Joe Colgan

Möllmann, @eckartstolle.bsky.social et al. report the first genome assembly for the European orchard bee and investigate its epigenomic architecture to find evidence for the limited role of methylation in gene regulation in Hymenopterans.

🔗 doi.org/10.1093/gbe/evaf224

#genome #evolution

New work from @miyapan.bsky.social and our team, bringing ant, bee, and wasp labs together. @chuanxinyu.bsky.social shows that the ANTSR locus we discovered in ants has determined sex for 150+ My across bees and stinging wasps 🐜🐝, despite virtually no sequence conservation 😮 doi.org/10.1073/pnas...

10 courses for my dream bioinformatics curriculum:

1. Unix Commands with Greg Wilson www.youtube.com/watch?v=U3i...
2. statistics and R with Rafael Irizarry rafalab.dfci.harvard.edu/pages/harva...

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.

1/n

📢 18-month PostDoc Fellowship – University of Montpellier (France)
🦠🦋 Interested in insect pathology, immunity, microbiome, or genomics?

We’re looking for a motivated candidate (<2 years post-PhD by mid-2026). 🧪
📩 Contact me ASAP for details!
⏳ Application deadline: 16/01/26
🔁 Please RT / Repost

PhD position available in evolutionary genomics/bioinformatics (hoehnalab.github.io/job_adverts/...). Topic: analyzing gene expression evolution across several firefly species and linking expression changes to genomic architecture. The position is jointly supervised with @anaevolcatalan.bsky.social

🧬 PhD Position: Evolutionary & Comparative Genomics 🕷️
Join us at @uni-goettingen.de for a 3-year PhD (65% TV-L E13).
We will investigate the genomic & phenotypic impact of gene duplication across 233 arthropod genomes!
More infos 👇 and s.gwdg.de/eDrAAY
#Evolution #Genomics #Bioinformatics

The relationship between sexual dimorphism and intersex correlation: do models support intuition? Abstract. The evolution of sexual dimorphism (the difference in average trait values between females and males, SD), is often thought to be constrained by

Full paper now out in GENETICS:
The relationship between sexual dimorphism and intersex correlation: do models support intuition?
🔗 academic.oup.com/genetics/art...
#Evolution #QuantGenetics @GeneticsGSA

1/ a single job opening receives >1000 applications. (I am not kidding).
How to stand out?

Most bioinformatics CVs look the same: Python, R, RNA-seq, pipelines.
But hiring managers don’t care about skills on paper.
They care about proof. 🧵

FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life Communications Biology - FANTASIA, a protein language model-based tool, enables large-scale functional annotation across ~1000 animal proteomes, revealing novel gene functions in both model and...

FANTASIA's paper is finally out! Check it out if you're interested in alternative methods to homology for functional annotation in nonmodel organisms 🦐🐙🪱🧬🐝🪲
@gemmaeling.bsky.social @amrojasm.bsky.social @ibe-barcelona.bsky.social @cabd-upo-csic.bsky.social
@csic.es www.nature.com/articles/s42...

🧬🖥️ Thrilled that our paper "Tree-based differential testing using inferential uncertainty for RNA-seq" genome.cshlp.org/content/earl..., led by @noorpratap.bsky.social, & in collab with @mikelove.bsky.social, @fennecpaaaw.bsky.social and Jason Fan is now accepted at @genomeresearch.bsky.social. 1/4

Partitioned Multi-MUM finding for scalable pangenomics Pangenome collections are growing to hundreds of high-quality genomes. This necessitates scalable methods for constructing pangenome alignments that can incorporate newly-sequenced assemblies. We prev...

Excited to share a new update to Mumemto, scaling MUM and conserved element finding to any size pangenome! Preprint out now w/ @benlangmead.bsky.social.
Mumemto scales to the new HPRC v2 release and beyond, and can merge in future assemblies without any recomputation! 1/n

Massive thanks to @tegangaetano.bsky.social and @fmanfredini.bsky.social for impecably hosting while I was over - fantastic to hear about all the exciting research going on in Aberdeen🏴󠁧󠁢󠁳󠁣󠁴󠁿, meeting great people🍻, as well as seeing the wildlife🦭🦭🦭

Annotation of 200 Insect Genomes with BRAKER for Consistent Comparisons across Species The annotation of genomes lags behind their sequencing and assembly. For example, of 5,092 insect species in GenBank, as one of the most widely used databases, only 375 currently have annotated genome...

Annotation of 200 insect genomes. Work driven by @stepbystepsolution.bsky.social and Mario Stanke within @gevol.bsky.social : www.biorxiv.org/content/10.1...

Simplify and elevate your data visualization with GGally, an R package designed to extend ggplot2.

Visualization: https://ggobi.github.io/ggally/

Details: https://statisticsglobe.com/online-course-data-visualization-ggplot2-r

#tidyverse #datavisualization #datasciencecourse #data #package

🐝Great to have this out @molbioevol.bsky.social and well done Hongfei Xu (not on BlueSky) for all the hard work

Review: Transcriptomics in the era of long-read sequencing www.nature.com/articles/s41... (read free: rdcu.be/efBjP) 🧬🖥️🧪

Using my Tidyverse local synteny visualization tools first time in 3 months. This a biosynthetic gene cluster with 2 P450s and a O-methyltransferase. Visualized across assemblies for 4 cultivars.

GitHub: github.com/cxli233/Tidy...

Our review on k-mers + pop gen is now published!

doi.org/10.1093/molb...

Friends, LiftOn is now published in @genomeresearch.bsky.social! LiftOn maps genes across genomes using a protein-centric, homology-based approach with both DNA & protein alignments
@stevensalzberg.bsky.social Mihaela Pertea, Jakob Heinz, Alaina Shumate, Celine Hoh, Alan Mao
doi.org/10.1101/gr.2...

From literature to biodiversity data: mining arthropod organismal and ecological traits with machine learning The fields of taxonomy and biodiversity research have witnessed an exponential growth in published literature. This vast corpus of articles holds information on the diverse biological traits of organi...

Resulting from an @snsf-ch.bsky.social SPARK grant this took some time to mature, but the outcome is very imformative and builds a foundation for where to head next - how to liberate facts/information locked in the published literature www.biorxiv.org/content/10.1... #textmining #biodiversity

Bitte am Sonntag wählen gehen! Noch nie war eine Wahl so wichtig für Deutschlands Zukunft.
#Btw2025

The Idiot's Guide to Effective Population Size This is a reference manual for the elegant, yet hideously complex concept of effective population size (Ne), inspired by a classic, self-published manual of automotive repair ‘for the compleat idiot’...

Wow. This is sooo good. Echoing @urbanevol.bsky.social this user’s manual for Ne should be required reading for popgen and conservation genetics folks. onlinelibrary.wiley.com/doi/10.1111/...

With @katiejenike.bsky.social and a bunch more of our fellow k-mer enthusiasts, we put together a manuscript on k-mers in biodiversity genomics. A guide if you will, that covers k-mers from basics to some really funky stuff...

genome.cshlp.org/content/35/2...

A century of theories of balancing selection Traits that affect organismal fitness are often very genetically variable. This genetic variation is vital for populations to adapt to their environments, but it is also surprising given that nature (...

Finally ready to see the world! Theories of balancing selection - past, present and future: www.biorxiv.org/content/10.1... A true collaborative effort that brought together theoreticians and empiricists, models, data, and fresh perspectives on how balancing selection can shape genetic variation.

Olá, Brasil! 🇧🇷 Interested in a research stay in Germany? Are you currently a postdoc at a uni or research institution in Brazil? Our CAPES #Fellowship offers you funding for a #research stay for 6-24 mth! Join our info event on 18 Feb! www.humboldt-foundation.de/en/connect/i...

Principled PCA separates signal from noise in omics count data www.biorxiv.org/content/10....

ggalign: Bridging the Grammar of Graphics and Biological Multilayered Complexity 🧬🖥️🧪
Paper: https://www.biorxiv.org/content/10.1101/2025.02.06.636847v1
#Rstats Code: https://github.com/Yunuuuu/ggalign
Docs: https://yunuuuu.github.io/ggalign/
Book (Quarto): https://yunuuuu.github.io/ggalign-book/

Estimating recombination using only the allele frequency spectrum Standard methods for estimating the population recombination parameter, rho, are dependent on sampling individual genotypes and calculating various types of disequilibria. However, recent machine lear...

New paper with Sarthak Mishra! Maybe it will bring you some joy given all this (waves arms around).

"Estimating recombination using only the allele frequency spectrum"

1/2

www.biorxiv.org/content/10.1...

What is a differentially expressed gene? The concept of 'Differentially Expressed Genes' (DEGs) is central to RNA-Seq studies, yet their identification suffers from reproducibility issues. This is largely a consequence of the inherent…

What is a differentially expressed gene? https://www.biorxiv.org/content/10.1101/2025.01.31.635902v1 🧬🖥️🧪 https://github.com/Morris-Research-Group/bayexpress