Databases compilations
- Osterman A., Overbeek R. 2003. Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol 7: 238-251.
- Galperin M. Y., Koonin E. V. 2010. From complete genome sequence to 'complete' understanding? Trends Biotechnol 28: 398-406.
- Sorokina M., Stam M., Medigue C., Lespinet O., Vallenet D. 2014. Profiling the orphan enzymes. Biol Direct 9: 10.
- Danchin A, Ouzounis C, Tokuyasu T, Zucker JD. No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects. Microb Biotechnol. 2018;11(4):588-605. doi:10.1111/1751-7915.13284
- Chen C, Huang H, Wu CH. Protein Bioinformatics Databases and Resources. Methods Mol Biol. 2017;1558:3-39. doi: 10.1007/978-1-4939-6783-4_1. PMID: 28150231.
- Zhulin IB. Databases for Microbiologists. J Bacteriol. 2015 Aug1;197(15):2458-67. doi: 10.1128/JB.00330-15. Epub 2015 May 26. Review. PMID: 26013493
- Rigden DJ, Fernández XM. The 2024 Nucleic Acids Research database issue and the online molecular biology database collection. Nucleic Acids Res. 2023 Nov 30:gkad1173. doi: 10.1093/nar/gkad1173. Epub ahead of print. PMID: 38035367.
Introduction on the Genomic revolution in Microbiology
- Relman DA. Microbial genomics and infectious diseases. N Engl J Med. 2011 Jul 28;365(4):347-57. doi: 10.1056/NEJMra1003071. Review. PMID: 21793746
- Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, Karpinets T, Lund O, Kora G, Wassenaar T, Poudel S, Ussery DW. Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics. 2015 Mar;15(2):141-61. doi: 10.1007/s10142-015-0433-4. Epub 2015 Feb 27. Review. PMID: 25722247.
- Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdorf AW, Amano Y, Ise K, Suzuki Y, Dudek N, Relman DA, Finstad KM, Amundson R, Thomas BC, Banfield JF. A new view of the tree of life. Nat Microbiol. 2016 Apr 11;1:16048. doi: 10.1038/nmicrobiol.2016.48. PMID: 27572647
- Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL. Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis. Clin Microbiol Rev. 2017 Oct;30(4):1015-1063. doi: 10.1128/CMR.00016-17. Review. PMID: 28855266
- Jagadeesan B, Gerner-Smidt P, Allard MW, Leuillet S, Winkler A, Xiao Y, Chaffron S, Van Der Vossen J, Tang S, Katase M, McClure P, Kimura B, Ching Chai L, Chapman J, Grant K. The use of next generation sequencing for improving food safety: Translation into practice. Food Microbiol. 2019 Jun;79:96-115. doi: 10.1016/j.fm.2018.11.005. Epub 2018 Nov 17. Review. PMID: 30621881
- Lachance JC, RodrigueS, PalssonBO. Minimal cells, maximal knowledge. Elife. 2019 PMID: 30860025
- Goldstein S, Beka L, Graf J, Klassen JL. Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing. BMC Genomics. 2019 Jan 9;20(1):23. doi: 10.1186/s12864-018-5381-7. PMID: 30626323.
- GEBA PROJECT: http://jgi.doe.gov/our-science/science-programs/microbial-genomics/phylogenetic-diversity/
- COMPILATION: https://www.intechopen.com/online-first/metagenomics-based-phylogeny-and-phylogenomic
Understanding RefSeq