People

Shan He

Shan is a Senior Lecturer (Tenured Associate Professor) in Computational Biology in School of Computer Science, the University of Birmingham. He is also an affiliate of the Centre for Computational Biology.

Shan's research interests include complex network analysis, machine learning, optimisation, agent-based modelling and their applications to biological and clinical problems.

Shan is an Associate Editor of IEEE Transactions on Nanobioscience. He also serves as the Editorial Board Member of Complex & Intelligent Systems (Springer).

Jiarui Zhou

Jiarui Zhou is a postdoc fellow in the School of Computer Science, University of Birmingham. He received his Ph.D. in Biomedical Engineering (Zhejiang University, 2014).

Jiarui's research interests include machine learning (ensemble, deep learning, etc.), complex networks (omics network reconstruction, multilayer, etc.), computational intelligence (memetic computing), and their applications on multi-omics data analysis. He is also working on omics database and workflow development. Jiarui is a researcher, functional programmer, tech nerd, and otaku.

Wen-Chi Yang

Wen-Chi recently passed his PhD viva and now is working as a RA with Dr Shan He. His primary interests are in the areas of Agent-based Simulation, Ecological Modelling and Game Theory. Currently he has completed an agent-based model to investigate the evolutionary trajectory of animal collective motion.

Wen-Chi earned his Bachelor degree from the Information Management Department at National Taiwan University, Taiwan in 2003, and his Master degree from the Department of Computer Science and Information Engineering at National Taiwan University, Taiwan in 2005.

James Bradbury

James started his PhD at 2012, sponsored by Natural Environmental Research Council (NERC). His research interests include Multi-objective optimisation, genome-wide metabolic reconstruction, metabolic network analysis and mass spectrometer optimisation.

James received his BSc in Computer Science from Reading University. Before joining our group he worked as a software engineer for 2 years.

Sharil Shafie

Sharil Shafie is a 3rd year PhD student Shan's supervision. He is developing metabolic network analysis algorithms. He received MEng in Aerospace Engineering at University of Manchester.

Weiqi Chen

Weiqi started her PhD under Shan's supervision in September 2013. Her main interest is in active module detection in multi-layer network constructed from time-course data. She has worked and developed methods to identify active module using multi-objective evolutionary algorithm.

Wei received his BSc in Biology at Peking University.

Benjapun Kaveelerdpotjana

Benjapun is a Ph.D. student under the supervision of Shan He and Professor Peter Tino. She focused on module identification in protein-protein interaction network and multi-layer networks specifically in time-course network.

Benjapun graduated with a B.S. in Mathematics from Kasetsart University, Bangkok, Thailand in March 2011 and earned her Master’s Degree in Apply Mathematic and Computational Science from Chulalongkorn University, Bangkok, Thailand in October 2013.

Dong Li

Dong started his PhD in Computer Science at the University of Birmingham in March 2015, under the supervision of Dr Shan He. His main interests are computational biology and machine learning. Currently, he is doing active module identification in multi-layer biological networks. His personal page can be found here.

Shi Ning

Ning is a PhD student under the supervision of Dr Shan He and Dr David Parker in Computer Science. He is interested in computational biology and probabilistic model checking. His current work focuses on gene regulatory network inference and control.

David McDonald

David is a first year PhD student under the supervision of Dr Shan He and Professor Peter Tino. He began work on his PhD in September 2016. He is interested in machine learning, natural computing, neural networks and complex network analysis. He is currently working on using self organizing maps to detect communities in networks, and hopes to move onto active module identification and to build networks containing an information layer that can produce testable hypotheses. He studied his BSc in Mathematics and Computer Science at the University of Birmingham and then went on to study his MSc, focusing in particular on evolving neural networks.

Han Zhang

Han Zhang is currently pursuing a PhD degree under the supervision of Dr Shan He in the departments of Computer Science at the University of Birmingham. His current research interest is metabolite identification using data obtained from mass spectrometry.

Alumni

Sam Benkwitz-Bedford: MRes student, graduated in 2016, currently a PhD student of Centre for Computational Biology at Univ. of Birmingham.

Yupeng Liu: MSc student and RA from 2012-2014, now a PhD student at MIT.

Guanbo Jia: PhD student, graduated in 2017. Now working as a research fellow at Queen's University Belfast.

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