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Thursday, September 5, 2013

Next Week’s ICG Meeting to Include Several SMRT Sequencing Talks

The International Conference on Genomics in the Americas (ICG), organized by BGI and UC Davis, is taking place on Sept 12-13 in Sacramento, CA. One of the keynote presentations in the opening session comes from Nobel Laureate Richard Roberts, Chief Scientific Officer of New England Biolabs. Entitled “Bacterial Methylomes,” the talk will cover some recent work Roberts has done using SMRT® Sequencing to characterize the full, genome-wide methylation marks in various strains of microbes. This kind of work “has yielded a plethora of new and interesting results,” Roberts told BioMed Central recently. Later that day, Ken Dewar from McGill University…

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Tuesday, July 30, 2013

Single-Molecule Sequencing Technology Q&A with Nobel Laureate Rich Roberts

BioMed Central has published an interesting Q&A session on its Biome blog with Nobel Laureate Richard Roberts about why he believes in SMRT Sequencing and thinks non-users should take another look at it, too. He also discusses the critical need for funding to support the functional annotation of the genomes being sequenced, including for new bioinformatics tools. “We should be greatly increasing our efforts to gain functional insights into the millions of genes we are discovering by sequencing and for which we either have no idea of what they do, or many of our predictions are simply wrong,” he says.…

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Monday, July 22, 2013

Whole-Genome Microbial Epigenetics: ASM Workshop videos highlight emerging application of SMRT Sequencing

We recently participated in a workshop on whole-genome microbial epigenetics at the American Society for Microbiology annual meeting in Denver. Using SMRT® Sequencing, the three most common types of bacterial methylation can be studied at base resolution across an entire genome. An exceptional lineup of speakers shared their latest research and we’re pleased to be able to share video of the presentations. Our CSO Jonas Korlach opened the workshop with a brief introduction describing how SMRT Sequencing generates epigenetic information. His presentation was followed by Brian Anton, from New England BioLabs, who presented data on restriction-modification systems and orphan methylases…

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Tuesday, April 23, 2013

Current Opinion in Microbiology: Bacterial Methylomes in Review – ‘An Exciting Era’

A new review paper from Brigid Davis, Michael Chao, and Matthew Waldor at Harvard Medical School considers a number of recent studies and findings that have used single molecule, real-time (SMRT®) sequencing to generate epigenomic information. “Entering the era of bacterial epigenomics with single molecule real time DNA sequencing” was recently published in Current Opinion in Microbiology. In the review, the authors note the importance of fully understanding and analyzing genome-wide methylation data, but say that technologies to date have not made it feasible to generate this information. “The advent of new sequencing platforms in the last decade has allowed…

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Wednesday, April 10, 2013

Rapid Genome Assembly: Salmonella Outbreak Strain Sequenced and Closed in Less Than One Week

A newly reported Salmonella genome showcases the utility of single molecule, real-time (SMRT®) sequencing for characterizing a foodborne outbreak pathogen. The outbreak strain, Salmonella enterica subsp. enterica serovar Javiana (S. Javiana), representing one of the top five most common forms of Salmonella associated with fresh-cut produce, was sequenced and analyzed late last year; its genome was published this month in Genome Announcements, a journal from the American Society for Microbiology. The study was led by the US Food & Drug Administration’s Center for Food Safety & Applied Nutrition. Scientists from Pacific Biosciences and New England BioLabs participated in the study,…

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Tuesday, April 9, 2013

It’s a Very Microbial Season

This springtime, we’ve got microbes on the brain! The annual meeting of the American Society for Microbiology is just over a month away, so we’ve been thinking a lot about microbial genomics and how we can contribute to this burgeoning field. Microbiology is a key application for customers using the PacBio® RS. With its throughput, turnaround time, cost-effectiveness, and long reads, it is the perfect tool for performing de novo sequencing of microbes and generating closed genomes — often bringing microbial genomes together in a single contig. Beyond that, the unique way in which SMRT® Sequencing produces epigenetic data together…

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Monday, March 18, 2013

Sequencing Innovations Offer a More Complete Picture for Microbes

We’re pleased to share with you a recent article from Microbe magazine, a publication of the American Society for Microbiology, from Eric Schadt, founding director of the Icahn Institute for Genomics and Multiscale Biology at Mount Sinai School of Medicine. Entitled “The Coming Revolution: Microbes and Multiscale Biology,” the article describes recent microbial studies Schadt participated in, including analyses of the cholera strain in the 2010 Haiti outbreak and the E. coli strain in the 2011 Germany outbreak. Schadt writes about the tremendous technological strides that have advanced the microbial research world: “Where we once relied on Southern blots to…

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Wednesday, March 13, 2013

Going to ASM? Register Now for the Microbial Epigenetics Workshop on May 18

If you’ll be heading to Denver for the American Society for Microbiology annual meeting on May 18-21, don’t miss the pre-conference workshop on whole-genome microbial epigenetics. New studies are continually demonstrating the importance of epigenetics in gene regulation and other biological functions of microbes, and this workshop features a panel of top-notch scientists to shed more light on these advances. Here’s the roster of presentations: Direct detection of bacterial epigenetics using SMRT Sequencing Jonas Korlach, Pacific Biosciences Comprehensive methylome analysis of the human gastric pathogen, Helicobacter pylori Sebastian Suerbaum, Hannover Medical School Large-scale analysis of restriction-modification systems using SMRT Sequencing…

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Tuesday, February 26, 2013

AGBT Day 4 Highlights: SMRT Sequencing for De Novo Genome Assemblies

Even as attendees’ energy was waning from three marathon days at AGBT, spirits were still high as we gathered for the final day’s Genomic Technologies session on Saturday morning. This session included two speakers presenting on applications using SMRT Sequencing: Eric Antoniou from Cold Spring Harbor Laboratory and Jonas Korlach, our CSO. Antoniou, a research investigator and manager of the genome sequencing center at Cold Spring Harbor Laboratory, presented on “Increased Read Length and Sequence Quality with Pacific Biosciences Magbead Loading System and a New DNA Polymerase.” In it, he reported on the sequencing and assembly of the 470-Mb rice…

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Thursday, February 21, 2013

AGBT Day 1 Highlights: Focus on Epigenetics

Years ago, “epigenetics” was largely synonymous with methylation — in particular, 5-methylcytosine, which could be analyzed through bisulfite sequencing. Today, technologies have advanced and so has our understanding of the biological mechanisms underlying epigenetics. Scientists are continually adding to the repertoire of methylation patterns and how they function, from virulence effects in microbes to DNA replication and new methylation marks in plants. Here at AGBT, the conference kicked off with some excellent talks focusing on epigenetics. In one, Leonid Moroz, a professor of neuroscience at the University of Florida, talked about the challenges of determining the biological function behind memory…

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Thursday, January 17, 2013

SMRT Sequencing Selected by 100K Pathogen Genome Project to Finish Genomes

A recently announced partnership with the University of California, Davis (UC Davis) highlights the benefits of one of the key applications for Single Molecule, Real-Time (SMRT®)  Sequencing: rapid and complete finishing of pathogen genomes. As part of the project, Pacific Biosciences’ SMRT technology will be used for the 100KPathogen Genome Project to sequence the genomes from at least 1,000 foodborne pathogen samples to completion, and to elucidate their epigenomes. These bacteria represent major illness-causing pathogens, including Salmonella, Campylobacter, E. coli, Vibrio, and Listeria. Speaking to GenomeWeb, Bart Weimer, Professor and Director of the 100K Genome Project, commented that building these…

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