literally who hurt genomics to make you all encode one specific kind of number as the ASCII characters from ! to ~ as an integer input to some logarithm function, but then others of you changed the function but kept encoding it as a single ASCII character ranging from -5 to 62 (???), and then later they decided that -5 to 62 was silly and so they changed that to 0-62 and throwing away half the original range for no reason, except actually it's 0-40 by convention.

did anyone consider "encoding it as a number"

https://doi.org/10.1093/nar/gkp1137

#DataStandards #FileFormats #Genomics

PhD studentship to characterise aphid immune evolution. Lots to uncover in an insect group with major ecological & economic impact. Aphid systemic immunity is a black box. The interested PhD candidate will both provide one of the first detailed descriptions of aphid immunity, but also uncover principles of immune evolution.

Deadline July 29th at #UoExeter
Email or DM for details🐘 📩
m.hanson@exeter.ac.uk

#Genomics #Aphid #Genetics #Immunity #Evolution #Drosophila

Stochasticity, determinism, and contingency shape genome evolution of endosymbiotic bacteria

https://www.nature.com/articles/s41467-024-48784-2

#evolution #microbiology #genomics

Stochasticity, determinism, and contingency shape genome evolution of endosymbiotic bacteria - Nature Communications

Endosymbionts often have small genomes that maintain minimal functions required to serve their hosts. This study examines cases of new endosymbiont acquisition and finds genome degeneration involves both stochastic and deterministic processes that sh…

^Nature

1) Want to know how much of your metagenome is eukaryotic? No references? No problem. We developed SingleM microbial fraction (SMF) and ran it on 250k metagenomes https://www.biorxiv.org/content/10.1101/2024.05.16.594470v1.

If you know what Eukaryotes are there, you can filter reads by mapping to their genomes. However, often you don’t know what’s in your sample, or the euk doesn’t have a genome.

#metagenomics #bioinformatics #genomics #microbiomes #microbialecology

Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns

Metagenomes often contain many reads derived from eukaryotes. However, there is usually no reliable method for estimating the prevalence of non-microbial reads in a metagenome, forcing many analysis techniques to make the often-faulty assumption that…

^bioRxiv

Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals

https://academic.oup.com/ve/advance-article/doi/10.1093/ve/veae039/7670984

#viruses #coral #evolution #genomics

Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals

Abstract:. Stony corals (Order Scleractinia) are central to vital marine habitats known as coral reefs. Numerous stressors in the Anthropocene are contribu

^{Stephens, Danae (Oxford University Press)}

Systematic identification of cargo-mobilizing genetic elements reveals new dimensions of eukaryotic diversity

https://doi.org/10.1093/nar/gkae327

#genomics #microbiology

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

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

#genomics #bioinformatics

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 Galaxy

^Nature

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 Sussex

^{www.FindAPhD.com}

Gene duplication as a major force driving the genome expansion in some giant viruses

https://journals.asm.org/doi/full/10.1128/jvi.01309-23

#GiantViruses #viruses #virology #genomics

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

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:

https://doi.org/10.1093/molbev/msad234

#Phylogeny #Genomics #bioinformatics #Phylogenomics

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

#microbiology #genomics #dna

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

'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

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"

https://doi.org/10.1016/j.cell.2023.08.017

#microbiology #genomics #genetics

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/

#bioinformatics #genomics