Research and PhD projects
CV & Publications
School of Informatics
10 Crichton Street
Tel: +44 131 650 5136
Fax: +44 131 651 1426
I am a Reader in Machine Learning the Institute for Adaptive and Neural Computation at the School of Informatics, University of Edinburgh. My interests focus on probabilistic modelling of biological systems, with particular emphasis on inference in dynamical systems. For more details of my research interests, including live projects and possible PhD projects, please see the research projects page.
Newly published papers
Andrea Ocone, Andrew J. Millar and Guido Sanguinetti, Hybrid Regulatory Models: a statistically tractable approach to model regulatory network dynamics, Bioinformatics 29(7) (2013) journal link
Samantha McLean, Ronald Begg, Helen E. Jesse, Brian E. Mann, Guido Sanguinetti, and Robert K Poole, Analysis of the bacterial response to Ru(CO)3Cl(glycinate) (CORM-3) and the inactivated compound identifies the role played by the ruthenium compound and reveals sulfur-containing species as a major target of CORM-3 action, Antioxidants and Redox Signalling, in press journal link.
Andrew Zammit-Mangion, Michael A. Dewar, Visakan Kadirkamanathan and Guido Sanguinetti, Point Process Modelling of the Afghan War Diary, Proceedings of the National Academy of Sciences of the USA (PNAS), Early Edition July 16th 2012 journal link. See also accompanying website here
Matthew D. Rolfe, Andrea Ocone, Melanie R. Stapleton, Simon Hall,
Eleanor W. Trotter, Robert K. Poole, Guido Sanguinetti and Jeffrey Green, Systems analysis of transcription factor activities in environments with stable and dynamic O2 concentrations, Royal Society Open Biology, in press (2012) journal link
Andrew Zammit-Mangion, Guido Sanguinetti and Visakan Kadirkamanathan, Variational Estimation in Spatiotemporal Systems from Continuous and Point-Process Observations, IEEE Transactions on Signal Processing, in press (2012), journal link.
Cozzarelli Prize 2012 Our PNAS paper "Point process Modelling of the Afghan War Diary" was awarded a Cozzarelli prize by the PNAS editorial board, an annual award to outstanding papers in the six main branches of the PNAS scope. Our paper won in the Engineering and Applied Science category. More details here
Andrew Zammit-Mangion wins IET Doctoral Prize in Control and Automation Congratulations to Andrew, whom until recently worked with us as a postdoc and whose PhD was jointly supervised by Visakan Kadirkamanathan at Sheffield and myself. The IET Prize is a prestigious award for doctoral students at UK Universities, and deservedly acknowledges Andrew's great work during his doctorate. Well done Andrew!
Gabriele Schweikert to talk at HiTSeq HiTSeq is the special interest group meeting on High Throughput Sequencing at the ISMB conference. Gabriele will speak about her research on nonparametric methods to detect differential binding in ChIP-Seq (paper to appear, stay tuned)
ERC Starting Grant I have been awarded an ERC Starting Independent Research Grant to investigate how machine learning techniques can be married with formal model descriptions of biological systems. This large project will run to 2017 and buy me out of teaching, as well as funding RAs and studentships. The official ads can be found here (postdoc) and here (studentship). If you are interested and would like some more info, do get in touch with me.
Arrivals and departures in the lab
Van Anh Huynh-Thu recently joined us to work on my ERC project from the University of Liege, where she worked on network reconstruction with Pierre Geurts and Louis Wehenkel.
David Schnoerr joined us and Ramon Grima's lab as a PhD student, after a theoretical physics degree in Heidelberg on renormalisation group techniques.
Daniel Trejo Banos arrived in February 2012 from the Universitad Nacional Autonoma de Mexico to pursue a PhD in computational systems biology. He will be looking to develop bioinformatics and machine learning methods to model plant oscillators.
Andrea Ocone submitted his thesis and is off to work in the Helmholtz Zentrum in Munich as a post doc with Fabian Theis.