High-throughput functional variant screens via in vivo production of single-stranded DNA

MG Schubert, DB Goodman… - Proceedings of the …, 2021 - National Acad Sciences
… a subsequent transformation of the genomic library into a strain bearing all folA mutations,
induced editing, and selected with increased TMP. Sequencing of retron plasmids identified …

[HTML][HTML] TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy

JP Meier-Kolthoff, M Göker - Nature communications, 2019 - nature.com
… type strain genomes, large-genome sequencing projects such as the Genomic Encyclopedia
… is publicly available, it might be difficult to verify its origin, especially in a complex situation …

[HTML][HTML] Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries

M Asplund, KR Kjartansdóttir, S Mollerup… - Clinical Microbiology …, 2019 - Elsevier
… with the same viral taxID at the first level (species/strain) … The factual origin(s) of viral sequences
could be verified by … method used for the initial identification of viral sequences, we find it …

… linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing …

Z Chen, L Pham, TC Wu, G Mo, Y Xia… - Genome …, 2020 - genome.cshlp.org
method having an average length of ∼20 kb, whereas genomic DNA from both strains of
E. … We also manually checked and confirmed the other eight SVs in the TELL-seq data as …

Combining genetically-encoded biosensors with high throughput strain screening to maximize erythritol production in Yarrowia lipolytica

X Qiu, P Xu, X Zhao, G Du, J Zhang, J Li - Metabolic engineering, 2020 - Elsevier
… To test this hypothesis, we checked the DNA sequence upstream … library containing 1152
mutant strains with UV and ARTP combinatorial mutagenesis. Each colony of the mutant library

Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria

TCA Hitch, T Riedel, A Oren, J Overmann… - ISME …, 2021 - academic.oup.com
… 16S rRNA gene sequence is checked by … sequences for the corresponding strains, hence
Barrnap was used to identify the presence of 16S rRNA genes within the genome sequences

High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome

W Zheng, S Zhao, Y Yin, H Zhang, DM Needham… - Science, 2022 - science.org
… We present Microbe-seq, a high-throughput method that yields the genomes of individual …
their DNA, which we then amplify, tag with droplet-specific barcodes, and sequence. We …

[HTML][HTML] Multi-functional genome-wide CRISPR system for high throughput genotype–phenotype mapping

J Lian, C Schultz, M Cao, M HamediRad… - Nature …, 2019 - nature.com
… comprehensive and diversified genomic libraries ever reported … We validated the ranking
criteria using the previously … mutant strains with similar performance as the SIZ1i-NAT1a strain (…

CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering

PLH Vo, C Ronda, SE Klompe, EE Chen, C Acree… - Nature …, 2021 - nature.com
… , we transformed our clonally integrated strain with a plasmid … first verified that this random
fragmentation-based method returned … to the NEBNext Ultra II DNA Library Prep Kit for Illumina …

Highthroughput identification and diagnostics of pathogens and pests: overview and practical recommendations

L Tedersoo, R Drenkhan, S Anslan… - Molecular ecology …, 2019 - Wiley Online Library
… and pathotypes or strains therein. … method by the end of this decade in spite of only negligible
technological improvements since 2015. The ultra-high throughput of Illumina sequencing