Dr. Yaoyong Li

Research Fellow in Bioinformatics
Faculty of Biology, Medicine and Health
University of Manchester
Michael Smith Building
Oxford Road
Manchester, M13 9PT, UK

Tel: +44 161 2756772
Email: Yaoyong.Li@manchester.ac.uk

Research experiences

December 2014 --- Present
Work as a research associate from 2014-2017 and then research fellow since 2017 in Professor Andrew Sharrocks's group. Perform integrative data analysis of ChIP-seq, RNA-seq, ATAC-seq and epigenetic data for several projects. Developed an HMM based pipeline for peak calling in ChIP-seq data, and a pipeline for analysing the Fluidigm gene expression data. Developed an R package geno2proteo to retrieve the protein sequences of any genomic regions and the genomic coordinates of any protein sequences, which was available in the R package repository CRAN, and an online tool ToFiGAPS based on geno2proteo. Downloading and analysing the sequencing data from the exteranal sources such as TGCA, Roadmap and GEO. Also provide general bioinformatics support for the group. Supervise the Masters students in the lab and gave the tutorial to MS student in bioinformatics.

May 2009 --- December 2014
Worked in the Applied Computational Biology and Bioinformatics group, led by Dr. Crispin Miller, at the Cancer Research UK Manchester Institute. I have been working on many projects by processing and analysing next-generation sequencing (NGS) data, microarray data, proteomic data, and siRNA data. The NGS projects that I have been working on involved the whole genome sequencing, whole exome sequencing, targeted genome sequencing, ChIP-seq, DamID-seq, and RNA-seq. The Microarray projects involved the Affymetrix Exon array, GeneArray, hgU133Plus2 array, and Agilent Human CGH Microarray. I developed several pipelines for analysing different types of NGS data. I designed and implemented a novel scan statistic based method for analysing the DamID-seq data. I also experimented and identified the best method for copy number variations (CNVs) analysis in the circulating tumor cells samples. For details about the research see the publications.

February 2004 --- April 2009
I worked in the GATE team, led by Professor Hamish Cunningham, in the Sheffield NLP Group, Sheffield University. Worked on an EU project LarKC. The aim of the LarKC is to build a platform and the essential plug-ins for massive distributed incomplete reasoning and semantic computing for the SemanticWeb. I have also worked in the project SAM for patent semantic annotations using the semi-automatic approach of GATE Teamware, and another EU project SEKT. My research focuses on developing effective and efficient machine learning algorithms for text mining, such as Perceptron with Uneven Margins, and SVM with Uneven Margins, and building up text mining system in the software GATE based on those machine learning algorithms. I also work on the applications of text mining, e.g. opinion mining, patent semant annotation, biomedical text mining, and bioinformatics. I also developed the advanced learning algorithms for other NLP tasks, such as Chinese word segmentation, cross-language information retrieval, cross-language document categorisation. I also worked on Semantic Web technology.

July 2001 --- January 2004:
I worked for Professor John Shawe-Taylor on an EU 5th Framework project 'Kernel Methods for Image and Text' (KerMIT), in Royal Holloway College, University of London. The project developed machine learning algorithms and software for classification, clustering, ranking and filtering of text and image. I have developed effective machine learning algorithms, such as Perceptron with Uneven Margins and SVM with Uneven Margins, for document categorisation, filtering and cross-language information retrieval. Our document filtering system scored the 2nd place in the adaptive filtering task in TREC 2002.

August 1999 --- July 2001:
I worked on the China founded project 'The Natural Language Understanding and HNC Theory', a part of National Key Fundamental Research Program (the 973 Program), in Professor Zengyang Huang's group, at Institute of Acoustics, CAS, China. The project developed a new theory of natural language understanding -- 'Hierarchical Networks of Concepts' (HNC) and a machine translation system using HNC. HNC develops knowledge and methods for semantically analysing natural language. One of its core knowledge is an ontology for analysing sentence.

September 1993 --- August 1999:
I worked at the Institute of Artificial Intelligence and Robotics, led by Professor Nanning Zheng, in Xi'an Jiaotong University, China. From 1997 to 1999 I worked on the 'Chaotic Neural Network models and intelligent information processing', a projected founded by National Natural Science Foundation of China (NSFC). This project involved studying the neurobiology-oriented dynamical neural network models and their applications to intelligent information processing. From 1993 to 1996 I worked on the 'Industrial Robot Vision' project. The project involved designing and developing state of the art Robot vision system in assembly line.

Software development

Developed a bioinformatics online tool ToFiGAPS, an online Tool for Finding Genomic And Protein Sequences of any genomic or protein regions. This on-line tool was based on the R package geno2proteo that I created.

I participate in developing the GATE, a well-known software for natural language engineering. In particular, I developed the machine learning facilities in GATE, the annotation merging plugin, and the inter-annotators agreement (IAA) computation. For more details about those works, see Chapter 11 and Chapter 9 in GATE User Manual, respectively.

A Chinese Word Segementater based on the Perceptron learning algorithm. It can be used for both the simplified Chinese and tranditional Chinese text. It obtained top scores in the SIGHAN-2005 Chinese word segmentation task. It has been integrated into GATE. Please contact me if you are interested in using it.

The PAUM models which were learned from the SIGHAN-05 training data and can be used in the Chinese word segmentation plugin of GATE:
The PAUM model learned from the PKU training data in UTF-8 code
The PAUM model learned from the PKU training data in GB2312 code

Teaching experiences

September 2015 --- Present, Research Associate at the University of Manchester
Give the tutorials to MS Bioinformatics students and co-supervise the research projects of the MS students.

September 1993 --- August 1999, Lecturer at Xi'an Jiaotong University
Courses taught:
Digital Signal Processing (both undergraduate and graduate level)
Computer Vision and Pattern Recognition (graduate level)
Machine Learning (co-taught, graduate level).
Supervised a two-week visiting and practising course at Changzhou Sound Equipment Factory for the final year students of Department of Information and Control, 1994.
Supervised a final year project on controlling a chaotic electrical circuit, 1996.

Other teaching experiences
Gave the tutorial to the MS students in bioinformatics, and supervised a Masters student in bioinformatics, Machester University, UK, 2015-2016.
JAVA Programming, Teaching Assistant, Sheffield University, UK, 2007.
FORTRAN and Algorithms, Lecturer, Xi'an Jiaotong University, China, 1992.
Methods of Mathematical Physics, Teaching Assistant, Xi'an Jiaotong University, China, 1990.


Li Y, Aguilar-Martinez E, Sharrocks AD (2019). "Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein Regions". Journal of Integrative Bioinformatics. 2019 Jul 13. DOI: 10.1515/jib-2018-0090.

Maiques-Diaz A, Spencer GJ, Lynch JT, Ciceri F, Williams EL, Amaral FMR, Wiseman DH, Harris WJ, Li Y, Sahoo S, Hitchin JR, Mould DP, Fairweather EE, Waszkowycz B, Jordan AM, Smith DL, Somervaille TCP (2018). "Enhancer Activation by Pharmacologic Displacement of LSD1 from GFI1 Induces Differentiation in Acute Myeloid Leukemia". Cell Report. 22(13): 3641–3659.

Karol Nowicki-Osuch, Yaoyong Li, Mairi Challinor, David T. Gerrard, Neil A. Hanley, and Andrew D. Sharrocks (2017). "EINCR1 is an EGF inducible lincRNA overexpressed in lung adenocarcinomas". PLoS One. 2017; 12(7).

Edward Britton, Connor Rogerson, Shaveta Mehta, Yaoyong Li, Xiaodun Li, the OCCAMS consortium, Rebecca C. Fitzgerald, Yeng S. Ang , Andrew D. Sharrocks (2017). "Open chromatin profiling identifies AP1 as a transcriptional regulator in oesophageal adenocarcinoma". PLoS Genetics, 13(8).

Louise Carter, Dominic G Rothwell, Barbara Mesquita, Christopher Smowton, Hui Sun Leong, Fabiola Fernandez-Gutierrez, Yaoyong Li, Deborah J Burt, Jenny Antonello, Christopher Morrow, Cassandra Hodgkinson, Karen Morris, Lynsey Franklin, Mathew Carter, Crispin Miller, Andrew Hughes, Fiona Blackhall, Caroline Dive and Ged Brady (2017). "Molecular analysis of circulating tumor cells identifies distinct copy number profiles in patients with chemosensitive and chemorefractory small cell lung cancer". Nature Medicine, 23, 114119.

Giulia Veluscek, Yaoyong Li, Shen-Hsi Yang, Andrew D. Sharrocks (2016). ``Jun-mediated changes in cell adhesion contribute to mouse embryonic stem cell exit from ground state pluripotency". Stem Cells, 34(5), 12131224. DOI: 10.1002/stem.2294.

Anna A Marusiak, Natalie L Stephenson, Hayeon Baik, Eleanor W Trotter, Yaoyong Li, Karen Blyth, Susan Mason, Phil Chapman, Lorena A Puto, Jon A Read, Claire Brassington, Hannah K Pollard, Chris Phillips, Isabelle Green, Ross Overman, Matthew Collier, Ewelina Testoni, Crispin Miller, Tony Hunter, Owen J. Sansom, and John Brognard (2016). ``Recurrent MLK4 Loss-of-Function Mutations Suppress JNK Signaling to Promote Colon Tumorigenesis". Cancer Research; 2016 Feb 1;76(3):724-35.

Roshana Thambyrajah, Milena Mazan, Rahima Patel, Victoria Moignard, Monika Stefanska, Elli Marinopoulou, Yaoyong Li, Christophe Lancrin, Thomas Clapes, Tarik Möröy, Catherine Robin, Crispin Miller, Shaun Cowley, Berthold Göttgens, Valerie Kouskoff and Georges Lacaud (2016). ``GFI1 proteins orchestrate the emergence of haematopoietic stem cells through recruitment of LSD1". Nature Cell Biology, 18, 2132 (2016) doi:10.1038/ncb3276.

Dominic G. Rothwell, Nigel Smith, Daniel Morris, Hui Sun Leong, Yaoyong Li, Antoine Hollebecque, Mahmood Ayub, Louise Carter, Jenny Antonello, Lynsey Franklin, Crispin Miller, Fiona Blackhall, Caroline Dive, Ged Brady (2016). ``Genetic profiling of tumours using both circulating free DNA and circulating tumour cells isolated from the same preserved whole blood sample". Molecular Oncology, 2016 Apr;10(4):566-74.

Jizhong Liu, Ashish Masurekar, Suzanne Johnson, Sohini Chakraborty, John Griffiths, Duncan Smith, Seema Alexander, Clare Dempsey, Catriona Parker, Stephanie Harrison, Yaoyong Li, Crispin Miller, Yujun Di, Zhumur Ghosh, Shekhar Krishnan, Vaskar Saha (2015). ``Stromal cell-mediated mitochondrial redox adaptation regulates drug resistance in childhood acute lymphoblastic leukemia", Oncotarget, 2015 Dec 15;6(40):43048-64.

Georges Lacaud, Roshana Thambyrajah, Milena Mazan, Rahima Patel, Victoria Moignard, Monika Stefanska, Elli Marinopoulou, Yaoyong Li, Christophe Lancrin, Thomas Clapes, Tarik Möröy, Catherine Robin, Crispin Miller, Shaun Cowley, Bertie Gottgens, Valerie Kouskoff (2015). ``New insights into the endothelial-to-haematopoietic transition leading to HSC emergence", Experimental Hematology, 09/2015; 43(9):S41. DOI: 10.1016/j.exphem.2015.06.043.

A. Marusiak,N. Stephenson,H. Baik,E. Trotter,Y. Li, E. Testoni,K. Blyth,S. Mason,L. Puto,C. Miller,T. Hunter,O. Sansom,J. Brognard (2014). "Frequent loss-of-function mutations in MLK4 suppresses signaling in the JNK-cJUN-p21/p15 pathway to promote growth of colon cancer cells". European Journal of Cancer, November 2014, Volume 50, Supplement 6, Page 164.

Dominic G Rothwell, Yaoyong Li, Mahmood Ayub, Catriona Tate, Gillian Newton, Yvonne Hey, Louise Carter, Suzanne Faulkner, Massimo Moro, Stuart Pepper, Crispin Miller, Fiona Blackhall, Giulia Bertolini, Luca Roz, Caroline Dive and Ged Brady (2014). "Evaluation and validation of a robust single cell RNA-amplification protocol through transcriptional profiling of enriched lung cancer initiating cells". BMC Genomics 2014, 15:1129. doi:10.1186/1471-2164-15-1129.

Malgorzata Gozdecka*, Stephen Lyons*, Saki Kondo, Janet Taylor, Yaoyong Li, Jacek Walczynski, Gerald Thiel, Wolfgang Breitwieser, Nic Jones (2014). "JNK Suppresses Tumor Formation via a Gene-Expression Program Mediated by ATF2". Cell Reports, Volume 9, Issue 4, p1361--1374, 20 November 2014. *Authors contributed equally.

Andrew M Hudson, Tim Yates, Yaoyong Li*, Eleanor Wendy Trotter*, Shameem Fawdar, Phil Chapman, Paul Lorigan, Andrew V Biankin, Crispin Miller, John Brognard (2014). "Discrepancies in Cancer Genomic Sequencing Highlight Opportunities for Driver Mutation Discovery". Cancer Research 09/2014; DOI: 10.1158/0008-5472.CAN-14-1020. *Authors contributed equally.

Sofie Björner, Paul A. Fitzpatrick, Yaoyong Li, Craig Allred, Anthony Howell, Anita Ringberg, Håkan Olsson, Crispin J. Miller, Håkan Axelson, Göran Landberg (2014) Epithelial and Stromal MicroRNA Signatures of Columnar Cell Hyperplasia Linking Let-7c to Precancerous and Cancerous Breast Cancer Cell Proliferation. PLoS ONE, 9(8): e105099. doi:10.1371/journal.pone.0105099

Lie-A-Ling M*, Marinopoulou E*, Li Y, Patel R, Stefanska M, Bonifer C, Miller C, Kouskoff V, Lacaud G (2014). RUNX1 positively regulates a cell adhesion and migration program in murine hemogenic endothelium prior to blood emergence. Blood, 07/2014; DOI:10.1182/blood-2014-04-572958. *Authors contributed equally.

Cassandra L. Hodgkinson*, Christopher J. Morrow*, Yaoyong Li, Robert L. Metcalf, Dominic Rothwell, Francesca Trapani, Radoslaw Polanski, Deborah J. Burt, Kathryn Simpson, Karen Morris, Stuart Pepper, Daisuke Nonaka, Alastair Greystoke, Paul Kelly, Becky Bola, Matthew G. Krebs, Jenny Antonello, Mahmood Ayub, Suzanne Faulkner, Lynsey Priest, Louise Carter, Catriona Tate, Crispin J. Miller, Fiona Blackhall, Ged Brady, Caroline Dive (2014). Tumorigenicity and Genetic Profiling of Circulating Tumor Cells in Small Cell Lung Cancer, Nature Medicine, 20, 897-903(2014), doi:10.1038/nm.3600. *Authors contributed equally.

Hui Sun Leong*, Keren Dawson*, Chris Wirth, Yaoyong Li, Yvonne Connolly, Duncan L Smith, Caroline Wilkinson, and Crispin J Miller (2014). A global non coding RNA system modulates fission yeast protein levels in response to stress, Nature Communications, 5, Article number: 3947, doi:10.1038/ncomms4947. *Authors contributed equally.

Christopher J Morrow, Cassandra L Hodgkinson, Yaoyong Li, Robert L. Metcalf, Dominic Rothwell, Francesca Trapani, Radoslaw Polanski, Deborah J. Burt, Kathryn Simpson, Karen Morris, Stuart Pepper, Daisuke Nonaka, Alastair Greystoke, Paul Kelly, Becky Bola, Matthew G. Krebs, Jenny Antonello, Mahmood Ayub, Suzanne Faulkner, Lynsey Priest, Louise Carter, Catriona Tate, Crispin J. Miller, Fiona Blackhall, Ged Brady, Caroline Dive (2014). Circulating tumor cells from small cell lung cancer patients are tumorigenic. AACR Annual Meeting 2014, San Diego, California, USA; 04/2014.

John S. Hall, Rohan Iype, Joana Senra, Janet Taylor, Lucile Armenoult, Kenneth Oguejiofor, Yaoyong Li, Ian Stratford, Peter L. Stern, Mark J. O'Connor, Crispin J. Miller, Catharine M. L. West (2014). Investigation of Radiosensitivity Gene Signatures in Cancer Cell Lines. PLoS ONE, 2014 Jan., 9(1): e86329. doi:10.1371/journal.pone.0086329.

Fawdar S, Trotter EW*, Yaoyong Li*, Stephenson N, Hanke F, Marusiak AA, Edwards ZC, Ientile S, Waszkowycz B, Miller CJ, Brognard J. (2013). Targeted Genetic Dependency Screen Facilitates Efficient Identification of Gain-of-Function Mutations in FGFR4, PAK5, and MAP3K9 in Lung Cancer. Proceedings of National Academy of Sciences, 2013 Jul 23;110(30):12426-31. doi: 10.1073/pnas.1305207110. *Authors contributed equally.

Elli Marinopoulou, Michael Lie-A-Ling, Yaoyong Li, Monika Lichtinger, Christopher Wirth, Crispin Miller, Constanze Bonifer, Valerie Kouskoff, Georges Lacaud (2013). Identification of the transcriptional programme controlled by RUNX1 in the haemogenic endothelium by utilising damid-seq. Experimental Hematology 08/2013; 41(8):S23. DOI:10.1016/j.exphem.2013.05.094.

Shameem Fawdar, Eleanor W. Trotter, Yaoyong Li, Sara Ientile, Crispin Miller, John Brognard (2013). Targeted depletion of all somatically mutated genes in lung cancer cells facilitates identification of mutationally activated novel drivers of lung cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2999. doi:10.1158/1538-7445.AM2013-2999.

Chicooree N, Connoly Y, Tan C, Malliri A, Li Y, Smith D, Griffiths J (2013). Enhanced detection of ubiquitin isopeptides using reductive methylation. Journal of The American Society for Mass Spectrometry. 2013 Jan 30.

Harris WJ, Huang X, Lynch JT, Spencer GJ, Hitchin JR, Li Y, Ciceri F, Blaser JG, Greystoke BF, Jordan AM, Miller CJ, Ogilvie DJ, Somervaille TC (2012). The histone demethylase KDM1A sustains the oncogenic potential of MLL-AF9 leukemia stem cells. Cancer Cell, 2012 Apr., 17;21(4):473-87.

Johansson M, Roberts A, Chen D, Li Y, Delahaye-Sourdeix M, Aswani N, Greenwood MA, Benhamou S, Lagiou P, Holcatova I, Richiardi L, Kjaerheim K, Agudo A, Castellsague X, Macfarlane TV, Barzan L, Canova C, Thakker NS, Conway DI, Znaor A, Healy CM, Ahrens W, Zaridze D, Szeszenia-Dabrowska N, Lissowska J, Fabianova E, Mates IN, Bencko V, Foretova L, Janout V, Curado MP, Koifman S, Menezes A, Wunsch-Filho V, Eluf-Neto J, Boffetta P, Franceschi S, Herrero R, Fernandez Garrote L, Talamini R, Boccia S, Galan P, Vatten L, Thomson P, Zelenika D, Lathrop M, Byrnes G, Cunningham H, Brennan P, Wakefield J, McKay JD (2012). Using prior information from the medical literature in GWAS of oral cancer identifies novel susceptibility variant on chromosome 4--the AdAPT method, PLoS One. 2012;7(5):e36888. doi: 10.1371/journal.pone.0036888.

Bitton D, Grallert A, Scutt P, Yates T, Li Y, Bradford J, Hey Y, Pepper SD, Hagan IM, Miller CJ (2011). Programmed fluctuations in sense/antisense transcript ratios drive sexual differentiation in S. pombe. Molecular Systems Biology, 7, Article number: 559, doi:10.1038/msb.2011.90.

Yaoyong Li, James Bradford, and Crispin J. Miller (2010), Evaluation of statistical methods for exon differential expressions using sequencing data, Proceedings of the 29th Leeds Annual Statistical Research Workshop -- High-throughput Sequencing, Proteins and Statistics, Leeds, UK, p117-120.

Bradford JR, Hey Y, Yates T, Li Y, Pepper SD, Miller CJ (2010). A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling. BMC Genomics, 2010, 11:282doi:10.1186/1471-2164-11-282.

Yaoyong Li, Kalina Bontcheva, Hamish Cunningham (2009). Adapting SVM for Data Sparseness and Imbalance: A Case Study on Information Extraction. Natural Language Engineering, 15(02), 241-271. On-line Link

Kalina Bontcheva, Brian Davis, Adam Funk, Yaoyong Li, Ting Wang (2009). Human Language Technologies. Semantic Knowledge Management, John Davies, Marko Grobelnik, and Dunja Mladenic (Eds.), Springer, 37-49. On-line Link

Yaoyong Li, Hamish Cunningham (2008). Geometric and Quantum Methods for Information Retrieval. SIGIR Forum, 42(2), 22-32. On-line Link

Yaoyong Li, Kalina Bontcheva (2008). Adapting Support Vector Machines for F-term-based Classification of Patents. ACM Transactions on Asian Language Information Processing, 7(2), 7:1--7:19. On-line Link

M. Agatonovic, N. Aswani, K. Bontcheva, H. Cunningham, T. Heitz, Y. Li, I. Roberts and V. Tablan (2008). Large-scale, Parallel Automatic Patent Annotation. Proceedings of 1st International CIKM Workshop on Patent Information Retrieval - PaIR'08, Napa Valley, California, USA, 30 October, p1-8. On-line Link

Adam Funk, Yaoyong Li, Horacio Saggion, Kalina Bontcheva, Christian Leibold (2008). Opinion Analysis for Business Intelligence, Proceedings of the First International Workshop on Ontology-supported Business Intelligence (OBI2008), ACM International Conference Proceedings Series, Vol. 308, ISBN 978-1-60558-219-1, ACM Press, 2008.

Yaoyong Li, John Shawe-Taylor (2007). Advanced learning algorithms for cross-language patent retrieval and classification. Information Processing and Management, 43(5), 1183-1199. On-line Link

Yaoyong Li, Kalina Bontcheva (2007). Hierarchical, Perceptron-like Learning for Ontology Based Information Extraction. Proceedings of the 16th International World Wide Web Conference (WWW2007), 777-786. (PDF version available )

Yaoyong Li, Kalina Bontcheva, Hamish Cunningham (2007). Cost Sensitive Evaluation Measures for F-term Patent Classification. Proceedings of the First International Workshop on Evaluating Information Access (EVIA 2007), 44-53. (PDF version available )

Yaoyong Li, Kalina Bontcheva, Hamish Cunningham (2007). SVM Based Learning System for F-term Patent Classification. Proceedings of the Sixth NTCIR Workshop Meeting on Evaluation of Information Access Technologies: Information Retrieval, Question Answering and Cross-Lingual Information Access, 396-402. (PDF version available )

Yaoyong Li, Kalina Bontcheva, Hamish Cunningham (2007). Experiments of Opinion Analysis on the Corpora MPQA and NTCIR-6. Proceedings of the Sixth NTCIR Workshop Meeting on Evaluation of Information Access Technologies: Information Retrieval, Question Answering and Cross-Lingual Information Access, 323-329. (PDF version available )

Diana Maynard, Yaoyong Li, Wim Peters (2007). NLP Techniques for Term Extraction and Ontology Population. Bridging the Gap between Text and Knowledge - Selected Contributions to Ontology Learning and Population from Text, P. Buitelaar and P. Cimiano (editors). IOS Press, 107-127. On-line Link

Yaoyong Li, John Shawe-Taylor (2006). Using KCCA for Japanese-English Cross-language Information Retrieval and Document Classification. Journal of Intelligent Information Systems, 27(2), 117-133. On-line Link

Diana Maynard, Wim Peters, Yaoyong Li (2006). Metrics for Evaluation of Ontology-based Information Extraction. Proceedings of WWW 2006 Workshop on Evaluation of Ontologies for the Web (EON 2006), Edinburgh, Scotland. (PDF version available )

Ting Wang, Yaoyong Li, Kalina Bontcheva, Hamish Cunningham, and Ji Wang (2006). Automatic Extraction of Hierarchical Relations from Text. Y. Sure and J. Domingue (Eds.): ESWC 2006, LNCS 4011, 215--229, Springer-Verlag Berlin Heidelberg. (PDF version available )

Hamish Cunningham, Kalina Bontcheva, Yaoyong Li (2005). Knowledge Manegement and Human Language: Crossing the Chasm. Journal of Knowledge Management, Vol. 9, No. 5. pp. 108--131.

Yaoyong Li, Kalina Bontcheva, Hamish Cunningham (2005). Using Uneven Margins SVM and Perceptron for Information Extraction. Proceedings of Ninth Conference on Computational Natural Language Learning (CoNLL-2005), 72-79. ( PDF version available )

Yaoyong Li, Chuanjiang Miao, Kalina Bontcheva, Hamish Cunningham (2005). Perceptron Learning for Chinese Word Segmentation. Proceedings of Fourth SIGHAN Workshop on Chinese Language processing (Sighan-05), 154-157. ( PDF version available )

Yaoyong Li, Kalina Bontcheva, Hamish Cunningham (2005). SVM Based Learning System For Information Extraction. J. Winkler, M. Niranjan and N. Lawerence (Eds.): Deterministic and Statistical Methods in Machine Learning, LNAI 3635, Springer Verlag, 319-339. ( PDF version available )

Yaoyong Li, Kalina Bontcheva, Hamish Cunningham (2005). SVM and Perceptron Based IE Systems For the Pascal Challenge. PASCAL Challenges Workshop, Southampton, UK. ( PPT version available )

Yaoyong Li and John Shawe-Taylor (2004), Combining Clustering with Canonical Correlation Analysis for Cross-Language Patent Retrieval, in Learning Methods for Text Understanding and Mining Workshop, Grenoble, France. (PDF version available )

Yaoyong Li and John Shawe-Taylor (2003). The SVM with uneven margins and Chinese document categorisation, in Proceedings of The 17th Pacific Asia Conference on Language, Information and Computation (PACLIC17), 216--227. ( PDF version available )

Nicola Cancedda, Nicolo Cesa-Bianchi, Alex Conconi, Claudio Gentile, Cyril Goutte, Thore Graepel, Yaoyong Li, Jean-Michel Renders, John Shawe-Taylor (2003), Kernel methods for document filtering. E. M. Voorhees and Lori P. Buckland, Editors, in Proceedings of The Eleventh Text Retrieval Conference (TREC 2002). ( PDF version available )

Yaoyong Li, Hugo Zaragoza, Ralf Herbrich, John Shawe-Taylor, and Jaz Kandola (2002), The Perceptron algorithm with uneven margins, in Proceedings of the 9th International Conference on Machine Learning (ICML-2002), 379--386. ( PDF version available )

Yaoyong Li (2001), Example-based Chinese-English machine translation by using HNC theory, in Natural Language Understanding and Machine Translation -- the Proceedings of the 6th Joint Conference of Computational Linguistics of China (JSCL-2001), 319-325. (in Chinese)

Yaoyong Li (2001), The Chinese-English machine translation system based on the Analysis of Sentence Category of HNC, in The HNC and Linguistics -- Proceeding of the 1st Conference on Natural Language Theory and HNC, 294-301. (in Chinese)

Yaoyong Li and Nanning Zheng (1998), Improved dynamical model for neural network and the stabilisation of associative memory, Progress in Natural Science, 8(5), 610-618.

Yaoyong Li and Nanning Zheng (1998), Controlling the chaotic neural network, Chinese Journal of Computers Science and Technology, 21(supplement), 142-146. (in Chinese)

Yaoyong Li and Nanning Zheng (1997), The self-organized and time-delayed hybrid neural network model and its application to the occluded object recognition, Pattern Recognition And Artificial Intelligence, 10(4), 317-325. (in Chinese)

Yaoyong Li and Nanning Zheng (1997), A new Hopfield-type neural network model with more biological plausibility, Chinese Journal of Neuroanatomy, 13(supplement), 313. (in Chinese)

Yaoyong Li and Nanning Zheng (1996), The relationship between the size and generalization ability of neural networks, Journal of Xi'an Jiaotong University, 30(9), 22-29. (in Chinese)

Yaoyong Li, and Nanning Zheng (1996), Letters to the editor - an explanation of Amirikian and Nishimura's neural net, Neural Networks, 9, 1085-1086.

Yaoyong Li, Nanning Zheng, and Lixing Yuan (1996), Controlling the chaotic neural network-a way of information integration, in Proceedings of the 1996 IEEE/SICE/RSJ Int. Conf. On Multisensor Fusion and Integration, 775-780.

Nanning Zheng, Yaoyong Li, and Wiek Houwers (1995), A local feature-based recognition of partially occluded objects using neural network, in Proceedings of the 1995 IEEE Industrial Electronics, Control, and Instrumentation , 1301-1306.

Yaoyong Li and Zili Zhang (1995), Solving the free boundary problem in continuous casting by using boundary element method, Applied Mathematics and Mechanics, 12(12), 1201-1208.

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