Andrew R. Jones
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View article: List of Contributors
List of Contributors Open
View article: Sparse Methods for Vector Embeddings of TPC Data
Sparse Methods for Vector Embeddings of TPC Data Open
Time Projection Chambers (TPCs) are versatile detectors that reconstruct charged-particle tracks in an ionizing medium, enabling sensitive measurements across a wide range of nuclear physics experiments. We explore sparse convolutional net…
View article: The promise of AlphaFold for gene structure annotation
The promise of AlphaFold for gene structure annotation Open
Background As sequencing technology improves, more genomes become available. Most lack annotation, automated methods are error prone, and few genomes are ever manually curated due to time and cost. Protein structure prediction software may…
View article: The functional landscape of the human ubiquitinome
The functional landscape of the human ubiquitinome Open
Protein ubiquitination regulates cell biology through diverse avenues, from quality control-linked protein degradation to signaling functions such as modulating protein-protein interactions and enzyme activation. Mass spectrometry-based pr…
View article: Hepatic cellular stress response pathways exhibit species differences in basal and inducible activity
Hepatic cellular stress response pathways exhibit species differences in basal and inducible activity Open
Cellular stress response pathways such as the NRF2 oxidative stress response, endoplasmic reticulum (ER) stress response and macroautophagy afford protection against many forms of drug toxicity, including the liver toxicity associated with…
View article: Elucidating tissue and subcellular specificity of the entire SUMO network reveals how stress responses are fine-tuned in a eukaryote
Elucidating tissue and subcellular specificity of the entire SUMO network reveals how stress responses are fine-tuned in a eukaryote Open
SUMOylation is essential in plant and animal cells, but it remains unknown how small ubiquitin-like modifier (SUMO) components act in concert to modify specific targets in response to environmental stresses. In this study, we characterize …
View article: Ubiquitin-like SUMO protease expansion in rice (<i>Oryza sativa</i>)
Ubiquitin-like SUMO protease expansion in rice (<i>Oryza sativa</i>) Open
Summary SUMOylation is a protein post-translational modification that is essential for plant growth and response to changing environments. However, past work in this area has mainly focused on simple sequence similarity methods for discove…
View article: Applying a Conservation-Based Approach for Predicting Novel Phosphorylation Sites in Eukaryotes and Evaluating Their Functional Relevance
Applying a Conservation-Based Approach for Predicting Novel Phosphorylation Sites in Eukaryotes and Evaluating Their Functional Relevance Open
Protein phosphorylation, a key post-translational modification, is central to cellular signaling and disease pathogenesis. The development of high-throughput proteomics pipelines has led to the discovery of large numbers of phosphorylated …
View article: Pharmacist-Led Transition of Care Services in Patients with Cardiovascular Disease: A Systematic Scoping Review
Pharmacist-Led Transition of Care Services in Patients with Cardiovascular Disease: A Systematic Scoping Review Open
Introduction: Transition of care (ToC) is a critical time that requires effective management, especially for patients with cardiovascular disease, who have complex health needs. Pharmacists can play an integral role in improving medication…
View article: Redox-regulated Aux/IAA multimerization modulates auxin responses
Redox-regulated Aux/IAA multimerization modulates auxin responses Open
Reactive oxygen species (ROS) function as key signals in plant adaptation to environmental stresses, such as drought. Roots respond to transient water unavailability by temporarily ceasing branching through the acclimative response xerobra…
View article: A novel INDEL-based next-generation sequencing assay for monitoring donor-derived cell-free DNA in renal transplant recipients—from bedside to results: a UK pilot study
A novel INDEL-based next-generation sequencing assay for monitoring donor-derived cell-free DNA in renal transplant recipients—from bedside to results: a UK pilot study Open
The INDEL-based NGS assay is a promising novel tool for detecting and monitoring dd-cfDNA in renal transplant recipients with an easy-to-implement workflow. These preliminary results support its clinical utility in a high-immunological-ris…
View article: Elucidating tissue and sub-cellular specificity of the entire SUMO network reveals how stress responses are fine-tuned in a eukaryote
Elucidating tissue and sub-cellular specificity of the entire SUMO network reveals how stress responses are fine-tuned in a eukaryote Open
SUMOylation is essential in plant and animal cells, but it remains unknown how SUMO components act in concert to modify specific targets in response to environmental stresses. In this study we characterise every SUMO component in the Arabi…
View article: Unsupervised Attributed Dynamic Network Embedding with Stability Guarantees
Unsupervised Attributed Dynamic Network Embedding with Stability Guarantees Open
Stability for dynamic network embeddings ensures that nodes behaving the same at different times receive the same embedding, allowing comparison of nodes in the network across time. We present attributed unfolded adjacency spectral embeddi…
View article: A pan-gene catalogue of Asian cultivated rice
A pan-gene catalogue of Asian cultivated rice Open
The rice genome underpins fundamental research and breeding, but the Nipponbare (japonica) reference does not fully encompass the genetic diversity of Asian rice. To address this gap, the Rice Population Reference Panel (RPRP) was develope…
View article: Searching for Sulfotyrosines (sY) in a HA(pY)STACK
Searching for Sulfotyrosines (sY) in a HA(pY)STACK Open
Protein sulfation can be crucial in regulating protein-protein interactions but remains largely underexplored. Sulfation is nearly isobaric to phosphorylation, making it particularly challenging to investigate using mass spectrometry. The …
View article: Applying a conservation-based approach for predicting novel phosphorylation sites in eukaryotes and evaluating their functional relevance
Applying a conservation-based approach for predicting novel phosphorylation sites in eukaryotes and evaluating their functional relevance Open
Protein phosphorylation, a key post-translational modification, is central to cellular signalling and disease pathogenesis. The development of high-throughput proteomics pipelines has led to the discovery of large numbers of phosphorylated…
View article: Integrated View of Baseline Protein Expression in Human Tissues Using Public Data Independent Acquisition Data Sets
Integrated View of Baseline Protein Expression in Human Tissues Using Public Data Independent Acquisition Data Sets Open
The PRIDE database is the largest public data repository of mass spectrometry-based proteomics data and currently stores more than 40,000 data sets covering a wide range of organisms, experimental techniques, and biological conditions. Dur…
View article: The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF
The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF Open
Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that are used for further downstream analysis of new spectra. There are many different formats u…
View article: Using Machine Learning to Examine Pre-Transplant Factors Influencing<i>De novo</i>HLA-Specific Antibody Development Post-Kidney Transplant
Using Machine Learning to Examine Pre-Transplant Factors Influencing<i>De novo</i>HLA-Specific Antibody Development Post-Kidney Transplant Open
The development of de novo donor-specific antibodies (DSAs) against HLA is associated with premature graft failure in kidney transplantation. However, rates and factors influencing de novo DSA formation vary widely across the literature. W…
View article: Phosphorylation in the <i>Plasmodium falciparum</i> Proteome: A Meta-Analysis of Publicly Available Data Sets
Phosphorylation in the <i>Plasmodium falciparum</i> Proteome: A Meta-Analysis of Publicly Available Data Sets Open
Malaria is a deadly disease caused by Apicomplexan parasites of the Plasmodium genus. Several species of the Plasmodium genus are known to be infectious to humans, of which P. falciparum is the most virulent. Post-tran…
View article: Searching for Sulfotyrosines (sY) in a HA(pY)STACK
Searching for Sulfotyrosines (sY) in a HA(pY)STACK Open
Protein sulfation can be crucial in regulating protein-protein interactions but remains largely underexplored. Sulfation is near-isobaric to phosphorylation, making it particularly challenging to investigate using mass spectrometry. The de…
View article: The Proteomics Standards Initiative standardized formats for spectral libraries and fragment ion peak annotations: mzSpecLib and mzPAF
The Proteomics Standards Initiative standardized formats for spectral libraries and fragment ion peak annotations: mzSpecLib and mzPAF Open
Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that are used for further downstream analysis of new spectra. There are many different formats u…
View article: mzIdentML 1.3.0 – Essential progress on the support of crosslinking and other identifications based on multiple spectra
mzIdentML 1.3.0 – Essential progress on the support of crosslinking and other identifications based on multiple spectra Open
The mzIdentML data format, originally developed by the Proteomics Standards Initiative in 2011, is the open XML data standard for peptide and protein identification results coming from mass spectrometry. We present mzIdentML version 1.3.0,…
View article: Charting the evolutionary path of the SUMO modification system in plants reveals molecular hardwiring of development to stress adaptation
Charting the evolutionary path of the SUMO modification system in plants reveals molecular hardwiring of development to stress adaptation Open
SUMO modification is part of the spectrum of Ubiquitin-like (UBL) systems that give rise to proteoform complexity through post-translational modifications (PTMs). Proteoforms are essential modifiers of cell signaling for plant adaptation t…
View article: Corrigendum: SUMOylation of OsPSTOL1 is essential for regulating phosphate starvation responses in rice and Arabidopsis
Corrigendum: SUMOylation of OsPSTOL1 is essential for regulating phosphate starvation responses in rice and Arabidopsis Open
[This corrects the article DOI: 10.3389/fpls.2024.1274610.].
View article: Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome
Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome Open
Phosphorylation is the most studied post-translational modification, and has multiple biological functions. In this study, we have reanalyzed publicly available mass spectrometry proteomics data sets enriched for phosphopeptides from Asian…
View article: Integrated Proteomics Analysis of Baseline Protein Expression in Pig Tissues
Integrated Proteomics Analysis of Baseline Protein Expression in Pig Tissues Open
The availability of an increasingly large amount of public proteomics data sets presents an opportunity for performing combined analyses to generate comprehensive organism-wide protein expression maps across different organisms and biologi…
View article: What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species
What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species Open
FungiDB (https://fungidb.org) serves as a valuable online resource that seamlessly integrates genomic and related large-scale data for a wide range of fungal and oomycete species. As an integral part of the VEuPathDB Bioinformatics Resourc…
View article: SUMOylation of OsPSTOL1 is essential for regulating phosphate starvation responses in rice and Arabidopsis
SUMOylation of OsPSTOL1 is essential for regulating phosphate starvation responses in rice and Arabidopsis Open
Although rice is one of the main sources of calories for most of the world, nearly 60% of rice is grown in soils that are low in phosphorus especially in Asia and Africa. Given the limitations of bioavailable inorganic phosphate (Pi) in so…
View article: Dynamic Changes in the Thylakoid Proteome of Cyanobacteria during Light-Regulated Thylakoid Membrane Development
Dynamic Changes in the Thylakoid Proteome of Cyanobacteria during Light-Regulated Thylakoid Membrane Development Open
Cyanobacteria were among the oldest organisms to undertake oxygenic photosynthesis and have an essential impact on the atmosphere and carbon/nitrogen cycles on the planet. The thylakoid membrane of cyanobacteria represents an intricate com…