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Trackplot: A flexible toolkit for combinatorial analysis of genomic data

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

09/18/2023

Research Article

Nowcasting the 2022 mpox outbreak in England

The 2022 mpox outbreak was characterised by long delays from individuals developing symptoms and reporting a positive case. This creates 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

Nowcasting the 2022 mpox outbreak in England

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Current Issue

Current Issue September 2023

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. A computational method was developed to dissociate these learning modes from behavioral data, addressing the challenges faced by current analytical methods when agents mix between different strategies

Image credit: Sur et al

Mixtures of strategies underlie rodent behavior during reversal learning

09/11/2023

Research Article

Emergence of belief-like representations through reinforcement learning

Here we show that an artificial recurrent neural network trained with TD learning can estimate value from observations, without explicitly estimating beliefs. The trained RNN’s error signals resembled the neural activity of dopamine neurons measured during the same tasks. Importantly, the RNN’s activity resembled beliefs, but only when the RNN had enough capacity..

Image credit: Ave Calver

Emergence of belief-like representations through reinforcement learning

08/17/2023

Perspective

The specious art of single-cell genomics

This article examines the practical implications of low-dimensional embedding of single-cell data and finds that extensive distortions and inconsistent practices make such embeddings counter-productive for exploratory, biological analyses. In lieu of this, the authors discuss alternative approaches for conducting targeted embedding and feature exploration to enable hypothesis-driven biological discovery.

The specious art of single-cell genomics

Image credit: Chari and Pachter

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