Faculty of Health and Life Sciences

Dr Zheng (Ron) Yang

Dr Zheng (Ron) Yang

Honorary Senior Lecturer

 Z.R.Yang@exeter.ac.uk

 Geoffrey Pope 

 

Geoffrey Pope Building, University of Exeter , Stocker Road, Exeter, EX4 4QD, UK

Overview

I am a bioinformacian with research interests covering sequence/structure bioinformatics and systems biology. In the last few years, my work mainly focused on developing novel algorithms for peptide classification, protein structure/function prediction. In collaborating with Oxford University, a tool called RONN was developed for predicting the disordered regions in proteins, which has been proved the best tool so far for predicting the short disordered regions in proteins. I am a member of the Molecules and cells research group.

Qualifications

1995-1997 PhD, Portsmouth University

Career

2000-2021 Senior lecturer in Bioinformatics, School of Biosciences, Exeter University
2004-2007 Senior lecturer in Computer Sciences, Department of Computer Sciences, Exeter University
2000-2004 Lecturer in Computer Sciences, Department of Computer Sciences, Exeter University
1999-2000 Research fellow, Heriot-Watt University
1997-1999 Research fellow, Southampton University

Links

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Research

Research interests

My current research interests are in gene-metabolite network construction, signaling pathway crosstalk modeling and systems dynamics. My main methodology is top-down data mining using various machine learning algorithms and differential as well as difference equations. In theoretical bioinformatics, I am currently working on developing novel neural network algorithms which can handle data complexity as conventional neural networks but provide the capability of quantitative interpretation to a model so that biological relevance in data can be well-explored through black-box-alike learning.

Research networks

  • Dr Robert Esnouf, Department of Structural Biology, Oxford University,
  • Dr Toby Gibson, European Molecular Biology Laboratory (Germany),
  • Prof L Wang, Nanyang Technology University, Singapore

Research grants

  • 2007 NERC
    The molecular diversity of microbial eukaryotes using a large-scale parallel tag sequencing strategy, the Linnean Society and Systematics Association

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Publications

Books

Yang ZR (In Press). machine learning approaches to bioinformatics. new jersey, world scientific.
Yang ZR, Everson R, Yin H (2004). Intelligent data engineering and automated learning--IDEAL 2004., Springer-Verlag New York Inc. Abstract.
Yin H, Yang ZR, Everson R (2004). Preface.
Yang R, Everson RM, Yin H (2004). Proceedings of the Fifth International Conference on Intelligent Data Engineering and Automated Learning -- IDEAL2004., Springer.

Journal articles

Wagley S, Morcrette H, Kovacs-Simon A, Yang Z, Power A, Tennant R, Love J, Murray N, Titball R, Butler C, et al (In Press). Bacterial dormancy: a subpopulation of viable but non-culturable cells demonstrates better fitness for revival. PLoS Pathogens
Yang ZR (2022). In silico prediction of Severe Acute Respiratory Syndrome Coronavirus 2 main protease cleavage sites. Proteins: Structure, Function and Bioinformatics, 90(3), 791-801. Abstract.
Morcrette H, Kovacs-Simon A, Tennant RK, Love J, Wagley S, Yang ZR, Studholme DJ, Soyer OS, Champion OL, Butler CS, et al (2020). Campylobacter jejuni 11168H Exposed to Penicillin Forms Persister Cells and Cells with Altered Redox Protein Activity. Frontiers in Cellular and Infection Microbiology, 10 Abstract.
Ireland PM, Bullifent HL, Senior NJ, Southern SJ, Yang ZR, Ireland RE, Nelson M, Atkins HS, Titball RW, Scott AE, et al (2019). Global Analysis of Genes Essential for Francisella tularensis Schu S4 Growth in Vitro and for Fitness during Competitive Infection of Fischer 344 Rats. J Bacteriol, 201(7). Abstract.  Author URL.
Yang ZR, Bullifent HL, Moore K, Paszkiewicz K, Saint RJ, Southern SJ, Champion OL, Senior NJ, Sarkar-Tyson M, Oyston PCF, et al (2017). A Noise Trimming and Positional Significance of Transposon Insertion System to Identify Essential Genes in Yersinia pestis. Sci Rep, 7 Abstract.  Author URL.
Senior NJ, Sasidharan K, Saint RJ, Scott AE, Sarkar-Tyson M, Ireland PM, Bullifent HL, Rong Yang Z, Moore K, Oyston PCF, et al (2017). An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions. BMC Microbiology, 17(1). Abstract.
Wappett M, Dulak A, Yang ZR, Al-Watban A, Bradford JR, Dry JR (2016). Multi-omic measurement of mutually exclusive loss-of-function enriches for candidate synthetic lethal gene pairs. BMC Genomics, 17 Abstract.  Author URL.
de Torres Zabala M, Zhai B, Jayaraman S, Eleftheriadou G, Winsbury R, Yang R, Truman W, Tang S, Smirnoff N, Grant M, et al (2016). Novel JAZ co-operativity and unexpected JA dynamics underpin Arabidopsis defence responses to Pseudomonas syringae infection. New Phytologist, 209(3), 1120-1134. Abstract.
Wu Y, Shi B, Ding X, Liu T, Hu X, Yip KY, Yang ZR, Mathews DH, Lu ZJ (2015). Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data. Nucleic Acids Res, 43(15), 7247-7259. Abstract.  Author URL.
Yang Z, Yang Z (2013). Prediction of heterogeneous differential genes by detecting outliers to a Gaussian tight cluster. BMC Bioinformatics, 14(1). Abstract.
Lau SK, Champion OL, Titball RW, Yang ZR, Winlove P, Moger J, Yang ZH (2012). A Bayesian Whittaker-Henderson smoother for general-purpose and sample-based spectral baseline estimation and peak extraction. Journal of Raman Spectroscopy Abstract.
Lau SK, Winlove P, Moger J, Champion OL, Titball RW, Yang ZH, Yang ZR (2012). A Bayesian Whittaker-Henderson smoother for general-purpose and sample-based spectral baseline estimation and peak extraction. JOURNAL OF RAMAN SPECTROSCOPY, 43(9), 1299-1305.  Author URL.
Yang Z, Yang Z, Eftestl T, Steen PA, Lu W, Harrison RG (2012). A Mixture model classifier and its application on the biomedical time series. Applied Artificial Intelligence, 26(6), 588-597. Abstract.
Al-Watban A, Yang ZH, Everson R, Yang ZR (2012). A novel data mining approach for differential genes identification in small cancer expression data. 2012 7th International Symposium on Health Informatics and Bioinformatics, HIBIT 2012, 1-6. Abstract.
Perera V, de Torres Zabala M, Florance H, Smirnoff N, Grant M, Yang ZR (2012). Aligning extracted LC-MS peak lists via density maximization. Metabolomics, 8, 175-185. Abstract.
Yang ZR, Grant M (2012). An ultra-fast metabolite prediction algorithm. PLoS One, 7(6). Abstract.  Author URL.
Sidhu A, Yang ZR (2012). Prediction of Signal Peptides Using Bio-Basis Function Neural Networks and Decision Trees. Applied Bioinformatics, 5(1), 13-19.
Perera V, De Torres Zabala M, Florance H, Smirnoff N, Grant M, Yang ZR (2011). Aligning extracted LC-MS peak lists via density maximization. Metabolomics, 1-11.
YANG ZR, LU W, HARRISON RG (2011). VIRTUAL OBJECT THEORY AND ITS APPLICATION TO FINANCE. International Journal of Theoretical and Applied Finance, 3(03), 605-606.
Yang ZR (2010). Neural networks. Methods Mol Biol, 609, 197-222. Abstract.  Author URL.
Felgner PL, Kayala MA, Vigil A, Burk C, Nakajima-Sasaki R, Pablo J, Molina DM, Hirst S, Chew JSW, Wang D, et al (2009). A Burkholderia pseudomallei protein microarray reveals serodiagnostic and cross-reactive antigens. Proc Natl Acad Sci U S A, 106(32), 13499-13504. Abstract.  Author URL.
Yang ZR, Lertmemongkolchai G, Tan G, Felgner PL, Titball R (2009). A genetic programming approach for Burkholderia pseudomallei diagnostic pattern discovery. Bioinformatics, 25(17), 2256-2262. Abstract.  Author URL.
Yang ZR (2009). Peptide bioinformatics- peptide classification using peptide machines. Methods Mol Biol, 458, 155-179. Abstract.
Yang ZR (2009). Predict collagen hydroxyproline sites using support vector machines. J Comput Biol, 16(5), 691-702. Abstract.  Author URL.
Yang ZR (2009). Predict prokaryotic proteins through detecting N-formylmethionine residues in protein sequences using support vector machine. Biosystems, 97(3), 141-145. Abstract.  Author URL.
Yang ZR (2009). Predicting sulfotyrosine sites using the random forest algorithm with significantly improved prediction accuracy. BMC Bioinformatics, 10 Abstract.  Author URL.
Yin H, Tino P, Magdon-Ismail M, Yang ZR, Corchado E (2008). INTRODUCTION. INTERNATIONAL JOURNAL OF NEURAL SYSTEMS, 18(6), V-V.  Author URL.
Yin H, Tino P, Magdon-Ismail M, Yang ZR, Corchado E (2008). International Journal of Neural Systems: Introduction. International Journal of Neural Systems, 18(6).
Yang ZR (2008). Peptide bioinformatics: peptide classification using peptide machines. Methods Mol Biol, 458, 159-183. Abstract.  Author URL.
Yang ZR (2007). A probabilistic peptide machine for predicting hepatitis C virus protease cleavage sites. IEEE Trans Inf Technol Biomed, 11(5), 593-595. Abstract.  Author URL.
Yang ZR, Hamer R (2007). Bio-basis function neural networks in protein data mining. Curr Pharm Des, 13(14), 1403-1413. Abstract.  Author URL.
Yang ZR (2007). Peptide machines for data mining protein peptides. AMINO ACIDS, 33(3), XII-XII.  Author URL.
Yang ZR, Dry J, Thomson R, Charles Hodgman T (2006). A bio-basis function neural network for protein peptide cleavage activity characterisation. Neural Netw, 19(4), 401-407. Abstract.  Author URL.
Yang ZR (2006). A novel radial basis function neural network for discriminant analysis. IEEE Trans Neural Netw, 17(3), 604-612. Abstract.  Author URL.
Esnouf RM, Hamer R, Sussman JL, Silman I, Trudgian D, Yang ZR, Prilusky J (2006). Honing the in silico toolkit for detecting protein disorder. Acta Crystallographica Section D: Biological Crystallography, 62(10), 1260-1266. Abstract.
Yang ZR (2006). Predicting hepatitis C virus protease cleavage sites using generalized linear indicator regression models. IEEE Trans Biomed Eng, 53(10), 2119-2123. Abstract.  Author URL.
Yang ZR, Thomson R (2005). Bio-basis function neural network for prediction of protease cleavage sites in proteins. IEEE Trans Neural Netw, 16(1), 263-274. Abstract.  Author URL.
Yang ZR, Dalby AR (2005). International Journal of Neural Systems: Introduction. International Journal of Neural Systems, 15(4).
Yang ZR (2005). Mining SARS-CoV protease cleavage data using non-orthogonal decision trees: a novel method for decisive template selection. Bioinformatics, 21(11), 2644-2650. Abstract.  Author URL.
Yang ZR (2005). Orthogonal kernel machine for the prediction of functional sites in proteins. IEEE Trans Syst Man Cybern B Cybern, 35(1), 100-106. Abstract.  Author URL.
Yang ZR, Wang L, Young N, Trudgian D, Chou K-C (2005). Pattern recognition methods for protein functional site prediction. Curr Protein Pept Sci, 6(5), 479-491. Abstract.  Author URL.
Senawongse P, Dalby AR, Yang ZR (2005). Predicting the phosphorylation sites using hidden Markov models and machine learning methods. J Chem Inf Model, 45(4), 1147-1152. Abstract.  Author URL.
Senawongse P, Dalby AR, Yang ZR (2005). Predicting the phosphorylation sites using hidden markov models and machine learning methods. Journal of Chemical Information and Modeling, 45(4), 1147-1152. Abstract.
Yang ZR, Johnson FC (2005). Prediction of T-cell epitopes using biosupport vector machines. J Chem Inf Model, 45(5), 1424-1428. Abstract.  Author URL.
Yang ZR, Johnson FC (2005). Prediction of T‐Cell Epitopes Using Biosupport Vector Machines. ChemInform, 36(49), no-no.
Yang, Z.R. (2005). Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks. Bioinformatics, 21(9), 1831-1837.
Yang ZR, Esnouf R, McNeil P, Thomson R (2005). RONN: use of the bio-basis function neural network technique for the detection of natively disordered regions in proteins. Bioinformatics, 21(16), 3369-3376.
Yang ZR, Dalby AR (2005). Special issue on bioinformatics - Introduction. INTERNATIONAL JOURNAL OF NEURAL SYSTEMS, 15(4), V-VI.  Author URL.
Yang ZR, Chou KC (2004). Bio-Support Vector Machines for Computational Proteomics. Bioinformatics, 20(5), 735-741.
Yang ZR (2004). Biological applications of support vector machines. Brief Bioinform, 5(4), 328-338. Abstract.  Author URL.
Venkatraman V, Dalby AR, Yang ZR (2004). Evaluation of mutual information and genetic programming for feature selection in QSAR. J Chem Inf Comput Sci, 44(5), 1686-1692. Abstract.  Author URL.
Yang ZR, Dalby AR, Qiu J (2004). Mining HIV protease cleavage data using genetic programming with a sum-product function. Bioinformatics, 20(18), 3398-3405. Abstract.  Author URL.
Yang, Z.R. (2004). Mining gene expression data using the template theory. Bioinformatics, 20(16), 2759-2766.
Yang ZR, Chou KC (2004). Predicting the O-linkage sites in glycoproteins using bio-basis function neural networks. Bioinformatics, 20(6), 903-908.
Berry EA, Dalby AR, Yang ZR (2004). Reduced bio basis function neural network for identification of protein phosphorylation sites: comparison with pattern recognition algorithms. Comput Biol Chem, 28(1), 75-85. Abstract.  Author URL.
Yang ZR, Berry EA (2004). Reduced bio-basis function neural networks for protease cleavage site prediction. J Bioinform Comput Biol, 2(3), 511-531. Abstract.  Author URL.
Yang ZR, Harrison RG (2003). An unsupervised probabilistic net for health inequalities analysis. IEEE Trans Neural Netw, 14(1), 46-57. Abstract.  Author URL.
Yang ZR, Doyle AK, Hodgman C, Thomson R (2003). Characterising proteolytic cleavage site activity using bio-basis function neural network. Bioinformatics, 19(14), 1741-1747.
Yang ZR, Chou K-C (2003). Mining biological data using self-organizing map. J Chem Inf Comput Sci, 43(6), 1748-1753. Abstract.  Author URL.
Yang ZR, Thomson R, Hodgman TC, Dry J, Doyle AK, Narayanan A, Wu X (2003). Searching for discrimination rules in protease proteolytic cleavage activity using genetic programming with a min-max scoring function. Biosystems, 72(1-2), 159-176. Abstract.  Author URL.
Yang ZR, Harrison RG (2002). Analysing company performance using templates. Intelligent Data Analysis, 6(1), 3-15. Abstract.
Narayanan A, Wu X, Yang ZR (2002). Mining viral protease data to extract cleavage knowledge. Bioinformatics, 18 Suppl 1, S5-13. Abstract.  Author URL.
Yang ZR, Lu W, Harrison RG (2001). Evolving stacked time series predictors with multiple window scales and sampling gaps. Neural Processing Letters, 13(3), 203-211. Abstract.
Zwolinski, M. (2001). Mutual information theory for adaptive mixture models. IEEE Transactions on Pattern Analysis and Machine Intelligence, 23(4), 396-403.
Yang ZR, Zwolinski M, Chalk CD, Williams AC (2000). Applying a robust heteroscedastic probabilistic neural network to analog fault detection and classification. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, 19(1), 142-151.
Zwolinski M, Yang ZR, Kazmierski TJ (2000). Applying mutual information theory to behavioural analogue fault modelling. International Journal of Electronics, 87(12), 1461-1471.
Wolinski MZ, Yang ZR, Kazmierski TJ (2000). Using robust adaptive mixing for statistical fault macromodelling. IEE Proceedings: Circuits, Devices and Systems, 147(5), 265-270. Abstract.

Chapters

Yang ZR, Yang Z (2014). Artificial Neural Networks. In  (Ed) Comprehensive Biomedical Physics, 1-17. Abstract.

Conferences

Mohammed S, Akman OE, Yang ZR (2014). A consensus approach to predict regulatory interactions. Abstract.
Yang Z, Alwatban A, Yang ZR (2014). A mean pattern model for integrative study - Integrative self-organizing map. Abstract.
Yang Z, Yang ZR (2014). Detection of non-structural outliers for microarray experiments. Abstract.
Dry JR, Wappett M, Yang R (2014). Integrating pan-molecular data sets by bimodality to nominate synthetic lethal gene pairs and biomarkers of drug response.  Author URL.
Yang ZH, Alwatban A, Everson R, Yang ZR (2014). Multi-scale Gaussian mixtures for cross-species study. Abstract.
King A, Yang Z, Yang ZR (2014). Multivariate multi-scale Gaussian for microarray unsupervised classification. Abstract.
Knocker L, Yang ZR (2014). SLC- and NDUF-genes expression dynamics in pre-implantation embryonic development between bovine and mouse - a bioinformatics study. Abstract.
Yang ZR (2008). Crosstalk and signalling pathway complexity - a case study on synthetic models. Abstract.
Yang ZR (2008). Explore residue significance in peptide classification. Abstract.
Yang ZR (2008). Single-layer neural net competes with multi-layer neural net. Abstract.
Trudgian DC, Yang ZR (2007). A sparse bayesian position weighted bio-kernel network. Abstract.
Yang ZR (2007). Peptide classification with genetic programming ensemble of generalised indicator models.  Author URL.
Yang ZR (2007). Predicting palmitoylation sites using a regularised bio-basis function neural network. Abstract.
Yang ZR, Young N (2007). Regressional inhibitive crosstalk models.  Author URL.
Trudgian DC, Yang ZR (2007). Substitution matrix optimisation for peptide classification. Abstract.
Yang ZR (2006). A fast algorithm for relevance vector machine.  Author URL.
Thomas AC, Zheng RY (2006). Improved prediction of HIV-1 protease genotypic resistance testing assays using a consensus technique. Abstract.
Young N, Yang ZR (2006). Multivariate crosstalk models.  Author URL.
Trudgian DC, Charles-Johnson F, Yang ZR (2006). Predicting HIV-1 T cell epitopes using bio-basis function neural networks. Abstract.
Yang ZR (2005). Bayesian radial basis function neural network. Abstract.
Yang ZR, Young N (2005). Bio-kernel self-organizing Map for HIV drug resistance classification. Abstract.
Yang ZR (2005). Probabilistic Mercer kernel clusters. Abstract.
Berry E, Yang ZR, Wu XK (2003). A Biology Inspired Neural Learning Algorithm for Analysing Protein Sequences. Abstract.
Yang ZR (2003). Support vector machines for company failure prediction.  Author URL.
Thomson R, Yang ZR (2002). A novel basis function neural network.  Author URL.
Yang ZR (2002). Artificial neural networks in analysing health inequalities. Abstract.
Yang ZR (2001). A Binary Probabilistic Model and genetic algorithm for HIV protease cleavage sites prediction and search.  Author URL.
Yang ZR (2001). A binary probabilistic classification tree for company failure prediction.  Author URL.
Yang ZR (2001). A new method for company failure prediction using probabilistic neural networks.  Author URL.
Yang ZR (2001). Analysing health inequalities using SOM.  Author URL.
Yang ZR, Zwolinski M (2000). Applying mutual information to adaptive mixture models. Abstract.
Yang ZR, Lu W, Yu D, Harrison RG (2000). Detecting false benign in breast cancer diagnosis. Proceedings of the IEEE-INNS-ENNS International Joint Conference on Neural Networks. IJCNN 2000. Neural Computing: New Challenges and Perspectives for the New Millennium.

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External Engagement and Impact

Committee/panel activities

Steering committee member of 7th International Conference on Intelligent Data Engineering and Automated Learning, Birmingham, UK, December, 2007. Program committee member of the 3rd International Conference on Natural Computation (ICNC'07) and the 4th International Conference on Fuzzy Systems and Knowledge Discovery (FSKD'07). Program committee member of the 9th International Conference on Software Engineering and Knowledge Engineering, 2007. Steering committee member of 7th International Conference on Intelligent Data Engineering and Automated Learning, Burgos, Spain, September, 2006. Steering committee member of 6th International Conference on Intelligent Data Engineering and Automated Learning, Australia, July, 2005. Program committee member of The Congress on Evolutionary Computation 2005. Program committee member of 6th International Conference on Intelligent Data Engineering and Automated Learning, Australia, July, 2005. Steering committee member of BCS summer school, Exeter, 2004. Program committee member of 5th International Conference on Intelligent Data Engineering and Automated Learning, Exeter, August, 2004. Program committee member of 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. Program committee member of The Congress on Evolutionary Computation 2004. Chair sessions in 4th International Conference on Intelligent Data Engineering and Automated Learning, 2003. Chair sessions in IEEE Neural Network Society 9th International Conference on Neural Information Processing, 2002. Chair sessions in IEEE Neural Network Society 8th International Conference on Neural Information Processing, 2001.

Editorial responsibilities

IEEE Trans on Systems, Man and Cybernetics – associate editor

Open Artificial Intelligence – associate editor

Trends in Applied Science Research – associate editor


Invited lectures

Invited talk for the 10th International Congress on Amino Acids and Proteins (ICAAP), August 2007. Keynote speech for the workshopPeptidomics: methods and applications, Royal Holloway, University of London, September, 2005. Predict protein functional sites using pattern recognition methods, Nanyang Technology University, Singapore, November 18, 2004. Bio-basis function neural networks, BCS Summer School, Exeter University, July 2003 A unified method in bioinformatics, Oxford University, March 2003. Bio-basis function neural network, Aberysterwyth University, November 2002. Bio-basis function neural networks for analysing protein sequences, Portsmouth University, September 2002. Protein sequences analysis, Guildhall University, August 2002.

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Teaching

My current taught modules are:
BIOM502 Tools and techniques
BIOM505 Machine learning and informatics
BIOM507 Research methodology
BIOM504 Sequence analysis
COM3507 Bioinformatics (for SECAM)

Modules

2023/24

Information not currently available


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Supervision / Group

Postgraduate researchers

  • Venura Perera PhD
  • Alex Thomas PhD
  • Dave Trudgain PhD
  • Natasha Young PhD

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