Citations

Discovery of Novel Rhabdoviruses in the Blood of Healthy Individuals from West Africa

March 2015

Authors:
Matthew H Stremlau, Kristian G Andersen, Onikepe A Folarin, Jessica N Grove, Ikponmwonsa Odia, Philomena E Ehiane, Omowunmi Omoniwa, Omigie Omoregie, Pan-Pan Jiang, Nathan L Yozwiak, Christian B Matranga, Xiao Yang, Stephen K Gire, Sarah Winnicki, Ridhi Tariyal, Stephen F Schaffner, Peter O Okokhere, Sylvanus Okogbenin, George O Akpede, Danny A. Asogun, Dennis E. Agbonlahor, Peter J Walker, Robert B Tesh, Joshua Z Levin, Robert F Garry, Pardis C Sabeti, Christian T Happi

Info:
In this PLOS Neglected Tropical Diseases paper, researchers utilized next-generation sequencing to identify RNA viruses in the blood of 195 patients with unexplained acute febrile illness and compared them with those found in 328 apparently healthy control individuals, all from communities in southeastern Nigeria. The researchers suggest that human infection with rhabdoviruses might be common. Carrier RNA was removed after cDNA synthesis using Pippin Prep size selection.

Citation:
PLoS Negl Trop Dis
9(3): e0003631. doi:10.1371/journal.pntd.0003631

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Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics

March 2015

Authors:
Stephanie J Yaung, Luxue Deng, Ning Li, Jonathan L Braff, George M Church, Lynn Bry, Harris H Wang, Georg K Gerber

Info:
In this Molecular Systems Biology paper, researchers from Harvard and Columbia discuss the use of metagenomic DNA to construct large-scale heterologous expression libraries that are tracked over time in vivo by deep sequencing and computational methods. This is the first demonstration of temporal functional metagenomics using shotgun libraries applied to the in vivo mammalian gut environment. Pippin Prep was used for size selection prior to Sanger sequencing.

Citation:
Mol Syst Biol. (2015) 11: 788
doi 10.15252/msb.20145866

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PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations

March 2015

Authors:
Min Wang, Christine R Beck, Adam C English, Qingchang Meng, Christian Buhay, Yi Han, Harsha V Doddapaneni, Fuli Yu, Eric Boerwinkle, James R Lupski, Donna M Muzny and Richard A Gibbs

Info:
In this BMC Genomics publication, scientists from Baylor College of Medicine report a new method for targeted sequencing of important structural variations in the human genome with the PacBio platform. Using oligo-based DNA capture with Pippin Prep or BluePippin sizing from Sage Science, the researchers demonstrated successful structural variant analysis at high accuracy and low cost.

Citation:
Wang et al. BMC Genomics (2015) 16:214
DOI 10.1186/s12864-015-1370-2

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A phylogenomic analysis of turtles

February 2015

Authors:
Nicholas G Crawford, James F Parham, Anna B Sellas, Brant C Faircloth, Travis C Glenn, Theodore J Papenfuss, James B Henderson, Madison H Hansen, W Brian Simison

Info:
In this Editor’s Choice article from the Molecular Phylogenetics and Evolution journal, researchers provide the first genome-scale analysis of turtle phylogeny using sequence data collected from thousands of ultraconserved elements. Through maximum likelihood, Bayesian, and species tree methods, they produced a single resolved phylogeny. BluePippin was used to prepare the libraries for PCR amplification.

Citation:
Molecular Phylogenetics and Evolution
doi:10.1016/j.ympev.2014.10.021

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Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

February 2015

Authors:
Francine E. Garrett-Bakelman, Caroline K. Sheridan, Thadeous J. Kacmarczyk, Jennifer Ishii, Doron Betel, Alicia Alonso, Christopher E. Mason, Maria E. Figueroa, and Ari M. Melnick

Info:
In this publication in the Journal of Visualized Experiments, scientists at Weill Cornell Medical College and the University of Michigan describe a protocol to map DNA methylation patterns across the genome with next-gen sequencing instead of microarrays. Where input amounts allow, the approach calls for automated DNA size selection using Pippin Prep.

Citation:
J Vis Exp. 2015; (96): 52246.
DOI: 10.3791/52246

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