Selected publications from the Computational Biology Facility.

Extracting Self-Reported COVID-19 Symptom Tweets and Twitter Movement Mobility Origin/Destination Matrices to Inform Disease Models  (Information – 2023)

Leveraging transcriptomics for precision diagnosis: lessons learned from cancer and sepsis (Frontiers in Genetics – 2023)

Whole Genome DNA Methylation and Mutational Profiles Identify Novel Changes in Proliferative Verrucous Leukoplakia (Oral Surg Oral Med Oral Pathol Oral Radiol – 2023)

Structural Insights into Pink-eyed Dilution Protein (Oca2)  (Biosci rep – 2023)

Deep Learning-based structure modelling illuminates structure and function in uncharted regions of β-solenoid fold space (Journal of Structural Biology – 2023)

A systems approach reveals species differences in hepatic stress response capacity  (Toxicological Sciences – 2023)

A bespoke analytical workflow for the confident identification of sulfopeptides and their discrimination from phosphopeptides (bioRxiV (on JPR) – 2023)

Trustworthy AI-Environments for Clinical Prediction: Application to Crisis-Risk in People with Depression (IEEE Journal of Biomedical and Health Informatics – 2023)

Mesenchymal Stromal Cell secretome is affected by tissue source, donor age and sex. (Stem Cells – 2023)

Tertiary structure assessment at CASP15 (Proteins – 2023)

Custom workflow for the confident identification of sulfotyrosine-containing peptides and their discrimination from phosphopeptides  (Journal of Proteome Research – 2023)

Multi-Omic Temporal Landscape of Plasma and Synovial Fluid-Derived Extracellular Vesicles Using an Experimental Model of Equine Osteoarthritis  (MDPI – 2023)

Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15 (Proteins – 2023)

Dynamic changes in the thylakoid proteome of cyanobacteria during light-regulated thylakoid membrane development (Plants – 2023)

Rapid evaporative ionization mass spectrometry (intelligent knife) for point-of-care testing in acute aortic dissection surgery (Interactive CardioVascular and Thoracic Surgery – 2022)

Data-driven learning of narcosis mode of action identifies a CNS transcriptional signature shared between whole organism caenorhabditis elegans and a fish gill cell line (Science of the Total Environment – 2022)

The INSR/AKT/mTOR pathway regulates the pace of myogenesis in a syndecan-3-dependent manner (Matrix Biology – 2022)

Temporal Extracellular Vesicle Protein Changes following Intraarticular Treatment with Integrin alpha 10 beta 1-selected Mesenchymal Stem Cells in Equine Osteoarthritis (Frontiers veterinary science – 2022)

Identification of tissue-dependent proteins in knee OA synovial fluid (Osteoarthritis cartilage – 2021)

Genomics and transcriptomics landscapes associated to changes in insulin sensitivity in response to endurance exercise training (Scientific Reports – 2021)

Systems analysis of miRNA biomarkers to inform drug safety (Arch Toxicol. – 2021)

A Proteome-Wide Immunoinformatics Tool to Accelerate T-Cell Epitope Discovery and Vaccine Design in the Context of Emerging Infectious Diseases: An Ethnicity-Oriented Approach (Frontiers in Immunology – 2021)

A snapshot of human leukocyte antigen (HLA) diversity using data from the Allele Frequency Net Database (Human Immunology – 2021)

lcmsWorld: High-Performance 3D Visualization Software for Mass Spectrometry (Journal of Proteome Research – 2021)

Temporal modulation of the NF-B RelA network in response to different types of DNA damage (Biochemical Journal – 2021)

An OMICs based meta-analysis to support infection state stratification (Bioinformatics – 2021)

Experimental and computational modeling for signature and biomarker discovery of renal cell carcinoma progression (Molecular Cancer – 2021)

Characterising proteolysis during SARS-CoV-2 infection identifies viral cleavage sites and cellular targets with therapeutic potential (Nature communications – 2021)

Four Weeks of Probiotic Supplementation Alters the Metabolic Perturbations Induced by Marathon Running: Insight from Metabolomics (Metabolites – 2021)

Serum protein signatures differentiate paediatric autoimmune/ inflammatory disorders (Clinical Immunology – 2021)

Exploring the potential of rapid evaporative ionization mass spectrometry (Intelligent Knife) for point-of-care testing in aortic surgery (European Journal of Cardio-Thoracic Surgery – 2021)

Genetic variants associated with mandibular osteoradionecrosis following radiotherapy for head and neck malignancy (Radiotherapy and Oncology 165 (2021) 87–93 – 2021)

Assessing Technical and Biological Variation in SWATH-MS Based proteomic Analysis of Chronic Lymphocitic Leukaemia Cells (Scientific Reports – 2021)

Machine learning to uncover differentiable signatures of bacterial and viral infections (Int. Journal of Infectious Diseases – 2020)

NMR-based metabolic profiling provides diagnostic and prognostic information in critically ill children with suspected infection (Scientific Reports – 2020)

Transcriptome Profiling Reveals New Insights into the Immune Microenvironment and Upregulation of Novel Biomarkers in Metastatic Uveal Melanoma (Cancers – 2020)

Transoral laser microsurgery and radiotherapy for oropharyngeal squamous cell carcinoma: Equitable survival and enhanced function compared with contemporary standards of care (European Journal of Surgical Oncology – 2020)

Increased Expression of Interleukin-1 Receptor Characterizes Anti-estrogen-Resistant ALDH+ Breast Cancer Stem Cells (Stem Cells Reports – 2020)

MMP13 and TIMP1 are functional markers for two different potential modes of action by mesenchymal stem/stromal cells when treating osteoarthritis (Stem Cells – 2020)

Use of the Polo-like kinase 4 (PLK4) inhibitor centrinone to investigate intracellular signaling networks using SILAC-based phosphoproteomics (Biochem J – 2020)

The Sodium Channel B4-Subunits are Dysregulated in Temporal Lobe Epilepsy Drug-Resistant Patients (International Journal of Molecular Sciences – 2020)

A novel panel of differentially-expressed microRNAs in breast cancer brain metastasis may predict patient survival (Scientific Reports – 2019)

Vision of a near future: Bridging the human health-environment divide. Toward an integrated strategy to understand mechanisms across species for chemical safety assessment (Toxicology in vitro – 2020)

Quality of Reporting in Human Aortic Tissue Research- A Systematic Review (Artery Research – 2019)

Allele frequency net database 2020 update (Nucleic Acids Res – 2019)

Computationally predicted gene regulatory networks in molluscan biomineralisation identify extracellular matrix production and ion transportaiton pathways (Bioinformatics – 2019)

VAPPER: High-throughput variant antigen profiling in African trypanosomes of livestock. (GigaScience – 2019)

Strong anion exchange-mediated phosphoproteomics reveals extensive human non-canonical phosphorylation (Embo – 2019)

Idiopathic degenerative thoracic aneurysms are associated with increased aortic medial amyloid (Amyloid – 2019)

Nonspecific effects of oral vaccination with live-attenuated Salmonella Typhi strain Ty21a (Science Advances – 2019)

Deciphering the complex role of thrombospondin-1 in glioblastoma development (Nat Commun. – 2019)

MzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics (Analytical Chemistry, 2019)

Chemical hazard prediction and hypothesis testing using quantitative adverse outcome pathways (ALTEX, 2019)

Non-specific effects of oral vaccination with live-attenuated Salmonella Typhi strain Ty21a (Science Advances, 2019)

Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets (Molecular & Cellular Proteomics, 2018)

Comparative qualitative phosphoproteomics analysis identifies shared phosphorylation motifs and associated biological processes in evolutionary divergent plants (Journal of Proteomics, 2018)

Incorporating suborganismal processes into dynamic energy budget models for ecological risk assessment (Integrated Environmental Assessment Management, 2018)

In Silico Computational Transcriptomics Reveals Novel Endocrine Disruptors in Largemouth Bass (Micropterus salmoides) (Environmental Science Technology, 2018)

Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions (Molecular Immunology, 2018)

The role of Eif6 in Skeletal Muscle Homeostasis Revealed by Endurance Training Co-Expression networks (Cell Rep, 2017)

Transcriptional mechanism of vascular endothelial growth factor-induced expression of protein kinase CBII in chronic lymphocytic leukaemia cells (Sci Rep, 2017)

Glaerosin: a novel sexually dimorphic urinary lipocalin in the bank vole, Myodes glareolus (Open Biology, 2017)

A network biology approach identifies molecular cross-talk between normal prostate epithelial and prostate carcinoma cells (PloS Computational Biology, 2016)

The centrosomal deubiquitylase UP21 regulates Gly1 trancriptional activity and stability (Journal of Cell Science, 2016)

Inference of low and high-grade glioma gene regulatory networks delineates the role of Rnd3 in establishing multiple hallmarks of cancer (PLoS Genetics, 2015)

Systems Biology Approach Reveals a Calcium-Dependent mechanism for basal toxicity in Daphnia Magna (Environmental Science Technology, 2015)

Adverse outcome pathways for regulatory applications: examination of four case studies with different degrees of completeness and scientific confidence (Toxicological Sciences, 2015)

Lpg0393 of Legionella pneumophila Is a Guanine-Nucleotide Exchange Factor for Rab5, Rab21 and Rab22 ( PloS One, 2015)

Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations (Nucleic Acids Research, 2014)

ProteomeXchange provides globally coordinated proteomics data submission and dissemination (Nature Biotechnology, 2014)


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