Author Archives: Alex

High-molecular weight DNA extraction, clean-up and size selection for long-read sequencing

July 2021 Authors: Ashley Jones ,Cynthia Torkel,David Stanley,Jamila Nasim,Justin Borevitz,Benjamin Schwessinger Info: The authors provide a protocol for preparing high molecular weight DNA sequencing libraries with a particular focus on difficult plant and fungal tissues, and also can be used … more »

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Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology

April 2021 Authors: Multiple authors, the SEQC2 Oncopanel Sequencing Working Group Info: A multi-site and cross-platform evaluation of circulating tumor DNA (ctDNA) NGS assays was conducted by the SEQC2 Oncopanel Sequencing Working Group and reported on in this comprehensive study. … more »

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Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples

May 2021 Authors: Samuel Martin, Darren Heavens, Yuxuan Lan, Samuel Horsfield, Matthew D Clark, Richard M Leggett Info: Oxford Nanopore adaptive sampling is a real-time sequencing method with which analysis software identifies several hundred sequence bases as they pass through … more »

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Gene by environment interaction mouse model reveals a functional role for 5-hydroxymethylcytosine in neurodevelopmental disorders

May 2021 Authors: Ligia A. Papale, Andy Madrid, Qi Zhang, Kailei Chen, Lara Sak, Sündüz Keles, and Reid S. Alisch Info: Researchers studying the role of 5-Hydroxymethylcytosine (5hmC) epigenetic modifications in neurological disorders report on the effect of prenatal stress … more »

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Circulating miRNA diversity, origin and response to changing metabolic and reproductive states, new insights from the rainbow trout

Authors: Emilie Cardona, Cervin Guyomar, Thomas Desvignes3, Jérôme Montfort , Samia Guendouz, John H. Postlethwait , Sandrine Skiba-Cassy, Julien Bobe Info: The researchers conducted a comprehensive study of circulating miRNAs (c-mRNAs) in biological fluids of the rainbow trout, with the … more »

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Chromosomal rearrangements but no change of genes and transposable elements repertoires in an invasive forest-pathogenic fungus

Authors: Arthur Demené , Benoît Laurent , Sandrine Cros-Arteil , Christophe Boury , Cyril Dutech Info: The authors present a high-quality de novo genome assembly of Cryphonectria parasitica, and invasive fungus that causes chestnut blight, using Oxford Nanopore and Illumina … more »

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Resetting of 24-nt siRNA landscape is initiated before the first zygotic division in rice

January 2021 Authors: Chenxin Li, Jonathan I. Gent, Hengping Xu, Hong Fu, Scott D. Russell, and Venkatesan Sundaresan Info: In this preprint, the authors report on a study of siRNA profiling in zygotes from the rice plant. They report that … more »

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A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol

January 2021 Authors: Dimitrios G Anastasakis, Alexis Jacob, Parthena Konstantinidou, Kazuyuki Meguro, Duncan Claypool, Pavol Cekan, Astrid D Haase, Markus Hafner Info: The authors offer an improvement to the PAR-CLIP method that is more streamlined and does not require the … more »

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isoCirc catalogs full-length circular RNA isoforms in human transcriptomes

January 2021 Authors: Ruijiao Xin, Yan Gao, Yuan Gao, Robert Wang, Kathryn E. Kadash-Edmondson, Bo Liu, Yadong Wang, Lan Lin & Yi Xing Info: The authors present a protocol, isoCirc, for the full-length sequence determination of circular RNAs. The method … more »

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ATAC-seq with unique molecular identifiers improves quantification and footprinting

November 2020 Authors: Tao Zhu, Keyan Liao, Rongfang Zhou, Chunjiao Xia & Weibo Xie Info: The authors suggest an improvement on the ATAC-seq method (Assay for Transposase-Accessible Chromatin with high-throughput sequencing). By using unique molecular identifiers to distinguish between transposase … more »

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