Stephen Taylor

SoftHybrid: A Hybrid Imputation Algorithm Optimised for Single-Cell Proteomics Data

SoftHybrid improves single-cell proteomics data imputation by jointly modeling missingness and protein abundance, outperforming existing methods at low input and matching them at the mini-bulk level.

ChatMDV: Democratising Bioinformatics Analysis Using Large Language Models

ChatMDV provides a natural language interface for generating interactive visualizations of biological data using large language models and the MDV platform.

Integrating diverse statistical methods to analyse stage-discriminatory cell interactions in colorectal neoplasia

The paper develops spatial descriptors using mathematical tools to analyze cell interactions in colorectal cancer progression and demonstrates their utility in identifying disease-related pathways.

Breathlessness in a virtual world: An experimental paradigm testing how discrepancy between VR visual gradients and pedal resistance during stationary cycling affects breathlessness perception.

This study uses a virtual reality paradigm to show that breathlessness perception is influenced by both expected and actual effort during cycling.

Multi Locus View: An Extensible Web Based Tool for the Analysis of Genomic Data

MLV is a web-based tool for visualizing, analyzing, and annotating genomic datasets, enabling multi-scale interaction and integration of multiple data tracks.

LanceOtron: a deep learning peak caller for ATAC-seq, ChIP-seq, and DNase-seq

LanceOtron improves peak calling in ATAC-seq, ChIP-seq, and DNase-seq by using deep learning to better capture peak shapes and outperforms MACS2 in selectivity and sensitivity.

CaptureCompendium: a comprehensive toolkit for 3C analysis.

CaptureCompendium provides software tools to simplify the design, analysis, and visualization of 3C experiments, addressing the need for specialized bioinformatics skills in genome folding studies.

An integrated platform to systematically identify causal variants and genes for polygenic human traits.

The paper develops a platform combining ATAC-seq, DNaseI footprints, NG Capture-C, and machine learning to identify causal variants and genes for polygenic human traits.

Reconstruction of the global neural crest gene regulatory network in vivo

The paper reconstructs the global neural crest gene regulatory network in vivo using epigenomic and single-cell transcriptome data combined with genome engineering.

CSynth: A Dynamic Modelling and Visualisation Tool for 3D Chromatin Structure

CSynth is a 3D genome browser and chromatin structure modeller that enables real-time visualization and interaction with Hi-C data using GPU acceleration and VR.