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   Articles with "taxonomic classification" as a keyword



Challenge accepted: Evolutionary lineages versus taxonomic classification of North American shrub willows (Salix).

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recommendations! Published in 2024 at "American journal of botany"

DOI: 10.1002/ajb2.16361

Abstract: PREMISE The huge diversity of Salix subgenus Chamaetia/Vetrix clade in North America and the lack of phylogenetic resolution within this clade has presented a difficult but fascinating challenge for taxonomists to resolve. Here we tested… read more here.

Keywords: classification; shrub willows; clade; north american ... See more keywords
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The "Chemistree" of Porous Coordination Networks: Taxonomic Classification of Porous Solids to Guide Crystal Engineering Studies.

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recommendations! Published in 2021 at "Small"

DOI: 10.1002/smll.202006351

Abstract: New approaches to gas/vapor storage and purification are urgently needed to address the large energy footprint, cost, and/or risk associated with existing technologies. In this context, new classes of porous physisorbents, exemplified by porous coordination… read more here.

Keywords: taxonomic classification; classification; crystal engineering; coordination networks ... See more keywords
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Does the genetic diversity among pubescent white oaks in southern Italy, Sicily and Sardinia islands support the current taxonomic classification?

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recommendations! Published in 2020 at "European Journal of Forest Research"

DOI: 10.1007/s10342-020-01334-z

Abstract: Molecular diversity analysis of deciduous pubescent oaks was conducted for populations from Calabria, Sicily and Sardinia. The aims of this study were twofold. First, to provide data on the genetic diversity of pubescent oaks from… read more here.

Keywords: taxonomic classification; diversity; genetic diversity; sicily sardinia ... See more keywords
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Perspective on taxonomic classification of uncultivated viruses.

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recommendations! Published in 2021 at "Current opinion in virology"

DOI: 10.1016/j.coviro.2021.10.011

Abstract: Historically, virus taxonomy has been limited to describing viruses that were readily cultivated in the laboratory or emerging in natural biomes. Metagenomic analyses, single-particle sequencing, and database mining efforts have yielded new sequence data on… read more here.

Keywords: taxonomic classification; virology; classification uncultivated; uncultivated viruses ... See more keywords

Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks

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recommendations! Published in 2022 at "Proceedings of the National Academy of Sciences of the United States of America"

DOI: 10.1073/pnas.2122636119

Abstract: Significance The correct assignment of DNA sequences to their origin is an important task. However, only a fraction of all species are available in today’s databases and thus easily assignable. Therefore, we present a method… read more here.

Keywords: classification dna; dna; dna sequences; beyond sequence ... See more keywords

RdRp-based sensitive taxonomic classification of RNA viruses for metagenomic data

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recommendations! Published in 2022 at "Briefings in Bioinformatics"

DOI: 10.1093/bib/bbac011

Abstract: Abstract With advances in library construction protocols and next-generation sequencing technologies, viral metagenomic sequencing has become the major source for novel virus discovery. Conducting taxonomic classification for metagenomic data is an important means to characterize… read more here.

Keywords: usepackage; classification; taxonomic classification; metagenomic data ... See more keywords

MetaSquare: an integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification

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recommendations! Published in 2022 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btac184

Abstract: Abstract Motivation Taxonomic classification of 16S ribosomal RNA gene amplicon is an efficient and economic approach in microbiome analysis. 16S rRNA sequence databases like SILVA, RDP, EzBioCloud and HOMD used in downstream bioinformatic pipelines have… read more here.

Keywords: 16s rrna; gene; taxonomic classification; metasquare ... See more keywords

Application and Comparison of Machine Learning and Database-Based Methods in Taxonomic Classification of High-Throughput Sequencing Data

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recommendations! Published in 2024 at "Genome Biology and Evolution"

DOI: 10.1093/gbe/evae102

Abstract: Abstract The advent of high-throughput sequencing technologies has not only revolutionized the field of bioinformatics but has also heightened the demand for efficient taxonomic classification. Despite technological advancements, efficiently processing and analyzing the deluge of… read more here.

Keywords: classification; database; biology; database based ... See more keywords

Genomic-based taxonomic classification of the order Sphingomonadales

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recommendations! Published in 2025 at "International Journal of Systematic and Evolutionary Microbiology"

DOI: 10.1099/ijsem.0.006769

Abstract: Abstract The order Sphingomonadales strains are globally distributed in various biomes and are renowned for their biodegradable and biosynthesis capabilities. At present, it consists of 4 families and 49 genera making it the third largest… read more here.

Keywords: based taxonomic; family; genomic based; taxonomic classification ... See more keywords

From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools

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recommendations! Published in 2022 at "Microbial Genomics"

DOI: 10.1099/mgen.0.000949

Abstract: In metagenomic analyses of microbiomes, one of the first steps is usually the taxonomic classification of reads by comparison to a database of previously taxonomically classified genomes. While different studies comparing metagenomic taxonomic classification methods… read more here.

Keywords: classification; database; parameter database; database choice ... See more keywords

Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets

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recommendations! Published in 2022 at "BMC Bioinformatics"

DOI: 10.1101/2022.01.31.478527

Abstract: Background Long-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher information content in long reads is useful for a variety of metagenomics analyses, including taxonomic classification and… read more here.

Keywords: precision; classification; classification profiling; taxonomic classification ... See more keywords