Dr James Smith

Dr James Smith

Profile

After graduating from the University of Leicester, I started a DPhil at the University of Oxford. An invitation of an industry-funded PhD in Computer-aided Drug Design lured me over to the University of Cambridge, with TeknoMed, a multi-site consortium that later became DeNovo Pharmaceuticals UK Ltd. This opportunity of cutting-edge research into inhibitor design of nucleotide binding site targets started my career in industry-related medicinal and computational chemistry in protein-ligand interactions and later xenobiotic metabolism. Drug target discovery in the interactome has remained a theme in my research. 

Postdoctoral research career prior to joining the University of Leeds

2013-2016, Senior Investigator Scientist at  MRC Human Nutrition Research, Elsie Widdowson Laboratory, Cambridge, UK.
2012-2013, Fixed-term Lectureship, BBSRC-funded SysMIC DTP consortium School of Biological Sciences, Birkbeck, and an Honorary Lecturer at the Research Department of Cell and Developmental Biology, University College London.
2009-2016, Affiliated Lecturer in Network and Computational Biology at the  Cambridge Computational Biology Institute, Department of Applied Mathematics and Theoretical Physics and additionally under Sir Tom Blundell, Department of Biochemistry, part of the Genome3D and the Open Source Drug Discovery Consortium, University of Cambridge.
2007-2010, Volkswagen Foundation-funded Research Fellow in Computational Systems Biology with Marc-Thorsten Hütt, Jacobs University Bremen, Germany.
2004-2007, Visting Research Fellow in Computational Chemistry, Computer Chemistry Center and the  Biophysics Group, Centre for Medical Physics and Technology, University of Erlangen-Nuremburg, Germany.
2004  MRC Centre for Protein Engineering at the MRC LMB with Sir Alan Ferscht peptidomimetic inhibitor design, University of Cambridge.
2001-2003 The Wellcome Trust (London), AstraZeneca and Unilever-funded Resarch Associate at the Centre for Molecular Informatics, University of Cambridge.
1999-2001 Molecular modeller in drug target discovery, The Drug Design Group, University of Cambridge and DeNovo Pharmaceuticals UK Ltd.

Responsibilities

  • School PGT Tutor and PGT Admissions
  • MNatSc Link Tutor - Joint Hons & NatSc committees and Progression & Awards Board.
  • Course Module Coordinator

Research interests

James Smith joined the School in September 2016 as a University Lecturer in Biochemistry initially in the Chemistry & Biochemistry Section. His personal research group is multi-disciplinary, focusing on structural biology and systems biology.  His nutritional and molecular epidemiology interests lie in developing statistical models useful for discriminating emergent states that could indicate metabolic phenotypes. His chemistry interests remain in structure-based drug design and pathway discovery.

External and International Collaborators

  • Nick Parker and Andrew Baggaley, Newcastle University, UK.
  • Chi-Ying Huang, National Yang Ming University, Taiwan.
  • Garstka Malgorzata Anna, Xi'an Jiaotong University, Xi’an City, Shaanxi, PR China - Diagnostic biomarker discovery in early GDM. 
  • Ahmed M. Ibrahim, Mansoura, Dakahlia, Egypt - Potential adjustment of  gut microbe populations with a pro-phylactic nutritional strategy for metabolic syndrome. 
  • Babiker Badri, Ahfad University for Women, Omdurman, Sudan - Natural product-derived re-design of leishmanicidal agents. 
  • Micheal J Wise, University of Western Australia, Australia.  
  • David Hauton, University of Oxford. 
  • Albert Koulman and Davide Chiarugi, University of Cambridge. 
  • Valerie Speirs, University of Aberdeen.
  • Richard Foster, University of Leeds.

Local Recognition

  • Personal Tutor Award  from the Faculty of Environment and shortlisted for the University of Leeds, Partnership Awards 2020.
  • Shortlisted for the Inspirational Teaching Award from the Faculty of Mathematics and Physical Sciences, Partnership Awards 2018.

Professional Activities

  • NIHR Peer reviewer
  • European Commission H2020 Registered Expert Evaluator
  • Peer Reviewer for Computational & Mathematical Methods in Medicine, Journal of Theoretical Biology

Recent Funding

  • Wellcome Trust (London)-funded University of Leeds Institutional Strategic Support Fund Discipline Hopping Fellowship for Iosifina Sampson 2020-2021. With Lucy Stead and Richard Bayliss, University of Leeds and Mariko Okada, Osaka University.
  • Machine Learning Exploration of Circulating Biochemical Biomarkers for Gestational Diabetes Wellcome Trust (London) UNS89407 2019.
  • British Council, Newton Funds, FAPESP (Brazilian Research agency) and ANII (Uruguayan Research Agency), UK, Brazil & Uruguay
    Exploring the potential of biological soft matter in AgriFood challenges 2018.
  • The validation of biomarkers of metabolic efficacy in infant nutrition BBSRC DRINC BB/M027252/1 and BB/M027252/2 with Albert Koulman, Core Metabolomics and Lipidomics Laboratory, University of Cambridge Metabolic Research Laboratories, UK.

Current Postgraduate Researchers

  • Yaowei Xun, jointly supervised by Richard Bayliss, University of Leeds - Structural molecular biology and inhibitor complexation of oncogenic fusion proteins in non-small cell lung cancer. 
  • Riannnon Morris,  co-supervised by Helen ChappellAntonia Borrissova and Andrew Scott, University of Leeds.
  • With Deirdre Devine and Andrew Scott co-supervising Oliver Hills, supervised by Helen Chappell, University of Leeds.
  • Yuwei Li,  jointlysupervised by Francisco M. Goycoolea, University of Leeds - Modelling bacterial spatio-temporal patterns on microfluidic droplet surfaces - Rock-paper-scissor dynamics, reciprical altruism and dispersity of microbial populations. 
  • John W. Holden, kindly funded by DEFRA (HMGov UK) and Newcastle University, co-supervised by Sam Grant, DEFRA, Nick Parker and Andrew Baggaley, Newcastle University, and Melvin Holmes and Rammile Ettelaie, University of Leeds - Lattice-based epidemic spread, and novel forecasting of disease velocities to inform effective containment strategies.
  • Nienyun Sharon Hsu, co-supervised by Richard Bayliss, University of Leeds - Drug target discovery and peptide-based drug design for novel Basal-like breast cancer chemotherapy targetting intrinsically disordered regions in membrane-associated signalling domains. 
<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, University of Cambridge, UK.
  • BSc (Hons) Biological Sciences, University of Leicester, UK.

Professional memberships

  • Biochemical Society (London)
  • British Biophysical Society
  • Society for Mathematical Biology
  • Natural Sciences Society

Student education

  • 2016-2020 Module Coordinator for FOOD2031 & FOOD5241M covering nutritional chemistry and food biochemistry.
  • 2016-2019 Network and Systems Modelling for FOOD3130 Food Research: Recent Revelations and Disputes,
  • 2019 Radical Reaction Mechanisms and Fatty Acid Oxdation for FOOD5196M Impacts of Processing on Nutritional Quality.

Undergraduate and Masters Research Projects

I welcome motivated Nutrition and Medical students wanting to explore the use of biomarkers and molecular epidemiology. I welcome Natural Sciences students motivated by research and in being trained further in multi-disciplinary areas including medicinal and biological chemistry, computational molecular biochemistry, or in research areas at a systems level including metabolic and nutritional state prediction in health and disease or metabolic modelling and computational systems biology. I am also keen to host students with experience in computing and mathematics especially formal methods for mathematical biology, biostatistics and machine learning.

Every year, I host Summer vacation internships and have collaborators interested in sharing students. Enquire early in the New Year if you are interested in joining my research group for a scholarship-funded project during the Summer. There are a number of organisations and societies listed here and here that offer funding and scholarships. 

Current and Former Research Students

  • X Shen (2020) Polysaccharide organisation of marine biofilms, understanding the physicochemical constraints for the design of repellent surfaces for culinary use.
  • S Wu (2020) Interactions of drugs on cysteine-rich kidney stones.
  • P Zhang (2020) Assessing HbA1c measurements by Statistical modelling and clustering of blood pressure measurements.
  • M Li (2020) Discussing uncertainties in using the OGTT and CGM in the third trimester of pregnancy.
  • K Zhang (2020) with Nienyun Sharon Hsu and Yaowei Xun - Binding sites of oncogenic fusion proteins of non-small cell lung cancer.
  • T Liu & CW Chan (2019-20) Statistical modelling and clustering of blood pressure measurements.
  • O Taylor (2019-20) Re-assessment of unsupervised clustering of retrospective early gestational diabetes and OGTT clinical data.
  • E Wong (2019-20) Computer-aided drug design of peptide inhibitor binding for targets in basal-like breast cancer.
  • Y Jiang (2019-20) Computational Systems Biochemistry - Cyclic and feed-forward motif behaviour from flux patterns of anaplerotic metabolic reactions in E.coli.
  • O Taylor (2019) Wellcome Trust-funded Summer Studentship: An unsupervised multivariate analysis of early gestational diabetes clinical biomarkers.
  • Y Xun (2019) 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) with  Yuwei Li – Microbial and metabolic modelling of repeated Stag Hunt competition in cyclic Rock-Paper-Scissor interactions.
  • A Shen (2019) Systematic review of coagulation biomarkers on early gestational diabetes. 
  • T He (2019) Systematic review of the hepatic and trace element biomarkers on early gestational diabetes.
  • Y Zhang (2019) Systematic review of the thyroid and anaemia biomarkers on early gestational diabetes.
  • H Tong (2018-9) with Helen Chappell – Modelling interactions of aflatoxins and their metabolites with calcium phosphate,
  • G Gornall (2018-9) with Helen Chappell – Water activity and hydration shells of polyphenols.
  • S Holmes (2018-9) Rock-paper-scissor dynamics - Development of a cellular automaton model for interacting bacterial colonies.
  • L Potts (2018-9)  Identifying metabolic biomarker correlations in clinical data from early gestational diabetes.
  • K Daly (2018) 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)  Phase I metabolism prediction of xenobiotics - A comparison of  mechanistic biotransformations by CYP2D6 and CYP2C9  predicted using SPORCalc.
  • Y Li (2018) Identification of functional motifs from GAB1 intrinsically disordered regions and an assessment of their stabilising interactions with SHC binding domains.
  • W Zhou (2018) 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. 
  • Z Ma (2017) Molecular recognition of isosterol and triterpenoid-based ligand-binding constraints to inform structure-based drug design.
  • D Wu (2017) 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 and EPSRC-funded Summer Studentship: Canonical correlation analysis  & combinatoric composition analysis of acyl abundance in phospholipids and neutral acylglycerol, derived from large scale lipidomics. 
  • M  Liu (2017) Discrimination of Her2 and Luminal-A breast cancer patients revealed by hierarchical clustering of nuclear receptor expression patterns.
  • W Pan (2017) 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). 
  • A  Ackroyd (2016-7) 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 (2016-7) 2D machine learning stratification of fat lipid biomarkers, useful for molecular epidemiology and fish-oil intervention studies.
  • M Harland (2016-7) 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.

 

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>