Publications

Selected recent publications

• Prior knowledge guided active modules identification: an integrated multi-objective approach (Weiqi Chen, Jing Liu, Shan He), APBC 2017, BMC Systems Biology, In press.
• Active module identification in intracellular networks using a memetic algorithm with a new binary decoding scheme (Dong Li, Zhisong Pan, Guyu Hu, Zexuan Zhu, Shan He), APCB 2017, BMC Genomics, In press.
• Cooperative Co-evolutionary Module Identification with Application to Cancer Disease Module Discovery (Shan He, Zexuan Zhu, Guanbo Jia, Daniel Tennant, Qiang Huang, Ke Tang, John Heath, Mirco Musolesi, Xin Yao), IEEE Transactions on Evolutionary Computation, 20(6), 2016.
• Inference of Low and High-Grade Glioma Gene Regulatory Networks Delineates the Role of Rnd3 in Establishing Multiple Hallmarks of Cancer (Kim Clarke, Thomas Daubon, Nil Turan, Fabienne Soulet, Maihafizah Mohd Zahari, Katie R Ryan, Sarah Durant, Shan He, John Herbert, John Ankers, John K Heath, Rolf Bjerkvig, Roy Bicknell, Neil A Hotchin, Andreas Bikfalvi, Francesco Falciani), PLoS Genetics 11(7), e1005325, 2015
• MUSCLE: automated multi-objective evolutionary optimisation of targeted LC-MS/MS analysis (James Bradbury, Grégory Genta-Jouve, J William Allwood, Warwick B Dunn, Royston Goodacre, Joshua D Knowles, Shan He*, Mark R Viant*), Bioinformatics 31 (6), 975-977, 2015. *equal contributing last author
• Robust twin boosting for feature selection from high-dimensional omics data with label noise (Shan He, Huanhuan Chen, Zexuan Zhu, Douglas G Ward, Helen J Cooper, Mark R Viant, John K Heath, Xin Yao ), Information Sciences 291, 1-18, 2015.
• HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries (Jiarui Zhou, Ralf JM Weber, J William Allwood, Robert Mistrik, Zexuan Zhu, Zhen Ji, Siping Chen, Warwick B Dunn, Shan He*, Mark R Viant*), Bioinformatics 30 (4), 581-583, 2014. *equal contributing last author
• DiME: a scalable disease module identification algorithm with application to glioma progression (Yunpeng Liu, Daniel A Tennant, Zexuan Zhu, John K Heath, Xin Yao, Shan He), PLOS ONE, 9(2), e86693, 2014.

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