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Matthew O'Meara

@maom.bsky.social
1.4K followers 1.9K following 23 posts

Assistant Professor at UMich with a focus on computational pharmacology (he/him)

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Reposted by Matthew O'Meara
Stephan Hacker @stephanhacker2.bsky.social · 22/08/2026
What is the function of diverse protein isoforms in human cells? An interesting bioRxiv preprint by the group of Abdullah Kahraman with first author @jakobsteuer.bsky.social addresses this question on a proteome-wide scale. www.biorxiv.org/content/10.6... (1/3) #Isoforms #DrugDiscovery #Alphafold
biorxiv.org
SPLISOFORMS: a Structure-Resolved Knowledge Base of Alternative Splicing Isoforms
Background Alternative splicing expands the coding capacity of single genes into diverse protein families, and its dysregulation is a recognized hallmark of cancer. Despite this, the characterization ...
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Reposted by Matthew O'Meara
Alex Guseman @alexguseman.bsky.social · 21/08/2026
Come be my colleague! We are hiring a structural biologist. I have thoroughly enjoyed starting my career here and both department(s) are full of exceptional scientists. apol-recruit.ucsd.edu/JPF04589
apol-recruit.ucsd.edu
Assistant Professor in Structural Biochemistry
University of California, San Diego is hiring. Apply now!
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MDRepo @mdrepo.bsky.social · 17/08/2026
mdrepo.org now has its own account (that's me!) Follow the account for updates on content and functionality.
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Reposted by Matthew O'Meara
Teresa O'Meara @teresaomeara.bsky.social · 14/08/2026
Hey #a2council Why do I have to push the button to get a pedestrian cross light? Why isn’t it automatic?
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Ruth Huttenhain @rhuttenhain.bsky.social · 13/08/2026
My lab at Stanford University School of Medicine is recruiting! We are looking for a postdoc at the interface of quantitative proteomics, structural biology and G protein-coupled receptor (GPCR) biology: postdocs.stanford.edu/prospective/...
postdocs.stanford.edu
Open Postdoctoral position, faculty mentor Ruth Huttenhain | Office of Postdoctoral Affairs
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Reposted by Matthew O'Meara
Alex Guseman @alexguseman.bsky.social · 11/08/2026
Im looking for a postdoc to help with protein engineering efforts. If you know who could be a good fit send them my way! see details below:
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Martin Pacesa @martinpacesa.bsky.social · 04/08/2026
We are looking for a lab manager starting from January 2027, you can find more information on our members page pacesalab.com#members. We are also starting to look into hosting master students starting 2027.
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ebospacr.bsky.social @ebospacr.bsky.social · 09/07/2026
How do intracellular parasites remodel host cells? We developed spaCR to connect parasite genes with spatial phenotypes by pooled imaging-based CRISPR screening, and used it to identify EAF1 as a Toxoplasma gondii effector involved in host ESCRT subversion. www.biorxiv.org/content/10.6...
biorxiv.org
A pooled image-based CRISPR screen identifies EAF1 as a T. gondii modulator of ESCRT subversion.
Intracellular pathogens remodel host cells by redirecting cellular machinery to the host-pathogen interface. The protozoan parasite Toxoplasma gondii co-opts host ESCRT proteins at the parasitophorous...
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Reposted by Matthew O'Meara
Nick Polizzi @nickpolizzi.bsky.social · 26/06/2026
Our lab's paper on the de novo design of small-molecule binding proteins is out! In it, we show how neural nets can be trained and used to design binders to drugs with very high success rates. www.nature.com/articles/s41...
nature.com
Zero-shot design of drug-binding proteins via neural iterative selection−expansion - Nature
 By pairing two neural networks in an iterative optimization algorithm, small-molecule binding proteins can be designed from scratch with high accuracy, affinity and success rates, showing p...
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Reposted by Matthew O'Meara
Teresa O'Meara @teresaomeara.bsky.social · 23/05/2026
Our paper on examining sequence-structure-function relationships and constraints on protein evolution is now published! www.nature.com/articles/s41...
nature.com
Deep homology and design of proteasome chaperone proteins in Candidozyma auris - Nature Communications
Protein structure modeling can generate hypotheses about sequence-structure-function relationships. Here, the authors used modern computational methods and experimental characterization to explore the...
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Reposted by Matthew O'Meara
Teresa O'Meara @teresaomeara.bsky.social · 14/05/2026
New preprint alert! www.biorxiv.org/content/10.6... from my lab and Evan Snitkin's lab Defining the Candidozyma auris pan-genome and essentiality
biorxiv.org
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Lauren Surface @lsurface.bsky.social · 24/03/2026
Come join us at University of Michigan! The School of Dentistry is inviting applications for a tenure-track faculty position at the Assistant Professor level (dual PhD and clinical dental degree required). Any area of biomedical research welcome! Please share widely! apply.interfolio.com/183598
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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Reposted by Matthew O'Meara
Marion Perrier @marionperrier.bsky.social · 10/03/2026
My research exchange at the University of Michigan in Ann Arbor is coming to an end! This stay was possible thanks to the scientist exchange funds grant of @microverse.bsky.social. Here is a thread🧵of thankfulness for my wonderful stay in Michigan!
A selfie of a woman with a green beanie smiling in front of a building. There is written on top of it "Medical Science Building" in capital letters. Sunset over a street with very warm orange and pink colors. There is a blue mailbox in front.A small park surrounded by buildings, with lights all around it. In the center there is a pole with a large US flag waving in the wind.8 people smiling in a bowling alley. 2 of them are holding a bowling ball in their hands.
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Teresa O'Meara @teresaomeara.bsky.social · 20/01/2026
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...
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
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Alice Ting @aliceyting.bsky.social · 08/01/2026
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
youtube.com
Alice Ting Rosettacon keynote 2025
YouTube video by Alice Ting
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Open Free Energy @openfree.energy · 18/12/2025
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
chemrxiv.org
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...
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Matthew O'Meara @maom.bsky.social · 16/12/2025
@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!
mlive.com
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.
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Noel O'Boyle @baoilleach.bsky.social · 15/12/2025
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
baoilleach.blogspot.com
Openings for Scientific Developers in the Chemical Biology Services team
As part of a collaboration with Open Targets on the development of a Side Effect Resource to guide target selection, we have two positions a...
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jeneyer.bsky.social @jeneyer.bsky.social · 10/12/2025
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
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Matthew O'Meara @maom.bsky.social · 10/12/2025
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.
nnw.org
Find a Watch Program | National Neighborhood Watch
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Matthew O'Meara @maom.bsky.social · 10/12/2025
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.
votejeneyer.com
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...
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Matthew O'Meara @maom.bsky.social · 10/12/2025
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."
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Matthew O'Meara @maom.bsky.social · 10/12/2025
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".
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Matthew O'Meara @maom.bsky.social · 10/12/2025
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.
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Matthew O'Meara @maom.bsky.social · 10/12/2025
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.
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Matthew O'Meara @maom.bsky.social · 10/12/2025
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.
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Matthew O'Meara @maom.bsky.social · 10/12/2025
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!
nnw.org
Find a Watch Program | National Neighborhood Watch
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Matthew O'Meara @maom.bsky.social · 10/12/2025
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?
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Matthew O'Meara @maom.bsky.social · 10/12/2025
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/...).
scholarship.law.upenn.edu
Neighborhood Watch: Invading the Community, Evading Constitutional Limits
By Adeoye Johnson, Published on 01/01/16
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Matthew O'Meara @maom.bsky.social · 10/12/2025
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".
scholarship.law.upenn.edu
Neighborhood Watch: Invading the Community, Evading Constitutional Limits
By Adeoye Johnson, Published on 01/01/16
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Alex Kalinin @alxndrkalinin.bsky.social · 23/10/2025
💡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
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Javier Santoyo @jsantoyo.bsky.social · 24/09/2025
Predicting the structural impact of human alternative splicing. #AlternativeSplicing #GenomeBiology genomebiology.biomedcentral.com/articles/10....
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 07/09/2025
Evaluation of De Novo Deep Learning Models on the Protein-Sugar Interactome www.biorxiv.org/content/10.1101/202…
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Jimmy 🇩🇰 🇨🇭 @jimmykromann.bsky.social · 05/07/2025
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...
linkedin.com
Roche hiring Scientist in Small Molecule Computer-Aided Drug Design (CADD) in Basel, Basel, Switzerland | LinkedIn
Posted 12:44:22 PM. At Roche you can show up as yourself, embraced for the unique qualities you bring. Our culture…See this and similar jobs on LinkedIn.
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Teresa O'Meara @teresaomeara.bsky.social · 16/05/2025
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...
biorxiv.org
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...
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AAUP @aaup.org · 12/04/2025
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.
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Matthew O'Meara @maom.bsky.social · 05/04/2025
Hands off protest in Canton MI
Large crowd of peaceful protesters
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Matthew O'Meara @maom.bsky.social · 05/03/2025
Inch worm!
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Roy Perlis, MD @royperlis.bsky.social · 08/02/2025
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...
brimr.org
BRIMR Rankings of NIH Funding in 2023 | BRIMR
The Blue Ridge Institute for Medical Research publishes rankings of institutions, departments, and investigators based on the funding they receive from the NIH.
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Gregg Gonsalves @gregggonsalves.bsky.social · 09/02/2025
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....
statnews.com
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.
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Zoe McElligott @nanopharmnc.bsky.social · 22/01/2025
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-...
unitedformedicalresearch.org
NIH In Your State - United For Medical Research
Select a state on the map to see the impact of NIH funding across America.
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Gregg Gonsalves @gregggonsalves.bsky.social · 13/01/2025
@defendpublichealth.bsky.social, a new national coalition of more than 1500 public health experts, has led an effort to send >3500 letters to US Senators to oppose RFK Jr.’s nomination to HHS. Concerns include his unfounded beliefs about vaccines, raw milk and HIV. 1/ docs.google.com/document/d/1...
docs.google.com
DPH Press Release.docx
FOR IMMEDIATE RELEASE January 13, 2025 Healthcare, Public Health, and Scientific Experts Call on the Senate to Reject RFK Jr. Nomination to Lead HHS CONTACT: Julie Scofield, 301-455-2558, jscofie...
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Jeffrey J. Gray @jeffreyjgray.bsky.social · 18/12/2023
Prepping for class this spring, this playlist of videos on diffusion models for proteins are great! Series is led by @maom.bsky.social and Nick Randolph of UNC. www.youtube.com/playlist?lis...
youtube.com
Molecular ML Reading Group
The Molecular ML Reading Group aims to explore foundational and recent applications of machine learning models to modeling molecular system.
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Reposted by Matthew O'Meara
Jeffrey J. Gray @jeffreyjgray.bsky.social · 14/12/2023
Hey #NeurIPS2023 folks - interested in protein design / computational biology? Check out Rosetta Commons labs. We have undergrad summer internships, post-baccalaureate gap-year positions, and PhD programs and postdocs at universities around the globe. www.rosettacommons.org/about
rosettacommons.org
About | RosettaCommons
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Matthew O'Meara @maom.bsky.social · 06/12/2023
^ Starting in 30 minutes!
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Matthew O'Meara @maom.bsky.social · 04/12/2023
The Rosetta Commons Molecular ML Reading Group is hosting Yeqing Lin from Mohammed AlQuraishi's lab to present Genie, a diffusion model for protein structure. GENIE:  doi.org/10.48550/arX... Join us! Wed. 12/6 at 11am EST Website and zoom link: maomlab.github.io/mol_ml_readi...
doi.org
Generating Novel, Designable, and Diverse Protein Structures by...
Proteins power a vast array of functional processes in living cells. The capability to create new proteins with designed structures and functions would thus enable the engineering of cellular...
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Matthew O'Meara @maom.bsky.social · 21/11/2023
Yes, we'll put it up on our youtube channel: www.youtube.com/@maomlab
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Matthew O'Meara @maom.bsky.social · 21/11/2023
At our Rosetta Commons Molecular ML Reading group Patrick Bryant (patrickbryant1.github.io) will present Umol, a method to predict protein ligand complexes from sequence and SMILES. Umol: doi.org/10.1101/2023... Tomorrow Wed. 11/22 11am EST Website and zoom link: maomlab.github.io/mol_ml_readi...
maomlab.github.io
Molecular ML Reading Group
Molecular ML Reading Group
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