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Advancing Genomics Research to Improve Global Health
Discover better vaccines, treatments and outcomes with full characterization of pathogens, their mobile elements and communities.
Comprehensive genetic information provided by Single Molecule, Real-Time (SMRT) Sequencing has radically increased our understanding of microbial genomics, pathogenicity, and antimicrobial resistance. The PacBio Systems empower scientists to:
- Elucidate microbial genomes and distinguish mobile elements using whole genome sequencing
- Investigate pathogenicity, virulence and evolution with targeted sequencing
- Characterize complex viral and bacterial populations to further successful design and evaluation of drugs and vaccines
- Explore epigenetic modifications as part of your sequencing reaction
Spotlight: Deciphere genome complexity in pathogens using SMRT sequencing
Scientists were able to successfully work through the well-known AT-bias challenge of the Plasmodium falciparum genome. De novo assembly revealed novel insights for genome architecture and complexity, providing a reference to better understand virulence, drug resistance and disease transmission. Explore this research further:
Vembar, S.S. et al., 2016. Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing. DNA Research, 23(4), pp.339–351.
Spotlight: Single-molecule sequencing to track HIV-1 mutations
The development of novel circular consensus algorithms enabled the tracking of viral evolution of the K103N drug resistant associate mutation in clinical samples. Explore this research further:
Laird Smith, M. et al., 2016. An improved circular consensus algorithm with an application to detect HIV-1 Drug Resistance Associated Mutations (DRAMs). In 2016 ASM Microbe. New Orleans, LA.
Selected Resources
- Liu, Qin et al. (2019) A chromosomal-level genome assembly for the insect vector for Chagas disease, Triatoma rubrofasciata. GigaScience
- Callahan, Benjamin J et al. (2019) High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic acids research
- Forde, Brian M et al. (2019) SMRT sequencing reveals differential patterns of methylation in two O111:H- STEC isolates from a hemolytic uremic syndrome outbreak in Australia. Scientific reports
- Davies, Mark R et al. (2019) Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics. Nature genetics
- Nye, Taylor M et al. (2019) DNA methylation from a Type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes. PLoS pathogens
- Stinson, Lisa F et al. (2019) The Not-so-Sterile Womb: Evidence That the Human Fetus Is Exposed to Bacteria Prior to Birth. Frontiers in microbiology
- Su, Bin et al. (2019) Detection of pretreatment minority HIV-1 reverse transcriptase inhibitor-resistant variants by ultra-deep sequencing has a limited impact on virological outcomes. The Journal of antimicrobial chemotherapy
- Lui, Wing-Yu et al. (2019) SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection. Emerging microbes & infections
- Ashton, P M et al. (2019) Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans. Nature communications
- Jayaraman, Siddharth et al. (2019) Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. PLoS neglected tropical diseases
- Murphy, Timothy F et al. (2019) Persistence of Moraxella catarrhalis in Chronic Obstructive Pulmonary Disease and Regulation of the Hag/MID Adhesin. The Journal of infectious diseases
- Sierra, Johanna C et al. (2019) a-Difluoromethylornithine reduces gastric carcinogenesis by causing mutations in Helicobacter pylori cagY. Proceedings of the National Academy of Sciences of the United States of America
- Beaulaurier, John et al. (2019) Deciphering bacterial epigenomes using modern sequencing technologies. Nature reviews. Genetics
- Pinzone, Marilia Rita et al. (2019) Longitudinal HIV sequencing reveals reservoir expression leading to decay which is obscured by clonal expansion. Nature communications
- Kingan, Sarah et al. (2019) A high-quality de novo genome assembly from a single mosquito using PacBio sequencing Genes
- Sullivan, Mitchell J et al. (2019) Complete genome screening of clinical MRSA isolates identifies lineage diversity and provides full resolution of transmission and outbreak events BioRxiv
- Liang, Quanhui et al. (2019) Sequencing and Genomic Diversity Analysis of IncHI5 Plasmids. Frontiers in microbiology
- Eren, Kemal et al. (2018) Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons. PLoS computational biology
- Beaulaurier, John et al. (2018) Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nature biotechnology
- Matthews, Benjamin J et al. (2018) Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature
- Campino, Susana et al. (2018) A forward genetic screen reveals a primary role for Plasmodium falciparum Reticulocyte Binding Protein Homologue 2a and 2b in determining alternative erythrocyte invasion pathways. PLoS pathogens
- Slager, Jelle et al. (2018) Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39. Nucleic acids research
- Müller, Laura S M et al. (2018) Genome organization and DNA accessibility control antigenic variation in trypanosomes. Nature
- Wen, Ming et al. (2018) Exploring the genome and transcriptome of the cave nectar bat Eonycteris spelaea with PacBio long-read sequencing. GigaScience
- Benavente, Ernest Diez et al. (2018) Global genetic diversity of var2csa in Plasmodium falciparum with implications for malaria in pregnancy and vaccine development. Scientific reports
- Castellanos, Mildred et al. (2018) A Borrelia burgdorferi mini-vls system that undergoes antigenic switching in mice: investigation of the role of plasmid topology and the long inverted repeat. Molecular microbiology
- Zhao, Nan et al. (2018) Influenza virus infection causes global RNAPII termination defects. Nature structural & molecular biology
- Yan, Bo et al. (2018) SMRT-Cappable-seq reveals complex operon variants in bacteria. Nature communications
- Löber, Ulrike et al. (2018) Degradation and remobilization of endogenous retroviruses by recombination during the earliest stages of a germ-line invasion. Proceedings of the National Academy of Sciences of the United States of America
- Atack, John M et al. (2018) Phasevarions of bacterial pathogens: Methylomics sheds new light on old enemies. Trends in microbiology
- Brese, Robin L et al. (2018) Ultradeep single-molecule real-time sequencing of HIV envelope reveals complete compartmentalization of highly macrophage-tropic R5 proviral variants in brain and CXCR4-using variants in immune and peripheral tissues. Journal of neurovirology
- Douglass, Alexander P et al. (2018) Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii: One species, four names. PLoS pathogens
- Verhey, Theodore B et al. (2018) Antigenic variation in the lyme spirochete: Insights into recombinational switching with a suggested role for error-prone repair. Cell reports
- Berná, Luisa et al. (2018) Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi. Microbial genomics
- Otto, Thomas D et al. (2018) Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres. Wellcome open research
- Poster: Boitano, M. et al. (2018) Full-length cDNA sequencing of prokaryotic transcriptome and metatranscriptome samples
- Poster: Heiner, Cheryl et al. (2018) Multiplexed complete microbial genomes on the Sequel System
- Poster: Lambert, C. et al. (2017) Multiplexing strategies for microbial whole genome sequencing using the Sequel System
- Poster: Kingan, Sarah et al. (2017) A high-quality genome assembly of SMRT sequences reveals long range haplotype structure in the diploid mosquito Aedes aegypti
- Poster: Hall, Richard et al. (2017) Using the PacBio Sequel System to taxonomically and functionally classify metagenomic samples in a trial of patients undergoing fecal microbiota transplantation
- Poster: Kingan, S. et al. (2017) A high-quality genome assembly of SMRT Sequences reveals long-range haplotype structure in the diploid mosquito Aedes aegypti
- Poster: Pollard, M. O. et al. (2016) The MHC Diversity in Africa Project (MDAP) pilot – 125 African high resolution HLA types from 5 populations
- Poster: Seetin, M. et al. (2016) Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome using long-read sequencing
- Poster: Laird Smith, M. et al. (2016) An improved circular consensus algorithm with an application to detect HIV-1 Drug Resistance Associated Mutations (DRAMs)
- Poster: Oh, S. et al. (2016) Minimization of chimera formation and substitution errors in full-length 16S PCR amplification
- Poster: Heiner, C. et al. (2016) WGS SMRT Sequencing of patient samples from a fecal microbiota transplant trial
- Poster: Hall, R. et al. (2016) Workflow for processing high-throughput, Single Molecule, Real-Time Sequencing data for analyzing the microbiome of patients undergoing fecal microbiota transplantation
- Poster: Hepler, N. Lance et al. (2016) An improved circular consensus algorithm with an application to detection of HIV-1 Drug-Resistance Associated Mutations (DRAMs)
- Poster: Seetin, Matthew et al. (2016) Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- Poster: Hall, Richard et al. (2016) Profiling the microbiome in fecal microbiota transplantation using circular consensus and Single Molecule, Real-Time Sequencing
- Poster: Seetin, Matthew G et al. (2016) Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- Ashby, Meredith (2020) Webinar: Opportunities for using PacBio long-read sequencing for COVID-19 research
- Mars, Kristin and Laird Smith, Melissa and Vinnere Pettersson, Olga and Hardigan, Michael (2020) Webinar: Sequencing 101 – How long-read sequencing improves access to genetic information
- (2020) Video: Introduction to PacBio highly accurate long-read sequencing
- Wheeler, Nic (2019) User Group Meeting: Long-read RNA Sequencing in neglected human parasites
- Ashby, Meredith (2019) Webinar: Long-read sequencing and infectious disease: New insights into longstanding challenges
- (2017) Tutorial: Minor variant analysis [SMRT Link v5.0.0]
- Neafsey, Daniel (2017) AGBT Conference: A community effort using multiple technologies to produce a dramatically improved genome assembly of the Zika virus mosquito vector
- Paulin, Lars (2017) AGBT Virtual Poster: Single-molecule sequencing reveals the presence of distinct JC polyomavirus populations in patients with progressive multifocal leukoencephalopathy
- Matthews, Ben (2017) PAG PacBio Workshop: Genome assembly and molecular genetics of the dengue, yellow fever, and zika vector Aedes aegypti
- Laird Smith, Melissa (2016) ASHG PacBio Workshop: SMRT Sequencing as a translational research tool to investigate germline, somatic and infectious diseases
- Pollard, Martin (2016) ASHG Virtual Poster: The MHC Diversity in Africa Project (MDAP) pilot – 125 African high resolution HLA types from 5 populations
- Korlach, J. and Kingan, S. (2016) i5K Webinar: High-quality de novo insect genome assemblies using PacBio sequencing
- Ameur, Adam (2016) AGBT Roche and PacBio Workshop: Clinical SMRT Sequencing – from single genes to complete genomes
- Murrell, Ben (2016) AGBT Roche and PacBio Workshop: Deeply sequencing entire genes from rapidly evolving viruses
- Paxinos, Ellen (2016) AGBT Virtual Poster: An improved circular consensus algorithm with an application to detect HIV-1 Drug Resistance Associated Mutations (DRAMs)
- Seetin, Matthew (2016) AGBT Virtual Poster: Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- Hall, Richard (2016) AGBT Virtual Poster: Profiling the microbiome in fecal microbiota transplantation using circular consensus and Single Molecule, Real-Time Sequencing
- Application Brief: Metagenomic sequencing with HiFi reads – Best Practices (2020)
- Application Brief: Microbial whole genome sequencing – Best Practices (2020)
- SMRT Sequencing Brochure: Delivering highly accurate long reads to drive discovery in life science (2019)
- Case Study: Sequencing an historic bacterial collection for the future (2019)
- Infographic: A brief history of microbiology (2019)
- PacBio Certified Service Providers (2019)
- Case Study: SMRT sequencing brings clarity to HIV vaccine and transplant research at the Wisconsin national primate research center (2017)
- Epigenetics Application Brochure: Characterize the epigenetic landscape of your genome (2016)