Citations

Harnessing the power of RADseq for ecological and evolutionary genomics

January 2016

Authors:
Kimberly R. Andrews, Jeffrey M. Good, Michael R. Miller, Gordon Luikart and Paul A. Hohenlohe

Info:
In this protocol review, scientists examine several approaches to restriction site-associated DNA sequencing and present their findings on how to choose the best method for a specific project. Pippin is included as a key step in the original RADseq protocol.

Citation:
Nature Reviews Genetics
doi:10.1038/nrg.2015.28

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CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

December 2015

Authors:
Zhonghui Tang, Oscar Junhong Luo, Xingwang Li, et al.

Info:
Scientists from the Jackson Lab and many collaborating institutes used the ChIA-PET strategy with other data sets to understand how genome organization affects transcription in human cells. They analyzed gene expression with the Iso-Seq method on a PacBio system, using SageELF for size selection.

Citation:
Cell 163, 1611–1627
DOI: 10.1016/j.cell.2015.11.024

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Population genomics of intrapatient HIV-1 evolution

December 2015

Authors:
Fabio Zanini, Johanna Brodin, Lina Thebo, Christa Lanz, Göran Bratt, Jan Albert, and Richard Neher

Info:
Researchers from Germany and Sweden sequenced several samples collected over time from each of nine patients with HIV-1 to assess genetic diversity and minor variants of the virus as it evolved. Sequencing was performed on an Illumina MiSeq, with size selection of the Nextera library conducted with BluePippin.

Citation:
eLife 2015;4:e11282
http://dx.doi.org/10.7554/eLife.11282

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MicroRNAs in the oriental fruit fly, Bactrocera dorsalis: extending Drosophilid miRNA conservation to the Tephritidae

October 2015

Authors:
Bernarda Calla and Scott M. Geib

Info:
Scientists analyzed small RNAs in Bactrocera dorsalis, the oriental fruit fly, and compared the resulting gene expression profile with that of Drosophila melanogaster. BluePippin was used to enrich for cDNAs between 92 bp and 118 bp prior to sequencing on an Ion Torrent PGM.

Citation:
BMC Genomics 2015 16:740
DOI: 10.1186/s12864-015-1835-3

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Scarless genome editing and stable inducible expression vectors for Geobacter sulfurreducens

August 2015

Authors:
Chi Ho Chan, Caleb E. Levar, Lori Zacharoff, Jonathan P. Badalamenti, Daniel R. Bond

Info:
Scientists from the University of Minnesota report in Applied and Environmental Microbiology the development of genetic system improvements for Geobacter sulfurreducens. BluePippin was used to size-select libraries prior to sequencing on PacBio.

Citation:
doi:10.1128/AEM.01967-15

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