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February 27, 2025

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09/11/2025

research article

A curriculum learning approach to training antibody language models

There is growing interest in pre-training antibody language models (AbLMs) with a mixture of unpaired and natively paired sequences, seeking to combine the proven benefits of training with natively paired sequences with the massive scale of unpaired antibody sequence datasets. However, given the novelty of this strategy, the field lacks a systematic evaluation of data processing methods and training strategies that maximize the benefits of mixed training data

Image credit: Pavel Czerwinski

A curriculum learning approach to training antibody language models

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Current Issue September 2025

09/08/2025

research article

Blood flow in the human cerebral cortex: Large-scale pial vascularization and 1D simulation

Understanding cerebral circulation is crucial for early diagnosis and patient-oriented therapies for brain conditions. However, blood flow simulations at the organ scale have been limited. This work introduces a framework for modeling extensive vascular networks in the human cerebral cortex and conducting pulsatile blood flow simulations.

Image credit: Zilves et al

Blood flow in the human cerebral cortex: Large-scale pial vascularization and 1D simulation

09/03/2025

research article

Optimal algorithms for controlling infectious diseases in real time using noisy infection data

The authors tackle the challenge of determining the best time to enforce or relax non-pharmaceutical interventions (NPIs), such as mandatory mask wearing, social distancing or quarantine, to manage the spread of infectious diseases. Making an optimal decision on NPIs requires balancing the risks and the burden of prevalent infections on the healthcare systems against the costs of restrictive measures to livelihood and life-quality.

Image credit: Markus Winkler

Optimal algorithms for controlling infectious diseases in real time using noisy infection data

08/26/2025

research article

Mixotrophy for carbon-conserving waste upcycling

Electrochemical and biological processes offer promise for upgrading waste streams, including recalcitrant carbon dioxide and plastic-derived wastes. However, the inherent heterogeneity and high energy requirements of upcycling the chemical endpoints of the “take-make-waste" economy remain challenging.

Mixotrophy for carbon-conserving waste upcycling

Image credit: Weldon and Euler

08/11/2025

research article

Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics

The authors present an approach that integrates AI with cryo-EM density-guided simulations to fit ligands into experimental maps. Using three inputs: 1) a protein amino acid sequence, 2) a ligand specification, and 3) an experimental cryo-EM map, they validated the approach on a set of biomedically relevant protein-ligand complexes including kinases, GPCRs, and solute transporters.

Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics

Image credit: Haloi, Howard, Lindahl

08/05/2025

research article

COEXIST: Coordinated single-cell integration of serial multiplexed tissue images

The authors developed COEXIST, a computational algorithm that combines shared molecular profiles with spatial information to match cells across serial sections, enabling more complete and accurate tissue profiling. COEXIST improves MTI utility, enhances single-cell resolution, and offers opportunities for integrating MTI with spatial transcriptomics for deeper biological insight.

COEXIST: Coordinated single-cell integration of serial multiplexed tissue images

Image credit: Heussner et al

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