Skip to main content

Search

Items tagged with: Genomics


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


[New paper]: Two subtle problems with over-representation analysis.
ORA is a type of enrichment analysis that analyses over-represented functional categories in gene lists. These tools have accumulated ~190k citations, but they have subtly different behaviours. Here we unpack the differences and investigate two subtle problems in some implementations, which may have negatively impacted those 190k research papers.
https://doi.org/10.1093/bioadv/vbae159
#genomics #bioinformatics


I've just been reminded of this masterwork book cover. I hope someday my work is cool enough to merit something even half as weird. #Science #ScientificIllustration #Genomics #EvolutionaryBiology


Now published in Peer Community Journal, #genomics section: High quality genome assembly and annotation (v1) of the eukaryotic terrestrial microalga Coccomyxa viridis SAG 216-4 https://doi.org/10.24072/pcjournal.447


New #ISEPpapers #preprint! Insights from comparative plastid #genomics of colorless facultative pathogens #Prototheca (Chlorophyta): Unveiling membrane transport and organelle division as key functions https://www.biorxiv.org/content/10.1101/2024.01.16.575923v1.abstract #protists #algae #parasites #microbes @biorxivpreprint


New #ISEPpapers! Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic #bacteria but does reveal the presence of #GiantViruses https://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1011218 #protists #symbiosis #viruses #genomics #microbes @PLOS by Anna Cho et al.


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


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


Small but mitey: long-read assembly of a streamlined mite genome from contaminated host plant sequencing data http://biorxiv.org/cgi/content/short/2024.05.17.594625v1?rss=1 #biorxiv #genomics #preprint


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


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

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

#genomics #microbiology


The Ribosomal Operon Database (ROD): A full-length rDNA operon database extracted from genome assemblies http://biorxiv.org/cgi/content/short/2024.04.19.590225v1?rss=1 #biorxiv #genomics #preprint


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 http://biorxiv.org/cgi/content/short/2024.03.06.583591v1?rss=1 #biorxiv #genomics #preprint


[New preprint] Direction-aware functional class scoring enrichment analysis of Infinium DNA methylation data
#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


Large language models improve annotation of prokaryotic viral proteins

https://www.nature.com/articles/s41564-023-01584-8

#virology #viruses #bioinformatics #genomics


Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

https://www.nature.com/articles/s41587-023-02100-3

#genomics #bioinformatics


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


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


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


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


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


Universal signatures of transposable element compartmentalization across eukaryotic genes http://biorxiv.org/cgi/content/short/2023.10.17.562820v1?rss=1 #biorxiv #genomics #preprint


Systematic identification of cargo-carrying genetic elements reveals new dimensions of eukaryotic diversity http://biorxiv.org/cgi/content/short/2023.10.24.563810v1?rss=1 #biorxiv #genomics #preprint


New #ISEPpapers! Long-read-based genome assembly reveals numerous endogenous viral elements in the green algal bacterivore Cymbomonas tetramitiformis https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evad194/7330633 #protists #algae #microbes #genomics #viruses by @DacksLabECB


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


Bacterial histones unveiled

https://www.nature.com/articles/s41564-023-01509-5

#microbiology #genomics #dna


Polinton-like Viruses Associated with Entomopoxviruses Provide Insight into Replicon Evolution http://biorxiv.org/cgi/content/short/2023.10.16.562556v1?rss=1 #biorxiv #genomics #preprint


A new look for the group's website - #Arthropod Evolutionary-Functional #Genomics at http://rmwaterhouse.org 🐞🧬🦟🧬🦋🧬🐝
New Environmental #Bioinformatics Group
@SIB - #DataScience solutions to address environmental challenges https://sib.swiss/environmental-bioinformatics 💻🧬📊🌍🛜🌦️🌄📋🔭


'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


What could go wrong?
#genomics #bioinformatics
https://www.biorxiv.org/content/10.1101/2023.09.08.556814v1


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


Phage-plasmids promote genetic exchanges between phages and plasmids and create novel ones. http://biorxiv.org/cgi/content/short/2023.08.08.552325v1?rss=1 #biorxiv #genomics #preprint


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


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

Lo, thar be cookies on this site to keep track of your login. By clicking 'okay', you are CONSENTING to this.