Circulomics - Nanobind Publications, HMW DNA, High MW DNA

Nanobind Publications and Presentations

2020

First Record of a Tandem-repeat Region Within the Mitochondrial Genome of Clonorchis Sinensis Using a Long-Read Sequencing Approach

Kinkar L et al. PLOS Neglected Tropical Diseases 14(8): e0008552.

A Highly Contiguous Genome for the Golden-fronted Woodpecker (Melanerpes aurifrons) via a Hybrid Oxford Nanopore and Short Read Assembly

Wiley G et al. G3: GENES, GENOMES, GENETICS June 1, 2020 vol. 10 no. 6 1829-1836; https://doi.org/10.1534/g3.120.401059

Targeted Nanopore Sequencing with Cas9-Guided Adapter Ligation

Gilpatrick T et al. Nature Biotech. 2020. https://doi.org/10.1038/s41587-020-0407-5

A Phased Canis Lupus Familiaris Labrador Retriever Reference Genome Utilizing High Molecular Weight DNA Extraction Methods and High Resolution Sequencing Technologies

Player RA et al. bioRxiv 2020.08.26.269076; doi:

Long-Read Sequencing to Interrogate Strain-Level Variation Among Adherent-Invasive Escherichia Coli Isolated from Human Intestinal Tissue

Wang J et al. bioRxiv 2020.03.10.985440; doi: https://doi.org/10.1101/2020.03.10.985440

A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea

Kirubakaran TG et al. G3: GENES, GENOMES, GENETICS Early online July 8, 2020 ; https://doi.org/10.1534/g3.120.401423

Strong Population Differentiation in Lingcod (Ophiodon elongatus ) is Driven by a Small Portion of the Genome

Longo GC et al. Evol Appl. 07 June 2020; doi:10.1111/eva.13037

Association Between Vancomycin-resistant Enterococcus faecium Colonization and Subsequent Infection: A Retrospective WGS Study

Rubin IMC et al. Journal of Antimicrobial Chemotherapy. 2020. dkaa074. doi: https://doi.org/10.1093/jac/dkaa074

A Draft Genome of Grass Pea (Lathyrus sativus), a Resilient Diploid Legume

Emmerich PMF et al. bioRxiv 2020.04.24.058164; doi:

Genome Sequencing of Four Culinary Herbs Reveals Terpenoid Genes Underlying Chemodiversity in the Nepetoideae

Bornowskii N et al. DNA Research, dsaa016,

Repeated Introduction and Spread of the MRSA Clone t304/ST6 in Northern Europe

Bartels MD et al. Clinical Microbiology and Infection 2020;

Establishment of an eHAP1 Human Haploid Cell Line Hybrid Reference Genome Assembled from Short and Long Reads

Law WD et al. Genomics; 2020 doi: https://doi.org/10.1016/j.ygeno.2020.01.009

Complete Genome of Isoprene Degrading Nocardioides sp. WS12

Gibson L et al. Microorganisms 2020, 8(6), 889;

Nanopore MinION Sequencing Reveals Possible Transfer of blaKPC-2 Plasmid Across Bacterial Species in Two Healthcare Facilities

Prussing C et al. Front. Microbiol., 19 August 2020 |

A Reference Genome Sequence for Giant Sequoia

Scott AD et al. G3: GENES, GENOMES, GENETICS Early online September 18, 2020.

The Giant Sequoia Genome and Proliferation of Disease Resistance Genes

Scott AD et al. bioRxiv 2020.03.17.995944; doi: https://doi.org/10.1101/2020.03.17.995944

Chromosomal-Level Genome Assembly of the Scimitar-Horned Oryx: Insights into Diversity and Demography of a Species Extinct in the Wild

Humble E et al. Molecular Ecology Resources.04 May 2020;

3D Printing-Enabled DNA Extraction for Long-Read Genomics

Agrawal P et al. ACS Omega 2020, 5, 33, 20817–20824;

Complete Vertebrate Mitogenomes Reveal Widespread Gene Duplications and Repeats

Formenti G et al. bioRxiv 2020.06.30.177956; doi:

Targeted Nanopore Sequencing by Real-Time Mapping of Raw Electrical Signal with UNCALLED

Kovaka S et al. bioRxiv 2020.02.03.931923; doi: https://doi.org/10.1101/2020.02.03.931923

Standardized Bacteriophage Purification for Personalized Phage Therapy

Luong T et al. Nat Protoc 15, 2867–2890 (2020);

Huntingtin Lowering Reduces Somatic Instability at CAG-Expanded Loci

Coffey SR et al. bioRxiv 2020.07.23.218347; doi:

Thiosulfinate Tolerance Is a Virulence Strategy of an Atypical Bacterial Pathogen of Onion

Stice SP et al. Current Biology. 2 July 2020;

The Genetic Architecture Underlying Ecological Adaptation in Atlantic Herring is not Consistent with the Infinitesimal Model

Han F et al. bioRxiv 2020.07.15.204214; doi:

A Singleton NLR of Recent Origin Causes Hybrid Necrosis in Arabidopsis thaliana

Barragan AC et al. bioRxiv 2020.05.18.101451; doi:

High Data Throughput and Low Cost Ultra Long Nanopore Sequencing

Kilburn, D et al. T2T / HPRC 2020 Conference

Generating Ultra Long Reads on Oxford Nanopore MinION/GridION/PromethION

Liu KJ et al. ABRF 2020. Palm Springs, CA

High Molecular Weight DNA Sample and Library Preparation for Long-Read Sequencing Using Clinical Tissue Specimens

Liu KJ et al. AGBT 2020. Marco Island, FL

Automated High Molecular Weight DNA Extraction for Production Scale Long-Read Sequencing

Burke JM et al. AGBT 2020. Marco Island, FL

High MW DNA Extraction from Diverse Animal and Plant Species

Kim M et al. PAGXXVIII 2020. San Diego, CA

2019

High Molecular Weight DNA Isolation Method from Diverse Plant Species for Use with Oxford Nanopore Sequencing

Vaillancourt B et al. bioRxiv 783159; doi: https://doi.org/10.1101/783159

Complete Genome Sequence of Luteibacter pinisoli MAH-14

Baltrus DA et al. Microbiology Resource Announcements. Jul 2019, 8 (29) e00774-19; DOI: 10.1128/MRA.00774-19

Resistance to Piperacillin/tazobactam in Escherichia coli Resulting from Extensive IS26-associated Gene Amplification of blaTEM-1

Hansen KH et al. Journal of Antimicrobial Chemotherapy. 2019. dkz349, doi.org/10.1093/jac/dkz349

Algal Nuclei Isolation for Nanopore Sequencing of HMW DNA

Auber R et al. protocols.io. doi: dx.doi.org/10.17504/protocols.io.5i2g4ge

High-Throughput High Molecular Weight DNA Extraction From Human Tissue Samples for Long-Read Sequencing

Liu KJ et al. ASHG 2019. Houston, TX

High-Throughput High MW DNA Extraction and Size Selection for Long-Read Sequencing

Liu KJ et al. NHGRI Advanced Genomic Technologies Meeting 2019. Boston, MA

The Fever Tree: Extracting and Preparing the DNA of Cinchona Pubescens

Costa V. London Calling 2019. London, UK

High-Throughput High MW DNA Extraction and Size Selection for Long-Read Sequencing

Liu KJ et al. ABRF2019. San Antonio, TX

Streamlined SMRTbell Library Generation Using Addition-Only, Single Tube Strategy for All Library Types Reduces Time to Results

Ekholm J et al. ABRF2019. San Antonio, TX

Rapid Extraction and Size Selection of High MW DNA for Long-Read Sequencing Using Nanobind Magnetic Disks.

Liu KJ et al. AGBT 2019. Marco Island, FL

Microbial Multiplexing Workflow on the Sequel System Using the SMRTbell Express Template Prep Kit 2.0.

Feb 2019. PacBio Application Note.

Rapid High MW DNA Extraction from Plant, Insect, Cell, and Tissue Samples for Long-Read Sequencing Using Nanobind Magnetic Disks

Liu KJ et al. PAGXXVII. 2019. San Diego, CA

Scaling Up Production of HMW DNA

Liu KJ et al. PAGXXVII. 2019. San Diego, CA

2018

Nanobind Magnetic Disks for Rapid High MW DNA Extraction and Library Preparation In Long-Read Sequencing and Optical Mapping Applications

Liu KJ et al. ASHG 2018. San Diego, CA

Single Chromosomal Genome Assemblies on the Sequel System with Circulomics High Molecular Weight DNA Extraction for Microbes

Wong J et al. ASM Conf on NGS 2018. Tysons, VA

Single Chromosomal Genome Assemblies on the Sequel System with Circulomics High Molecular Weight DNA Extraction for Microbes

Wong J et al. Lake Arrowhead Microbial Genomics 2018. Lake Arrowhead, CA

Nanobind High MW DNA Extraction and Library Preparation For Long-Read Sequencing and Optical Mapping

Liu K et al. G10K Annual Meeting 2018. New York

Get it Bigger, Better, Barcoded

Fuentes-Utrilla P et al. Genome Science 2018. Nottingham, UK

Single Chromosomal Genome Assemblies on the Sequel System with Circulomics High Molecular Weight DNA Extraction for Microbes

Heiner C et al. A SM Microbe 2018. Atlanta, GA

Nanobind Magnetic Disks for Rapid High MW DNA Extraction and Library Preparation in Long-Read Sequencing and Optical Mapping Applications

Liu K et al. NHGRI Advanced Sequencing Meeting 2018. Boston, MA

High Molecular Weight DNA Extraction from Recalcitrant Plant Species for Third Generation Sequencing

Workman R et al. Protocol Exchange (2018) doi: 10.1038/protex.2018.059

PromethION Sequencing of Complex Plant Genomes

Wittenberg A et al. London Calling 2018. London, UK

Optimizing High Molecular Weight Conifer gDNA Extraction and Single Molecule Sequencing in the Redwood Genome Project

Workman R et al. SFAF 2018. Santa Fe, NM

Optimizing High Molecular Weight gDNA Extraction for Single Molecule Sequencing in the Redwood Genome Project

Workman R et al. ABRF 2018. Myrtle Beach, FL

Nanopore Sequencing in the Redwood Genome Project: DNA Extraction to Sequencing Optimization

Workman, R et al. Nanopore Day DC 2018. Washington DC

High Molecular Weight Conifer DNA Extraction for Nanopore Sequencing

Workman R et al. AGBT 2018. Orlando, FL

2017

Extracting DNA for Nanopore Sequencing in the Redwood Genome Project

Timp, W et al. Nanopore Community Meeting 2017. New York

2016

A Simple Thermoplastic Substrate Containing Hierarchical Silica Lamellae for High-Molecular-Weight DNA Extraction

Zhang Y et al. Adv Mater. 2016 Dec;28 (48):10630-10636. doi: 10.1002/adma.201603738.

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