The efficacy of natural selection differs between lifestages in haploid-diploid Marchantia. #bryophyte #population #genomics Preprint out doi.org/10.1101/2024.0…

If you liked #SQANTI, you're gonna love our latest #SQANTI-reads to support raw-long-read QC in multi-sample experiments. Detect outliers, find biases, and assess discovery power in your LRS dataset. Great collaboration with Lauren M McIntyre team. Preprint biorxiv.org/content/10.110…

PoreMeth2 is an R package for the identification of Differentially Methylated Regions from Nanopore methylation data (inferred by methcallers such as Nanopolish, DeepSignal, Dorado or Guppy) of paired samples and for their functional interpretation.

out today in Molecular Ecology, daniel cadena & I show that extant reference genomes do not accurately reflect the latitudinal gradient of species richness, and that scientists in the global south are less likely to use reference genome-based approaches: doi.org/10.1111/mec.17…

Come work with us! We are looking for a post-doc to work on 🐝 🦠 🌸 in a collaborative project with Phil Stevenson. Help us understand how landscapes support wild bee health! Deadline for applications 29 Nov jobs.royalholloway.ac.uk/vacancy.aspx?r…

We (Maximilian Bolder and I) are offering a funded research internship on social insects🐜🐝 through DAAD RISE Germany for a BSc student from USA🇺🇸, Canada🇨🇦, UK🇬🇧, or Ireland🇮🇪, to undertake research Universität Mainz🇩🇪 Summer 2025. Please RT - deadline Nov 30th: tinyurl.com/47xm6jj9

Does 6mA exist in eukaryotic DNA? This is our take on this dispute: yes it does, and can be very abundant, but mostly correlates with presence of the MT-A70 writer AMT1. Then, 6mA is associated with transcriptionally-permissive chromatin (H3K4me3) 1/6: biorxiv.org/content/10.110…

This is great! NIAID News have launched a collection of public domain illustrations (currently 550 individual icons) bioart.niaid.nih.gov

New paper: "Density-dependent dispersal reduces conflict over the sex ratio" (#OpenAccess), w/ Chedhawat Chokechaipaisarn doi.org/10.1098/rsbl.2… Sex-ratio optima for haplodiploid parents converge in viscous populations when dispersal is density-dependent Royal Society Publishing #OA

Exploring gene duplications! Our study reveals how duplicated genes diverge in function using structural and expression analysis across 36 species. Check out our paper: biorxiv.org/content/10.110… Thanks to Alex WV, Natasha Glover, Paul Thomas, Christophe Dessimoz #Genomics #Evolution

Vcfexpress: flexible, rapid user-expressions to filter and format VCFs biorxiv.org/content/10.110… work with Aaron Quinlan lua expressions and a sandbox feature so it can be run safely.

UPDATE: #Arthropod #Genome Assembly Assessment Catalogue: #A3Cat v.2024-11-01 🐝🦋🐞🦂 232 new assemblies making a total of 6'849 a3cat.unil.ch Methods & Motivation GigaScience doi.org/10.1093/gigasc…

I recently discovered the tidyplots package in R, and it’s impressive how effortlessly it enables you to create beautiful, publication-ready plots. Designed with scientific papers in mind, tidyplots lets you build, adjust, and refine plot components gradually, all with a

OrthoHMM: Improved Inference of Ortholog Groups using Hidden Markov Models biorxiv.org/content/10.110… 🧬🖥️🧪 github.com/JLSteenwyk/ort…

Clair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data biorxiv.org/content/10.110…

CorrAdjust unveils biologically relevant transcriptomic correlations by efficiently eliminating hidden confounders biorxiv.org/content/10.110…

The Borzoi manuscript is now out in Nature Genetics: doi.org/10.1038/s41588… Borzoi predicts RNA-seq profiles in many tissues & cell types from DNA sequence as its only input. With it, we can score the impact of genetic variants on a number of gene-regulatory functions. 1/

Struggling to visualize complex intersections in your data? ComplexUpset, an extension of ggplot2, makes it easy to create advanced UpSet plots, offering a clear way to display overlapping sets and their relationships. ✔️ Visualize complex set intersections with clarity. ✔️

Two tools for plotting genomics data: figeno: Tool for making genomics figures in #python. github.com/CompEpigen/fig… Plotting Multi-omic Data with plotgardener in #rstats phanstiellab.github.io/plotgardener/i…

Working with survival analysis in R? survminer, a ggplot2 extension, makes it simple to create clean and informative survival curves, helping you effectively communicate survival data insights. ✔️ Easily plot Kaplan-Meier survival curves with customizable aesthetics. ✔️ Add risk