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Title Microbiome analysis : methods and protocols / edited by Robert G. Beiko, Will Hsiao, John Parkinson
Published New York, NY : Humana Press, [2018]
©2018

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Location Call no. Vol. Availability
 W'PONDS  579.078 Bei/Mam  DUE 30-06-20
Description xi, 324 pages : illustrations (chiefly color) ; 27 cm
Series Methods in molecular biology ; 1849
Springer protocols
Methods in molecular biology (Clifton, N.J.) ; v. 1849
Springer protocols (Series)
Contents Characterizing the deep terrestrial subsurface microbiome / Rebecca A. Daly, Kelly C. Wrighton, and Michael J. Wilkins -- Freshwater viromes : from sampling to evaluation / Catherine Putonti, Zoe Diener, and Siobhan C. Watkins -- Characterization of eukaryotic microbiome using 18S amplicon sequencing / Ana Popovic and John Parkinson -- Culture and molecular profiling of the respiratory tract microbiota / Fiona J. Whelan, Laura Rossi, Jennifer C. Stearns, and Michael G. Surette -- Methods and strategies to examine the human breastmilk microbiome / Lauren LeMay-Nedjelski, Julia Copeland, Pauline W. Wang, James Butcher, Sharon Unger, Alain Stintzi, and Deborah L. O'Connor -- Quantification of vitamin B12-related proteins in marine microbial systems using selected reaction monitoring mass spectrometry / Erin M. Bertrand -- Single-cell genomics of microbial dark matter / Christian Rinke -- 16S rRNA gene analysis with QIIME2 / Michael Hall and Robert G. Beiko -- Processing a 16S rRNA sequencing dataset with the microbiome helper workflow / Gavin M. Douglas, Andre M. Comeau, and Morgan G.I. Langille -- Normalization of microbiome profiling data / Paul J. McMurdie -- Predicting the functional potential of the microbiome from marker genes using PICRUSt / Gavin M. Douglas, Robert G. Beiko, and Morgan G.I. Langille -- Metagenome assembly and contig assignment / Qingpeng Zhang -- From RNA-seq to biological inference : using compositional data analysis in meta-transcriptomics / Jean M. Macklaim and Gregory B. Gloor -- Subsampled assemblies and hybrid nucleotide composition/differential coverage binning for genome-resolved metagenomics / Laura A. Hug -- Transkingdom networks : a systems biology approach to identify causal members of host-microbiota interactions / Richard R. Rodrigues, Natalia Shulzhenko, and Andrey Morgun -- Constructing and analyzing microbiome networks in R / Mehdi Layeghifard, David M. Hwang, and David S. Guttman -- Bayesian inference of microbial community structure from metagenomic data using BioMiCo / Katherine A. Dunn, Katelyn Andrews, Rana O. Bashwih, and Joseph P. Bielawski -- Analyzing metabolic pathways in microbiomes / Mobolaji Adeolu, John Parkinson, and Xuejian Xiong -- Sparse treatment-effect model for taxon identification with high-dimensional metagenomic data / Zhenqiu Liu and Shili Lin
Summary This volume aims to capture the entire microbiome analysis pipeline, sample collection, quality assurance, and computational analysis of the resulting data. Chapters detail several example applications of microbiome research, and the protocols described in this book are complemented with short perspectives about the history, current state, and future directions of protocols in microbiomics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls
Bibliography Includes bibliographical references and index
Subject Microbiology -- Laboratory manuals.
Genre/Form Laboratory manuals.
Laboratory manuals.
Author Beiko, Robert G., editor
Hsiao, Will, editor
Parkinson, John, 1968- editor
LC no. 2018955280
ISBN 1493987267 (hardback)
9781493987269 (hardback)