Base calling for high-throughput short-read sequencing: dynamic programming solutions [PDF]
, 2013 Shreepriya Das and Haris Vikalo are with the Electrical and Computer Engineering Department, The University of Texas at Austin, Austin, Texas 78712, USABackground: Next-generation DNA sequencing platforms are capable of generating millions of reads in ...
Das, Shreepriya, Vikalo, Haris
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Ion torrent high throughput mitochondrial genome sequencing (HTMGS).
PLoS ONE, 2019 The implementation and popularity of next generation sequencing (NGS) has led to the development of various rapid whole mitochondrial genome sequencing techniques. We summarise an efficient and cost-effective NGS approach for mitochondrial genomic DNA in
N R Harvey +10 more
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Effects of propidium monoazide (PMA) treatment on mycobiome and bacteriome analysis of cystic fibrosis airways during exacerbation [PDF]
, 2016 Introduction and Purpose : Propidium monoazide (PMA)-pretreatment has increasingly been applied to remove the bias from dead or damaged cell artefacts, which could impact the microbiota analysis by high-throughput sequencing. Our study aimed to determine
Audebert, Christophe +8 more
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High throughput genomic sequencing of bioaerosols in broiler chicken production facilities [PDF]
, 2016 Chronic inhalation exposure to agricultural dust promotes the development of chronic respiratory diseases among poultry workers. Poultry dust is composed of dander, chicken feed, litter bedding and microbes.
Bair, Thomas +6 more
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From meadows to milk to mucosa – adaptation of Streptococcus and Lactococcus species to their nutritional environments [PDF]
, 2011 Lactic acid bacteria (LAB) are indigenous to food-related habitats as well as associated with the mucosal surfaces of animals. The LAB family Streptococcaceae consists of the genera Lactococcus and Streptococcus.
Adab, P. +12 more
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HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing
Nucleic Acids Res., 2016 Mitochondrial DNA (mtDNA) profiles can be classified into phylogenetic clusters (haplogroups), which is of great relevance for evolutionary, forensic and medical genetics.
H. Weissensteiner +8 more
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Targeted high throughput sequencing in hereditary ataxia and spastic paraplegia. [PDF]
PLoS ONE, 2017 Hereditary ataxia and spastic paraplegia are heterogeneous monogenic neurodegenerative disorders. To date, a large number of individuals with such disorders remain undiagnosed.
Zafar Iqbal +8 more
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High‐Throughput
Molecular Ecology, 2018 AbstractReconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA ...
Marianne Ramstein +37 more
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Nature Communications, 2023 MicroRNAs (miRNAs) regulate fundamental biological processes by silencing mRNA targets and are dysregulated in many diseases. Therefore, miRNA replacement or inhibition can be harnessed as potential therapeutics.
Lien D. Nguyen +11 more
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Phigaro: high-throughput prophage sequence annotation [PDF]
Bioinformatics, 2020 Abstract Summary Phigaro is a standalone command-line application that is able to detect prophage regions taking raw genome and metagenome assemblies as an input. It also produces dynamic annotated ‘prophage genome maps’ and marks possible transposon insertion spots inside prophages.
Elizaveta V Starikova +6 more
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