Short Read Eliminator 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. https://doi.org/10.1371/journal.pntd.0008552

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

A linked‐read approach to museomics: Higher quality de novo genome assemblies from degraded tissues

Colella JP et al. Molecular Ecology Resources; https://doi.org/10.1111/1755-0998.13155

Analysis Procedures for Assessing Recovery of High Quality, Complete, Closed Genomes from Nanopore Long Read Metagenome Sequencing

Arumugam K et al. bioRxiv 2020.03.12.974238; doi: https://doi.org/10.1101/2020.03.12.974238

High-quality genome assembly of Fusarium oxysporum f. sp. lini

Krasnov GS et al. Front. Genet., 27 August 2020 | https://doi.org/10.3389/fgene.2020.00959

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: https://doi.org/10.1101/2020.08.26.269076

SILEX: A fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species

Vilanova S et al. Plant Methods. DOI: 10.21203/rs.3.rs-29518/v1

Complete Genome Sequence of Oryctes Rhinoceros Nudivirus Isolated from Coconut Rhinoceros Beetle in the Solomon Islands

Etebari K et al. Virus Research 2020; https://doi.org/10.1016/j.virusres.2020.197864

Complete Genome Sequence of Geobacillus sp. Strain E55-1, Isolated from Mine Geyser in Japan

Miyazaki K et al. Microbiology Resource Announcements May 2020, 9 (20) e00339-20; DOI: 10.1128/MRA.00339-20

Complete Genome Sequence of Pseudomonas otitidis Strain MrB4, Isolated from Lake Biwa in Japan

Miyazaki K et al. Microbiology Resource Announcements Apr 2020, 9 (16) e00148-20; DOI: 10.1128/MRA.00148-20

Complete Genome Sequences of Rhodothermus marinus Strains AA2-13 and AA3-38, Isolated from Arima Onsen Hot Spring in Japan

Tomariguchi N et al. Microbiology Resource Announcements Jan 2020, 9 (2) e01475-19; DOI: 10.1128/MRA.01475-19

Complete Genome Sequence of Bacillus cereus Strain PL1, Isolated from Soil in Japan

Miyazaki K et al. Microbiology Resource Announcements Mar 2020, 9 (12) e00195-20; DOI: 10.1128/MRA.00195-20

Complete Genome Sequence of Vibrio rotiferianus Strain AM7

Miyazaki K et al. Microbiology Resource Announcements May 2020, 9 (21) e01591-19; DOI: 10.1128/MRA.01591-19

High Contiguity De Novo Genome Sequence Assembly of Trifoliate Yam (Dioscorea dumetorum) Using Long Read Sequencing

Siadjeu C et al. Genes 2020, 11(3), 274; https://doi.org/10.3390/genes11030274

Complete Genome Sequence of Pseudomonas coronafaciens pv. oryzae 1_6

Baltrus DA et al. Microbiology Resource Announcements Jan 2020, 9 (3) e01564-19; DOI: 10.1128/MRA.01564-19

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

Emmerich PMF et al. bioRxiv 2020.04.24.058164; doi: https://doi.org/10.1101/2020.04.24.058164

Draft Genome Resource for Macrophomina phaseolina Associated with Charcoal Rot in Sorghum

Purushotham N et al. Molecular Plant-Microbe Interactions. 2020. doi: https://doi.org/10.1094/MPMI-12-19-0356-A

Insertion of an endogenous Jaagsiekte Sheep Retrovirus element into the BCO2 - gene abolishes its function and leads to yellow discoloration of adipose tissue in Norwegian Spælsau (Ovis aries)

Kent M et al. bioRxiv 2020.06.11.145755; doi: https://doi.org/10.1101/2020.06.11.145755

The Complete Mitochondrial Genome Sequence of Oryctes Rhinoceros (Coleoptera: Scarabaeidae) Based on Long-read Nanopore Sequencing

Filipovic I et al. bioRxiv 2020.04.27.065235; doi: https://doi.org/10.1101/2020.04.27.065235

Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus​
Lee HT et al. Front. Plant Sci., 28 April 2020; https://doi.org/10.3389/fpls.2020.00496

Complete and Validated Genomes from a Metagenome

Giguere DJ et al. bioRxiv 2020.04.08.032540; doi: https://doi.org/10.1101/2020.04.08.032540

A Single Gene Underlies the Dynamic Evolution of Poplar Sex Determination

Muller NA et al.  Nat. Plants 6, 630–637 (2020). https://doi.org/10.1038/s41477-020-0672-9

Comparison of Long Read Methods for Sequencing and Assembly of a Plant Genome

Murigneux V et al. bioRxiv 2020.03.16.992933; doi: https://doi.org/10.1101/2020.03.16.992933

Exploring Rain as Source of Biological Control Agents for Fire Blight on Apple

Llongtop MEM et alFront Microbiol. 2020; 11: 199. doi: 10.3389/fmicb.2020.00199

Complete vertebrate mitogenomes reveal widespread gene duplications and repeats

Formenti G et al. bioRxiv 2020.06.30.177956; doi: https://doi.org/10.1101/2020.06.30.177956

Chromosome-level Genome Construction of a Japanese Stickleback Species Using Ultra-dense Linkage Analysis Using Single-cell Sequencing of Sperms

Yoshitake K et al. bioRxiv 2020.05.12.092221; doi: https://doi.org/10.1101/2020.05.12.092221

The stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that direct genome-wide DNA methylation

Sperschneider J et al. bioRxiv 469338; doi: https://doi.org/10.1101/469338

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

Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information

Chen Z et al. Genome Res. 2020. 30: 898-909; June 15, 2020, doi:10.1101/gr.260380.119

Nanopore Sequencing and the Shasta Toolkit Enable Efficient De Novo Assembly of Eleven Human Genomes

Shafin et al. Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0503-6

Caenorhabditis elegans Dauers Vary Recovery in Response to Bacteria from Natural Habitat

Bubrig LT et al. bioRxiv 2020.04.01.020693; doi: https://doi.org/10.1101/2020.04.01.020693

Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression

Yano R et al. Communications Biology volume 3, Article number: 432 (2020); https://doi.org/10.1038/s42003-020-01172-0

The Knockout of the HMG Domain of the Porcine SRY Gene Causes Sex Reversal in Gene-edited Pigs

Kurtz S et al. bioRxiv 617589; doi: https://doi.org/10.1101/617589

Unraveling molecular mechanisms of immunity and cancer-resistance using the genomes of the Neotropical bats Artibeus jamaicensis and Pteronotus mesoamericanus

Scheben A et al. bioRxiv 2020.09.09.290502; doi: https://doi.org/10.1101/2020.09.09.290502

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

Alonge M et al. Cell. Volume 182, Issue 1, 9 July 2020, Pages 145-161.e23. https://doi.org/10.1016/j.cell.2020.05.021

 

The human Origin Recognition Complex is essential for pre-RC assembly, mitosis and maintenance of nuclear structure

Chou HC et al. bioRxiv 2020.08.06.240358; doi: https://doi.org/10.1101/2020.08.06.240358
 

Oxford Nanopore Sequencing: New Opportunities for Plant Genomics? 

Dumschott K et al. Journal of Experimental Botany. 2020. eraa263; https://doi.org/10.1093/jxb/eraa263

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

Higher quality de novo genome assemblies from degraded museum specimens: a linked-read approach to museomics

Colella JP et al. bioRxiv 716506; doi: https://doi.org/10.1101/716506

Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit

Shafin K et al. bioRxiv 715722; doi: https://doi.org/10.1101/715722

Complete Genome Sequences of Thermus thermophilus Strains AA2-20 and AA2-29, Isolated from Arima Onsen in Japan.

Miyazaki K et al. Microbiology Resource Announcements. 2019. 8(31): e00820-19. DOI: 10.1128/MRA.00820-19

Complete Genome Sequencing of Thermus thermophilus Strain HC11, Isolated from Mine Geyser in Japan

Miyazaki K. Microbiology Resource Announcements Sep 2019, 8 (39) e00873-19; DOI: 10.1128/MRA.00873-19

Complete Genome Sequence of Alteromonas sp. Strain I4, Isolated from the Japan Sea

Miyazaki K et al. Microbiology Resource Announcements. 2019. 8(47): e01277-19; DOI: 10.1128/MRA.01277-19

Complete Genome Sequence of Rubrobacter xylanophilus Strain AA3-22, Isolated from Arima Onsen in Japan

Tomariguchi N et al. Microbiology Resource Announcements. 2019. 8(34): e00818-19. DOI: 10.1128/MRA.00818-19

Enhancer Hijacking Determines Intra- and Extrachromosomal Circular MYCN Amplicon Architecture in Neuroblastoma

Helmsauer et al. bioRxiv 2019.12.20.875807; doi: https://doi.org/10.1101/2019.12.20.875807

Nanopore Sequencing of DNA Concatemers Reveals Higher-Order Features of Chromatin Structure

Ulahannan N et al. bioRxiv 833590; doi: https://doi.org/10.1101/833590

Ultra-Low Input Single Tube Linked-Read Library Method Enables Short-Read NGS Systems to Generate Highly Accurate and Economical Long-Range Sequencing Information for de novo Genome Assembly and Haplotype Phasing

Chen Z et al. bioRxiv 852947; doi: https://doi.org/10.1101/852947

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

Generating High-Quality Human Reference Genomes Using PromethION Nanopore Sequencing

Jain M et al. London Calling 2019. London, UK

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

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

Generating High-Quality Human Reference Genomes Using PromethION Nanopore Sequencing

Miga K et al. AGBT 2019. Marco Island, FL

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