Research group 

University of Leeds, UK

• Wang HaoChen (2024) MSc student – joint supervisor with Helen F Chappell.  First Principles Modelling of Interactions between Novel Quorum Sensing Pqs receptor Inhibitors and Pseudomonas aeruginosa extracellular alginate. 

• Jia Xu (2024) MSc student Network analysis of fatty acid data

• Jian Chen (2024) MSc student Systematic review on Vitamin D supplementation

• Stella Ning Li (2024) MSc student – Network analysis of public-health co-morbidities - a pilot survival analysis and CapStone Project Innovation to Impact Grant funding  proposal of joint lung bacterial infections with pancreatic ductal adenocarcinoma (PDAC).

• Runyan Zhu (2024). MSc student –  Evidence of the risks of the spread of air-borne Antimicrobial Resistance from Secondary processed and Ultra-processed food stuffs

• Meagan G. D'Souza (2024) MSc student – Evaluation of  low molecular weight molecules  that share similar physicochemical properties to nutrients, used as antimicrobials for Gram negative bacteria lung infections.

• An-nie Yuan Wang  (2024) MSc student – Informing  predictive toxicology – A structural bioinformatics analysis of D-residues in Proteins and Peptides.

• Giselle X Lim (2023-24) BSc student– Molecular endocrinology structural bioinformatics - Molecular recognition and receptor complexation of oligopeptide hormones (Award winning poster).

• H Horsley (2023-24) BSc student – Nutritional incompatibilities and ethics of a ketogenic diet with chemotherapies.

• C Zhang, SA Chen (2023) MSc students – Investigating the metabolon of redox enzymes (specifically dehydrogenases) and the impact of somatic mutations and variants on protein-protein interaction partners.

• NT Johnson (2023) MSc student Joint supervisor with Amie Lister – Development of an extraction and isolation protocol  for determining  the surface charge and buffering characteristics of  soluble plant proteins.

• Isaac Noble  (2022 – present) EPSRC-funded PhD student joint supervisor with Helen F Chappell – Computational modelling of bacterial biofilm permeability and the design of novel antimicrobial therapeutics.

• J Chen, S Li, X Lin & Y Huang (2022) MSc students joint-supervisor with Lijing Ke – Tri-partite network descriptions of natural product chemistry from Traditional Chinese Medicine ingredients, their recognised protein targets and roles in  symptoms of long-COVID syndrome.

• Dr  Bhaveshkumar Bharatiya (2022) Molecular interactions within model membranes and the impact for bioadhesion and antimicrobial resistance.  Currently atthe  Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany. 

• G Sergalyte (2021 – 2022) MSci student joint-supervisor with Helen F Chappell and with  Rhiannon Morris – DFT modelling of kidney microtubular urinary metabolite fragments with calcium oxalate.

• T Ensor (2021 – 2022) BSc student joint-supervisor with Mark Hopkins – Bayesian cluster analysis of psychometric indices to indicate mis-reporting in cohorts returning self-reported dietary assessments of their own energy intake.

• H Panesar, S Yuan & Y Wang (2021) MSc students – Tri-partite network descriptions of natural product chemistry from Traditional Chinese Medicine ingredients, their recognised protein targets and roles in  symptoms of long-COVID syndrome.

• Y Jiang (2021) MSc student – Functional analysis and mathematical modelling of continuous glucose measurement time series from Type 1 diabetics. 

• Y Zhang (2021) MSc student – Data analyses of breast milk fatty acid profile distributions under JASP. 

• Dr Iosifina Sampson Wellcome Trust ISSF Discipline Hopping Research Fellow  (2021 – 2023) with Richard Bayliss  & Lucy Stead – Bio-modelling of EML4-ALK V3 binding sites and its resistance signalling in NSCLC cells.

• R Chauhan (2020 – 2021) MSci student – Molecular integrity of the cell tight junction affected by fat-soluble vitamins in the gut.

• L Donaghy  (2020 – 2021) BSc student – Understanding Spatial and Temporal Alteration to the Gut Microbiome and the Impact on interspecies interactions.

• A  Blick (2020 – 2021)  BSc student – Analysis of individual dietary patterns and food intake and the misreporting when carrying out self-reported dietary assessments.

• J Wills (2020 – 2021)  BSc student – Analysis of historical trends of child-stunting with crop yield and rainfalls in Kenya. 

• I Blicknell (2020 – 2021)  BSc student & P Chalmers (2020 – 2021)  MSci student – Analysis of de novo lipogenesis-associated TAG lipid abundances between organs. 

• X Shen (2020) MSc student– Polysaccharide organisation of marine biofilms, understanding the physicochemical constraints for the design of repellent surfaces for culinary use.

• S Wu (2020) MSc student with Rhiannon Morris – Thiol drugs in cystine stones treatment.

• P Zhang (2020) MSc student – Assessment of  HbA1c measurements by statistical component analysis and clustering of blood pressure measurements.

• M Li (2020) MSc student – Discussion on  uncertainties in OGTT and CGM in the third trimester of pregnancy.

• K Zhang (2020) MSci student with Nienyun Sharon Hsu and Yaowei Xun  – Structural Bioinformatics: binding sites of oncogenic fusion proteins of non-small cell lung cancer.

• T Liu & CW Chan (2019 – 2020) BSc student – Statistical component modelling and clustering of blood pressure measurements.

• O Taylor (2019 – 2020) MSci student – A reassessment of unsupervised clustering of retrospective early gestational diabetes and OGTT clinical data. 

• E Wong (2019 – 2020) BSc student with Nienyun Sharon Hsu – Computer-aided drug design of peptide inhibitor binding for targets in basal-like breast cancer.

• Y Jiang (2019 – 2020) Nanjing Tech University Study Abroad Programme BSc student  with Yuwei Li –  Computational Systems Biochemistry: cyclic and feed-forward motif behaviour from flux patterns of anaplerotic metabolic reactions in Escherichia coli.

• O Taylor (2019) Wellcome Trust-funded Summer Studentship MSci (International) student 3rd year student Rank Prize Award (declined) – Unsupervised multivariate analysis of early gestational diabetes clinical biomarkers. 

• Y Xun (2019) MSc student with Nienyun Sharon Hsu  – Molecular docking of SHC domains to short linear motifs from intrinsically disordered regions in proteins related to intracellular signalling. 

• J Shu (2019) MSc student with Yuwei Li –  Ecological Modelling for exploring microorganism and cellular interactions.

• A Shen (2019) MSc student – Systematic review of coagulation biomarkers on early GDM. 

• T He (2019) MSc student– Systematic review of the hepatic and trace element biomarkers on early GDM. 

• Y Zhang (2019) MSc student – Systematic review of the thyroid and anaemia biomarkers on early GDM. 

• Rhiannon Morris (2019 – 2023) EPSRC-funded PhD student   co-supervised with Helen F Chappell – First Principles DFT and molecular dynamics modelling of organic-inorganic interactions contributing to crystal nucleation of kidney stones. 

• Oliver Hills (2019 – 2022), PhD student co-supervised with Helen F Chappell – First Principles DFT and molecular dynamics modelling of a Mucoid Pseudomonas aeruginosa Biofilm Extracellular Matrix.

• H Tong (2018 – 2019) BSc student with Helen F Chappell – Modelling interactions of aflatoxins and their metabolites with calcium phosphate.

• G Gornall (2018 – 2019) BSc student with Helen F Chappell – Water activity and hydration shells of polyphenols.

• S Holmes (2018 – 2019) BSc student with Yuwei Li – Rock-paper-scissor dynamics: development of a cellular automaton model for interacting bacterial colonies.

• L Potts (2018 – 2019) BSc student with Matthew Campbell – Identification of  metabolic biomarker correlations in clinical data from early gestational diabetes.

• K Daly (2018) Erasmus+ funded research project from DIT Dublin, Ireland BSc student – Quantitative methods for exploring metabolomics:
  i) biostatistical methods for anthropometry landscape modelling according to dominant phospholipids in circulating lymphocytes.
  ii) unsupervised machine learning pattern recognition to characterise physiological biomarkers indicative of gestational diabetes in the first trimester. 

• L Yeo (2018) MSc student – Phase I metabolic prediction of xenobiotics. A comparison of hydroxylations by CYP2D6 and CYP2C9 P450s predicted using SPORCalc.

• Y Li (2018) MSc student with Nienyun Sharon Hsu – Identification of functional motifs from GAB1 intrinsically disordered regions and an assessment of their stabilising interactions with SHC binding domains.

• W Zhou (2018) MSc student with Nienyun Sharon Hsu – Characterising PPI binding motifs in intrinsically disordered regions used by KIT protein signalling, for peptidomimetic drug target discovery in signalling protein aggregates in breast cancer. 

• Yuwei Li  (2018 – 2024)  PhD student jointly supervised with Francisco M Goycoolea and co-supervised by Helen F Chappell – Synthetic Molecular Biology and Biotechnology.  An engineered Escherichia coli consortium for studying quorum sensing. 

• John W Holden (2018 – 2022)  DEFRA & University of Newcastle co-funded PhD student  jointly supervised with Nick Parker and co-supervised by Andrew Baggaley (Newcastle U),  Sam Grant (DEFRA) and  Melvin Holmes & Rammile Ettelaie – Modelling spatio-temporal tree disease epidemics in Great Britain. BioRxiv

• Z Ma (2017) MSc student with Sharon Nienyun Hsu – Molecular recognition of isosterol and triterpenoid-based ligand-binding constraints to inform structure-based drug design.

• D Wu (2017) MSc student with Sharon Nienyun Hsu – Identification of potential drug targets from hub-associated motifs from transcription factor networks, found in basal (triple-negative) breast cancer patients. 

• H Tong (2017) University of Leeds & EPSRC-funded Summer Studentship MMath (3rd Year) student joint supervisor with Jianhua Wu – Canonical correlation analyses and  combinatorial composition analysis of acyl abundance in phospholipids and  triacylglycerols, derived from large scale lipidomics. 

• M  Liu (2017) MSc student with Nienyun Sharon Hsu – Discrimination of Her2/Neu and Luminal type patients: A breast cancer patients revealed by hierarchical clustering of nuclear receptor expression patterns.

• W Pan (2017) MSc student with Helen Chappell and with  Denise Li – Explicit solvent molecular modelling.  Hydrogen-bonding networks determined from conformational sampling of MD-generated conformational ensembles (with AMBER) followed by geometry optimisation with DFT (with CASTEP). 

• ​​Sharon Nienyun Hsu (2017 – 2021) PhD student and jointly supervised with  Richard Bayliss and co-supervised by Iosifina Sampson ​​​​​​ –  Revealing Putative Drug Targets for Basal-Like Breast Cancer.  (2021-2022) Bioinformatician, University of Sheffield. (2022-2030) MD Programme at National Cheng Kumg University Medical School, Taiwan.

• A  Ackroyd (2016 – 2017) BSc student with Alan Mackie – Time-dependent correlation clustering analysis to reveal coherence between self-reported satiety with physiological  data collected from lateral MRI imaging and circulating blood biomarkers linked to gastric emptying.

• A  Bawden (2016 – 2017) BSc student – 2D machine learning stratification of fat lipid biomarkers, useful for molecular epidemiology and fish-oil intervention studies.

• M Harland (2016 – 2017) BSc student with David Hauton – Regressing cardiac QT and RR interval signals to both logarithmic and parabolic models to determine  the accuracy of QTc interval changes during cardiovascular exercise and nitrate supplementation.

• Dr Ahmed M Ibrahim (2016 – present) Independent Research Pharmacist, Mansoura, Dakahlia, Egypt – Game theoretic consideration of transgenic bacteria in the human gut microbiota as a pro-biotic prophylactic for metabolic syndrome, BioRxiv

MRC Human Nutrition Research, Elsie Widdowson Laboratory, Cambridge, UK.
The Dept of Biochemistry,  University of Cambridge, UK.
The Cambridge Computational Biology Institute,  DAMTP,  University of Cambridge, UK.

• K Loell (2016) MPhil student (Computational Biology) co-supervised with Albert Koulman,  Wellcome-MRC Institute of Metabolic Sciences & MRC Epidemiology Unit – Revealing Biomarker Mixtures in Lipid Pools from large-scale Lipidomics.

• R Galiwango (2015) MPhil student (Computational Biology) – Metabolic & nutritional phenotypic landscape models in population data. A method development for the InterAct component of the EPIC consortium. 

• R Crawford (2015) MSci student  (Biochemistry) PartII (3rd year) – Stochastic modelling of fatty acid metabolism in rats and humans.

• A Zardilis (2014) MPhil student (Computational Biology) Executable & Synthetic Biology – Extensible and executable stochastic models of fatty acid and lipid metabolism. 

• Dr Luke Marney (2014-2016) MRC Investigator Scientist, co-supervised with Albert Koulman – Bootstrapping, statistical component clustering, lipidomics data analysis, computational analytical chemistry. (2020-present) Oregan State University, USA.

• Z Zhou (2014) MPhil student (Computational Biology) Correlation Network Analysis – Investigating metabolomics data from T1D mouse models using Dirichlet Process clustering to stratify and generate biomarker signals.

• Dr Animesh Acharjee (2013 - 2016) MRC Investigator Scientist  – Maximum likelihood estimation, random forest regression and classification, computational  biology and chemistry, metabolomics data analysis  (2016 – present) University of Birmingham UK.

• Hsin-Wei Wang (2012) NTOU Taiwan–UK Exchange-funded PhD student co-supervised with Tom Blundell – Investigating fragment and functional group composition using a latent feature Bayesian hierarchical classification model for HTS virtual screening.

Jacobs University Bremen, Germany.

• Shuban  Jain (2010)  MSc student (Mol Life Sci) with Marc T Huett Computational strategy for the metabolic engineering of Saccharomyces cerevisiae to optimize the production of metabolic intermediates.

University of Erlangen-Nuremberg, Germany.

• Gerold Diez (2006 – 2008)  DFG-funded PhD student co-supervised with Wolfgang Goldmann – Lipid-binding interactions on the vinculin tail domain helical bundle.

• Nicolas Bernhard (2005) BSc student (Mol Life Sci) - Investigating tetracycline analogues: developing a molecular discrimination approach using electronic and steric descriptors.

• Ula  Uciechowska (2004) Erasmus+ funded MSciEng (Computational Chemistry) student  Institute of Physical and Theoretical Chemistry, Technical University of Wroclaw, Poland – Analysis of the conformational behaviour of two TrxA peptide fusion constructs by MD simulations.

Dept of Chemistry, University of Cambridge, UK.

• Mike Burke (2002 – 2003) MSci (Biochemistry) Part III (4th year) student – Prediction of xenobiotic metabolism by CYP P450 isoforms.

• Laura  Guerra-Arias (2002 – 2003) MSci (Biochemistry) Part III (4th year) student  with John Christodoulou – Molecular modelling approaches for a potential drug target: Calcium-Dependent Protein Kinase.

• Victor Stein (2002) Wellcome Trust (London) & Trinity College Cambridge-funded  MSci (Biochemistry) 1B (2nd year) summer student. – Predicting the P450 site of metabolism of active compounds and xenobiotics SPORCalc.

• Helen F Chappell (2002) MRes (Biomolecular Science) student University of York,  with John Mitchell Examination of percentage amino acid compositions of protein architecture.

• Nicola Kerrison (2001 – 2002) MSci (Biochemistry) Part II (3rd year) student – DNA duplex recognition by polypeptides: an analysis of base pair step conformations.

• James Torrance  (2001 – 2002) MSci (Biochemistry) Part III (4th year) student– Ligand-centred analysis of NADP(H)–protein interactions.