Biology subjects

Johnstone, T.

Publications and source records attributed to Johnstone, T..

5 recordsLinked to original sources

bioRxiv2026

Foundation Models Improve Perturbation Response Prediction

Predicting cellular responses to genetic or chemical perturbations has been a long-standing goal in biology. Recent applications of foundation models to this task have yielded contradictory results regarding their superiority over simple baselines. We conducted an extensive analysis of over 600 different models across various prediction tasks and evaluation metrics, demonstrating that while some foundation models fail to outperform simple baselines, others significantly improve predictions for both genetic and chemical perturbations. Furthermore, we developed and evaluated methods for integrating multiple foundation models for perturbation prediction. Our results show that with sufficient data, these models approach fundamental performance limits, confirming that foundation models can improve cellular response simulations. Code and Data: https://github.com/genbio-ai/foundation-models-perturbation

bioinformatics↗

bioRxiv2022

Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging

Neuroimaging data analysis often requires purpose-built software, which can be challenging to install and may produce different results across computing environments. Beyond being a roadblock to neuroscientists, these issues of accessibility and portability can hamper the reproducibility of neuroimaging data analysis pipelines. Here, we introduce the Neurodesk platform, which harnesses software containers to support a comprehensive and growing suite of neuroimaging software (https://www.neurodesk.org/). Neurodesk includes a browser-accessible virtual desktop environment and a command line interface, mediating access to containerized neuroimaging software libraries on various computing platforms, including personal and high-performance computers, cloud computing and Jupyter Notebooks. This community-oriented, open-source platform enables a paradigm shift for neuroimaging data analysis, allowing for accessible, flexible, fully reproducible, and portable data analysis pipelines.

neuroscience↗

bioRxiv2020

Intolerance of uncertainty is associated with heightened responding in the prefrontal cortex during instructed threat of shock

Heightened responding to uncertain threat is considered a hallmark of anxiety disorder pathology. Here, we sought to determine if individual differences in self-reported intolerance of uncertainty (IU), a key transdiagnostic dimension in anxiety-related pathology, underlies differential recruitment of neural circuitry during instructed outcome uncertainty of threat (n = 42). In an instructed threat of shock task, cues signalled uncertain threat of shock (50%) or certain safety from shock outcomes. Ratings of arousal and valence, skin conductance response (SCR) and functional magnetic resonance imaging were acquired. Overall, participants displayed greater ratings of arousal and negative valence, SCR, and amygdala activation to uncertain threat vs. safe cues. IU was not associated with greater arousal ratings, SCR or amygdala activation to uncertain threat vs. safe cues. However, we found that high IU was associated with greater ratings of negative valence and greater activity in the medial prefrontal cortex and dorsomedial rostral prefrontal cortex to uncertain threat vs safe cues. These findings suggest that during instructed outcome uncertainty of threat, individuals high in IU rate uncertain threat as aversive and engage prefrontal cortical regions known to be involved in safety-signalling and conscious threat appraisal. Taken together, these findings highlight the potential of IU in modulating safety-signalling and conscious appraisal mechanisms in situations with instructed outcome uncertainty of threat, which may be relevant to models of anxiety-related pathology.

neuroscience↗

bioRxiv2019

EEG-fMRI reveals rapid representation of personal relevance of faces in social cognition and reward-related brain regions

The faces of those most personally relevant to us are our primary source of social information, making their timely perception a priority. Recent research indicates that gender, age and identity of faces can be decoded from EEG/MEG data within 100ms. Yet the time course and neural circuitry involved in representing the personal relevance of faces remain unknown. We applied simultaneous EEG-fMRI to examine neural responses to emotional faces of female participants romantic partners, friends, and a stranger. Combining EEG and fMRI in cross-modal representational similarity analyses, we provide evidence that representations of personal relevance start prior to structural encoding at 100ms, with correlated representations in visual cortex, but also in prefrontal and midline regions involved in value representation, and monitoring and recall of self-relevant information. Our results add to an emerging body of research that suggests that models of face perception need to be updated to account for rapid detection of personal relevance in cortical circuitry beyond the core face processing network.

neuroscience↗

bioRxiv2018

Inter-slice leakage and intra-slice aliasing in simultaneous multi-slice echo-planar images

Simultaneous multi-slice (SMS) imaging is a popular technique for increasing acquisition speed in echo-planar imaging (EPI) fMRI. However, SMS data are prone to motion sensitivity and slice leakage artefacts, which spread signal between simultaneously acquired slices. Relevant to motion sensitivity, artefacts from moving anatomic structures propagate along the phase-encoding (PE) direction. This is particularly relevant for eye movement. As signal from the eye is acquired along with signal from simultaneously excited slices during SMS, there is potential for signal to spread in-plane and between spatially remote slices. After identifying an artefact temporally coinciding with signal fluctuations in the eye and spatially distributed in correspondence with multiband slice acceleration and parallel imaging factors, we conducted a series of small experiments to investigate eye movement artefacts in SMS data and the contribution of PE direction to the invasiveness of these artefacts. Five healthy adult volunteers were scanned during a blinking task using a standard SMS-EPI protocol with posterior-to-anterior (P>>A), anterior-to-posterior (A>>P) or right-to-left (R>>L) PE direction. The intensity of signal fluctuations (artefact severity) was measured at expected artefact positions and control positions. We demonstrated a direct relationship between eye movements and artefact severity across expected artefact regions. Within-brain artefacts were apparent in P>>A- and A>>P-acquired data but not in R>>L data due to the shift in artefact positions. Further research into eye motion artefacts in SMS data is warranted but researchers should exercise caution with SMS protocols. We recommend rigorous piloting of SMS protocols and switching to R>>L/L>>R PE where feasible.

neuroscience↗