@hverdonk.bsky.social, Callan & @sergeilkp.bsky.social present CAPHEINE, a computational workflow that starts with a set of unaligned pathogen sequences and a reference genome and performs a comprehensive exploratory evolutionary analysis. 🔗 doi.org/10.1093/gbe/evag173 #societyjournal #compbio

CAPHEINE, or Everything and the Kitchen Sink: A Workflow for Automating Selection Analyses Using HyPhy

Abstract. Here, we present CAPHEINE, a computational workflow that starts with a set of unaligned pathogen sequences and a reference genome and performs a

doi.org

@sergeilkp.bsky.social @hverdonk.bsky.social et al. present B-STILL, a hierarchical Bayesian framework designed to resolve the selective landscape of protein-coding genes near the zero-rate limit. 🔗 doi.org/10.1093/gbe/evag184 #societyjournal #compbio

Beyond Invariable Sites: Using Evolutionary Stasis to Map Multilayered Constraints on the Evolution of Viral and Mammalian Genomes

Abstract. The quantification of genomic conservation has progressed from foundational statistical modeling of evolutionary rates to state-of-the-art deep l

doi.org

I built a neural cell type classifier in under an hour using AI. The goal wasn’t speed alone — it was to test how models implement workflows from a detailed prompt, the assumptions they make, and what gets lost. Here’s what effective AI-assisted development actually looks like:

Just now catching my breath after a fantastic #SMBE2025 a few weeks back. I’m deeply grateful to the local organizers and to @official-smbe.bsky.social for the Graduate Student Excellence Award and for the chance to share my work. It was an honor to present among such brilliant researchers.

Thank you very much! It was a great conference.

Avery Davis Bell@averydb.bsky.social · last yr.

Cc @hverdonk.bsky.social Great talk, great work!

So many great talks from all the students in @lablabella.bsky.social! Let's keep in touch!

LaBella Lab@lablabella.bsky.social · last yr.

First up from the lab is Stevie Clemens! His work is aimed at disentangling the relationship between selection on Codon Usage Bias and growth rate in the yeasts #Evol25 #Evol2025

Really enjoyed your talk @averydb.bsky.social! I'd never considered that frequent transcription of tRNA genes would drive up the local mutation rate, but it makes sense in hindsight.

LaBella Lab@lablabella.bsky.social · last yr.

Wild worm 🪱 tRNA with @averydb.bsky.social How do tRNAs evolve? Caenorhanditis species can help us answer this question. #evol25 #evol2025

@hverdonk.bsky.social et al. expand on multiclass synonymous substitution (MSS) models, revealing widespread selection on synonymous codon usage across ~12K Drosophila genes. 🔗 doi.org/10.1093/molb... #evobio #molbio #selection

A New Comparative Framework for Estimating Selection on Synonymous Substitutions

Abstract. Selection on synonymous codon usage is a well-known and widespread phenomenon, yet existing models often do not account for it or its effect on s

doi.org

I'm honored to receive the Graduate Student Excellence Award and excited to present my research in Beijing this summer!

Society for Molecular Biology and Evolution@official-smbe.bsky.social · last yr.

👋 For the next two weeks, we will highlight our GSEA recipients - we start with Hannah Verdonk, Bioinformatics PhD student at @temple.edu Hannah works on improving bioinformatic tools to account for weak selection on synonymous codon usage. 💻 More on Hannah ⬇️ and follow her: @hverdonk.bsky.social