Four principles to establish a universal virus taxonomy
A universal taxonomy of viruses is essential for a comprehensive view of the virus world and
for communicating the complicated evolutionary relationships among viruses. However …
for communicating the complicated evolutionary relationships among viruses. However …
Horizontal gene transfer in eukaryotes: not if, but how much?
J Van Etten, D Bhattacharya - Trends in Genetics, 2020 - cell.com
Horizontal gene transfer (HGT), the movement of genetic material across branches of the
tree of life, is well established in prokaryotes and uncontroversial. This is explained in part …
tree of life, is well established in prokaryotes and uncontroversial. This is explained in part …
Roseobacters in a Sea of Poly- and Paraphyly: Whole Genome-Based Taxonomy of the Family Rhodobacteraceae and the Proposal for the Split of the “Roseobacter Clade” Into …
KYH Liang, FD Orata, YF Boucher… - Frontiers in Microbiology, 2021 - frontiersin.org
The family Rhodobacteraceae consists of alphaproteobacteria that are metabolically,
phenotypically, and ecologically diverse. It includes the roseobacter clade, an informal …
phenotypically, and ecologically diverse. It includes the roseobacter clade, an informal …
Identifying genetic variants underlying phenotypic variation in plants without complete genomes
Structural variants and presence/absence polymorphisms are common in plant genomes,
yet they are routinely overlooked in genome-wide association studies (GWAS). Here, we …
yet they are routinely overlooked in genome-wide association studies (GWAS). Here, we …
The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features
W Qi, YW Lim, A Patrignani, P Schläpfer… - …, 2022 - academic.oup.com
Abstract Background Cassava (Manihot esculenta) is an important clonally propagated food
crop in tropical and subtropical regions worldwide. Genetic gain by molecular breeding has …
crop in tropical and subtropical regions worldwide. Genetic gain by molecular breeding has …
Large-scale network analysis captures biological features of bacterial plasmids
Many bacteria can exchange genetic material through horizontal gene transfer (HGT)
mediated by plasmids and plasmid-borne transposable elements. Here, we study the …
mediated by plasmids and plasmid-borne transposable elements. Here, we study the …
When less is more: sketching with minimizers in genomics
The exponential increase in sequencing data calls for conceptual and computational
advances to extract useful biological insights. One such advance, minimizers, allows for …
advances to extract useful biological insights. One such advance, minimizers, allows for …
Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification
Genetic tools are increasingly used to identify and discriminate between species. One key
transition in this process was the recognition of the potential of the ca 658bp fragment of the …
transition in this process was the recognition of the potential of the ca 658bp fragment of the …
DeLUCS: Deep learning for unsupervised clustering of DNA sequences
We present a novel De ep L earning method for the U nsupervised C lustering of DNA S
equences (DeLUCS) that does not require sequence alignment, sequence homology, or …
equences (DeLUCS) that does not require sequence alignment, sequence homology, or …
Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy
Information theoretic approaches are ubiquitous and effective in a wide variety of
bioinformatics applications. In comparative genomics, alignment-free methods, based on …
bioinformatics applications. In comparative genomics, alignment-free methods, based on …