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Alissa Hummer

@alissahummer.com
118 followers 171 following 23 posts

Schmidt Science Fellow | Postdoc @ Stanford | Prev. DPhil @ Oxford || AI for Molecule & Cell Modeling

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Alissa Hummer @alissahummer.com · 15/06/2026
I am beyond grateful to everyone who supported me throughout my DPhil. Charlotte, thank you for being an awesome supervisor and trailblazer – this thesis would not have been possible without you! Thank you to everyone in the Oxford Protein Informatics Group for making my DPhil experience so much fun
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Alissa Hummer @alissahummer.com · 15/06/2026
Thank you to the Corcoran family, the Department, Frank Windmeijer, Simon Myers, Garrett Morris, and Beverley Lane for this award and for the wonderful lecture and ceremony! I had the pleasure (and pressure) of speaking after a fantastic talk by Frank Noé.
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Alissa Hummer @alissahummer.com · 15/06/2026
I am honoured to have been awarded the Corcoran Memorial Prize from @oxfordstatistics.bsky.social for my DPhil research on ML for antibody design. The Corcoran Memorial Prize & Lectures are named in memory of Stephen Corcoran, who was a graduate student in the Department of Statistics.
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Alissa Hummer @alissahummer.com · 04/10/2025
Immensely grateful to the Schmidt Science Fellowship, my mentors, and all the wonderful & inspiring people I have worked with over the past years.
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Alissa Hummer @alissahummer.com · 04/10/2025
Excited to be pivoting from molecules to cells for my Schmidt Science Fellowship, advised by Emma Lundberg and Wah Chiu! I’m looking forward to building ML models that better reflect how molecules & cells look in real life 🔬
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Alissa Hummer @alissahummer.com · 26/08/2025
Huge thanks to my co-authors @cschneider.bsky.social, Lewis Chinery, Charlotte Deane @opig.stats.ox.ac.uk!
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Alissa Hummer @alissahummer.com · 26/08/2025
More information about the paper: bsky.app/profile/alis...
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Alissa Hummer @alissahummer.com · 26/08/2025
Link to the paper: www.nature.com/articles/s43...
nature.com
Investigating the volume and diversity of data needed for generalizable antibody–antigen ΔΔG prediction - Nature Computational Science
Predicting the effects of mutations on antibody–antigen binding is a key challenge in therapeutic antibody development. Orders of magnitude more data will be needed to unlock accurate, robust predicti...
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Alissa Hummer @alissahummer.com · 26/08/2025
Our paper on generalizable antibody-antigen binding affinity prediction has been featured on the cover of the August Issue of @natcomputsci.nature.com! 📔🎉
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Reposted by Alissa Hummer
Nature Computational Science @natcomputsci.nature.com · 25/08/2025
🚨Our August issue is now live and includes research on antibody-antigen binding, molecular screening for zeolite synthesis, psychological experiments with LLMs, and much more! www.nature.com/natcomputsci...
Yellow and orange antibody binding to purple and blue membrane proteins
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Reposted by Alissa Hummer
Nature Computational Science @natcomputsci.nature.com · 08/07/2025
Out now! @alissahummer.com @opig.stats.ox.ac.uk and colleagues present Graphinity, a method to predict change in antibody-antigen binding affinity (∆∆G). Also featuring synthetic datasets of ~1 million FoldX-generated and >20,000 Rosetta Flex ddG-generated ∆∆G values! www.nature.com/articles/s43...
nature.com
Investigating the volume and diversity of data needed for generalizable antibody–antigen ΔΔG prediction - Nature Computational Science
Predicting the effects of mutations on antibody–antigen binding is a key challenge in therapeutic antibody development. Orders of magnitude more data will be needed to unlock accurate, robust predicti...
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Alissa Hummer @alissahummer.com · 09/07/2025
Paper link: www.nature.com/articles/s43...
nature.com
Investigating the volume and diversity of data needed for generalizable antibody–antigen ΔΔG prediction - Nature Computational Science
Predicting the effects of mutations on antibody–antigen binding is a key challenge in therapeutic antibody development. Orders of magnitude more data will be needed to unlock accurate, robust predicti...
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Alissa Hummer @alissahummer.com · 09/07/2025
And thank you to my co-authors @cschneider.bsky.social, Lewis Chinery, and Charlotte Deane – @opig.stats.ox.ac.uk!
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Alissa Hummer @alissahummer.com · 09/07/2025
Thank you very much to the reviewers and editors who made this work stronger!
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Alissa Hummer @alissahummer.com · 09/07/2025
The Graphinity code and synthetic datasets are publicly available at the following links. GitHub: github.com/oxpig/Graphi... Zenodo (code): doi.org/10.5281/zeno... Zenodo (data): doi.org/10.5281/zeno... OPIG (data): opig.stats.ox.ac.uk/data/downloa...
github.com
GitHub - oxpig/Graphinity: Graphinity: Equivariant Graph Neural Network Architecture for Predicting Change in Antibody-Antigen Binding Affinity
Graphinity: Equivariant Graph Neural Network Architecture for Predicting Change in Antibody-Antigen Binding Affinity - oxpig/Graphinity
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Alissa Hummer @alissahummer.com · 09/07/2025
Since the release of our preprint, we have made key updates including: 📊 Generation of a second synthetic dataset using Rosetta Flex ddG (20,829 ΔΔG values) 🕸️ Evaluation of additional ML architectures (incl. FLAML, CNN, Rotamer Density Estimate, Equiformer)
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Alissa Hummer @alissahummer.com · 09/07/2025
Antibody-antigen binding affinity lies at the heart of therapeutic antibody development. We show that orders of magnitude more data will be needed to unlock generalizable ΔΔG prediction. Our findings provide a lower bound on data requirements to inform future method development & data collection.
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Alissa Hummer @alissahummer.com · 09/07/2025
Our work exploring the ability of and requirements for ML to predict the effects of mutations on antibody-antigen binding affinity (ΔΔG) is out now in @natcomputsci.nature.com!
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Reposted by Alissa Hummer
Rachael Kretsch @rachael-kretsch.bsky.social · 20/05/2025
What is the status of nucleic acid structure prediction? Our analysis of CASP16 (doi.org/10.1101/2025...) reveals human expertise is still necessary for the most accurate prediction, but accuracy still heavily relies on templates; having seen a similar structure already.
doi.org
Assessment of nucleic acid structure prediction in CASP16
Consistently accurate 3D nucleic acid structure prediction would facilitate studies of the diverse RNA and DNA molecules underlying life. In CASP16, blind predictions for 42 targets canvassing a full ...
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Alissa Hummer @alissahummer.com · 14/05/2025
See the full analysis, led by @rachael-kretsch.bsky.social, in our preprint: www.biorxiv.org/content/10.1...
biorxiv.org
Assessment of nucleic acid structure prediction in CASP16
Consistently accurate 3D nucleic acid structure prediction would facilitate studies of the diverse RNA and DNA molecules underlying life. In CASP16, blind predictions for 42 targets canvassing a full ...
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Alissa Hummer @alissahummer.com · 14/05/2025
It was great to be involved in the evaluation of nucleic acid structure prediction in CASP16! 🧬 RNA modeling remains challenging for deep learning, esp. in the absence of templates and for long-range tertiary/quaternary interactions. Encouraging signs from deep evolutionary data though.
biorxiv.org
Assessment of nucleic acid structure prediction in CASP16
Consistently accurate 3D nucleic acid structure prediction would facilitate studies of the diverse RNA and DNA molecules underlying life. In CASP16, blind predictions for 42 targets canvassing a full ...
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Alissa Hummer @alissahummer.com · 04/04/2025
Thank you so much, Nick!
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Alissa Hummer @alissahummer.com · 03/04/2025
If you’re interested in building the data & ML to create molecular-resolution Virtual Cell Models, I would love to chat 🧫💻
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Alissa Hummer @alissahummer.com · 03/04/2025
And thank you to the @schmidtsciences.bsky.social program for encouraging and supporting disciplinary pivots to enable greater impact for our science!
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Alissa Hummer @alissahummer.com · 03/04/2025
A huge thank you to all my mentors & lab-mates who have shaped my scientific journey and supported my pivots so far! Special thanks to Charlotte Deane & @opig.stats.ox.ac.uk, @deboramarks.bsky.social, Madan Babu, @pstansfeld.bsky.social, @rdaslab.bsky.social
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Alissa Hummer @alissahummer.com · 03/04/2025
I'm so excited to join this interdisciplinary community as a 2025 Schmidt Science Fellow! After years behind a keyboard, I will be pivoting toward the wet lab. To unlock the true potential of ML for biology/biomedicine, we need high-quality data and robust evaluation 🔬🧫🧪
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Reposted by Alissa Hummer
Oxford Protein Informatics Group (OPIG) @opig.stats.ox.ac.uk · 27/03/2025
AntiFold, our antibody inverse folding model, has been published at Bioinformatics Advances. Work led by @magnushoie.bsky.social & @alissahummer.com. Paper: academic.oup.com/bioinformati... Webserver: opig.stats.ox.ac.uk/webapps/anti... Codebase available on Github: github.com/oxpig/AntiFold
academic.oup.com
AntiFold: Improved structure-based antibody design using inverse folding
AbstractSummary. The design and optimization of antibodies requires an intricate balance across multiple properties. Protein inverse folding models, capabl
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