Research
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
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BBSRC BBR BB/S020160/1 ‘PlantRTD’ 2019-2022 (£391,401) (PI)
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BBSRC Response Mode ‘The Generation Gap – Mechanisms of maternal control on grain’ BB/W002590/1 2022-2025 (£744,015) (Co-I)
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BBSRC International Partnering Award ‘BarleyEUNetwork’ BB/V018906/1 2021-2024 (£30,000) (Co-I)
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BBSRC International Partnering Award ‘UK Australia’ BB/V018299/1 2021-2024 (£30,000) (Co-I)
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BBSRC ERA-CAPS BB/S004610/1 ‘BARN’ 2018-2022 (£649,658) (Co-I)
Publications
Journals
- Puliasis, S.; Wypijewska, D.; Hemsley, P.; Zhang, R. (2023) ProtView: A Versatile Tool for In Silico Protease Evaluation and Selection in a Proteomic and Proteogenomic Context, Journal of Proteomic Research, 22(7), 2400-2410
- Daszkowska-Golec, A.; Mascher, M.; Zhang, R. (2023) Applications of longread sequencing in plant genomics and transcriptomics, Frontiers in Plant Science, 14, Art. 1141429
- 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 transcript-specific RNA-seq 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
- Guo, W.; Coulter, M.; Waugh, R.; Zhang, R. (2022) The value of genotypespecific reference for transcriptome analyses, Life Science Alliance, 5(8), Art. e202101255
- Wypijewska, D.; Orr, J.; Schreiber, M.; Colas, I.; Ramsay, L.; Zhang, R.; Waugh, R. (2022) The proteome of developing barley anthers during meiotic prophase I, Journal of Experimental Botany, 73(5), 1464-1482
- 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
- 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
- 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
- Kuo, R.I.; Cheng, Y.; Zhang, R.; Brown, J.W.S.; Smith, J.; Archibald, A.L.; Burt, D.W. (2020) Illuminating the dark side of the human transcriptome with long read transcript sequencing., BMC Genomics, 21, Article No. 751.
- 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.
- 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.
- Lewandowska, D.; Zhang, R.; Colas, I.; Uzrek, N.; Waugh, R. (2019) Application of a sensitive and reproducible label-free proteomic approach to explore the proteome of individual meiotic-phase barley anthers., Frontiers in Plant Science, 10, Article No. 393.
- 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.
- Bonar, N.; Liney, M.; Zhang, R.X.; Austin, C.; Dessoly, J.; Davidson, D.; Stephens, J.; McDougall, G.; Taylor, M.; Bryan, G.J.; Hornyik, C. (2018) Potato miR828 is associated with purple tuber skin and flesh colour., Frontiers in Plant Sciences, 9, Article No. 1742.
- 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.
- 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.
- 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.
- 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.
- Zhang, R.X.; Calixto, C.P.G.; Marquez, Y.; Venhuizen, P.; Tzioutziou, N.A.; Guo, W.B.; Spensley, M.; Entizne, J.C.; Lewandowska, D.; ten Have, S.; Frey, N.F.D.; Hirt, H.; James, A.B.; Nimmo, H.G.; Barta, A.; Kalyna, M.; Brown, J.W.S. (2017) A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing., Nucleic Acids Research, 45(9), 5061-5073.
- Brown, J.W.S.; Calixto, C.P.G.; Zhang, R.X. (2017) High quality reference transcript datasets hold the key to transcript-specific RNA-seq analysis in plants., New Phytologist, 213, 525-530.
- Zhang, R.X.; Tucker, M.R.; Burton, R.A.; Shirley, N.J.; Little, A.; Morris, J.; Milne, L.; Houston, K.; Hedley, P.E.; Waugh, R.; Fincher, G.B. (2016) The dynamics of transcript abundance during cellularization of developing barley endosperm., Plant Physiology, 170, 1549-1565.
- Katsarou, K.; Wu, Y.; Zhang, R.X.; Bonar, N.; Morris, J.; Hedley, P.E.; Bryan, G.J.; Kalantidis, K.; Hornyik, C. (2016) Insight on genes affecting tuber development in potato upon Potato spindle tuber viroid (PSTVd) infection., PLoS ONE, 11, Article No. e0150711.
- Zhang, R.X.; Calixto, C.P.G.; Tzioutziou, N.A.; James, A.B.; Simpson, C.G.; Guo, W.B.; Marquez, Y.; Kalyna, M.; Patro, R.; Eyras, E.; Barta, A.; Nimmo, H.G.; Brown, J.W.S. (2015) AtRTD – a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana., New Phytologist, 208, 96-101.
- 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
- Wu, X.; Hornyik, C.; Bayer, M.; Marshall, D.; Waugh, R.; Zhang, R.X. (2014) In silico identification and characterization of conserved plant microRNAs in barley., Central European Journal of Biology, 9, 841-852.
- Hancock, R.D.; Morris, W.L.; Ducreux, L.J.D.; Morris, J.A.; Usman, M.; Verrall, S.R.; Fuller, J.; Simpson, C.G.; Zhang, R.; Hedley, P.E.; Taylor, M.A. (2014) Physiological, biochemical and molecular responses of the potato (Solanum tuberosum L.) plant to moderately elevated temperature., Plant Cell and Environment, 37, 439-450.
- Jupe, J.; Stam R.; Howden A.J.M.; Morris J.A.; Zhang R.; Hedley P.E.; Huitema E. (2013) Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle., Genome Biology, 14, Article No. R63.
- Zhang, R.; Marshall, D.F.; Bryan, G.J.; Hornyik, C. (2013) Identification and characterization of miRNA transcriptome in potato by high-throughput sequencing., PLoS ONE, 8, Article No. e57233.
Books / chapters
- 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
- Simpson, C.G.; Barrero, R.A.; Bayer, M.; Flavell, A.; Rapazote-Flores, P.; Bellgard, M.I.; Hedley, P.E.; Zhang, R.; Waugh, R. (2018) The expressed portion of the barley genome, In: Stein, N. & Muehlbauer, G. (eds.) The Barley Genome, Compendium of Plant Genomes. Springer, Cham, Switzerland, 789-107
Conference papers
- 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.
Conference posters / abstracts
- 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).
