Episode 11: Back to December

We chat about travels, new preprints, and vibe coding.

Preprints:

• Improving Cryo-EM Optimization Robustness with an Optimal Transport Loss Function for Noisy Images

• Protein folding success depends on the direction and speed of polypeptide chain appearance

• Jeremy Reiter’s gene list

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Episode 10: Science Tree Farm

Topics:

• Year in Review
• 2026 Predictions

Prachee Avasthi Substack Post:

• How to Not Make a Scientific Journal by Accident

Preprints:

• Rewriting protein alphabets with language models

• Fine-tuning protein language models on human spatial constraint yields state-of-the-art variant effect prediction

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Topics:

• Government Shutdown/Reopening
• Travels
• The impact of Jane Richardson
• New science funding structures and Arena BioWorks closing

• AI Peer Review tools

• Big experiments are only big if they can fail

Preprints: ⁠

• Hit or Miss: Understanding Emergence and Absence of Homo-oligomeric Contacts in Protein Language Models

• The Drain of Scientific Publishing

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Topics:

• Compact for Academic Excellence in Higher Education
• Government Shutdown
• HHMI’s new open science policies
• Shrinking PhD pools
• The Nobel Prizes
• The Bear
• TLOS Reactions

Preprint: ⁠Experiment-guided AlphaFold3 resolves accurate protein ensembles⁠

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Episode 7 is out now!

Latest News: H1B changes & chaos; who determines what gets into PubMed (Literature Selection Technical Review Committee).

Preprints:

• Generative design of novel bacteriophages with genome language models
• Improved cryo-EM reconstruction of sub-50 kDa complexes using 2D template matching

• High-resolution ab initio reconstruction enables cryo-EM structure determination of small particles (see the great bioRxiv comment thread).

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