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Items tagged with: genomics
Systematic identification of cargo-mobilizing genetic elements reveals new dimensions of eukaryotic diversity
The Ribosomal Operon Database (ROD): A full-length rDNA operon database extracted from genome assemblies
Current rDNA reference sequence databases are tailored towards shorter DNA markers, such as parts of the 16/18S marker or the ITS region.bioRxiv
Interested in evolutionary genomics/population genomics and plant genetics? Want to do your PhD in beautiful Stockholm?
We have two 4-year PhD student positions available in my group at Stockholm University. More info, see tanjaslottelab.se
Please repost.
#evolution #genomics #popgen #distyly #CropWildRelatives #PlantGenetics #ecrchat #phd 1/4
MotifScope: a multi-sample motif discovery and visualization tool for tandem repeats
Tandem repeats (TRs) constitute a significant portion of the human genome, exhibiting high levels of polymorphism due to variations in size and motif composition.bioRxiv
#Genomics #Epigenetics #Bioinformatics
In this article we outline a refined method for pathway enrichment of infinium array data that is more sensitive and precise as compared to existing over-representation approaches. Feedback welcome.
https://www.biorxiv.org/content/10.1101/2024.02.22.581670v1
Direction-aware functional class scoring enrichment analysis of Infinium DNA methylation data
Infinium Methylation BeadChip arrays remain one of the most popular platforms for epigenome-wide association studies, but tools for downstream pathway analysis have their limitations.bioRxiv
Large language models improve annotation of prokaryotic viral proteins
https://www.nature.com/articles/s41564-023-01584-8
#virology #viruses #bioinformatics #genomics
Large language models improve annotation of prokaryotic viral proteins - Nature Microbiology
Ocean viral proteome annotations are expanded by a machine learning approach that is not reliant on sequence homology and can annotate sequences not homologous to those seen in training.Nature
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy
https://www.nature.com/articles/s41587-023-02100-3
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy - Nature Biotechnology
Nature Biotechnology - Scalable, accessible and reproducible reference genome assembly and evaluation in GalaxyNature
Gotta check these out!
Robust, scalable, and informative clustering for diverse biological networks
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03062-0
#bioinformatics #genomics #genetics #statistics
Robust, scalable, and informative clustering for diverse biological networks - Genome Biology
Clustering molecular data into informative groups is a primary step in extracting robust conclusions from big data.BioMed Central
Apply for our Phd project on "Discovering and characterising novel defence systems in pathogenic Serratia spp using microbiology and genomics"
#genomics #microbiology #omics
FindAPhD : Pathogens and Host Defences Doctoral Training Partnership PhD Studentships at University of Sussex
https://www.findaphd.com/phds/program/pathogens-and-host-defences-doctoral-training-partnership-phd-studentships/?p6353
FindAPhD : Pathogens and Host Defences Doctoral Training Partnership PhD Studentships at University of Sussex
Apply for a PhD: Pathogens and Host Defences Doctoral Training Partnership PhD Studentships at University of Sussexwww.FindAPhD.com
Gene duplication as a major force driving the genome expansion in some giant viruses
Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts
https://www.nature.com/articles/s41467-023-43236-9
#phages #viruses #evolution #genomics
Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts - Nature Communications
Proteins are composed of distinct functional domains, each serving a specific role. Here, Smug et al. show that phages are able to shuffle fragments of their proteins and this predominantly occurs in proteins involved in bacterial host interactions.Nature
Postdoctoral Fellow in Phylogenomics/Bioinformatics
#academicjobs #postdocjobs #genomics #evolution #microbiology
https://jobrxiv.org/job/uc-santa-barbara-27778-postdoctoral-fellow-in-phylogenomics-bioinformatics/
Postdoctoral Fellow in Phylogenomics/Bioinformatics
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!jobRxiv
New #ISEPpapers! The #protist #Aurantiochytrium has universal subtelomeric rDNAs and is a host for #mirusviruses: Jackie Collier et al. https://www.cell.com/current-biology/fulltext/S0960-9822(23)01368-4
#protists #microbes #protistology #microbiology #viruses #virology #genomics
PhD position in viral evolution and diversity @foaylward
Virginia Tech
Funded PhD positions in the Aylward Lab to study the #evolution and #genomics of giant #viruses. Both computational and wet-lab projects available.
See the full job description on jobRxiv: https://jobrxiv.org/job/virginia-tech-27778-funded-phd-position/?feed_id=64662
#ScienceJobs #hiring #research
Blacksburg #UnitedStatesUS ...
https://jobrxiv.org/job/virginia-tech-27778-funded-phd-position/?feed_id=64662
PhD position in viral evolution and diversity
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!jobRxiv
My latest preprint exploring transposable element (TE) activity in the genomes of sparrows.
https://biorxiv.org/cgi/content/short/2023.10.26.564301v1
We found remarkably high levels of repeat content in the newly generated genomes of
Bell's, Song, and Savannah Sparrow. 31% of the Bell's sparrow genome is spanned by repetitive elements.
This is ~3x as much as previously reported in most songbirds.
Thanks to all my co-authors for their contributions to this project!
#Genomics
#TransposableElements
#ornithology
#sparrows
Remarkably high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery.
Transposable elements (TE) play critical roles in shaping genome evolution. However, the highly repetitive sequence content of TEs is a major source of assembly gaps.bioRxiv
Universal signatures of transposable element compartmentalization across eukaryotic genes
The evolutionary mechanisms shaping the origins of genome architecture remain poorly understood but can now be assessed with unprecedented power due to the abundance of genome assemblies spanning phylogenetic diversity.bioRxiv
Systematic identification of cargo-carrying genetic elements reveals new dimensions of eukaryotic diversity
Cargo-carrying mobile elements (CCEs) are genetic entities that transpose diverse protein coding sequences. Although common in bacteria, we know little about the biology of eukaryotic CCEs because no appropriate tools exist for their annotation.bioRxiv
Long-read-based genome assembly reveals numerous endogenous viral elements in the green algal bacterivore Cymbomonas tetramitiformis
Abstract. The marine tetraflagellate Cymbomonas tetramitiformis has drawn attention as an early diverging green alga that uses a phago-mixotrophic mode of nutriGyaltshen, Yangtsho (Oxford University Press)
PhylteR: efficient identification of outlier sequences in phylogenomic datasets.
PhylteR can automatically identify sequences likely to be hidden paralogs or horizontally transferred genes in very large datasets. Removing those sequences therefore reduces noise in downstream analyses.
Available as an R package on CRAN or as docker and singularity images.
Package:
https://cran.r-project.org/web/packages/phylter/index.html
Paper:
Ancestral genome reconstructions are changing the field of #comparative #genomics. Want to learn more?
Watch the talks by Hugues Roest Crollius & Matthieu Muffato in the last #ERGA BioGenome Analysis and Applications Seminar!
👉https://www.youtube.com/watch?v=9QDgRHlLdmU
Learn more about the seminar series & stay tuned for the upcoming sessions! 👉https://www.erga-biodiversity.eu/post/erga-biogenome-analysis-and-applications-seminars
Earth BioGenome Project Biodiversity Genomics Europe
ERGA BioGenome Analysis and Applications Seminars
The ERGA BioGenome Analysis and Applications Seminars represent a joint endeavor of the ERGA Data Analysis Committee (DAC) and the Biodiversity Genomics Europe Work Package 11 - Genome Applications.erga
Bacterial histones unveiled
https://www.nature.com/articles/s41564-023-01509-5
Bacterial histones unveiled - Nature Microbiology
Computational, molecular and structural analyses reveal the presence of bacterial histones that bind DNA to form dense, DNA-enveloping fibres in Bdellovibrio bacteriovorus.Nature
Polinton-like Viruses Associated with Entomopoxviruses Provide Insight into Replicon Evolution
Polinton-like viruses (PLVs) are a diverse group of small integrative dsDNA viruses that infect diverse eukaryotic hosts. Many PLVs are hypothesized to parasitize viruses in the phylum Nucleocytoviricota for their own propagation and spread.bioRxiv
New Environmental #Bioinformatics Group
@SIB - #DataScience solutions to address environmental challenges https://sib.swiss/environmental-bioinformatics 💻🧬📊🌍🛜🌦️🌄📋🔭
Robert M. Waterhouse
Waterhouse Group Arthropoda Assembly Assessment Catalogue | DrosOMA Orthology Database | GO-Figure! Gene Ontology Visualisationrmwaterhouse.org
'Both genomes had been analysed before, but the fragmented assemblies had scaffold sizes comparable to the length of long reads prior to assembly. Our new assemblies illustrate how long-read technologies allow for a much better representation of species genomes. We are now able to conduct more accurate downstream assays based on more complete gene and transposable element predictions.'
#Preprint #Evolution #Genomics
https://www.biorxiv.org/content/10.1101/2023.10.06.561169v1
Revisiting genomes of non-model species with long reads yields new insights into their biology and evolution
High-quality genomes obtained using long-read data allow not only for a better understanding of heterozygosity levels, repeat content, and more accurate gene annotation, and prediction when compared to those obtained with short-read technologies, but…bioRxiv
#genomics #bioinformatics
https://www.biorxiv.org/content/10.1101/2023.09.08.556814v1
Automated Bioinformatics Analysis via AutoBA
With the fast-growing and evolving omics data, the demand for streamlined and adaptable tools to handle the analysis continues to grow.bioRxiv
Cool paper! Also glad we are moving towards Patescibacteria and not CPR:
"Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle"
Phage-plasmids promote genetic exchanges between phages and plasmids and create novel ones.
Phages and plasmids have key roles in bacterial evolution and are usually very different. Yet, they must recombine, since they sometimes carry nearly identical accessory genes.bioRxiv
Preprint from Salzberg team questioning a 2020 Nature paper from Rob Knight 😮
"the raw read counts were vastly over-estimated for nearly every bacterial species, often by a factor of 1000 or more."
"Our conclusion after re-analysis is that the near-perfect association between microbes and cancer types reported in the study is, simply put, a fiction."
Major data analysis errors invalidate cancer microbiome findings
https://www.biorxiv.org/content/10.1101/2023.07.28.550993v1
#microbiome #genomics #research #science
Major data analysis errors invalidate cancer microbiome findings
We re-analyzed the data from a recent large-scale study that reported strong correlations between microbial organisms and 33 different cancer types, and that created machine learning predictors with near-perfect accuracy at distinguishing among cance…bioRxiv
I wrote a short guide on how to build both alignment-free and reference-based prokaryote phylogenetic trees from SNP alignments without using snippy, check it out
https://www.bacpop.org/guides/building_trees_with_ska/
Building trees with SKA
SKA is a tool for comparing small and highly similar genomes using split k-mers. This guide will explain how to use SKA to build a phylogenetic tree for different Escherichia coli lineages in a few minutes.www.bacpop.org
https://www.wur.nl/en/vacancy/phd-researcher-in-bioinformatics-investigating-protein-evolution-using-machine-learning.htm
#PhD #PhDPosition #Evolution #Genomics #ProteinStructure #MachineLearning
Or is there a ready to go solution here?
i.e. give all genomes and get them back soft-masked.
#bioinformatics #genomics
Three new genome assemblies of blue mussel lineages: North and South European Mytilus edulis and Mediterranean Mytilus galloprovincialis
The blue mussel species complex ( Mytilus edulls ) is of particular interest both as model species in population genetics and ecology, but also as an economic resource in many regions.bioRxiv
Unraveling the tangled #evolution of #figs.
#genomics #phylogenetics #introgression #Ficus
https://phys.org/news/2023-07-unraveling-tangled-evolution-figs.html
Unraveling the tangled evolution of figs
Containing more than 850 species, fig trees are one of the most diverse groups of plants in the world.Amanda Morris (Phys.org)
Hello everyone!
I’m an associate prof at Virginia Tech studying viral diversity. Lately my group has been focusing on giant viruses, but we are also interested in other protist viruses, and the role of viral endogenization in host genome evolution.
#GiantViruses #ViralDiversity #TreeOfLife #Protists #Microbiology #Bioinformatics #Evolution #Virology #Genomics
Recently we have been examining the strange and complex genes encoded in giant virus genomes!
https://doi.org/10.1093/femsre/fuad053
Studying some phage genes with scattered, partial alignments in varying degrees (40~+90%) of ID against closely related cousins (~93% ANI).
I'm thinking intragenic insertion/shuffling - but what kind of signals could I look for here? Common scars? Models to reference? #phage #bioinformatics #genomics
https://www.biorxiv.org/content/10.1101/2023.06.03.543588v1 #bioinformatics #HumanGenome #genomics
miniBUSCO: a faster and more accurate reimplementation of BUSCO
Motivation Assembly completeness evaluation of genome assembly is a critical assessment of the accuracy and reliability of genomic data. An incomplete assembly can lead to errors in gene predictions, annotation, and other downstream analyses.bioRxiv
Empirical Evidence That Complexity Limits Horizontal Gene Transfer
https://academic.oup.com/gbe/article/15/6/evad089/7180211?login=false
Empirical Evidence That Complexity Limits Horizontal Gene Transfer
Abstract. Horizontal gene transfer (HGT) is a major contributor to bacterial genome evolution, generating phenotypic diversity, driving the expansion of proteinBurch, Christina L (Oxford University Press)
Built Into the Genome of the Microbes – Scientists Uncover Over 30,000 “Hidden” Viruses
Built Into the Genome of the Microbes – Scientists Uncover Over 30,000 “Hidden” Viruses
Unveiled within the DNA of unicellular organisms lie thousands of enigmatic viruses. Researchers at the University of Innsbruck, utilizing the high-performance computing cluster known as "Leo," have identified more than 30,000 new viruses embedded wi…Colin Collins (SciTechDaily)
Important study from Bellas et al showing that protists have a huge diversity of endogenous DNA viruses in their genomes!
Large-scale invasion of unicellular eukaryotic genomes by integrating DNA viruses
https://www.pnas.org/doi/10.1073/pnas.2300465120
And a commentary about these exciting findings from @giant_virus and myself -
Endogenous DNA viruses take center stage in eukaryotic genome evolution
Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk
https://www.nature.com/articles/s41588-023-01390-2
Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk - Nature Genetics
MEGAnE is a new tool to detect and genotype mobile element variants (MEVs) from short-read whole-genome sequencing datasets. Genetic analyses implicate MEVs as population-specific drivers of gene expression variation and disease risk.Nature
https://www.nature.com/articles/d41586-023-01300-w
#genomics #bioinformatics
Every base everywhere all at once: pangenomics comes of age
Multi-genome assemblies called pangenomes can capture genetic diversity in a species, but researchers are still working out how best to build and explore them.Eisenstein, Michael