Software
- Latent Variable Stochastic Ensemble of Trees (LAVASET) is freely available from GitHub.
- Natural language processing tools for omics data are available from the omicsNLP GitHub.
- Covariate Adjusted PLS (CAPLS) v1.5 (June 2018) is freely available from BitBucket.
- PanViz v1.4 is freely available from BioConductor.
- SubseT Optimization by Reference Matching (STORM) v2.0 (September 2017) is freely available from BitBucket.
- Resolution EnhanceD STORM (RED-STORM) is freely available from BitBucket.
- MetaboNetworks v2.1 (September 2017) is freely available from the MATLAB File Exchange.
- MetaboNetworks v2.2 (June 2018) is available from BitBucket.
- MetaboPathways v1.0 (June 2018) is freely available from BitBucket.
Guest Lectures
Host genomic influence on the gut microbial metabolite-blood pressure relationship, International Society of Hypertension conference, Kyoto, Japan, 2022
URINARY METABOLIC PHENOTYPE OF BLOOD PRESSURE, ESH ISH ON AIR Joint Meeting, Glasgow (online), 2021
An issue of life and breadth: how a urine test can help a nation on aslender bender, Health Data Research UK, London, 2020
Monitoring diet more accurately to aid healthy living (in a post-COVID society), Health Data Research UK, London, 2020
Integrating omics to understand blood pressure variation, MRC London Institute of Medical Sciences, London, United Kingdom, 2020
A Systems Biological Approach to the Interpretation of Multi-omics Data, Stellenbosch University, Stellenbosch, South Africa, 2019
Systemic nutriome-metabolome interactions to understand pathways to disease risk in humans, Murdoch University, Perth, Australia, 2019
Research Student Supervision
Alloula,A, Phenotypic Classification using Deep Learning in Metabolomics
Anholt,L, Leveraging geometric learning for community detection in biological networks that integrate polymorphic and metabolic data
Anholt,L, Expanding the systems view of biology and disease by integrating genome-wide association catalog data in the visualization of metabolic reaction networks
Bai,P, Topological machine learning to analyse metabolomic networks for idiopathic pulmonary fibrosis
Chaitrakulthong,N, Expanding the systems view of colorectal cancer risk by integrating genome-wide association catalog data in the visualization of metabolic reaction networks with MetaboNetworks
Cheng,Z, A framework for spatial metabolomics data analysis of fatty liver disease and liver fibrosis
Faghih Mirzaei,N, What-the-bug?! Named entity recognition of bacteria and microbiota in biomedical text using recurrent neural networks
Gao,M, Data visualization and analysis of intravital microscopy multi-layered video (4D) data to identify how splenic neutrophils are controlled in their activation, location and migration by other splenic players
Hu,Y, Natural language processing of biomedical literature: automated mining of metabolome-wide association studies
Hydyrova,L, UROP: Creation of a Multi-Task Corpus for Metabolite, Enzyme and Pathway Named Entity Recognition
Ibrahim,M, Natural language processing of biomedical literature: automated mining of genome-wide association studies
Jarosinska,O, Multi population assessment of urinary metabolome stability over time
Jin,W, Auto-CORPus: Automated Abbreviation and Definition Detection of Biomedical Literature
Kasapi,M, Integration of faecal metabolic phenotypes and gut microbiota in subtypes of irritable bowel syndrome
Krauss Souper,C, Harmonisation of UKBB data for the prediction of cardiomyopathy through machine learning
Li,ZJ, “A picture is worth a thousand words”: translating images found in biomedical literature to text
Liu,W, Can I Have Your (Un)Divided Attention? Single- versus multitasking in biomedical natural language processing
Mailijia,J, Visualization, Data Mining and Automated Molecular Identification in Spatial Metabolomics of Chronic Liver Disease
Makraduli,F, Find The Assay: named entity recognition of techniques used for genome-wide and metabolome-wide association study data generation
McQuibban,NAR, GWAS Metadata Extraction: GWAS MNER
Money-Kyrle,S, Scaling As A Hyperparameter
Ni,Y, Understanding the impact of two extreme diets on gut microbiota and microbial metabolites variability in people at risk of cardiovascular disease
Patel,D, UROP: Integrating Natural Language Processing into Bioinformatics Analysis of Idiopathic Pulmonary Fibrosis Microbiome Data
Popovici,CM, Automated Mining of Preprint and Peer-reviewed Literature for Cohort Characteristics
Scotcher,J, Understanding the Role of Host-Microbiome Interactions in the Pathophysiology of Irritable Bowel Syndrome and Its Subtypes
Son,W, NLP in Radiology Report: Auto-Label Generation for CXR Image Classification
Stotzem,N, AstraZeneca Sponsored Project: Remodelling of immunometabolism in chronic liver disease using novel data integration and visualisation tools
Sun,A, Natural language processing of biomedical literature to support automated mining of genome-wide association studies
Talay,A, Natural language processing of biomedical literature to extract genome-wide association study data
Tambini,DR, Expanding the configuration of Auto-CORPus with Scientific Journals for Broader Data Coverage in Natural Language Processing Pipelines
Truong,A, Data visualization and analysis of intravital microscopy multi-layered video data using statistical machine learning
Tsagkarakis,N, Natural Language Processing to Standardize Biomedical Scientific Literature
Wang,M, Named Entity Recognition for enzymes in biomedical text
Xu,K, UROP: Natural language processing of electronic health records to augment deep learning on lung radiology imaging
Xu,K, UROP: incorporating latent variables in ensemble methods
Yassin,SM, Class-based directional feature importance for tree-based classifiers
Yeung,C, MetaboListem and TABoLiSTM: Two Deep Learning Algorithms for Metabolite Named Entity Recognition
Yoon,G, LABP: Integrating bioinformatics and literature knowledge into models to predict 1-year mortality in Idiopathic Pulmonary Fibrosis patients using baseline genomics data