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Large-scale simulations of biological cell sorting driven by differential adhesion follow diffusion-limited domain coale...

Published in PLoS computational biology

Cell sorting, whereby a heterogeneous cell mixture segregates and forms distinct homogeneous tissues, is one of the main collective cell behaviors at work during development. Although differences in interfacial energies are recognized to be a possible driving source for cell sorting, no clear consensus has emerged on the kinetic law of cell sorting...

Ten simple rules for good research practice

Published in PLoS Computational Biology

Ten simple rules for improving communication among scientists

Published in PLoS Computational Biology

Communication is a fundamental part of scientific development and methodology. With the advancement of the internet and social networks, communication has become rapid and sometimes overwhelming, especially in science. It is important to provide scientists with useful, effective, and dynamic tools to establish and build a fluid communication framew...

Stress generation, relaxation and size control in confined tumor growth

Published in PLoS Computational Biology

Image-based parameter inference for epithelial mechanics

Published in PLoS Computational Biology

Thanks to recent advances in imaging techniques, researchers can track various events that occur during development, such as collective cell movement, morphogen signaling, and transcription from specific genome loci. A new challenge is to extract biologically important information from large and complex image data. Here, we developed an efficient a...

Epidemic management and control through risk-dependent individual contact interventions

Published in PLoS Computational Biology

During the ongoing COVID-19 pandemic, exposure notification apps have been developed to scale up manual contact tracing. The apps use proximity data from mobile devices to automate notifying direct contacts of an infection source. The information they provide is limited because users receive only rare and binary alerts. Here we present network data...

Quantifying biochemical reaction rates from static population variability within incompletely observed complex networks

Published in PLoS Computational Biology

Statistical models are the dominant tool to interpret co-variability of molecular components in cellular processes because they can be formulated for a subset of components while leaving the full complexity of the processes unspecified. Their drawback lies in the difficulty of translating statistical associations into causal interactions. In contra...

A method for the inference of cytokine interaction networks

Published in PLoS Computational Biology

Cytokines are the messenger molecules of the immune system, allowing intercellular communication and mediating effective immune responses. They are an important therapeutic target in immune mediated inflammatory diseases such as inflammatory bowel disease (IBD) and rheumatoid arthritis. Cytokines interact in a tightly regulated network and dependin...

Active inference unifies intentional and conflict-resolution imperatives of motor control

Published in PLoS Computational Biology

Most of our everyday actions are motivated by the "intentional" imperative to achieve some goal. However, several studies reveal that when we experience a multisensory conflict, such as for example during the rubber hand illusion or when we embody an avatar in virtual reality, we execute movements that are not intentional in the traditional sense, ...

Direct reciprocity between individuals that use different strategy spaces

Published in PLoS Computational Biology

Direct reciprocity can lead to cooperation between individuals who meet in repeated encounters. The shadow of the future casts an incentive to cooperate. If I cooperate today, you may cooperate tomorrow. But if I defect today, you may defect tomorrow. In most studies of direct reciprocity it is assumed that both players explore the same space of po...