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Tuesday, September 9, 2014

Genome Analysis of Unicellular Organism Reveals Frequent, Massive Reshuffling

A recent publication from senior author Laura Landweber at Princeton University offers a remarkable and unexpected look at sweeping genomic rearrangements in a unicellular organism. “The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development,” published in Cell, comes from lead authors Xiao Chen and John Bracht as well as other collaborators from Princeton, the Icahn School of Medicine at Mount Sinai, Benaroya Research Institute, and other institutions. The project focused on Oxytricha trifallax, a single-celled eukaryote that lives in ponds. Despite its unicellular simplicity, the organism has an extensive ability to scramble and rearrange its…

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Wednesday, August 6, 2014

Plant and Animal Genomes: New Web Resource Available

After so many compelling customer projects for microbial genomes, it’s been rewarding to see more scientists turning to Single Molecule, Real-Time (SMRT®) Sequencing for larger genomes, such as plants and animals. Many PacBio users are performing de novo sequencing and assembly or upgrading draft genomes initially generated by short-read technologies. Extraordinarily long reads and throughput improvements have allowed scientists to affordably assemble and close genomes such as the Atlantic cod, spinach, and Orpinomyces, an anaerobic fungus found in the rumen of cows, to name a few. As reported by several customers at the 2014 Plant & Animal Genome conference in…

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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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Thursday, May 29, 2014

Research Studies Use Sequencing to Track Path of Infection Outbreaks

A talk at last week’s ASM conference continued the recent trend of scientists using Single Molecule, Real-Time (SMRT®) Sequencing in research projects designed to better understand the transmission path of hospital-acquired infections. The presentation, entitled “Tracking Hospital Patients and Environment with Complete Genome Sequencing of Carbapenem-Resistant Klebsiella pneumoniae and other Enterobacteriaceae,” came from Julie Segre, a chief investigator at the National Human Genome Research Institute. Segre spoke of Klebsiella as “the nightmare bug.” From the earliest reports of it in 2001, it is now in more than 40 states in the US and shows strong resistance to antibiotics. The study…

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Wednesday, May 28, 2014

The Sequence Analysis Meeting: SFAF 2014

The Sequencing, Finishing, and Analysis in the Future (SFAF) meeting kicks off today in Santa Fe, New Mexico. The conference is hosted by Los Alamos National Laboratory and focuses on the analytical details that are so important as the community assesses how to get the most out of all this sequence data. This year, we will have two PacBio speakers, and there will be a number of other talks from users of our long-read sequence data. Steve Turner, our CTO, will speak on Wednesday morning about the use of Single Molecule, Real-Time (SMRT®) Sequencing for generating highly contiguous genome assemblies…

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Tuesday, May 13, 2014

A New Approach for HLA Typing: SMRT Sequencing

Two recent news announcements demonstrate the utility of our Single Molecule, Real-Time (SMRT®) Sequencing technology in the challenging realm of HLA typing.  HLA typing — or analysis of genes in the human leukocyte antigen region of the human genome — is of critical importance for research in tissue transplantation matching, autoimmune disease-association studies, drug hypersensitivity research, and other applications. But analyzing those genes, which are highly polymorphic and contain thousands of alleles that code for proteins important in recognizing foreign antigens, has proven difficult with most technologies. Use of Sanger or short-read sequencing technologies has required other methods for confirmation…

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Tuesday, May 6, 2014

Retroviral Study Reveals Potential for Influencing HIV Replication

Scientists from the Icahn School of Medicine at Mount Sinai in New York City and the MRC National Institute for Medical Research in London published a paper using Single Molecule, Real-Time (SMRT®) Sequencing to gain a better understanding of how human endogenous retroviruses may be interacting with HIV infection. They pursued a new avenue of research that could shed light on how to interfere with HIV replication. “HIV-1 interacts with HERV-K (HML-2) Envelopes derived from human primary lymphocytes” was recently published in the Journal of Virology, a publication of the American Society for Microbiology. Daria Brinzevich and George R. Young…

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Monday, May 5, 2014

Webinar Recap: New Insights in Genome and Transcriptome Research

This week, our CSO Jonas Korlach hosted a webinar entitled “Gain New Insights in Genome and Transcriptome Research with Greater than 10,000 bp Reads.” He spoke to attendees about the PacBio® technology, elements of sequencing, and applications of the ultra-long reads generated by Single Molecule, Real-Time (SMRT®) Sequencing. Here’s a quick recap. Jonas offered a look at how PacBio’s technology performs in the four key sequencing characteristics that one should consider for any sequencing work: contiguity, accuracy, uniformity, and originality. For contiguity, or how much of a DNA fragment can be sequenced in a single pass, the PacBio platform outperforms…

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Wednesday, April 16, 2014

Innovation Centre in Quebec Uses SMRT Sequencing for
Cost-Effective, Complete Microbial Genomes

At the McGill University and Génome Québec Innovation Centre, many projects conducted in the sequencing core facility fall under the umbrella of life sciences rather than biomedical research. To the scientists responsible for making the core facility operate as smoothly as possible, that makes a world of difference. “When you’re in the life sciences in addition to human biomedical [research], you’re out there in the world of things that haven’t been sequenced before, or haven’t been sequenced particularly well,” says Ken Dewar, a principal investigator at the Innovation Centre. To navigate this type of uncharted territory, scientists at the center…

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Monday, March 31, 2014

New Software Release: SMRT Analysis Upgrade for Iso-Seq Analysis and HLA Allele Phasing

Today we announced the release of a software upgrade for our Single Molecule, Real-Time (SMRT®) DNA Sequencing platform. SMRT Analysis 2.2 provides enhanced functionality to support two additional applications that uniquely benefit from our long-read sequencing technology: Iso-Seq™ full-length transcript /isoform sequencing, and human leukocyte antigen (HLA) allele phasing. The study of mRNA transcript isoforms has been challenging due to the short read lengths of other sequencing technologies. Since Iso-Seq analysis allows for the capture of full-length transcripts, scientists can use this approach to identify alternatively spliced forms of a gene, detect novel genes and isoforms, or perform transcriptome-wide analysis…

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Monday, March 31, 2014

This Week: Sample Prep Webinar on 10 Kb Template Prep

If you love long reads, you won’t want to miss this week’s webinar on sample prep for Single Molecule, Real-Time (SMRT®) Sequencing. We will focus on automation solutions for 10 Kb template preparation, including new high-throughput sample prep kits, compatible automated liquid handling platforms, and sample data. Register now for the webinar, with your choice of times: Tuesday, April 1 5:00 p.m. PDTWednesday, April 2 8:00 a.m. PDT Our presenters will be PacBio scientists Kristi Spittle Kim and Michael Weiand. Kristi, an applications scientist in our technical support group, has been working in the genomics field since 2006. At PacBio,…

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Thursday, March 27, 2014

As Genome Editing Gains Traction, SMRT Sequencing Provides Accurate View of Results

A new paper published in Cell Reports describes how Single Molecule, Real-Time (SMRT®) Sequencing can be used to greatly improve outcome reporting for a variety of popular genome-editing approaches. “Quantifying genome-editing outcomes at endogenous loci with SMRT sequencing” comes from lead authors Ayal Hendel and Eric Kildebeck from the Porteus lab at Stanford University, along with other collaborators at Stanford and the Georgia Institute of Technology. The goal for this study was to contribute to the tremendous innovations occurring in the genome editing field — from CRISPR to TALENs and more — by finding a better tool to measure results…

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