Short Read Eliminator Publications and Presentations


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;

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

Colella JP et al. Molecular Ecology Resources;

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:

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

Krasnov GS et al. Front. Genet., 27 August 2020 |

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:

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/

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

Etebari K et al. Virus Research 2020;

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;

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:

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

Purushotham N et al. Molecular Plant-Microbe Interactions. 2020. doi:

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:

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:

Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus​
Lee HT et al. Front. Plant Sci., 28 April 2020;

Complete and Validated Genomes from a Metagenome

Giguere DJ et al. bioRxiv 2020.04.08.032540; doi:

A Single Gene Underlies the Dynamic Evolution of Poplar Sex Determination

Muller NA et al.  Nat. Plants 6, 630–637 (2020).

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

Murigneux V et al. bioRxiv 2020.03.16.992933; doi:

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:

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:

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:

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

Kovaka S et al. bioRxiv 2020.02.03.931923; doi:

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).

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

Bubrig LT et al. bioRxiv 2020.04.01.020693; doi:

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);

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:

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:

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.


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:

Oxford Nanopore Sequencing: New Opportunities for Plant Genomics? 

Dumschott K et al. Journal of Experimental Botany. 2020. eraa263;


High molecular weight DNA isolation method from diverse plant species for use with Oxford Nanopore sequencing

Vaillancourt B et al. bioRxiv 783159; doi:

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

Colella JP et al. bioRxiv 716506; doi:

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

Shafin K et al. bioRxiv 715722; doi:

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:

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

Ulahannan N et al. bioRxiv 833590; doi:

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:

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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