Matthew O'Meara

graphical abstract. Left is a fungal cell surrounded by bacteria, and the Hog1 cascade is turned on. Right is a fungal cell covered in mannan fibrils that prevent IgA and caspofungin and increase CLR recognition by macrophages

Candida albicans is usually hanging out with bacterial neighbors, so what happens to the fungus during co-culture?
The bacteria secrete metabolites that induce massive cell wall remodeling that change immune recognition and drug resistance. Read more in our new paper: www.cell.com/current-biol...

YouTube video by Alice Ting Alice Ting Rosettacon keynote 2025

Video introduction to our new “Conformational Biasing” method for computational design of mutations that bias proteins towards desired conformational states

CB part starts at 14:55

Thanks to Peter Cavanagh and Andrew Xue – amazing graduate students who co-led this work

Large-scale collaborative assessment of binding free energy calculations for drug discovery using OpenFE Accurately measuring compound binding affinities is key to driving the pharmaceutical development process. Rigorous physics-based in silico approaches, particularly alchemical free energy methods, hav...

OpenFE is ready for production! chemrxiv.org/engage/chemr...

In collaboration with our industry partners, we ran benchmarking simulations of our hybrid-topology RBFE protocol on a large collection of both public and private protein-ligand binding datasets.

#compchem

Here’s why ‘Neighborhood Crime Watch’ signs in Ann Arbor are going away There are hundreds of them throughout Ann Arbor and they've been around since the 1970s.

@jeneyer.bsky.social and Cynthia Harrison (www.votecynthiaharrison.com) have put forward a resolution to codify the removal of the signs and put a timeline on the work!

My team has roles available for scientific developers either as Technical Lead (more senior) or as part of the development of a Side Effect Resource.

baoilleach.blogspot.com/2025/12/open...

#chemsky #chemjobs #bionformatics #cheminformatics #datascience #techlead

Thank you, @maom.bsky.social, for surfacing the issue and to Chief Anderson for acting so quickly. We are an inclusive community that is committed to safety practices rooted in trust rather than suspicion. These signs communicate the opposite and it’s long past time for them to go. #a2council

Find a Watch Program | National Neighborhood Watch

Taking apart the racist "Tough on Crime" Neighborhood Watch program is far from over--going to the National Neighborhood Watch Find a Watch Program (nnw.org/find-a-watch...) still lists over 2400 program nationwide, and surely many of them similarly have signs that should be removed.

Ann Arbor City Council | Vote Jen Eyer for Ann Arbor City Council Jen Eyer is a longtime 4th Ward resident, small business owner, community volunteer and mother of two. She is running to lead Ann Arbor to a better future — a future that lives up to our community’s p...

Many thanks to Jen Eyer and her staff (www.votejeneyer.com), the Ann Arbor transportation office and the Ann Arbor police for making this happen! This is long overdue. I was shocked that all it took to make change was to ask. Participatory governance for the win.

Yesterday, Jen Eyer wrote, "Transportation Manager Malisa McCreedy has directed the Signs and Signals team to begin scheduling their removal. There are more than 600 signs citywide, so the work will take some time, but they are now officially in the queue and will be removed over the coming months."

Remarkably, a week later, I got an email from the Ann Arbor chief of police, Andre Anderson, who recognizing my concern about removing the signs. He said that it was "being looked into immediately".

Fast-forward to three weeks ago, at a fund-raiser for Christina Hines (@cbhines586.bsky.social), who is running for Michigan's 10th District. There, I met Jen Eyer, our city council representative, and I brought up removing the Neighborhood Watch signs. She said, "Email me", which I did.

Susan Casey at the AA Police department was receptive to the idea of removing the signs, but said the biggest hurdle was the cost. She transferred me to the transportation department, and they said they would look into, but never got back to me.

I reached out to the Ann Arbor police department to learn more about the Neighborhood Watch and community policing. I spoke with Susan Casey, and she said that while there are still "block captains", the program was largely inactive.

Find a Watch Program | National Neighborhood Watch

Going to the "Find a Watch Program" on the National Neighborhood Watch website (nnw.org/find-a-watch...), the Ann Arbor "Crime Prevention Specialist" listed retired in 2016. Also, the Ann Arbor Neighborhood Watch "Weekly crime bulletin" hotline 734-994-8775 plays a recording from 2010!

I think the Neighborhood Watch signs should be removed, as they don't represent our values of inclusion. So, I first wanted to know if the program was still active--was it just the signs or did we need to take apart the program too?

A good scholarly article critical of the Neighborhood Watch program is "Neighborhood Watch: Invading the Community, Evading Constitutional Limits" authored by (Johnson, et al., 2016, scholarship.law.upenn.edu/jlasc/vol18/...).

In 2020, I started to run every street in Ann Arbor and noticed the Neighborhood Watch signs around town. I was curious and learned that they came out of the 1994 Crime Bill effort for "community policing", and are part of a deeply racist tradition that aims to exclude people that "don't belong".

💡Just presented our new paper at the @iccv.bsky.social BioImage Computing workshop: cubic: CUDA-accelerated 3D Bioimage Computing. We introduce a simple way to add GPU acceleration to scikit-image–based bioimage processing pipelines by swapping import statements. 🧵
1/6 #iccv2025

Predicting the structural impact of human alternative splicing. #AlternativeSplicing #GenomeBiology
genomebiology.biomedcentral.com/articles/10....

Evaluation of De Novo Deep Learning Models on the Protein-Sugar Interactome https://www.biorxiv.org/content/10.1101/2025.09.02.673778v1

Roche is hiring a small-molecule computer-aided drug design researcher in Basel, Switzerland. Go for it! #rdkit #compchem #chemsky www.linkedin.com/jobs/view/42...

@bmoore-beth.bsky.social We are delighted to announce that Dr. Teresa O'Meara ‪was awarded the Henry Russel award at U-M. Our highest honor for an early-mid career faculty member for her outstanding research and teaching! @teresaomeara.bsky.social ‬ @umichmicroimmuno.bsky.social

Deep homology and design of proteasome chaperone proteins in Candida auris A central tenet of biology is that protein structure mediates the sequence-function relationship. Recently, there has been excitement about the promise of advances in protein structure modeling to gen...

I'm so excited to share a new preprint on exploring sequence, structure, and function relationships and how we can use evolutionary information to help us design new proteins that work in the native context of a cell
www.biorxiv.org/content/10.1...

BREAKING: Harvard AAUP & the nat'l AAUP have jointly filed a lawsuit & TRO to block the Trump admin from demanding that Harvard restrict speech & undermine academic freedom or else lose $8.7 billion in federal funds. This action challenges the Trump admin's misuse of funds for coercion. Stay tuned.

Large crowd of peaceful protesters

Hands off protest in Canton MI

Inch worm!

For those curious about the impact of the 15% IDC rate, here's data on total NIH funding by institution: brimr.org/brimr-rankin... ... and here's a brief synopsis of hardest-hit: www.forbes.com/sites/michae...

The NIH’s drastic cut to indirect cost rates is a critical threat to U.S. research infrastructure The drastic reduction in indirect costs is not a path to innovation or cost savings — it’s a threat to U.S.’s position as global leader in medical research.

My #Yale colleague Harlan Krumholz explains why the cuts to indirect costs are a disaster for biomedical research in the United States. Want to do something about it? I'll list those who have to hear from us below. Share, recruit friends and family to help. 1/ www.statnews.com/2025/02/08/n....

NIH In Your State - United For Medical Research Select a state on the map to see the impact of NIH funding across America.

I just reached out to my senators about the NIH situation. If you need to find out how much impact NIH has in your state in terms of dollars in and their economic impact here's a link: www.unitedformedicalresearch.org/nih-in-your-...