Skip to navigation Skip to content

Runxuan Zhang

Staff picture: Runxuan Zhang
Information and Computational Sciences
Information and Computational Sciences
Quantitative Geneticist / Computational Biologist
+44 (0)1382 568886

The James Hutton Institute
Dundee DD2 5DA
Scotland UK


Runxuan is a computational biologist, who was trained in machine learning and artificial neural networks for his PhD. His 20 years of research have focused on developing computational and analysis methods/tools for high throughput experimental data, such as RNA-seq for gene expression analysis. His team has published several widely used and easily accessible software and tools for analyzing sequencing data.

He has gained extensive experience in computational biology by taking up postdoc positions in Systems Biology Group of Institut Pasteur, Paris, Center for Model Organisms Proteome, University of Zurich, Zurich and Translational Medicine Research Collaboration lab, Dundee, where his research focused on the development of novel and cutting-edge computational methods for high throughput experimental data, especially for transcriptomics and proteomics experiments.



Current research interests

His research group focuses on the development of novel and cutting-edge computational methods for analysing high throughput experimental data. He pioneered the development of methods for accurately measuring gene expression from plant RNA-seq experiments by developing the quality control pipelines that were essential for constructing a comprehensive Reference Transcript Dataset in Arabidopsis (AtRTD2). AtRTD2 allows rapid and accurate quantification of differential expression and alternative splicing (AS) analysis. This method has been translated into barley, potato and other plant species. His group also developed novel analytical tools for time-series RNA-seq data that capture the dynamics of expression and AS changes, including the first tool (R package TSIS) for characterising transcript isoform switches in a time series. These methods have now been incorporated into an easy-to-use tool for rapid and accurate RNA-seq and alternative splicing analysis (3D RNA-seq) which has been taken up by >6,000 users from ~60 countries. His group recently developed Protview, which optimizes the enzyme scheme to increase the protein coverage for proteomics experiments.

Current research projects

  • BBSRC BBR BB/S020160/1 ‘PlantRTD’ 2019-2022 (£391,401) (PI)
  • BBSRC Response Mode ‘The Generation Gap - Mechanisms of maternal control on grain’ BB/W002590/1 2022-2025 (£744,015) (Co-I)
  • BBSRC International Partnering Award ‘BarleyEUNetwork’ BB/V018906/1 2021-2024 (£30,000) (Co-I)
  • BBSRC International Partnering Award ‘UK Australia’ BB/V018299/1 2021-2024 (£30,000) (Co-I)
  • BBSRC ERA-CAPS BB/S004610/1 ‘BARN’ 2018-2022 (£649,658) (Co-I)


  • Hornyik, C.; Zhang, R.; Prashar, A.; Marshall, D.F.; Bryan, G.J. (2013) Characterisation of micro RNAs in the tuber bearing crop potato., UK PlantSci 2013, University of Dundee, Dundee, 16-17 April 2013.

  • Bonar, N.; Rahamkulov, I.; Dangol, S.D.; Zhang, R.; Dessoly, J.; Stephens, J.; Barakate, A.; Taylor, M.; Hornyik, C. (2019) Post-transcriptional gene regulation and gene editing in potato., 6th Plant Genomics and Gene Editing Congress and Micobiome for Agriculture Congress, Asia, Kuala Lumpur, Malaysia, 29-30 July 2019. (Abstract).
  • Zhang, R.; Liney M.; Marshall, D.; Dalmay, T.; Bryan, G.J.; Hornyik, C. (2014) The micro RNA transcriptome change during tuberization in potato., Post-transcriptional Gene Expression Regulation in Plants, Poznan, Poland, 30 June - 2 July 2014.
  • Morris, W.L.; Ducreux, L.; Usman, M.; Hedley, P.; Verrall, S.; Zhang, R.; Morris, J.; Hancock, R.D. (2013) A physiological, biochemical and transcriptomic approach to understanding the response of potato to elevated temperature., UK Plant Science Conference, West Park Centre, Dundee, 16-17 April 2013. (Poster)
  • Hein, I.; Gilroy, E.; Hornyik, C.; Bryan, G.; Milne, I.; Toth, I.K.; Ducreux, L.; Torrance, L.; Milne, L.; Cock, P.; Pritchard, L.; Sharma, K.; MacFarlane, S.; Zhang, R.; Hedley, P.; Jones, J.; Birch, P.; Taylor, M.; Dale, F.; McNaughton, I.; Wright, J.; Prashar, A.; Blok, V.; Carnegie, P.; Chapman, S. (2013) Utilising the potato genome., Potatoes in Practice 2013, Balruddery Farm, Invergowrie, Dundee, 8 August 2013.
  • Zhang, R.; Burton, R.; Hedley, P.E.; Morris, J.; Fincher, G.; Marshall, D.F.; Waugh, R. (2012) Network analysis of genes expressed in endosperm during barley grain development., Plant and Animal Genome XX. San Diego, California, 14-18 January 2012 (Poster).
  • Hornyik, C.; Zhang, R.; Marshall, D.F.; Bryan, G.J. (2012) Exploring the miRNA transcriptome of a tuber bearing crop, potato., EMBO/EMBL Symposium: The Complex Life of mRNA, Heidelberg, Germany, 7-10 October 2012 (Poster).

Printed from /staff/runxuan-zhang on 22/02/24 08:53:58 PM

The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.