Matthew O'Meara
@maom.bsky.social
📤 1247
📥 1796
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Assistant Professor at UMich with a focus on computational pharmacology (he/him)
reposted by
Matthew O'Meara
Alex Kalinin
23 days ago
💡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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reposted by
Matthew O'Meara
Javier Santoyo
about 2 months ago
Predicting the structural impact of human alternative splicing.
#AlternativeSplicing
#GenomeBiology
genomebiology.biomedcentral.com/articles/10....
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reposted by
Matthew O'Meara
bioRxiv Biophysics
2 months ago
Evaluation of De Novo Deep Learning Models on the Protein-Sugar Interactome
https://www.biorxiv.org/content/10.1101/2025.09.02.673778v1
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reposted by
Matthew O'Meara
Jimmy 🇩🇰 🇨🇭
4 months ago
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...
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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.
https://www.linkedin.com/jobs/view/4260858154
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reposted by
Matthew O'Meara
U. Mich Micro-Immuno Dept
5 months ago
@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
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reposted by
Matthew O'Meara
Teresa O'Meara
6 months ago
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...
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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...
https://www.biorxiv.org/content/10.1101/2025.05.14.654010v1
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reposted by
Matthew O'Meara
AAUP
7 months ago
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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Hands off protest in Canton MI
7 months ago
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reposted by
Matthew O'Meara
Roy Perlis, MD
9 months ago
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...
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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.
https://brimr.org/brimr-rankings-of-nih-funding-in-2023/
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reposted by
Matthew O'Meara
Gregg Gonsalves
9 months ago
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...
.
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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.
https://www.statnews.com/2025/02/08/nih-indirect-research-cost-rate-cuts-universities-threat/#:~:text=Indirect%20costs%20cover%20expenses%20like,function%20at%20their%20full%20capacity
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reposted by
Matthew O'Meara
Zoe McElligott
10 months ago
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-...
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NIH In Your State - United For Medical Research
Select a state on the map to see the impact of NIH funding across America.
https://www.unitedformedicalresearch.org/nih-in-your-state/
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reposted by
Matthew O'Meara
Gregg Gonsalves
10 months ago
@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...
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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...
https://docs.google.com/document/d/1DV6hRITXNLYGhHwEyVqqMiZgj9EncjZS/edit?usp=sharing&ouid=115135685989254406499&rtpof=true&sd=true
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reposted by
Matthew O'Meara
Jeffrey J. Gray
almost 2 years ago
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...
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Molecular ML Reading Group
The Molecular ML Reading Group aims to explore foundational and recent applications of machine learning models to modeling molecular system.
https://www.youtube.com/playlist?list=PLiCkhHjoTvgASb7smvU4KFxXuV2ZgON6-
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reposted by
Matthew O'Meara
Jeffrey J. Gray
almost 2 years ago
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
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About | RosettaCommons
https://www.rosettacommons.org/about
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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...
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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...
https://doi.org/10.48550/arXiv.2301.12485
almost 2 years ago
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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...
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Molecular ML Reading Group
Molecular ML Reading Group
https://maomlab.github.io/mol_ml_reading_group/
almost 2 years ago
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The Rosetta Commons Molecular ML Reading group is hosting Joey Bose to present FoldFlow, a flow-matching model for protein backbone generation. Join us! When: Wed. 11/8 11am EST:
zoom.us/j/9932387699...
FoldFlow:
arxiv.org/abs/2310.02391
Website:
maomlab.github.io/mol_ml_readi...
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SE(3)-Stochastic Flow Matching for Protein Backbone Generation
The computational design of novel protein structures has the potential to impact numerous scientific disciplines greatly. Toward this goal, we introduce $\text{FoldFlow}$ a series of novel...
https://arxiv.org/abs/2310.02391
about 2 years ago
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Fred Dietrich's sac genome update is artisanal bioinformatics 😙👌 "It is the opinion of the authors that it is time to raise the bar and that published evidence that a gene is real should be necessary to keep questionable open reading frames from being relegated to dubious."
doi.org/10.1101/2023...
about 2 years ago
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