September 5, 2023

Trackplot: A flexible toolkit for combinatorial analysis of genomic data

The authors present Trackplot, a comprehensive tool that delivers high-quality plots via a programmable and interactive web-based platform. Trackplot seamlessly integrates diverse data sources and utilizes a multi-threaded process, enabling users to explore genomic signal in large-scale sequencing datasets.

Image credit: NCI

10/17/2023

Research Article

Integrated information theory (IIT) 4.0: Formulating the properties of phenomenal existence in physical terms

This paper presents Integrated Information Theory (IIT) 4.0. IIT aims to account for the properties of experience in physical (operational) terms. It identifies the essential properties of experience (axioms), infers the necessary and sufficient properties that its substrate must satisfy (postulates), and expresses them in mathematical terms.

Image credit: Albantakis et al

Integrated information theory (IIT) 4.0: Formulating the properties of phenomenal existence in physical terms

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Current Issue November 2023

10/06/2023

Research Article

Force-dependent focal adhesion assembly and disassembly: A computational study

This study presents a differential equation-based mechano-chemical computational model, to investigate how substrate stiffness influences adhesion formation, maturation and disassembly. It explicitly includes the role of talin and vinculin-based reinforcement in these processes.

Image credit: Shankar et al

Force-dependent focal adhesion assembly and disassembly: A computational study

10/16/2023

Research Article

Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies

This study describes a comprehensive workflow to simulate a variety of different types of heterogeneity and evaluate the performances of different integration methods together with batch normalization.

Image credit: NCI

Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies

10/04/2023

Research Article

Mechanistic characterization of oscillatory patterns in unperturbed tumor growth dynamics: The interplay between cancer cells and components of tumor microenvironment

This work highlights the oscillatory dynamics observed in the tumor growth over time curves and proposes a novel semi-mechanistic model capable of describing the non-monotonic growth in the tumor microenviroment.

Image credit: NCI

10/02/2023

Research Article

Mouse visual cortex as a limited resource system that self-learns an ecologically-general representation

This study takes a computational approach to seek an overall understanding of the mouse’s visual cortex, and how it supports a range of behaviors. It uses a high-fidelity quantitative model of mouse visual cortex and identifies key structural and functional principles underlying that model’s success.

Image credit: Ricky Kharawala

09/18/2023

Research Article

Nowcasting the 2022 mpox outbreak in England

The 2022 mpox outbreak was characterized by long delays from individuals developing symptoms and reporting a positive case, creating an underestimate of the true extent of the outbreak. The authors developed a mathematical model that accounts for these reporting delays to estimate the true shape of the epidemic curve in real-time. This model was used continuously throughout the outbreak response to provide insight to the incident management team at the UK Health Security Agency.

Image credit: Midas Hofstra

09/14/2023

Research Article

Mixtures of strategies underlie rodent behavior during reversal learning

Using a reversal learning task, the authors showed that mice displayed a much more variable behavior than would be expected from a uniform strategy, suggesting that they mix between multiple behavioral modes in the task.

Image credit: Sur et al

09/11/2023

Research Article

Emergence of belief-like representations through reinforcement learning

This study shows that an artificial recurrent neural network trained with TD learning can estimate value from observations, without explicitly estimating beliefs.

Image credit: Ave Calver

09/05/2023

Research Article

What constrains food webs? A maximum entropy framework for predicting their structure with minimal biases

The authors present a novel framework to identify feeding relationship variables by applying the principle of maximum entropy to the analysis of food-web structure.

Image credit: Alex Belogub

08/10/2023

Education

Ten simple rules for a mom-friendly Academia

Image credit: PLOS pcbi.1010627

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PLOS Computational Biology | ISSN: 1553-7358 (online)

Trackplot: A flexible toolkit for combinatorial analysis of genomic data

Integrated information theory (IIT) 4.0: Formulating the properties of phenomenal existence in physical terms

Recently Published Articles

Force-dependent focal adhesion assembly and disassembly: A computational study

Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies

Mechanistic characterization of oscillatory patterns in unperturbed tumor growth dynamics: The interplay between cancer cells and components of tumor microenvironment

Mouse visual cortex as a limited resource system that self-learns an ecologically-general representation

Nowcasting the 2022 mpox outbreak in England

Mixtures of strategies underlie rodent behavior during reversal learning

Emergence of belief-like representations through reinforcement learning

What constrains food webs? A maximum entropy framework for predicting their structure with minimal biases

Ten simple rules for a mom-friendly Academia

Topic Pages

Developing Computational Biology

Education

Benchmarking

PLOS Biology

PLOS Neglected Tropical Diseases

PLOS Pathogens

PLOS Medicine

Publish with PLOS

Recently Published Articles

Publish with PLOS

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