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CV

last updated: 2023-12

Yi Liu, Research Fellow, MRC Integrative Epidemiology Unit, University of Bristol

  • Complex network analysis
  • Computational and statistical methods in causal inference
  • Machine learning and predictive analytics
  • Natural language processing

Professional experience

2023-08 -- present, Research fellow, MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol

2018-11 -- 2023-07, Senior research associate in health data science, MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol

I am affiliated with the Data Mining Epidemiological Relationships programme of Tom Gaunt.

2017-06 -- 2018-10, Postdoctoral Research Fellow, College of Social Sciences & International Studies, University of Exeter

I worked on the ESRC funded project “Inclusion and the academisation of English secondary schools: trends in the placement of pupils with significant SEN and those permanently excluded”.

Projects

Futher details here

Education

2012-09 -- 2017-07, PhD in Economics, Department of Economics, University of Birmingham

2011-09 -- 2012-08, MSc Money Banking and Finance, Department of Economics, University of Birmingham

2007-09 -- 2011-07, Financial management, School of Economics and Management, China University of Geosciences

Research output

Journal articles

Lloyd, O., Liu, Y., Gaunt, T.R., 2023. Assessing the Effects of Hyperparameters on Knowledge Graph Embedding Quality. Journal of Big Data. https://doi.org/10.1186/s40537-023-00732-5

Liu, Y., Elsworth, B.L., Gaunt, T.R., 2023. Using language models and ontology topology to perform semantic mapping of traits between biomedical datasets. Bioinformatics. https://doi.org/10.1093/bioinformatics/btad169

Zheng, J., Zhang, Y., Zhao, H., Liu, Y., Baird, D., Karim, M.A., Ghoussaini, M., Schwartzentruber, J., Dunham, I., Elsworth, B., Roberts, K., Compton, H., Miller-Molloy, F., Liu, X., Wang, L., Zhang, H., Davey Smith, G., Gaunt, T.R., 2022. Multi-ancestry Mendelian randomization of omics traits revealing drug targets of COVID-19 severity. eBioMedicine 81, 104112. https://doi.org/10.1016/j.ebiom.2022.104112

Zhao, H., Rasheed, H., Nøst, T.H., Cho, Y., Liu, Y., Bhatta, L., Bhattacharya, A., Hemani, G., Davey Smith, G., Brumpton, B.M., Zhou, W., Neale, B.M., Gaunt, T.R., Zheng, J., 2022. Proteome-wide Mendelian randomization in global biobank meta-analysis reveals multi-ancestry drug targets for common diseases. Cell Genomics 2, 100195. https://doi.org/10.1016/j.xgen.2022.100195

Liu, Y., Elsworth, B., Erola, P., Haberland, V., Hemani, G., Lyon, M., Zheng, J., Lloyd, O., Vabistsevits, M., Gaunt, T.R., 2020. EpiGraphDB: a database and data mining platform for health data science. Bioinformatics 37, 1304–1311. https://doi.org/10.1093/bioinformatics/btaa961

Zheng, J., Haberland, V., Baird, D., Walker, V., Haycock, P.C., Hurle, M.R., Gutteridge, A., Erola, P., Liu, Y., Luo, S., Robinson, J., Richardson, T.G., Staley, J.R., Elsworth, B., Burgess, S., Sun, B.B., Danesh, J., Runz, H., Maranville, J.C., Martin, H.M., Yarmolinsky, J., Laurin, C., Holmes, M.V., Liu, J.Z., Estrada, K., Santos, R., McCarthy, L., Waterworth, D., Nelson, M.R., Smith, G.D., Butterworth, A.S., Hemani, G., Scott, R.A., Gaunt, T.R., 2020. Phenome-wide Mendelian randomization mapping the influence of the plasma proteome on complex diseases. Nat Genet. https://doi.org/10.1038/s41588-020-0682-6

Liu, Y., Bessudnov, A., Black, A., Norwich, B., 2020. School autonomy and educational inclusion of children with special needs: Evidence from England. British Educational Research Journal 46, 532–552. https://doi.org/10.1002/berj.3593

Black, A., Bessudnov, A., Liu, Y., Norwich, B., 2019. Academisation of Schools in England and Placements of Pupils With Special Educational Needs: An Analysis of Trends, 2011–2017. Frontiers in Education 4. https://doi.org/10.3389/feduc.2019.00003

Working papers and preprints

Vabistsevits, M., Robinson, T., Elsworth, B., Liu, Y., Gaunt, T., 2022. Integrating Mendelian randomization and literature-mined evidence for breast cancer risk factors. medRxiv. https://doi.org/10.1101/2022.07.19.22277795

Liu, Y., Gaunt, T.R., 2022. Triangulating evidence in health sciences with Annotated Semantic Queries. medRxiv. https://doi.org/10.1101/2022.04.12.22273803

Zheng, J., Liu, Y., Elsworth, B., Bronson, P.G., Nounu, A., Haycock, P., Robinson, J.W., Babaei, M.S., Kanzaria, S., John, S., Prins, B., Runz, H., Hurle, M., Hemani, G., Butterworth, A., Scott, R.A., Davey Smith, G., Gaunt, T.R., 2022. Multi-omics Mendelian randomization powering drug targets prioritization for common diseases. In preparation.

Zheng, J., Lu, J., Cui, B., Qi, J., Yang, Q., Xu, M., Xu, Y., Wang, T., Li, M., Zhao, Z., Zheng, R., Wang, S., Lin, H., Hu, C., Cui, C.S.L., Yeung, S.L.A., Luo, S., Dimopoulou, O., Dixon, P., Harrison, S., Liu, Y., Robinson, J., Yarmolinsky, J., Haycock, P., Yuan, J., Lewis, S., Gaunt, T.R., Davey Smith, G., Martin, R., 2022. Effect of sodium-glucose cotransporter 2 inhibition on prostate cancer risk: evidence from Mendelian randomization and electronic health-care study. Submitted.

Elsworth, B., Lyon, M., Alexander, T., Liu, Y., Matthews, P., Hallett, J., Bates, P., Palmer, T., Haberland, V., Davey Smith, G., Zheng, J., Haycock, P., Gaunt, T.R., Hemani, G., 2020. The MRC IEU OpenGWAS data infrastructure. bioRxiv. https://doi.org/10.1101/2020.08.10.244293

Conference presentations

Liu, Y., Gaunt, T.R., 2023. Triangulating evidence in health sciences with Annotated Semantic Queries. 2023 Research Software Engineering in Data Science & AI Workshop. Warwick, UK.

Elsworth, B., Liu, Y., Gaunt, T.R., 2019. Vectology – exploring biomedical variable relationships using sentence embedding and vectors. 1st International “Alan Turing” Conference on Decision Support and Recommender Systems. London, UK.

Liu, Y., Gaunt, T.R., 2019. Computing systematic polygenic risk scores associations using biobank-wide association scan. 4th International Mandelian randomization conference. Bristol, UK.

Liu, Y., Elsworth, B., Erola P., Haberland V., Gaunt, T.R., 2019. EpiGraphDB: a database and data mining platform for health data science. 4th International Mandelian randomization conference. Bristol, UK.

Liu, Y., Bessudnov, A., Black, A., Norwich, B., 2018. The effects of the academisation of English schools on educational trajectories of children with Special Educational Needs. London, UK.

Liu, Y., Bessudnov, A., Black, A., Norwich, B., 2018. Estimating the causal effects of academisation of English schools with the data from the National Pupil Database. 2018 International Conference for Administrative Data Research. Belfast, UK.

Liu, Y., Black A., 2017. Trends on pupils with special education needs and disabilities (SEND) and the academisation effect. National Pupil Database User Group. London, UK.

Black, A., Liu, Y., Bessudnov A., Norwich, B., 2018. Inclusion and the academisation of English secondary schools: trends in the placement of pupils with significant SEN and those permanently excluded. Social Mobility Conference. Exeter, UK.

Software

Liu, Y., IEU software coordination team, 2022. MRC IEU wiki. https://mrcieu.github.io/wiki

Liu, Y., Gaunt, T.R., 2022. Ontology harmonization annotator. https://annotator.epigraphdb.org

Liu, Y., IEU software coordination team, 2021. MRC IEU GitHub pages. https://mrcieu.github.io/

Liu, Y., Elsworth B., Haberland V., Gaunt, T.R. 2020. EpiGraphDB software. https://mrcieu.github.io/software/epigraphdb

Liu, Y., Haberland V., Vabistsevits M., Gaunt, T.R., 2020. epigraphdb R package. https://cran.rstudio.com/web/packages/epigraphdb

Liu, Y., Elsworth, B., Gaunt, T.R., 2019. Vectology. http://vectology.mrcieu.ac.uk/

Liu, Y., IEU OpenGWAS team, 2019. OpenGWAS reports. https://github.com/MRCIEU/opengwas-reports

Academic activities

Grants

Assessing capability of large AI models in text mining of cancer studies, University of Bristol Cancer Research Fund seedcorn funding, 2023, Liu, Y. (Co-PI), Xu, Z. (Co-PI), Sobczyk-Barad, M., Gaunt T.R., Simpson, E.

Data acquisition and pilot study on BioRxiv and MedRxiv full text data to facilitate comprehensive data mining on biomedical literature, Elizabeth Blackwell Institute Rapid Research Funding Call Award 2023, 2023, Liu, Y. (PI), Gaunt T.R.

Automation in systematic reviews. WCRF UK. 2023 -- 2026. Liu, Y. (Co-PI), Sobczyk-Barad, M. (Co-PI), Millard, L., Martin, R., Gaunt T.R.

Local authority responses to diversity: school placement trends. 2018 -- 2019. BA/Leverhulme Small Research Grants, Sakellariadis, A. (PI), Liu, Y., Black, A., Norwich, B.

PhD Student supervisions

Marina Vabistsevits. Supervised by Tom Gaunt, Tim Robinson, Yi Liu, Benjamin Elsworth

Oliver Lloyd. Supervised by Tom Gaunt, Yi Liu, Patrick Rubin-Delanchy

Winfred Gatua. Supervised by Tom Gaunt, Yi Liu, Deborah Lawlor, Maria Sobzcyk-Barad, Jie Zheng

Referee for Journals

Journal of Personalized Medicine; Healthcare; Applied Sciences; Genes; Symmetry; Behavioural Sciences; BioData Mining; Electronics;