Author Archives: Alex

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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At the University of Florida, SageELF Delivers Better Sizing for ddRAD-seq and Long-Read Pipelines

Posted on October 12, 2016 by Alex

Clients of the NextGen DNA Sequencing core at the University of Florida in Gainesville rely on Scientific Director David Moraga Amador to find and validate the best technologies for their projects. In addition to bringing in the best sequencers, that … 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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Poster: Better Cell-Free DNA Analysis with Pippin + Rubicon Genomics

Posted on October 5, 2016 by Alex

Recently we blogged about the rise of cell-free DNA studies, and how precise size selection is one tool that can help researchers isolate DNA of interest for further analysis (such as sorting out fetal from maternal genetic material). At the AGBT … more »

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Size Selection Has Utility for Cell-Free DNA Studies

Posted on September 23, 2016 by Alex

The rise of research studies and diagnostic tests looking at cell-free DNA — particularly fetal DNA in a mother’s bloodstream — has happened with astonishing speed. Prenatal genetic testing, for instance, has already supplanted many invasive clinical tests such as … 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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Association of MicroRNAs with Antibody Response to Mycoplasma bovis in Beef Cattle

Posted on September 20, 2016 by Alex

August 2016 Authors: Eduardo Casas, Guohong Cai, Larry A. Kuehn, Karen B. Register, Tara G. McDaneld, John D. Neill Info: USDA scientists performed a longitudinal study of young cows to identify microRNAs linked to a serum antibody produced after exposure … more »

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Where Illumina Users Gather, Great Science Is on Display

Posted on September 15, 2016 by Alex

The Sage team is pleased to be sponsoring the slate of upcoming Illumina user group meetings. We’ve attended many of these events over the years, and they’re excellent venues that showcase truly impressive work from the company’s broad customer base. … more »

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