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Wednesday, February 28, 2018

Join Us in Recognizing Rare Disease Day

The last day of February each year is designated as Rare Disease Day, a unique opportunity to recognize people who sometimes seem to be forgotten by the mainstream medical community. Once again PacBio is an official sponsor of the day, which will be marked with awareness-raising events in 80 countries around the world. It’s a beautiful way to remember the hundreds of millions of people affected by a rare disease, as well as the caretakers, researchers, and clinicians who work so hard to make their lives better. The thing about rare diseases is that, while each individual disease might affect…

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Wednesday, February 21, 2018

Hummingbird Study Uses Iso-Seq Method to Hunt for Metabolic Function

Photo of ruby-throated hummingbird by Michelle Lynn Reynolds UPDATED February 21, 2018 Congratulations to Winston Timp’s team on the publication of their Iso-Seq analysis of hummingbird! The paper is now available at GigaScience. ORIGINAL POST April 4, 2017 A new preprint offers an enticing look at transcriptome results from analysis of a hummingbird using SMRT Sequencing. In this study, scientists found new clues to explain unique attributes of the bird’s metabolism. The work was made possible through full-length isoform sequencing, which allowed deep, assembly-free analysis even though no reference genome was available. “Single molecule, full-length transcript sequencing provides insight into…

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Tuesday, February 20, 2018

Pre-AGBT Workshop: Reference Genomes and Diversity Representation

We can’t resist a good reference genome, so the pre-AGBT workshop entitled “Updating Reference Assemblies: New Technologies, New Sources of Diversity” was right up our alley. Hosted by the McDonnell Genome Institute, a member of the Genome Reference Consortium, the event offered conference attendees useful updates on efforts to expand the diversity of human reference genome sequences by incorporating samples from multiple continents of origin (the Americas, Africa, and Asia in addition to Europe). NCBI’s Valerie Schneider spoke about opportunities and challenges in mining assemblies other than the current GRCh38 build. There are more human genome assemblies than ever, she…

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Friday, February 9, 2018

JGI Sequencing Fungus for Clues to Better Biofuel Production

Aspergillus ochraceus The Department of Energy has its eyes on an unassuming solution to our bioenergy needs: Aspergillus. The fungal genus contains hundreds of variations, which include powerful pathogens, industrial cell factories, and prolific producers of bioactive secondary metabolites. The DOE’s Joint Genome Institute (JGI) has embarked on an ambitious plan to sequence, annotate and analyze the genomes of 300 Aspergillus fungi, and the first results are in. In a study published in the Proceedings of the National Academy of Sciences, “Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species,” a team led by researchers at…

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Wednesday, February 7, 2018

Review: SMRT Sequencing ‘Is Revolutionizing’ Human Sequencing Applications

A new review in Nucleic Acids Research offers a sweeping look at human sequencing applications for SMRT Sequencing, finding that “[t]he myth that SMRT sequencing is too error prone … is being expunged and replaced by evidence that it offers advantages over short-read sequencers.” The authors conclude with a prediction about the ultimate potential for SMRT Sequencing and other “third-generation” platforms: “Just as second-generation platforms stepped beyond Sanger sequencing and enabled a revolution in genomics medicine, third-generation single molecule sequencing platforms will likely be the next genetic diagnostic revolution.” “Single molecule real-time (SMRT) sequencing comes of age: applications and utilities…

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Monday, February 5, 2018

Illuminating the Origin and Evolution of Bioluminescence

A project that sparked widespread interest and a successful science crowdsourcing campaign has inspired an international collaboration that produced two high-quality reference genomes, as well as a draft genome of a related beetle. And the results have shed light on the evolution of bioluminescence. We’ve been following the progress of Team Firefly since the team of scientists from MIT, University of Rochester, Brigham Young University, Indiana University, Cornell University, and Tufts University narrowly lost our 2016 SMRT Grant competition. The project to sequence the genome of the Big Dipper Firefly, Photinus pyralis, was ultimately crowdfunded through the Experiment site and…

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