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Tuesday, July 29, 2014

Novel Study of Genome-wide PT Modifications in Bacteria Performed with SMRT Sequencing

A recent paper from scientists in China and the United States demonstrates a novel view of phosphorothioate (PT) DNA modifications in two bacterial genomes. Scientists from Shanghai Jiao Tong University, Massachusetts Institute of Technology, Wuhan University, and Pacific Biosciences teamed up to deploy Single Molecule, Real-Time (SMRT®) Sequencing to generate the first genome-wide view of PT modifications and to better understand their function. “Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences” by Cao et al. was published in Nature Communications. The authors note that PT modifications, which replace a non-bridging phosphate oxygen with sulphur, were only recently…

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Tuesday, July 22, 2014

At ISMB, Gene Myers’ Keynote Offers History, Future of Genome Assembly

At ISMB 2014 in Boston earlier this month, Gene Myers of the Max-Planck Institute for Molecular Cell Biology and Genetics, presented a keynote address entitled “DNA Assembly: Past, Present, and Future.”  Myers received the prestigious Senior Scientist Accomplishment Award from the International Society for Computational Biology (ISCB) at the event. The ISCB Senior Scientist Accomplishment Award honors respected leaders in computational biology and bioinformatics for their significant contributions to these fields through research, education, and service. Myers is being honored as the 2014 winner for his outstanding contributions to the bioinformatics community, particularly for his work on sequence comparison algorithms,…

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Friday, July 11, 2014

ISMB 2014: The World Cup of Bioinformatics

We’re eager for the #ISMB conference — it’s the 22nd annual Intelligent Systems for Molecular Biology event — kicking off this weekend in Boston. As we continue to push our technology to deliver longer read lengths, we have been honored to work with many leading bioinformaticians to optimize the processing and analysis of our data. Several of those experts will be speaking at ISMB this year. On Sunday, attendees will hear from Adam Phillippy of the National Biodefense Analysis and Countermeasures Center. He’ll be presenting at noon on producing complete genome assemblies using Single Molecule, Real-Time (SMRT®) Sequencing data. Adam’s…

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Wednesday, July 9, 2014

Optimizing Eukaryotic De Novo Genome Assembly: Webinar Recording Available

Our webinar on eukaryotic genome assembly attracted a great crowd, and now we’re making the full recording available to the community. The session featured great hands-on information and best practices for working with Single Molecule, Real-Time (SMRT®) Sequencing data. “Optimizing Eukaryotic Genome Assembly with Long-Read Sequencing” featured three excellent speakers — Michael Schatz and James Gurtowski from Cold Spring Harbor Laboratory and Sergey Koren from the National Biodefense Analysis and Countermeasures Center — and was hosted by our own CSO Jonas Korlach. Schatz kicked off the session with an overview of assemblers for PacBio® data (as well as recommendations for…

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Tuesday, July 1, 2014

Scientists Generate the First Personal Transcriptome Using SMRT Sequencing

A new paper from scientists at Stanford University and Yale University describes the use of Single Molecule, Real-Time (SMRT®) Sequencing to generate transcriptomes for three individuals. The work is believed to be the first personal transcriptome analysis using long-read sequencing. The paper, entitled “Defining a personal, allele-specific, and single-molecule long-read transcriptome,” was published in PNAS by Hagen Tilgner, Fabian Grubert, Donald Sharon, and Michael Snyder. Last year, the same authors published a study using SMRT Sequencing to analyze transcriptomes across tissue samples from human organs. In the PNAS publication, they compare metrics from the new data set to those from…

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