Dr. Armita Nourmohammad

437 posts

Dr. Armita Nourmohammad

Dr. Armita Nourmohammad

@TheArmita

physicist, interested in biology --- Assoc. Prof. of physics @UW (Seattle)

Beigetreten Temmuz 2016
409 Folgt873 Follower
Dr. Armita Nourmohammad
Dr. Armita Nourmohammad@TheArmita·
check out our new manuscript (led by @GMarcoVisani) structure-based machine learning model for TCR-pMHC complexes, predicting T-cell affinity to peptide-MHC complexes, quantifying T-cell receptor specificity, and designing de-novo immunogenic peptides: arxiv.org/abs/2503.00648
Dr. Armita Nourmohammad tweet media
English
5
18
80
6.5K
Dr. Armita Nourmohammad retweetet
Giulio Isacchini
Giulio Isacchini@giulioisacchini·
Curious about generative modeling for T and B cell receptor repertoires and its role in understanding immune system diversity? Watch my talk here youtu.be/HVUYG-UmRH8?t=…. Thanks to the @airr_community and @victorgreiff for the opportunity to share our work!
YouTube video
YouTube
English
1
4
18
1.3K
Dr. Armita Nourmohammad retweetet
Oskar Hallatschek
Oskar Hallatschek@ohallats·
🚨 Job Alert! 🚨 Join the UC Berkeley Physics Department! We’re hiring an Assistant Professor in soft condensed matter (broadly defined). Both experimentalists and theorists are encouraged to apply! aprecruit.berkeley.edu/JPF04653
English
1
16
32
10.8K
Dr. Armita Nourmohammad retweetet
Manu Setty
Manu Setty@SettyM·
Are you an early career scientist who wants to pursue a research project in the lab of a Fred Hutch Computational Biologist mentor? If yes, then the #MahanFellowship is for you. Apply by Dec. 20, 2024! Learn more: apply.interfolio.com/157470
English
1
7
8
2.4K
Dr. Armita Nourmohammad retweetet
Biology+AI Daily
Biology+AI Daily@BiologyAIDaily·
HERMES: Holographic Equivariant neuRal network model for Mutational Effect and Stability prediction 1. HERMES introduces a cutting-edge 3D rotationally equivariant neural network model to predict the effects of mutations on protein stability and binding, significantly improving performance compared to previous models. 2. A key feature of HERMES is its pre-training on atomic 3D structures to predict amino acid identities, which enhances accuracy when fine-tuned to predict mutation effects. 3. HERMES offers substantial improvements in speed (2.75× faster) over its predecessor H-CNN while retaining high accuracy in mutation effect predictions, making it a practical choice for large datasets. 4. The model’s architecture respects permutation anti-symmetry in mutations, ensuring that the effect of reversing a mutation is predicted as the negative of the forward mutation, a feature that most models achieve through data augmentation. 5. When tested on experimental and computational protein structures, HERMES outperformed state-of-the-art models, including Stability-Oracle and ProteinMPNN, in predicting protein stability and binding effects. 6. HERMES was rigorously benchmarked across multiple datasets, showing excellent performance even when using computationally predicted protein structures, such as those from ESMFold, for both training and testing. 7. The paper highlights HERMES' ability to predict not only stability effects but also the binding affinity changes of mutations using the SKEMPI dataset, showing high correlation with experimental data. 8. HERMES is open-source, enabling users to fine-tune the model on their specific datasets for customized mutation effect predictions, potentially accelerating discoveries in protein engineering and disease-related mutation analysis. @TheArmita @GMarcoVisani 💻Code: github.com/StatPhysBio/he… 📜Paper: doi.org/10.1101/2024.0…
Biology+AI Daily tweet media
English
0
2
8
1.6K
Dr. Armita Nourmohammad retweetet
APS Division of Biological Physics
Are you an undergraduate interested in pursuing graduate studies biological physics? Join us for a virtual panel “Applying to Graduate School in Biophysics” with panelists who have been on both sides of the application process! Oct. 3 at 3pm ET. Register: apsphysics.zoom.us/webinar/regist…
English
1
20
12
3.7K
Dr. Armita Nourmohammad retweetet
Fernanda Pinheiro
Fernanda Pinheiro@fepinheiromycin·
My 'Predicting the evolution of antibiotic resistance' is out now 🤓🥹 tinyurl.com/3pkyejwp I review a topic that's very dear to my ❤️- how quantitative models of resource allocation can help predict bacterial behavior under stress 🦠💊 #AntibioticResistance #compbio
Fernanda Pinheiro tweet media
English
1
41
172
15.1K
Dr. Armita Nourmohammad retweetet
Paul Francois
Paul Francois@p_r_francois·
We are hiring post-docs! Please do not hesitate to share. We are especially looking for candidates with strong theory and computational backgrounds, who dream about 1. applying their skills and 2. developing new ones to understand squishy, non-linear, evolving ... stuff ! 😉
Paul Francois tweet media
English
0
13
28
5.5K
Dr. Armita Nourmohammad retweetet
Prof. Stefan Rahmstorf 🌏 🦣
Is the #AMOC approaching a tipping point? Here's my take after researching this topic for over 30 years. Open access, peer-reviewed, in full colour & understandable for non-experts. tos.org/oceanography/a…
Prof. Stefan Rahmstorf 🌏 🦣 tweet media
English
146
1.4K
3.1K
738.4K
Dr. Armita Nourmohammad retweetet
NSF-Simons NITMB
NSF-Simons NITMB@NITMB_Chicago·
Do you have an excellent idea for an NITMB Long Program? Learn how the NITMB can support you as you develop your idea into an exceptional program! 🧵(1/5)
NSF-Simons NITMB tweet media
English
1
4
3
646
Dr. Armita Nourmohammad retweetet
Sara Mostafavi
Sara Mostafavi@sara_mostafavi·
Joins us for Machine Learning in Computational Biology (MLCB) 2024 mlcb.github.io Submission deadline: June 15 Conference dates: Sept 5 & 6
English
1
41
146
22.6K
Dr. Armita Nourmohammad retweetet
Alvaro E Chavarria
Alvaro E Chavarria@ChavarriaAlvaro·
Dr. John C. Mather from @NASA will give the next Frontiers of Physics Public Lecture at @UW Seattle on May 8th. Register for free at frontiers.uw.edu and come learn about @NASAWebb !
Alvaro E Chavarria tweet media
English
0
2
4
663
Nikta Fakhri
Nikta Fakhri@FakhriLab·
Had a wonderful visit to Physics Department @UW. Thank you @TheArmita for hosting me. And got to see the peak bloom on campus…
Nikta Fakhri tweet media
Seattle, WA 🇺🇸 English
1
0
22
2.2K