Tag Archives: BluePippin

Plasmids from Shiga Toxin-Producing Escherichia coli Strains with Rare Enterohemolysin Gene (ehxA) Subtypes Reveal Pathogenicity Potential and Display a Novel Evolutionary Path

Posted on December 9, 2016 by Alex

November 2016 Authors: Sandra C. Lorenz, Steven R. Monday, Maria Hoffmann, Markus Fischer and Julie A. Kase Info: Scientists from the US FDA and the University of Hamburg used PacBio sequencing to characterize plasmids associated with heightened virulence in Shiga … more »

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Very Short Mitochondrial DNA Fragments and Heteroplasmy in Human Plasma

Posted on December 9, 2016 by Alex

November 2016 Authors: Ruoyu Zhang, Kiichi Nakahira, Xiaoxian Guo, Augustine M.K. Choi & Zhenglong Gu Info: Scientists at Cornell University studied cell-free mitochondrial DNA found in plasma samples collected from sepsis patients. Along the way, they optimized sample prep protocols … more »

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Preprints Galore!

Posted on December 8, 2016 by Alex

We normally wait until papers come out in scientific journals before reporting on them here, but there are so many great preprints featuring Sage Science tools we couldn’t resist pointing them out. (On a side note, the rising numbers of … more »

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Nanopore Sequencers Give Optimal Results with BluePippin Size Selection

Posted on November 1, 2016 by Alex

The Oxford Nanopore team has been speaking recently about their use of our BluePippin automated size selection system for optimizing the read length obtained from nanopore sequencers. For anyone interested in the Oxford platforms who hasn’t seen this information, here’s … more »

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Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data

Posted on October 15, 2016 by Alex

September 2016 Authors: Jianwei Zhang, Ling-Ling Chen, Shuai Sun, et al. Info: In this paper, researchers report generating two reference-quality genome assemblies for Oryza sativa subspecies. They publicly released both assemblies, which were built using PacBio and Illumina sequencing technology. … more »

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Production of the Bioactive Compounds Violacein and Indolmycin Is Conditional in a maeA Mutant of Pseudoalteromonas luteoviolaceaS4054 Lacking the Malic Enzyme

Posted on October 12, 2016 by Alex

September 2016 Authors: Mariane S. Thøgersen, Marina W. Delpin, Jette Melchiorsen, Mogens Kilstrup, Maria Månsson, Boyke Bunk, Cathrin Spröer, Jörg Overmann, Kristian F. Nielsen, and Lone Gram Info: A team of scientists analyzed biological compounds produced by Pseudoalteromonas luteoviolacea, a … more »

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The two chromosomes of the mitochondrial genome of a sugarcane cultivar: assembly and recombination analysis using long PacBio reads

Posted on October 9, 2016 by Alex

August 2016 Authors: Jeremy R. Shearman, Chutima Sonthirod, Chaiwat Naktang, Wirulda Pootakham, Thippawan Yoocha, Duangjai Sangsrakru, Nukoon Jomchai, Somvong Tragoonrung, and Sithichoke Tangphatsornruang Info: Scientists in Thailand used long-read sequencing to assemble the mitochondrial genome of a sugarcane cultivar from … more »

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A draft genome of the brown alga, Cladosiphon okamuranus, S-strain: a platform for future studies of ‘mozuku’ biology

Posted on September 20, 2016 by Alex

August 2016 Authors: Koki Nishitsuji, Asuka Arimoto, Kenji Iwai, Yusuke Sudo, Kanako Hisata, Manabu Fujie, Nana Arakaki, Tetsuo Kushiro, Teruko Konishi, Chuya Shinzato, Noriyuki Satoh and Eiichi Shoguchi Info: Scientists from Japan sequenced the genome of Cladosiphon okamuranus, an edible … more »

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DSBCapture: in situ capture and sequencing of DNA breaks

Posted on September 20, 2016 by Alex

August 2016 Authors: Stefanie V Lensing, Giovanni Marsico, Robert Hänsel-Hertsch, Enid Y Lam, David Tannahill & Shankar Balasubramanian Info: Scientists at Cancer Research UK developed and validated a new sequencing-based protocol to spot double-stranded DNA breaks in situ; these regions … more »

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At the University of Delaware, Early Adopter Genomics Core Spots New Science Trends

Posted on August 24, 2016 by Alex

The genomics core facility at the University of Delaware has set itself apart from other service providers by being among the first to adopt new sequencing technologies. The strategy has been a success: today, the facility serves customers around the … more »

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