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Items tagged with: genomics
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011032
#genomics #bioinformatics
JASPER: A fast genome polishing tool that improves accuracy of genome assemblies
Advances in long-read sequencing technologies have dramatically improved the contiguity and completeness of genome assemblies.journals.plos.org
https://academic.oup.com/bioinformatics/article/39/3/btad121/7072460
#genomics
NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes
AbstractSummary. Large-scale comparative genomic studies have provided important insights into species evolution and diversity, but also lead to a great challenHe, Weiming (Oxford University Press)
https://www.nature.com/articles/s43705-023-00231-x
#genomics #microbiology
Linking prokaryotic genome size variation to metabolic potential and environment - ISME Communications
ISME Communications - Linking prokaryotic genome size variation to metabolic potential and environmentNature
The methanogen core and pangenome: conservation and variability across biology’s growth temperature extremes
"Increased methanogenic growth temperature is associated with reduced genome size, and thermotolerant organisms...have larger core genome fractions, suggesting that genome size is governed by temperature rather than phylogeny. "
https://academic.oup.com/dnaresearch/article/30/1/dsac048/6862058
#genomics #pangenomics #microbiology
The methanogen core and pangenome: conservation and variability across biology’s growth temperature extremes
Abstract. Temperature is a key variable in biological processes. However, a complete understanding of biological temperature adaptation is lacking, in part becaProndzinsky, Paula (Oxford University Press)
Scaling of Protein Function Across the Tree of Life
"The abundance of functional categories in a given genome scales with genome size, suggesting that universal constraints shape category abundance. Here we look across the tree of life to understand how genome evolution may be related to functional scaling. "
https://www.biorxiv.org/content/10.1101/2023.03.08.531481v1.abstract
#genomics #microbiology
Scaling of Protein Function Across the Tree of Life
Scaling laws are a powerful way to compare genomes because they put all organisms onto a single curve and reveal non-trivial generalities as genomes change in size.bioRxiv
This paper outlines an approach ranging from population genetics to functional #genomics in which the researchers identified four important #alleles and their likely #regulatory function.
Title: "Regulatory dissection of the severe #COVID-19 risk locus introgressed by #Neanderthals" (Jagoda et al. 2023)
Link: https://elifesciences.org/articles/71235
Regulatory dissection of the severe COVID-19 risk locus introgressed by Neanderthals
Key functional variants, discovered using Massively Parallel Reporter Assay (MPRA) and reporter assays in the context of SARS-CoV-2 infection, support the importance of two critical chemokine receptor genes CCR1 and CCR5 in severe Covid-19 illness.Evelyn Jagoda (eLife Sciences Publications, Ltd)
@NCBI
nt and nr (I certainly have!)
From https://youtu.be/2FW1dk5YQ3I?t=484 and https://youtu.be/KLBE0AuH-Sk?t=692 (cued to the right spots in the video)
#Bioinformatics #Genomics
NCBI Minute: Using BLAST Well
Presented October 3, 2018. In this webinar, the NCBI BLAST team lead will show you how to be more effective with NCBI’s standalone BLAST applications. You wi...YouTube
https://phys.org/news/2023-02-decades-old-crustaceans-coaxed-lake-mud.html
Resurrection #genomics provides molecular and phenotypic evidence of rapid adaptation to #salinization in a keystone aquatic species https://www.pnas.org/doi/10.1073/pnas.2217276120
They revived decades-old #Daphnia resting eggs from lake sediments. Tanners Lake has suffered significant salt #pollution, stemming from the widespread use of road deicing salts in its watershed.
Decades-old crustaceans coaxed from lake mud give up genetic secrets revealing evolution in action
Human actions are changing the environment at an unprecedented rate. Plant and animal populations must try to keep up with these human-accelerated changes, often by trying to rapidly evolve tolerance to changing conditions.Science X (Phys.org)
#Microbiology #Evolution #ExperimentalEvolution #EcoEvo #popgen #PopulationDynamics #Genomics
Quantifying the local adaptive landscape of a nascent bacterial community - Nature Communications
Fitness landscapes largely shape the dynamics of evolution, but it is unclear how they shift upon ecological diversification. By engineering genome-wide knockout libraries of a nascent bacterial community, Ascensao et al.Nature
Giant Transposons in Eukaryotes: Is Bigger Better?
https://academic.oup.com/gbe/article/11/3/906/5364020
"...the size limitations previously placed on mobilizable DNA units in eukaryotes may have been due in part to our inability to assemble large contiguous stretches of repetitive DNA in complex genomes."
#genetics #genomics
Giant Transposons in Eukaryotes: Is Bigger Better?
Abstract. Transposable elements (TEs) are ubiquitous in both prokaryotes and eukaryotes, and the dynamic character of their interaction with host genomes bringsArkhipova, Irina R (Oxford University Press)
https://www.nature.com/articles/s41576-022-00554-w
#genomics #genetics #evolution
Current advances in primate genomics: novel approaches for understanding evolution and disease - Nature Reviews Genetics
In this Review, the authors describe how advances in comparative primate genomics — complemented by multi-layered omic resources and primate cell systems — are providing insights into the evolution of primates and the genetic underpinnings of key tra…Nature
Ten things you should know about transposable elements
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1577-z
#genomics #transposons #evolution #genetics
Ten things you should know about transposable elements - Genome Biology
Transposable elements (TEs) are major components of eukaryotic genomes. However, the extent of their impact on genome evolution, function, and disease remain a matter of intense interrogation.BioMed Central
What other genomics/evolution classics do people always keep around?
#genomics #bioinformatics #evolution #microbiology
