Genome Sequences 

 

Metabolism Databases

 

Methods

Sample prep, sequencing & bioinformatic Methods

  • Miller, Bronwen, Beverley van Rooyen, Heather Whitehorn, Piet Jones, Martin Ranik, Eric van der Walt, Maryke Appel, Nguyet Kong, Carol Huang, Dylan Storey, Bart C. Weimer. 2015, A novel, single-tube enzymatic fragmentation and library construction method enables fast turnaround times and improved data quality for microbial whole-genome sequencing. Kapa Biosystems Application Note (072314 KK1234; DOI: 10.13140/RG.2.1.4534.3440).
  • Kong, Nguyet, Whitney Ng, and Bart C. Weimer. 2015. Quality Control of Library Construction Pipeline for PacBio SMRTbell 10kb Library Using Agilent 2200 TapeStation. Agilent Technologies application note (5991-6521EN; DOI: 10.13140/RG.2.1.4339.4644)
  • Kong, Nguyet, Whitney Ng, Lucy Cai, Alvin Leonardo, and Bart C. Weimer. 2014. Integrating the DNA Integrity Number (DIN) to Assess Genomic DNA (gDNA) Quality Control Using the Agilent 2200 TapeStation System. Agilent Technologies application note (5991-5442EN; DOI: 10.13140/RG.2.1.3616.8409).
  • Kong, Nguyet, Whitney Ng, Azarene Foutouhi, B. Carol Huang, and Bart C. Weimer. 2014. Quality Control of High-Throughput Library Construction Pipeline for KAPA HTP Library Using an Agilent2200 TapeStation. Agilent Technologies application note (5991-5141EN; DOI: 10.13140/RG.2.1.4927.5604).
  • Jeannotte, Richard, Eric Lee, Narine Arabyan, Nguyet Kong, Kao Thao, Carol Huang and Bart C. Weimer. 2014. Optimization of Covaris settings for shearing bacterial genomic DNA by focused ultrasonication and analysis using Agilent 2200 TapeStation. Agilent Technologies application note. (5991-5075EN; DOI: 10.13140/RG.2.1.4424.1444).
  • Jeannotte, Richard, Eric Lee, Nguyet Dao Kong, Whitney Ng, and B. C. Weimer. 2014. High-Throughput Analysis of Foodborne Bacterial Genomic DNA Using Agilent 2200 TapeStation and Genomic DNA ScreenTape System. Agilent Technologies application note. (5991-4003EN; DOI: 10.13140/RG.2.1.3354.6961).
  • Kong, Nguyet, Kao Thao, Whitney Ng, Kristi Spittle Kim, Jonas Korlach, Luke Hickey, Lenore Kelly, Stephen Lappin, and Bart C. Weimer. 2014. Automation of PacBio SMRTbell 10 kb Template Preparation on an Agilent NGS Workstation. Agilent Technologies application note. (5991-4482EN; DOI: 10.13140/RG.2.1.4403.2725).
  • Kong, Nguyet, Kao Thao, Carol Huang, Maryke Appel, Stephen Lappin, Lisa Knapp, Lenore Kelly, and B. C. Weimer. 2014. Automated Library Construction Using KAPA Library Preparation Kits on the Agilent NGS Workstation Yields High-Quality Libraries for Whole-Genome Sequencing on the Illumina Platform. Agilent Technologies application note (5991-4296EN; DOI: 10.13140/RG.2.1.2306.1203).
  • Kong, N., W. Ng, V. Lee, L. Kelly, and B. C. Weimer. 2013. Production and Analysis of High Molecular Weight Genomic DNA for NGS Pipelines Using Agilent DNA Extraction Kit. Agilent Technologies application note (5991-3722EN; DOI: 10.13140/RG.2.1.2961.4807).
  • Stevens, John R., Todd R. Jones, Michael Lefevre, Balasubramanian Ganesan, and Bart C. Weimer. 2017. SigTree: identifying and visualizing significantly responsive branches in a phylogenetic tree. Computational and Structural Biology Journal 15:372-376. (PMID:28748045)
  • Kaufman, James H., Christopher A. Elkins, Matthew Davis, Allison M Weis, Bihua C. Huang, Mark K Mammel, Isha R. Patel, Kristen L. Beck, Stefan Edlund, David Chambliss, Simone Bianco, Mark Kunitomi, Bart C. Weimer*. 2017. Microbiogeography and microbial genome evolution. arXiv:1703.07454 [q-bio.GN].
  • Draper, Jenny L., Lori M. Hansen, David Bernick, Samar Abedrabbo, Jason G. Underword, Nguyet Kong, Carol B. Huang, Allison M. Weis, Bart C. Weimer, Arnoud Van Vliet, Nader Pourmand, Jay V. Solnick, Kevin Karplus, Karen M. Ottemann. 2017. Fallacy of the unique genome: Sequence diversity within single Helicobacter pylori strains. mBio 8:e02321-16. (PMID: 28223462).
  • Kong, Nguyet, Whitney Ng, Kao Thao, Regina Agulto, Allison Weis, Kristi Spittle, and Bart C. Weimer. 2017. Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing. Standards in Genomic Sciences. 12:27-37 (PMID: 28344744). (highly accessed notation by journal)
  • Chen, Poyin, Henk C. den Bakker, Jonas Korlach, Meredith Ashby, Tyson Clark, Khai Luong, R. J. Roberts, Martin Wiedmann, and Bart C. Weimer. 2017. Comparative Genomics Reveals the Diversity of Restriction-Modification Systems and DNA Methylation Sites in Listeria monocytogenes.App. Environ. Microbiol. 83:e02091-16. (PMID: 27836852).
  • Hu, Yongfei, Xi Yang, Jing Li, Na Lv, Fei Liu, Jun Wu, Ivan Lin, Na Wu, Bart C. Weimer, George Gao, Yulan Liu, Baoli Zhu. 2016. The transfer network of bacterial mobile resistome connecting animal and human microbiome. App. Environ. Microbiol. 82:6672-6681 (PMID: 27613679)
  • Weimer, Bart C., Dylan Bobby Storey, Christopher A. Elkins, Robert C. Baker, Peter Markwell, David Chambliss, Stefan Edlund, James H. Kaufman. 2016. Defining the food microbiome for authentication, safety, and process management.  IBM Journal of Research and Development, 60 (5/6):1.1-1.13. (DOI: 10.1147/JRD.2016.2582598).
  • Edlund, Stefan, Kristen L. Beck, Niina Haiminen, Laxmi Parida, Dylan Bobby Storey, Bart C. Weimer, James H. Kaufman, David Chambliss. 2016. Design of the MCAW Compute Service for Food Safety Bioinformatics. IBM Journal of Research and Development, 60 (5/6):2.1-2.12 (DOI: 10.1147/JRD.2016.2584798).
  • Shah, Jigna, Prerak T. Desai, & Bart C. Weimer. 2014. Genetic mechanisms underlying pathogenicity of cold-stressed Salmonella Typhimurium in cultured intestinal epithelial cells. Appl. Environ. Microbiol. 80:6943-53. (PMID: 25192993)
  • Chen, Poyin, Richard Jeannotte, and Bart C. Weimer. 2014. Exploring Bacterial Epigenomics in the NGS Era—A New Approach for an Emerging Frontier. Trends in Microbiology 22:292–300. (PMID: 24725482)
  • Deng, Xiangyu, Prerak T. Desai, Henk C. den Bakker, Matthew Mikoleit, Beth Tolar, Eija Trees, Rene S. Hendriksen, Jonathan Frye, Steffen Porwollik, Bart C. Weimer, Martin Wiedmann, George M. Weinstock, Michael McClelland, Patricia I. Fields. 2014. Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages. Emerging and Infectious Diseases. 20:1481-9. (PMID: 25147968)
  • Latta, L.C. IV, M. Baker, T. Crowl, J.J. Parnell, B. Weimer, D. DeWald, M.E. Pfrender. 2011.  Species and genotype diversity drive community and ecosystem properties in experimental microcosms. Evolutionary Ecology 25:1107-1125. DOI 10.1007/s10682-010-9457-3
  • Parnell, John, Giovanni Rompato, Todd Crowl, Bart C. Weimer, and Michael Pfrender. 2011. The effect of disturbance on phylogenetic diversity in microbial communities. Aquatic Microbial Ecology 64:267–273. DOI: 10.3354/ame01527
  • Parnell, John, Giovanni Rompato, Leigh Latta IV, Michael Pfrender, Joy Van Nostrand, Zhili He, Jizhong Zhou, Gary Andersen, Patti Champine, Balasubramanian Ganesan, and Bart C. Weimer. 2010. Functional biogeography as evidence of gene transfer in hypersaline microbial communities. PLoS One 5(9):e12919. (PMID: 20957119)
  • Stevens, John R., Balasubramanian Ganesan, Prerak Desai, Sweta Rao, and Bart C. Weimer. 2008. Statistical issues for normalization of multi-species microarray data. 20:47–62. In: Proceedings of the 20th Annual Kansas State University Conference on Applied Statistics in Agriculture. Ed. Gary L. Gadbury. New Prairie Press, Manhattan, KS.
  • Lee, J-H., V.N. Karamychev, S.A. Kozyavkin, D. Mills, A.R. Pavlov, N.V. Pavlov, N.N. Polouchine, P.M. Richardson, V.V. Shakhova, A.I. Slesarev, B. Weimer, D.J. O’Sullivan. 2008. Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth. BMC Genomics 9:247-265. (PMID: 18505588)

 

 

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