Dr James Smith

Dr James Smith

Profile

Dr James Smith joined the Chemistry & Biochemistry Section in the School in September 2016 as a University Lecturer in Biochemistry (Metabolic & Biophysical Modelling).  Before arriving in Leeds, he was an MRC Senior Investigator Scientist at the MRC Human Nutrition Research, Elsie Widdowson Laboratory, Cambridge and previously a temporary Lecturer at Birkbeck College, London and University College London. For many years, he was also an Affiliated Lecturer at the Dept of Applied Mathematics & Theoretical Physics, University of Cambridge.  During his research career, he held positions at the MRC Centre for Protein Engineering, and Depts of Chemistry and Biochemistry, University of Cambridge, UK  and also worked in Germany at the University of Erlangen Nuremberg and at Jacobs University Bremen, Germany as a Volkswagen Foundation Research Fellow. 

Responsibilities

  • PGT Tutor & Admissions

Research interests

Dr Smith’s research focuses on aspects of computational structural and systems biochemistry. He has a particular interest in molecular recognition questions involving allostery  in ligand-protein and protein-protein interaction networks in signalling and metabolic pathways in health and disease.

<h4>Research projects</h4> <p>Any research projects I'm currently working on will be listed below. Our list of all <a href="https://environment.leeds.ac.uk/dir/research-projects">research projects</a> allows you to view and search the full list of projects in the faculty.</p>

Qualifications

  • PhD Computer-aided Drug Design (Cantab)
  • BSc (Hons) Biological Sciences (University of Leicester)

Professional memberships

  • Biochemical Society (London)
  • Nutrition Society (London)
  • British Pharmacological Society (London)
  • Quantitative Systems Pharmacology Network
  • British Biophysical Society
  • Society for Mathematical Biology
  • Society for Natural Sciences

Student education

Dr Smith teaches Biochemistry at undergraduate level and  also on postgraduate programmes at Masters level. Dr Smith supervises a number of PhD students and mentors Early Career Researchers. He is enthusiastic to hear from individuals with research interests that align with his. If you are interested in conducting post-graduate or post-doctoral research in his group, please enquire by  email, attaching a copy of your CV and if possible information on a particular funding call to apply to. Members of the group have been previously funded by The Rank Prize Funds, The Wellcome Trust, UKRI EPSRC and BBSRC and the EU.  Undergraduate students are welcomed to enquire by email in January and February, if  interested in joining the research group for a 10 week Summer Research Scholarship Project.

Present & past colleagues and their research projects

  • Isaac Nobel PhD student (2022 – present) co-supervisor with Helen Chappell 

  • Dr Bhaveshkumar N Bharatiya  (2021 – present) Scientist, Deutsches Elektronen Synchrotron (DESY) Hamburg, Germany, and jointly mentored by Helen Chappell  – Understanding molecular interactions within model membranes and their impact on bioadhesion and antimicrobial resistance.

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

  • G Sergalyte (2021 – 2022) MSci with Helen Chappell and Riannnon Morris  – DFT modelling of kidney microtubular urinary metabolite fragments with calcium oxalate.

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

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

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

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

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

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

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

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

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

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

  • P Zhang (2020) MSc – Assessment of  HbA1c measurements by statistical coponent modelling and clustering of blood pressure measurements.

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

  • K Zhang (2020) MSci 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 – Statistical modelling and clustering of blood pressure measurements.

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

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

  • Y Jiang (2019 – 2020) BSc (Nanjing Tech University and University of Leeds Study Abroad Programme)  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) MSci (International) (3rd year Rank Prize Award (declined), Wellcome Trust-funded Summer Studentship)  – Unsupervised multivariate analysis of early gestational diabetes clinical biomarkers. 

  • Yaowei Xun (2019) MSc 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 with Yuwei Li –  Ecological Modelling for exploring Microorganism and Cellular Interactions.

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

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

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

  • Rhiannon Morris PhD student (2019 – present) jointly supervised with Helen Chappell  – DFT modelling of organic-inorganic interactions contributing to crystal nucleation of kidney stones. 

  • Oliver Hills PhD student (2019 – present) co-supervisor with Helen Chappell – First Principles and Molecular Dynamics Modelling of a Mucoid Pseudomonas aeruginosa Biofilm Extracellular Matrix.

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

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

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

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

  • K Daly (2018) BSc (Erasmus+ Project Student from DIT Dublin, Ireland)  – 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 – Phase I metabolic prediction of xenobiotics. A comparison of hydroxylations by CYP2D6 and CYP2C9 predicted using SPORCalc.

  • Y Li (2018) MSc 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 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 PhD student (2018 – present) jointly supervised with Francisco M. Goycoolea  – Synthetic biology of community quorum sensing strains in Escherichia coli

  • John W Holden PhD student (2018 – 2022) 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.

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

  • D Wu (2017) MSc with Nienyun Sharon 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) MMath (3rd Year) with Jianhua Wu (University of Leeds & EPSRC-funded Summer Studentship) –  Canonical correlation analyses and  combinatoric composition analysis of acyl abundance in phospholipids and  tri acylglycerols, derived from large scale lipidomics. 

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

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

  • ​​Nienyun Sharon Hsu PhD student (2017 – 2021) and co-supervised by Iosifina Sampson ​​​​​​ and  Richard Bayliss –  Revealing Putative Drug Targets for Basal-Like Breast Cancer.  Visiting Research Fellow in Structural Bioinformatics (from U Sheffield, 2021 – 2022).​ 

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

  • M Harland (2016 – 2017) BSc 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.

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

MRC Human Nutrition Research, Elsie Widdowson Laboratory, and University of Cambridge, UK.

  • K Loell (2016) MPhil (Computational Biology) with Albert Koulman, MRC Epidemiology Unit – Revealing Biomarker Mixtures in Lipid Pools from large-scale Lipidomics.

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

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

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

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

Jacobs University Bremen, Germany

  • S Jain (2010)  MSc (Mol Life Sci) – Computational strategy for the metabolic engineering of Saccharomyces cerevisiae to optimize the production of metabolic intermediates.

University of Erlangen-Nuremberg, Germany

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

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

  • U  Uciechowska (2004) Erasmus+ MSciEng (Computational Chemistry)  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.

University of Cambridge, UK

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

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

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

  • HF Chappell (2002) MRes (Biomolecular Science) University of York. – Examination of percentage amino acid compositions of protein architecture.

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

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

Current postgraduate researchers

<h4>Postgraduate research opportunities</h4> <p>We welcome enquiries from motivated and qualified applicants from all around the world who are interested in PhD study. Our <a href="https://phd.leeds.ac.uk">research opportunities</a> allow you to search for projects and scholarships.</p>