HyPhy

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

Glad to see Alex Lucaci sharing work built with HyPhy at EEBG 2025. Always great to see the tools in use by folks who know them inside and out.

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

I'm so grateful to be speaking alongside so many other talented graduate students! Looking forward to sharing ideas and connecting at SMBE - hope to see you there!

Congrats Dr. @averyselberg! Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors elifesciences.org/reviewed-prepr…

Even more coauthors for this great paper! Carole C. Baldwin, Guillermo Ortí, Lily C. Hughes, Sergei L. Kosakovsky Pond, @R_BetancurR and @arciladk Congrats all!! 👏👏

1/8 Excited to share our new paper in Science Advances! We investigated the evolution of endothermy in ray-finned fishes by integrating phylogenomics, ecomorphology, fossil occurrence, and comparative genomics across 205 marine vertebrates. 👉 science.org/doi/10.1126/sc…

Recent work Ecological interactions and genomic innovation fueled the evolution of ray-finned fish endothermy science.org/doi/full/10.11…

RNA Viromes of subways and other urban biomes by Alexander Lucaci! #RdRpSummit2025

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

1/ Genome-wide (and other) positive selection screens in genomes may be severely biased by alignment and other errors. biorxiv.org/content/10.110… we (@averyselberg, @NathanClark111, @ChikinaLab, @nekrut, @stvnwvr, @aglucaci, @timsackton) propose a simple fix.

Watch @hannahverdonk's talk entitled "MSS: A codon model with Multiple classes of Synonymous Substitutions" at #Evol2024. She highlights the impact of using independent pairs of synonymous substitution rates on diverse datasets. youtu.be/X1ZQIXi9vAY?si…

Watch @aglucaci's presentation on "Quantifying natural selection in coding sequences" given last week at the @metasub 2024 conference in Tokyo! He features application and technical description of the BUSTED and aBSREL methods. youtube.com/live/jcA_lwcGb…

Excited to have been selected to receive the @NIH_LRP from @theNCI. Thank you for all the support and mentorship from @LabMelnick @mason_lab @sergeilkp

Last week at #SMBE2024, grad student @hannahverdonk presented her work on the Multiclass Synonymous Substitution (MSS) model implemented in HyPhy! Her poster detailed how MSS estimates relative rates for synonymous codons to explore selection on codon usage. Fantastic, Hannah!