Wenbin Guo
Wenbin is a bioinformatician and his work focuses on developing computational and mathematical models for high-throughput experimental data analysis. He has developed several easy-to-use tools and novel pipelines for accurate transcriptomics data analysis, including RTDBox for reference transcript data (RTD) construction with Illumina short read sequencing and high-resolution single molecule long read sequencing data, Splice Junction Usage Score (SJUS) for RTD assembly quality evaluation, 3D RNA-seq App for differential expression and differential alternative splicing analysis, and RLowPC for co-expression regulatory network construction. These tools have been applied in a wide range of projects, such as RTD constructions and data analyses in barley (BART1, BART2 and pan transcriptome studies of 20 barley genotypes), Arabidopsis (AtRTD1, AtRTD2, and AtRTD3), rice, potato, raspberry, lettuce, pumpkin as well as animal and human disease data. The 3D RNA-seq App he developed has over 6,000 users and won the Best Innovation Award in the School of Life Sciences at the University of Dundee as it is a real game-changer that allows biologists to conquer complex RNA-seq analysis in a couple of hours. The outputs of his work have engaged various opportunities for research commercialisation, internal and external collaborations with excellent research groups.
Current research interests
- BBSRC BBR BB/S020160/1 “PlantRTD” 2019-2022 (£391,401) (Leading researcher)
- FAPESP 2019/13158-8 “Heat-induced alternative splicing in rice” 2021-2026 (R$766,868) (Co-I)
- FAPESP 2021/00394-5 “Camara growth house for plant” 2021-2026 (U$73,276) (Co-I)
- Serrapilheira R-2011-37880 “Rice temperature memory” 2021-2024 (R$650,000) (Co-I)
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.
- PhD project: Computational analysis and method development for high throughput transcriptomics and transcriptional regulatory inference in plants.
Bibliography
- Guo, W.; Coulter, M.; Waugh, R.; Zhang, R. (2022) The value of genotypespecific reference for transcriptome analyses, Life Science Alliance, 5(8), Art. e202101255
- Coulter, M.; Entizne, J.C.; Guo, W.; Bayer, M.; Wonneberger, R.; Milne, L.; Schreiber, M.; Haaning, A.; Muehlbauer, G.J.; McCallum, N.; Fuller, J.; Simpson, C.; Stein, N.; Brown, J.W.S.; Waugh, R.; Zhang, R. (2022) BaRTv2 A highly resolved barley reference transcriptome for accurate transcriptspecific RNAseq quantification, The Plant Journal,111(4),1183-1202
- Zhang, R.; Kuo, R.; Coulter, M.; Calixto, C.P.G.; Entizne, J.C.; Guo, W.; Marquez, Y.; Milne, L.; Riegler, S.; Matsui, A.; Tanaka, M.; Harvey, S.; Gao, Y.; Wießner-Kroh, T.; Paniagua, A.; Crespi, M.; Denby, K.; ben Hur, A.; Huq, E.; Jantsch, M.; Jarmolowski, A.; Koester, T.; Laubinger, S.; Li, Q.Q.; Gu, L.; Seki, M.; Staiger, D.; Sunkar, R.; Szweykowska-Kulinska, Z.; Tu, S.; Wachter, A.; Waugh, R.; Xiong, L.; Zhang, X.N.; Conesa, A.; Reddy, A.S.N.; Barta, A.; Kalyna, M.; Brown, J.W.S. (2022) A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis, Genome Biology 23, Art. 149
- Coulter, M.; Entizne, J.; Guo, W.; Bayer, M.; Wonneberger, R.; Milne, L.; Schreiber, M.; Haaning, A.; Muehlbauer, G.J.; McCallum, N.; Fuller, J.; Simpson, C.; Stein, N.; Brown, J.; Waugh, R.; Zhang, R. (2022) BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification, The Plant Journal, 111(4), 1183-1202
- Ding, P.; Sakai, T.; Krishna Shrestha, R.; Manosalva Perez, N.; Guo, W.; Pok Man Ngou, B.; He, S.; Liu, C.; Feng, X.; Zhang, R.; Vandepoele, K.; MacLean, D.; D G Jones, J. (2021) Chromatin accessibility landscapes activated by cellsurface and intracellular immune receptors, Journal of Experimental Botany, 72(22), 7927-7941
- 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, 18, 1574-1587
- Tzioutziou, N.; James, A.B.; Guo, W.; Calixto, C.; Zhang, R.; Nimmo, H.G.; Brown, J. (2021) Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing, In: Staigner, D.; Davis, S. & Davis, A.M. (eds.). Plant Circadian Networks. Methods in Molecular Biology, Volume 2398. Cham: Springer, Chapter 14, pp 173-188
- 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.
- Zhang, R.; Calixto, C.; Marquez, Y.; Venhuizen, P.; Tzioutziou, N.; Guo, W.; Spensley, M.; Entizne, J.; Lewandowska, D.; ten Have, S.; Frei dit Frey, N.; Hirt, H.; B. James, A.; Nimmo, H.G.; Barta, A.; Kalyna, M.; Brown, J. (2017) A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing, Nucleic Acids Research, 45(9), 5061-5073
- 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.
- Zhang, R.; Calixto, C.; Tzioutziou, N.; Simpson, C.; B. James, A.; Guo, W.; Marquez, Y.; Kalyna, M.; Patro, R.; Eyras, E.; Barta, A.; G. Nimmo, H.; Brown, J. (2015) AtRTD a comprehensive reference transcript dataset resource for accurate quantification of transcriptspecific expression in Arabidopsis thaliana, New Phytologist, 208(1), 96-101
- Guo, W.; Coulter, M.; Waugh, R.; Zhang, R. (2022) The value of genotypespecific reference for transcriptome analyses, Life Science Alliance, 5(8), Art. e202101255
- Coulter, M.; Entizne, J.C.; Guo, W.; Bayer, M.; Wonneberger, R.; Milne, L.; Schreiber, M.; Haaning, A.; Muehlbauer, G.J.; McCallum, N.; Fuller, J.; Simpson, C.; Stein, N.; Brown, J.W.S.; Waugh, R.; Zhang, R. (2022) BaRTv2 A highly resolved barley reference transcriptome for accurate transcriptspecific RNAseq quantification, The Plant Journal,111(4),1183-1202
- Zhang, R.; Kuo, R.; Coulter, M.; Calixto, C.P.G.; Entizne, J.C.; Guo, W.; Marquez, Y.; Milne, L.; Riegler, S.; Matsui, A.; Tanaka, M.; Harvey, S.; Gao, Y.; Wießner-Kroh, T.; Paniagua, A.; Crespi, M.; Denby, K.; ben Hur, A.; Huq, E.; Jantsch, M.; Jarmolowski, A.; Koester, T.; Laubinger, S.; Li, Q.Q.; Gu, L.; Seki, M.; Staiger, D.; Sunkar, R.; Szweykowska-Kulinska, Z.; Tu, S.; Wachter, A.; Waugh, R.; Xiong, L.; Zhang, X.N.; Conesa, A.; Reddy, A.S.N.; Barta, A.; Kalyna, M.; Brown, J.W.S. (2022) A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis, Genome Biology 23, Art. 149
- Coulter, M.; Entizne, J.; Guo, W.; Bayer, M.; Wonneberger, R.; Milne, L.; Schreiber, M.; Haaning, A.; Muehlbauer, G.J.; McCallum, N.; Fuller, J.; Simpson, C.; Stein, N.; Brown, J.; Waugh, R.; Zhang, R. (2022) BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification, The Plant Journal, 111(4), 1183-1202
- Ding, P.; Sakai, T.; Krishna Shrestha, R.; Manosalva Perez, N.; Guo, W.; Pok Man Ngou, B.; He, S.; Liu, C.; Feng, X.; Zhang, R.; Vandepoele, K.; MacLean, D.; D G Jones, J. (2021) Chromatin accessibility landscapes activated by cellsurface and intracellular immune receptors, Journal of Experimental Botany, 72(22), 7927-7941
- 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, 18, 1574-1587
- 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.
- Zhang, R.; Calixto, C.; Marquez, Y.; Venhuizen, P.; Tzioutziou, N.; Guo, W.; Spensley, M.; Entizne, J.; Lewandowska, D.; ten Have, S.; Frei dit Frey, N.; Hirt, H.; B. James, A.; Nimmo, H.G.; Barta, A.; Kalyna, M.; Brown, J. (2017) A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing, Nucleic Acids Research, 45(9), 5061-5073
- 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.
- Zhang, R.; Calixto, C.; Tzioutziou, N.; Simpson, C.; B. James, A.; Guo, W.; Marquez, Y.; Kalyna, M.; Patro, R.; Eyras, E.; Barta, A.; G. Nimmo, H.; Brown, J. (2015) AtRTD a comprehensive reference transcript dataset resource for accurate quantification of transcriptspecific expression in Arabidopsis thaliana, New Phytologist, 208(1), 96-101
- Tzioutziou, N.; James, A.B.; Guo, W.; Calixto, C.; Zhang, R.; Nimmo, H.G.; Brown, J. (2021) Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing, In: Staigner, D.; Davis, S. & Davis, A.M. (eds.). Plant Circadian Networks. Methods in Molecular Biology, Volume 2398. Cham: Springer, Chapter 14, pp 173-188
- Runxuan, Z.; Calixto Cristiane, P.G.; Tzioutziou, N.A.; James, A.B.; Simpson, C.G.; Guo, W.; Marquez, Y.; Kalyna, M.; Patro, R.; Eyras, E.; Barta, A.; Nimmo. H.G.; Brown, J.W.S. (2015) A comprehensive and non-redundant transcript reference enables accurate quantification of transcript-specific expression in Arabidopsis thaliana., Plant Genomes and Biotechnology: from Genes to Networks, Cold Spring Harbor lab., Long Island, USA, 2-5 December 2015.
