of plague,” Nature, vol. 413, no. 6855, pp. 523–527, 2001. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  21. M. Eppinger, M. J. Rosovitz, W. F. Fricke et al., “The complete genome sequence of Yersinia pseudotuberculosis IP31758, the causative agent of Far East scarlet-like fever,” PLoS Genetics, vol. 3, no. 8, pp. 1508–1523, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  22. T. M. Fuchs, K. Brandt, M. Starke, and T. Rattei, “Shotgun sequencing of Yersinia enterocolitica strain W22703 (biotype 2, serotype O:9): genomic evidence for oscillation between invertebrates and mammals,” BMC Genomics, vol. 12, article 168, pp. 1–12, 2011. View at Publisher · View at Google Scholar · View at PubMed
  23. X. Wang, Y. Li, H. Jing et al., “Complete genome sequence of a Yersinia enterocolitica “old world” (3/O:9) strain and comparison with the “new world” (1B/O:8) strain,” Journal of Clinical Microbiology, vol. 49, no. 4, pp. 1251–1259, 2011. View at Publisher · View at Google Scholar · View at PubMed
  24. J. Batzilla, U. Antonenka, D. Höper, J. Heesemann, and A. Rakin, “Yersinia enterocolitica palearctica serobiotype O:3/4—a successful group of emerging zoonotic pathogens,” BMC Genomics, vol. 12, pp. 1–37, 2011. View at Publisher · View at Google Scholar · View at PubMed
  25. J. M. Rouillard and E. Gulari, “OligoArrayDb: pangenomic oligonucleotide microarray probe sets database,” Nucleic Acids Research, vol. 37, no. 1, pp. D938–D941, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  26. S. B. Plaisier, R. Taschereau, J. A. Wong, and T. G. Graeber, “Rank-rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures,” Nucleic Acids Research, vol. 38, no. 17, pp. e169–e169, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  27. H. He, H. Zhang, X. Wang et al., “Development of a versatile, target-oriented tiling microarray assay for measuring allele-specific gene expression,” Genomics, vol. 96, no. 5, pp. 308–315, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  28. M. N. Miller, B. W. Okaty, S. Kato, and S. B. Nelson, “Activity-dependent changes in the firing properties of neocortical fast-spiking interneurons in the absence of large changes in gene expression,” Developmental Neurobiology, vol. 71, no. 1, pp. 62–70, 2011. View at Publisher · View at Google Scholar · View at Scopus
  29. R. Schwarz, B. Joseph, G. Gerlach et al., “Evaluation of one- and two-color gene expression arrays for microbial comparative genome hybridization analyses in routine applications,” Journal of Clinical Microbiology, vol. 48, no. 9, pp. 3105–3110, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  30. S. Kim, J. Hu, Y. Oh et al., “Combining ChIP-chip and expression profiling to model the MoCRZ1 mediated circuit for Ca/calcineurin signaling in the rice blast fungus,” PLoS Pathogens, vol. 6, no. 5, Article ID e1000909, 2010. View at Publisher · View at Google Scholar · View at PubMed
  31. M. Gauthier, B. Bonnaud, M. Arsac et al., “Microarray for hepatitis B virus genotyping and detection of 994 mutations along the genome,” Journal of Clinical Microbiology, vol. 48, no. 11, pp. 4207–4215, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  32. B. Quiñones, M. S. Swimley, A. W. Taylor, and E. D. Dawson, “Identification of Escherichia coli O157 by using a novel colorimetric detection method with DNA microarrays,” Foodborne Pathogens and Disease, vol. 8, no. 6, pp. 705–711, 2011. View at Publisher · View at Google Scholar · View at PubMed
  33. R. Z. Wu, S. N. Bailey, and D. M. Sabatini, “Cell-biological applications of transfected-cell microarrays,” Trends in Cell Biology, vol. 12, no. 10, pp. 485–488, 2002. View at Publisher · View at Google Scholar · View at Scopus
  34. R. Natrajan, S. E. Little, J. S. Reis-Filho et al., “Amplification and overexpression of CACNA1E correlates with relapse in favorable histology Wilms' tumors,” Clinical Cancer Research, vol. 12, no. 24, pp. 7284–7293, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  35. P. Simpson, C. Jones, A. Mackay, and S. R. Lakhani, “Gene expression analysis using filter cDNA microarrays,” Methods in molecular medicine., vol. 120, pp. 415–424, 2006. View at Google Scholar · View at Scopus
  36. T. Hart, A. Zhao, A. Garg, S. Bolusani, and E. M. Marcotte, “Human cell chips: adapting DNA microarray spotting technology to cell-based imaging assays,” PLoS One, vol. 4, no. 10, Article ID e7088, pp. 1–7, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  37. H. Lee, B. D. O'Connor, B. Merriman et al., “Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing,” BMC Genomics, vol. 10, article 646, pp. 1–12, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  38. L. H. Saal, C. Troein, J. Vallon-Christersson, S. Gruvberger, A. Borg, and C. Peterson, “BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data,” Genome Biology, vol. 3, no. 8, Article ID SOFTWARE0003, pp. 1–6, 2002. View at Google Scholar · View at Scopus
  39. H. Huang, W. L. Ma, X. Q. Dong, B. Zhang, Q. Wu, and W. L. Zheng, “DNA microarray for the detection of Yersinia pesits,” Di Yi Jun Yi Da Xue Xue Bao, vol. 24, no. 1, pp. 47–49, 2004. View at Google Scholar · View at Scopus
  40. K. M. Myers, J. Gaba, and S. F. Al-Khaldi, “Molecular identification of Yersinia enterocolitica isolated from pasteurized whole milk using DNA microarray chip hybridization,” Molecular and Cellular Probes, vol. 20, no. 2, pp. 71–80, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  41. M. Ikeda, N. Yamaguchi, K. Tani, and M. Nasu, “Detection of food poisoning bacteria in fresh vegetables using DNA microarray,” Journal of Health Science, vol. 52, no. 1, pp. 36–42, 2006. View at Google Scholar · View at Scopus
  42. H. J. Kim, S. H. Park, T. H. Lee, B. H. Nahm, Y. R. Kim, and H. Y. Kim, “Microarray detection of food-borne pathogens using specific probes prepared by comparative genomics,” Biosensors and Bioelectronics, vol. 24, no. 2, pp. 238–246, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  43. M. Boye, A. A. Feenstra, C. Tegtmeier, L. O. Andresen, S. R. Rasmussen, and V. Bille-Hansen, “Detection of Streptococcus suis by in situ hybridization, indirect immunofluorescence, and peroxidase-antiperoxidase assays in formalin-fixed, paraffin-embedded tissue sections from pigs,” Journal of Veterinary Diagnostic Investigation, vol. 12, no. 3, pp. 224–232, 2000. View at Google Scholar · View at Scopus
  44. U. Gasanov, D. Hughes, and P. M. Hansbro, “Methods for the isolation and identification of Listeria spp. and Listeria monocytogenes: a review,” FEMS Microbiology Reviews, vol. 29, no. 5, pp. 851–875, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  45. F. Dziva, A. P. Muhairwa, M. Bisgaard, and H. Christensen, “Diagnostic and typing options for investigating diseases associated with Pasteurella multocida,” Veterinary Microbiology, vol. 128, no. 1-2, pp. 1–22, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  46. A. G. Gehring, P. L. Irwin, S. A. Reed et al., “Enzyme-linked immunomagnetic chemiluminescent detection of Escherichia coli O157:H7,” Journal of Immunological Methods, vol. 293, no. 1-2, pp. 97–106, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  47. V. M. Bohaychuk, G. E. Gensler, R. K. King, J. T. Wu, and L. M. McMullen, “Evaluation of detection methods for screening meat and poultry products for the presence of foodborne pathogens,” Journal of Food Protection, vol. 68, no. 12, pp. 2637–2647, 2005. View at Google Scholar · View at Scopus
  48. L. M. Clotilde, C. Bernard IV, G. L. Hartman, D. K. Lau, and J. M. Carter, “Microbead-based immunoassay for simultaneous detection of Shiga toxins and isolation of Escherichia coli O157 in foods,” Journal of Food Protection, vol. 74, no. 3, pp. 373–379, 2011. View at Publisher · View at Google Scholar · View at PubMed
  49. A. Roggenkamp, K. Ruckdeschel, L. Leitritz, R. Schmitt, and J. Heesemann, “Deletion of amino acids 29 to 81 in adhesion protein YadA of Yersinia enterocolitica serotype O:8 results in selective abrogation of adherence to neutrophils,” Infection & Immunity, vol. 64, no. 7, pp. 2506–2514, 1996. View at Google Scholar · View at Scopus
  50. B. Ngom, Y. Guo, X. Wang, and D. Bi, “Development and application of lateral flow test strip technology for detection of infectious agents and chemical contaminants: a review,” Analytical & Bioanalytical Chemistry, vol. 397, no. 3, pp. 1113–1135, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  51. M. J. Taussig and U. Landegren, “Progress in antibody arrays,” Drug Discovery Today, vol. 2, no. 4, pp. 169–176, 2003. View at Google Scholar · View at Scopus
  52. C. Wingren and C. A. K. Borrebaeck, “Progress in miniaturization of protein arrays-a step closer to high-density nanoarrays,” Drug Discovery Today, vol. 12, no. 19-20, pp. 813–819, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  53. K. L. Kellar and K. G. Oliver, “Multiplexed microsphere assays for protein and DNA binding reactions,” Methods in Cell Biology, vol. 2004, no. 75, pp. 409–429, 2004. View at Google Scholar · View at Scopus
  54. S. Derveaux, B. G. Stubbe, K. Braeckmans et al., “Synergism between particle-based multiplexing and microfluidics technologies may bring diagnostics closer to the patient,” Analytical & Bioanalytical Chemistry, vol. 391, no. 7, pp. 2453–2467, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  55. M. Magliulo, P. Simoni, M. Guardigli et al., “A rapid multiplexed chemiluminescent immunoassay for the detection of Escherichia coli O157:H7, Yersinia enterocolitica, Salmonella typhimurium, and Listeria monocytogenes pathogen bacteria,” Journal of Agricultural and Food Chemistry, vol. 55, no. 13, pp. 4933–4939, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  56. A. Sreekumar, M. K. Nyati, S. Varambally et al., “Profiling of cancer cells using protein microarrays: discovery of novel radiation-regulated proteins,” Cancer Research, vol. 61, no. 20, pp. 7585–7593, 2001. View at Google Scholar · View at Scopus
  57. V. C. Rucker, K. L. Havenstrite, and A. E. Herr, “Antibody microarrays for native toxin detection,” Analytical Biochemistry, vol. 339, no. 2, pp. 262–270, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  58. B. Li, L. Jiang, Q. Song et al., “Protein microarray for profiling antibody responses to Yersinia pestis live vaccine,” Infection & Immunity, vol. 73, no. 6, pp. 3734–3739, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  59. J. Hoorfar, D. L. Baggesen, and P. H. Porting, “A PCR-based strategy for simple and rapid identification of rough presumptive Salmonella isolates,” Journal of Microbiological Methods, vol. 35, no. 1, pp. 77–84, 1999. View at Publisher · View at Google Scholar · View at Scopus
  60. M. R. Stratton, P. J. Campbell, and P. A. Futreal, “The cancer genome,” Nature, vol. 458, no. 7239, pp. 719–724, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  61. S. Brenner, M. Johnson, J. Bridgham et al., “Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays,” Nature Biotechnology, vol. 18, no. 6, pp. 630–634, 2000. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  62. T. D. Harris, P. R. Buzby, H. Babcock et al., “Single-molecule DNA sequencing of a viral genome,” Science, vol. 320, no. 5872, pp. 106–109, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  63. W. Brockman, P. Alvarez, S. Young et al., “Quality scores and SNP detection in sequencing-by-synthesis systems,” Genome Research, vol. 18, no. 5, pp. 763–770, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  64. J. A. Shendure, G. J. Porreca, and G. M. Church, “Overview of DNA sequencing strategies,” Current Protocols in Molecular Biology, chapter 7: unit 7.1, no. 81, pp. 7.1.1–7.1.11, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  65. X. Zhou, L. Ren, Q. Meng et al., “The next-generation sequencing technology and application,” Protein & Cell, vol. 1, no. 6, pp. 520–536, 2010. View at Google Scholar
  66. F. Sanger, “Sequences, sequences, and sequences,” Annual Review of Biochemistry, vol. 57, pp. 1–28, 1988. View at Google Scholar · View at Scopus
  67. K. V. Voelkerding, S. A. Dames, and J. D. Durtschi, “Next-generation sequencing:from basic research to diagnostics,” Clinical Chemistry, vol. 55, no. 4, pp. 641–658, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  68. J. C. Dohm, C. Lottaz, T. Borodina, and H. Himmelbauer, “SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing,” Genome Research, vol. 17, no. 11, pp. 1697–1706, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  69. M. J. Chaisson and P. A. Pevzner, “Short read fragment assembly of bacterial genomes,” Genome Research, vol. 18, no. 2, pp. 324–330, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  70. D. Hernandez, P. François, L. Farinelli, M. Østerås, and J. Schrenzel, “De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer,” Genome Research, vol. 18, no. 5, pp. 802–809, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  71. A. D. Smith, Z. Xuan, and M. Q. Zhang, “Using quality scores and longer reads improves accuracy of Solexa read mapping,” BMC Bioinformatics, vol. 9, article 128, pp. 1–8, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  72. R. L. Warren, G. G. Sutton, S. J. M. Jones, and R. A. Holt, “Assembling millions of short DNA sequences using SSAKE,” Bioinformatics, vol. 23, no. 4, pp. 500–501, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  73. A. V. Zimin, D. R. Smith, G. Sutton, and J. A. Yorke, “Assembly reconciliation,” Bioinformatics, vol. 24, no. 1, pp. 42–45, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  74. J. R. Miller, A. L. Delcher, S. Koren et al., “Aggressive assembly of pyrosequencing reads with mates,” Bioinformatics, vol. 24, no. 24, pp. 2818–2824, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  75. K. Prüfer, U. Stenzel, M. Dannemann, R. E. Green, M. Lachmann, and J. Kelso, “PatMaN: rapid alignment of short sequences to large databases,” Bioinformatics, vol. 24, no. 13, pp. 1530–1531, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  76. B. D. Ondov, A. Varadarajan, K. D. Passalacqua, and N. H. Bergman, “Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications,” Bioinformatics, vol. 24, no. 23, pp. 2776–2777, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  77. D. Campagna, A. Albiero, A. Bilardi et al., “PASS: a program to align short sequences,” Bioinformatics, vol. 25, no. 7, pp. 967–968, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  78. J. Butler, I. MacCallum, M. Kleber et al., “ALLPATHS: de novo assembly of whole-genome shotgun microreads,” Genome Research, vol. 18, no. 5, pp. 810–820, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  79. N. Navin and J. Hicks, “Future medical applications of single-cell sequencing in cancer,” Genome Medicine, vol. 3, no. 5, pp. 1–12, 2011. View at Publisher · View at Google Scholar · View at PubMed
  80. A. C. Fierro, F. Vandenbussche, K. Engelen, Y. Van de Peer, and K. Marchal, “Meta analysis of gene expression data within and across species,” Current Genomics, vol. 9, no. 8, pp. 525–534, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  81. Y. Surget-Groba and J. I. Montoya-Burgos, “Optimization of de novo transcriptome assembly from next-generation sequencing data,” Genome Research, vol. 20, no. 10, pp. 1432–1440, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  82. F. B. Rahmatpanah, S. Carstens, S. I. Hooshmand et al., “Large-scale analysis of DNA methylation in chronic lymphocytic leukemia,” Epigenomics, vol. 1, no. 1, pp. 39–61, 2009. View at Google Scholar
  83. D. S. Johnson, A. Mortazavi, R. M. Myers, and B. Wold, “Genome-wide mapping of in vivo protein-DNA interactions,” Science, vol. 316, no. 5830, pp. 1497–1502, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  84. O. Wurtzel, M. Dori-Bachash, S. Pietrokovski, E. Jurkevitch, and R. Sorek, “Mutation detection with next-generation resequencing through a mediator genome,” PLoS One, vol. 5, no. 12, Article ID e15628, 2010. View at Publisher · View at Google Scholar · View at PubMed
  85. J. M. Kidd, Z. Cheng, T. Graves, B. Fulton, R. K. Wilson, and E. E. Eichler, “Haplotype sorting using human fosmid clone end-sequence pairs,” Genome Research, vol. 18, no. 12, pp. 2016–2023, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  86. C. A. Cummings, C. A. Chung, R. Fang et al., “Accurate, rapid and high-throughput detection of strain-specific polymorphisms in Bacillus anthracis and Yersinia pestis by next-generation sequencing,” Investigative Genetics, vol. 1, no. 1, article 5, 2010. View at Publisher · View at Google Scholar · View at PubMed
  87. G. Morelli, Y. Song, C. J. Mazzoni et al., “Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity,” Nature Genetics, vol. 42, no. 12, pp. 1140–1143, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  88. P. E. Chen, C. Cook, A. C. Stewart et al., “Genomic characterization of the Yersinia genus,” Genome Biology, vol. 11, no. 1, article R1, 2010. View at Publisher · View at Google Scholar · View at PubMed