Application of machine learning in spatial proteomics

M Mou, Z Pan, M Lu, H Sun, Y Wang… - Journal of Chemical …, 2022 - ACS Publications
Spatial proteomics is an interdisciplinary field that investigates the localization and dynamics
of proteins, and it has gained extensive attention in recent years, especially the subcellular …

A subcellular map of the human proteome

PJ Thul, L Åkesson, M Wiking, D Mahdessian… - Science, 2017 - science.org
INTRODUCTION A complete view of human biology can only be achieved by studying the
molecular components of its smallest functional unit, the cell. Cells are internally organized …

Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics

A Geladaki, N Kočevar Britovšek, LM Breckels… - Nature …, 2019 - nature.com
The study of protein localisation has greatly benefited from high-throughput methods
utilising cellular fractionation and proteomic profiling. Hyperplexed Localisation of Organelle …

Bioinformatic analysis of temporal and spatial proteome alternations during infections

M Rahmatbakhsh, A Gagarinova, M Babu - Frontiers in Genetics, 2021 - frontiersin.org
Microbial pathogens have evolved numerous mechanisms to hijack host's systems, thus
causing disease. This is mediated by alterations in the combined host-pathogen proteome in …

[HTML][HTML] Spatiotemporal proteomic profiling of the pro-inflammatory response to lipopolysaccharide in the THP-1 human leukaemia cell line

CM Mulvey, LM Breckels, OM Crook… - Nature …, 2021 - nature.com
Protein localisation and translocation between intracellular compartments underlie almost
all physiological processes. The hyperLOPIT proteomics platform combines mass …

Using hyperLOPIT to perform high-resolution mapping of the spatial proteome

CM Mulvey, LM Breckels, A Geladaki, NK Britovšek… - Nature protocols, 2017 - nature.com
The organization of eukaryotic cells into distinct subcompartments is vital for all functional
processes, and aberrant protein localization is a hallmark of many diseases. Microscopy …

Exploiting transfer learning for the reconstruction of the human gene regulatory network

P Mignone, G Pio, D D'Elia, M Ceci - Bioinformatics, 2020 - academic.oup.com
Motivation The reconstruction of gene regulatory networks (GRNs) from gene expression
data has received increasing attention in recent years, due to its usefulness in the …

Multi-task learning for the simultaneous reconstruction of the human and mouse gene regulatory networks

P Mignone, G Pio, S Džeroski, M Ceci - Scientific reports, 2020 - nature.com
Abstract The reconstruction of Gene Regulatory Networks (GRNs) from gene expression
data, supported by machine learning approaches, has received increasing attention in …

A Bayesian mixture modelling approach for spatial proteomics

OM Crook, CM Mulvey, PDW Kirk… - PLoS computational …, 2018 - journals.plos.org
Analysis of the spatial sub-cellular distribution of proteins is of vital importance to fully
understand context specific protein function. Some proteins can be found with a single …

Separating Golgi Proteins from Cis to Trans Reveals Underlying Properties of Cisternal Localization

HT Parsons, TJ Stevens, HE McFarlane… - The Plant …, 2019 - academic.oup.com
The order of enzymatic activity across Golgi cisternae is essential for complex molecule
biosynthesis. However, an inability to separate Golgi cisternae has meant that the cisternal …