This documentary film features the wave of cutting-edge technologies that now provide the opportunity to create predictive models of living systems, and gain wisdom about the fundamental nature of life itself. The potential impact for humanity is immense: from fighting complex diseases such as cancer, enabling proactive surveillance of virulent pathogens, and increasing food crop production.
Part I of The New Biology documentary. This documentary film features the wave of cutting-edge technologies that now provide the opportunity to create predictive models of living systems, and gain wisdom about the fundamental nature of life itself. The potential impact for humanity is immense: from fighting complex diseases such as cancer, enabling proactive surveillance of virulent pathogens, and increasing food crop production.
Part II of The New Biology documentary. This documentary film features the wave of cutting-edge technologies that now provide the opportunity to create predictive models of living systems, and gain wisdom about the fundamental nature of life itself. The potential impact for humanity is immense: from fighting complex diseases such as cancer, enabling proactive surveillance of virulent pathogens, and increasing food crop production.
Part III of The New Biology documentary. This documentary film features the wave of cutting-edge technologies that now provide the opportunity to create predictive models of living systems, and gain wisdom about the fundamental nature of life itself. The potential impact for humanity is immense: from fighting complex diseases such as cancer, enabling proactive surveillance of virulent pathogens, and increasing food crop production.
Part IV of The New Biology documentary. This documentary film features the wave of cutting-edge technologies that now provide the opportunity to create predictive models of living systems, and gain wisdom about the fundamental nature of life itself. The potential impact for humanity is immense: from fighting complex diseases such as cancer, enabling proactive surveillance of virulent pathogens, and increasing food crop production.
Jonas Korlach, CSO of PacBio, discusses the revival of finished genomes the microbial community will see with long read data, emphasizing that for certain organisms such as rapidly evolving microbes, having a de novo finished genome will be more useful than creating a draft based on a previous related reference genome. Korlach describes two bioinformatic methods from PacBio, a hierarchical genome assembly process (HGAP) and an consensus caller (Quiver), which are used to generate finished genomes from just long-read PacBio data, with final genome sequence accuracies over 99.999%. Korlach demonstrates the ability of PacBio data to generate closed, high-quality de…
In this AGBT plenary talk, Jonas Korlach presented a number of collaborative studies between PacBio and other institutions to make use of highly accurate, long-read sequence data, which has led to a revival of finished genomes. Examples from the infectious disease or pathogen realm included Pertussis, Salmonella, and Listeria, all of which now have closed genomes from PacBio-generated data. Korlach also reported on epigenomic information in Salmonella and Listeria, indicating potential new forms of DNA modifications.
Peter Evans from the US FDA shares insights on whole-genome sequencing for bacteria of importance to public health. Comparing data across PacBio, 454, and MiSeq sequencers, he says having closed genomes, long reads, and methylation patterns are critical for gleaning comprehensive information about a microbe.
UC Davis’s Bart Weimer describes foodborne pathogens and their proclivity for rapid genome rearrangement. The 100K Pathogen Genome Project he leads is using PacBio long-read sequencing to close genomes and analyze methylation; Weimer reports that his team has already discovered new epigenetic modifications in Salmonella and Listeria with the technology.
In this webinar, the presenters describe a targeted sequencing workflow that combines Roche NimbleGen’s SeqCap EZ enrichment technology with PacBio’ SMRT Sequencing to provide a more comprehensive view of variants and haplotype information over multi-kilobase, contiguous regions. They demonstrate that 6 kb fragments can also be utilized to enrich for long fragments that extend beyond the targeted capture site and well into (and often across) the adjacent intronic regions. When combined with SMRT Sequencing, multi-kilobase genomic regions can be phased and variants, including complex structural variants, can be detected in exons, introns and intergenic regions.
Robert Henry, Professor of Innovation in Agriculture and Director of the Queensland Alliance for Agriculture and Food Innovation at the University of Queensland, Australia, discusses how whole genome analysis of Australian wild rice is being used to better understand rice domestication, with the goal of making a diverse genetic resource available for increased rice food security worldwide. The wild “A genome” species represent an effective gene pool for rice. SMRT Sequencing and assembly of two taxon of wild Australian rice has allowed analysis of the relationships with this group. Domesticated rice (Oryza sativa ssp. japonica) nuclear genome shows close relationship…
In this AGBT 2017 poster, the University of Helsinki’s Petri Auevinen reports on efforts to understand bacteria that grow on, and subsequently spoil, food. This analysis monitored DNA modifications and transcriptomic changes in three species of lactic acid bacteria. Scientists discovered that the organisms’ metabolic profiles change substantially when grown together compared to those cultured individually, and are now studying how Cas protein activity changes under these conditions too.
In this PacBio User Group Meeting presentation, Nic Wheeler of University of Wisconsin-Madison, speaks about RNA sequencing for filarial nematodes associated with understudied tropical diseases. His team used Iso-Seq analysis to improve gene models and achieve better transcriptome coverage for these worms, which typically have poorly annotated and fragmented genome assemblies. While getting enough RNA to study is a technical challenge, the group still managed to generate full-length isoforms, many of which were novel or contained novel junctions.
In a push to develop insect-based food sources for people, Brenda Oppert from the USDA has been sequencing bug genomes with PacBio technology. Long reads are essential because of the highly repetitive sequences and large genomes. On the Sequel II System, a single SMRT Cell is sufficient to generate 350-fold coverage and produce a high-quality assembly for some of the insects she’s studying.
Studying microbial genomics and infectious disease? Learn how the PacBio Sequel II System can help advance your research, with first-hand perspectives from scientists who are investigating SARS-CoV-2 and COVID-19. In this webinar, Melissa Laird-Smith (Mt. Sinai School of Medicine) discusses her work evaluating the impact of host immune restriction in health and disease with high resolution HLA typing. She is joined by Corey Watson (University of Louisville School of Medicine) who talks about overcoming complexity to elucidate the role of IGH haplotype diversity in antibody-mediated immunity. Hosted by Meredith Ashby, Director of Microbial Genomics at PacBio. Access additional PacBio resources…