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Wenbin Guo
Wenbin completed a BSc (Hons) in Applied Mathematics at Zhejiang University of Technology, China in July 2012 and an MSc in Mathematical Biology at the University of Dundee in September 2013. During his study, he focused on how to use mathematical models to solve biological problems, such as PDE models in pest control and differential equation models in gene network analysis. Now he is registered at the University of Dundee and working on the PhD project ‘Constructions of regulatory networks and integration of large scale experimental data in plants’. He has great interests in the fields of mathematical biology and gene network analysis which involves large scale data integrating and interpreting, gene network construction, mathematical models for network dynamics investigation and network simplification and optimisation.
Current research interests
PhD Studentship
Constructions of regulatory networks and integration of large scale experimental data in plants
Methods for integrating and interpreting these data in a meaningful way are therefore powerful tools for identifying known and unknown links between components, in turn helping to identify genetic and molecular mechanisms that provide a more holistic understanding of the process under investigation.
The aim of the project is:
- (a) to integrate and interpret the large scale gene data of crops in a meaningful way
- (b) to construct gene network from experimental data
- (c) to identify functional modules from genetic perturbations, further to use mathematical models to investigate the dynamics
- (d) to find solutions for complex models.
Co-supervisor: Professor Ping Lin (University of Dundee)
Past research
- Project in Zhejiang University of Technology: Set up mathematical models to investigate the ozone in greenhouse pest control.
- Honours year project: Set up spatiotemporal PDE mathematical models to investigate the population movement of insects, such as locusts and aphids. The outcome is expected to provide an idea to detect and control the insect swarm. Further to reduce the chemical use and to protect the environment.
- MSc project: Detect how to acquire and process gene expression data, how to construct gene networks from experimental data, how to simplify and optimise the network models. The goal is to have a basic scope of how to construct gene networks from large scale experimental data.
Bibliography
- Jabre, I.; Chaudhary, S.; Guo, W.; Kalyna, M.; Reddy, A.S.N.; Chen, W.; Zhang, R.; Wilson, C.; Syed, N.H. (2021) Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana., New Phytologist, 229, 1937-1945
- Guo, W.; Tzioutziou, N.A.; Stephen, G.; Milne, I.; Calixto, C.P.G.; Waugh, R.; Brown, J.W.S.; Zhang, R. (2021) 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists., RNA Biology.Published online.
- Harvey, S.; Hickman, R.; Kumari, P.; Lapin, D.; Griebel, T.; Beynon, J.; Guo, W.; Zhang, R.; Parker, J.E.; Denby, K.; Steinbrenner, J. (2020) Downy mildew effector HaRxL21 interacts with the transcriptional repressor TOPLESS to promote pathogen susceptibility., PLOS Pathogen, 16, Article No. e1008835.
- Harb, A.; Simpson, C.G.; Guo, W.; Govindan, G.; Kakani, V.G.; Sunkar, R. (2020) The effect of drought on transcriptome and hormonal profiles in barley genotypes with contrasting drought tolerance., Frontiers in Plant Science, 11, Article No. 618491.
- Raxwal, V.K.; Simpson, C.G.; Gloggnitzer, J.; Entinze, J.C.; Guo, W.; Zhang, R.; Brown, J.W.S.; Riha, K. (2020) Nonsense-mediated RNA decay factor UPF1 is critical for posttranscriptional and translational gene regulation in arabidopsis., The Plant Cell, 32, 2725-2741.
- Calixto, C.P.G.; Tzioutziou, N.A.; James, A.B.; Hornyik, C.; Guo, W.B.; Zhang, R.X.; Nimmo, H.G.; Brown, J.W.S. (2019) Cold-dependent expression and alternative splicing of arabidopsis long non-coding RNAs., Frontiers in Plant Science, 10, Article No. 235.
- Rapazote-Flores, P.; Bayer, M.; Milne, L.; Mayer, C-D.; Fuller, J.; Guo, W.; Hedley, P.E.; Morris, J.; Halpin, C.; Kam, J.; McKim, S.M.; Zwirek, M.; Casao, C.; Barakate, A.; Schreiber, M.; Stephen, G.; Zhang, R.; Brown, J.W.S.; Waugh, R.; Simpson, C.G. (2019) BaRTv1.0: a barley reference transcript dataset for quantitative measurement barley transcriptomes using RNA-seq., BMC Genomics, 20, Article No. 968.
- Calixto, C.P.G.; Guo, W.; James, A.B.; Tzioutziou, N.A.; Entizne, J.C.; Panter, P.E.; Knight, H.; Nimmo, H.G.; Zhang, R.X.; Brown, J.W.S. (2018) Rapid and dynamic alternative splicing impacts the arabidopsis cold response transcriptome., Plant Cell, 30, 1424-1444.
- James, A.B.; Calixto, C.P.G.; Tzioutziou, N.A.; Guo, W.; Zhang, R.X.; Simpson C.G.; Jiang. W.Y.; Nimmo, G.A.; Brown, J.W.S.; Nimmo, H.G. (2018) How does temperature affect splicing events? Isoform switching of splicing factors regulates splicing of LATE ELONGATED HYPOCOTYL (LHY)., Plant Cell and Environment, 41, 1539-1550.
- Guo, W.B.; Calixto, C.P.G.; Brown, J.W.S.; Zhang, R.X. (2017) TSIS: an R package to infer alternative splicing isoform switches for time-series data., Bioinformatics, 33, 3308-3310.
- Gou, W.; Calixtio, C.P.G.; Tzioutziou, N.; Ping, L.; Waugh, R.; Brown, J.W.S.; Zhang, R. (2017) Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size., BMC Systems Biology, 11, Article No. 62.
- Bull, H.; Casao, M.C.; Zwirek, M.; Flavell, A.J.; Thomas, W.T.B.; Guo, W.B.; Zhang, R.X.; Rapazote-Flores, P.; Kyriakidis, S.; Russell, J.; Druka, A.; McKim, S.M.; Waugh, R. (2017) Barley SIX-ROWED SPIKE3 encodes a putative Jumonji C-type H3K9me2/me3 demethylase that represses lateral spikelet fertility., Nature Communications, 8, Article No. 936.
- Jabre, I.; Chaudhary, S.; Guo, W.; Kalyna, M.; Reddy, A.S.N.; Chen, W.; Zhang, R.; Wilson, C.; Syed, N.H. (2021) Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana., New Phytologist, 229, 1937-1945
- Guo, W.; Tzioutziou, N.A.; Stephen, G.; Milne, I.; Calixto, C.P.G.; Waugh, R.; Brown, J.W.S.; Zhang, R. (2021) 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists., RNA Biology.Published online.
- Harvey, S.; Hickman, R.; Kumari, P.; Lapin, D.; Griebel, T.; Beynon, J.; Guo, W.; Zhang, R.; Parker, J.E.; Denby, K.; Steinbrenner, J. (2020) Downy mildew effector HaRxL21 interacts with the transcriptional repressor TOPLESS to promote pathogen susceptibility., PLOS Pathogen, 16, Article No. e1008835.
- Harb, A.; Simpson, C.G.; Guo, W.; Govindan, G.; Kakani, V.G.; Sunkar, R. (2020) The effect of drought on transcriptome and hormonal profiles in barley genotypes with contrasting drought tolerance., Frontiers in Plant Science, 11, Article No. 618491.
- Raxwal, V.K.; Simpson, C.G.; Gloggnitzer, J.; Entinze, J.C.; Guo, W.; Zhang, R.; Brown, J.W.S.; Riha, K. (2020) Nonsense-mediated RNA decay factor UPF1 is critical for posttranscriptional and translational gene regulation in arabidopsis., The Plant Cell, 32, 2725-2741.
- Calixto, C.P.G.; Tzioutziou, N.A.; James, A.B.; Hornyik, C.; Guo, W.B.; Zhang, R.X.; Nimmo, H.G.; Brown, J.W.S. (2019) Cold-dependent expression and alternative splicing of arabidopsis long non-coding RNAs., Frontiers in Plant Science, 10, Article No. 235.
- Rapazote-Flores, P.; Bayer, M.; Milne, L.; Mayer, C-D.; Fuller, J.; Guo, W.; Hedley, P.E.; Morris, J.; Halpin, C.; Kam, J.; McKim, S.M.; Zwirek, M.; Casao, C.; Barakate, A.; Schreiber, M.; Stephen, G.; Zhang, R.; Brown, J.W.S.; Waugh, R.; Simpson, C.G. (2019) BaRTv1.0: a barley reference transcript dataset for quantitative measurement barley transcriptomes using RNA-seq., BMC Genomics, 20, Article No. 968.
- Calixto, C.P.G.; Guo, W.; James, A.B.; Tzioutziou, N.A.; Entizne, J.C.; Panter, P.E.; Knight, H.; Nimmo, H.G.; Zhang, R.X.; Brown, J.W.S. (2018) Rapid and dynamic alternative splicing impacts the arabidopsis cold response transcriptome., Plant Cell, 30, 1424-1444.
- James, A.B.; Calixto, C.P.G.; Tzioutziou, N.A.; Guo, W.; Zhang, R.X.; Simpson C.G.; Jiang. W.Y.; Nimmo, G.A.; Brown, J.W.S.; Nimmo, H.G. (2018) How does temperature affect splicing events? Isoform switching of splicing factors regulates splicing of LATE ELONGATED HYPOCOTYL (LHY)., Plant Cell and Environment, 41, 1539-1550.
- Guo, W.B.; Calixto, C.P.G.; Brown, J.W.S.; Zhang, R.X. (2017) TSIS: an R package to infer alternative splicing isoform switches for time-series data., Bioinformatics, 33, 3308-3310.
- Gou, W.; Calixtio, C.P.G.; Tzioutziou, N.; Ping, L.; Waugh, R.; Brown, J.W.S.; Zhang, R. (2017) Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size., BMC Systems Biology, 11, Article No. 62.
- Bull, H.; Casao, M.C.; Zwirek, M.; Flavell, A.J.; Thomas, W.T.B.; Guo, W.B.; Zhang, R.X.; Rapazote-Flores, P.; Kyriakidis, S.; Russell, J.; Druka, A.; McKim, S.M.; Waugh, R. (2017) Barley SIX-ROWED SPIKE3 encodes a putative Jumonji C-type H3K9me2/me3 demethylase that represses lateral spikelet fertility., Nature Communications, 8, Article No. 936.
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