Curated Literature for Amplicon Metagenomics

  • Comeau, André M., Gavin M. Douglas, and Morgan G. I. Langille. 2017. “Microbiome Helper: A Custom and Streamlined Workflow for Microbiome Research.” Edited by Jonathan Eisen. mSystems 2 (1): e00127–16, /msys/2/1/e00127–16.atom. https://doi.org/10.1128/msystems.00127-16.

  • Franzosa, Eric A, and Galeb Abu-Ali. n.d. “Introduction to Metagenomic Analysis,” 80.

  • Goodrich, Julia K., Sara C. Di Rienzi, Angela C. Poole, Omry Koren, William A. Walters, J. Gregory Caporaso, Rob Knight, and Ruth E. Ley. 2014. “Conducting a Microbiome Study.” Cell 158 (2): 250–62. https://doi.org/10.1016/j.cell.2014.06.037.

  • Koren, Omry, Dan Knights, Antonio Gonzalez, Levi Waldron, Nicola Segata, Rob Knight, Curtis Huttenhower, and Ruth E. Ley. 2013. “A Guide to Enterotypes Across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets.” Edited by Jonathan A. Eisen. PLoS Computational Biology 9 (1): e1002863. https://doi.org/10.1371/journal.pcbi.1002863.

  • Kuczynski, Justin, Christian L. Lauber, William A. Walters, Laura Wegener Parfrey, José C. Clemente, Dirk Gevers, and Rob Knight. 2012. “Experimental and Analytical Tools for Studying the Human Microbiome.” Nature Reviews Genetics 13 (1): 47–58. https://doi.org/10.1038/nrg3129.

  • Kunin, V., A. Copeland, A. Lapidus, K. Mavromatis, and P. Hugenholtz. 2008. “A Bioinformatician’s Guide to Metagenomics.” Microbiology and Molecular Biology Reviews 72 (4): 557–78. https://doi.org/10.1128/MMBR.00009-08.

  • Pollock, Jolinda, Laura Glendinning, Trong Wisedchanwet, and Mick Watson. 2018. “The Madness of Microbiome: Attempting to Find Consensus ‘Best Practice’ for 16S Microbiome Studies.” Edited by Shuang-Jiang Liu. Applied and Environmental Microbiology 84 (7): e02627–17, /aem/84/7/e02627–17.atom. https://doi.org/10.1128/AEM.02627-17.

  • Raja, Huzefa A., Andrew N. Miller, Cedric J. Pearce, and Nicholas H. Oberlies. 2017. “Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community.” Journal of Natural Products 80 (3): 756–70. https://doi.org/10.1021/acs.jnatprod.6b01085.

  • Washburne, Alex D., James T. Morton, Jon Sanders, Daniel McDonald, Qiyun Zhu, Angela M. Oliverio, and Rob Knight. 2018. “Methods for Phylogenetic Analysis of Microbiome Data.” Nature Microbiology 3 (6): 652–61. https://doi.org/10.1038/s41564-018-0156-0.

  • Wooley, John C., Adam Godzik, and Iddo Friedberg. 2010. “A Primer on Metagenomics.” Edited by Philip E. Bourne. PLoS Computational Biology 6 (2): e1000667. https://doi.org/10.1371/journal.pcbi.1000667.

2020

Guide to improve Python performance.

9 minute read

The primary objective of this guide is to summarize all of the popular approaches for boosting the execution speed of your Python code.

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2019

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