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Hannah Kim @hannahkimincompbio.bsky.social · 25/09/2026

MBE is an open-access journal, so check out the paper for all the details! ✔️article: academic.oup.com/mbe/article/... ✔️web application: v3.datamonkey.org ✔️cli: github.com/veg/hyphy (also see article Supplementary Notes p.18) 9/9

academic.oup.com

The physicochemical basis of protein evolution: property-informed evolutionary models (PRIME)

Abstract. Standard probabilistic models of coding sequence evolution effectively identify where and when selection acts but remain agnostic to the mechanis

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Hannah Kim @hannahkimincompbio.bsky.social · 25/09/2026

📋 We tested PRIME on simulated datasets to understand how much substitutional information is needed for the framework to be effective. We then evaluated PRIME on benchmark datasets and mammalian genomic data and examined how it improves upon existing methods. 8/9

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Hannah Kim @hannahkimincompbio.bsky.social · 25/09/2026

Because the very existence--therefore survival--of input DNA/RNA sequences suggests that physicochemical properties (e.g., amino acid hydrophobicity and volume) are constraints to changes, we were able to estimate their effects. 7/9

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Hannah Kim @hannahkimincompbio.bsky.social · 25/09/2026

Imagine a blob of protein sequence folded and floating in water. For the protein to have a function, it should interact with other molecules in the environment. Mutations happen at random, and some translate to proteins that are improperly folded or interacting differently with its environment. 6/9

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Hannah Kim @hannahkimincompbio.bsky.social · 25/09/2026

📨 Using maximum likelihood estimation methods and rigorous statistical tests, we identify signals that indicate how a property noticeably took part in a change or conservation of an amino acid at a particular site of the input sequences. 5/9

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Hannah Kim @hannahkimincompbio.bsky.social · 25/09/2026

In other words, PRIME 📨 takes multiple aligned DNA/RNA sequences and their evolutionary tree as inputs 📥, and returns the degree to which a chemical property influenced natural selection at the highest resolution of protein synthesis (codon) as outputs 📤. 4/9

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Hannah Kim @hannahkimincompbio.bsky.social · 25/09/2026

At the intersection of evolutionary biology and chemistry, PRIME aims to resolve the biophysical basis of selective constraint across both the sequence and the phylogeny. 3/9

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Hannah Kim @hannahkimincompbio.bsky.social · 25/09/2026

🧬 DNA/RNA sequences keep the record of changes that biological entities go through, and yet ⚗️ chemical properties that dictate the behavior of matters are rarely used to explain ❓ _how_ these changes were shaped. 2/9

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Hannah Kim @hannahkimincompbio.bsky.social · 25/09/2026

We are delighted to share that our paper, "The physicochemical basis of protein evolution: property-informed evolutionary models (PRIME)", has been published in Molecular Biology and Evolution! 🧵 1/9

MBE journal front page with the title, "The physicochemical basis of protein evolution: property-informed evolutionary models (PRIME)". It was authored by Hannah Kim, Konrad Scheffler, Anton Nekrutenko, Darren P. Martin, Steven Weaver, Ben Murrell, and Sergei L. Kosakovsky Pond.

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Hannah Kim @hannahkimincompbio.bsky.social · 30/07/2026

"I do not know, but I will try." - Betsy Ross when asked to sew the first American flag

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Reposted by Hannah Kim

Spyros Lytras @spyroslytras.bsky.social · 23/07/2026

Come work on exciting AI for biology projects in Paris!! 🇫🇷 Details and application below, deadline sept 1st!

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Hannah Kim @hannahkimincompbio.bsky.social · 23/07/2026

Google scholar pdf reader chrome extension has been working well for me whenever I wanted to check the source.

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Hannah Kim @hannahkimincompbio.bsky.social · 26/04/2026

Thank you for the useful tips, as always. Just to add my 2-cent, if people are looking for simple image editing tools, free tier of figma and/or canva may do wonders. I personally found some of the figma community's plugins and widgets to be lifesavers.

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Hannah Kim @hannahkimincompbio.bsky.social · 21/01/2026

They should get surnames! Mantis of Spatial Metabolomics and Mantis of Search Sequence Indexing.

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Reposted by Hannah Kim

Michael Hoffman @michaelhoffman.bsky.social · 10/01/2026

What genetic change to Indian wheat led to superior baking in a tandoor? A naan sense mutation

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Hannah Kim @hannahkimincompbio.bsky.social · 09/01/2026

Personally, 1. People sometimes use Bak or Pak instead of Park to write their surnames in English to be in line with the original pronunciation.

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Hannah Kim @hannahkimincompbio.bsky.social · 24/12/2025

I am glad that things worked out well for you. Happy Holidays!

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Reposted by Hannah Kim

Cindy Fuller-Zastudil @czastudil.bsky.social · 27/10/2025

I’m at #ASSETS2025 in Denver to present our paper on the impacts of using generative AI to scaffold just-in-time (JIT) configuration of visual scene displays (VSDs) by novice communication partners! You can catch my presentation in Session 5B on Tuesday at 11:15 MDT. Here are some highlights👇

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Reposted by Hannah Kim

Claus Wilke @clauswilke.com · 02/10/2025

Some thoughts about the research-plan component of the NSF GRFP application. blog.genesmindsmachines.com/p/how-to-wri...

blog.genesmindsmachines.com

How to write an NSF GRFP research plan

This is my second post about the NSF GRFP.

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