CV and Publications



Education

I obtained my DPhil in Mathematics from Wadham College in the University of Oxford. The title of my thesis was "Complex Geometry of Dual Isomonodromic Systems" and I was supervised by Dr N.M.J.Woodhouse. You can see the main results of my thesis here.

My first degree was in Physics from the University of Genova; my MSc dissertation was about dualities in string theory and was supervised by Prof. U. Bruzzo. The main results of my dissertation can be found here and were further built upon in here.


Scholarships and awards

Throughout my DPhil studies I was supported first by a scholarship of the Fondazione Angelo Della Riccia and then by a bursary from the University of Oxford. During my MSc dissertation I was partly supported by a bursary from the mathematical physics sector of S.I.S.S.A.

I was awarded a Keeley Senior Scholarship by Wadham College, Oxford, for the year 2000/2001. In 1999 I was awarded the Franco Tricerri memorial prize, a biennial prize awarded by the Italian Mathematical Union to the most deserving MSc dissertation of geometric argument.


Employment history

I have started my current job of SICSA lecturer in the school of informatics at Edinburgh in April 2010. Previously, I was a lecturer (2006-10) and an RA (2004-06) in the Department of Computer Science at the University of Sheffield.


Publications

Books and book chapters

J. Noirel, G. Sanguinetti and P.C. Wright, Mixture Model on Graphs: A Probabilistic Model for Network-Based Analysis of Proteomic Data, In S.Choi (ed), Systems Biology for Signalling Networks, Springer, Berlin, 2010 publisher's page

V. Kadirkamanathan, G. Sanguinetti, M. Girolami and M. Niranjan (eds), Pattern Recognition in Bioinformatics, LNBI, Springer, Berlin, 2009 publisher's page

N.D. Lawrence, M. Girolami, M.Rattray and G. Sanguinetti (eds), Learning in Computational Systems Biology, MIT press, Cambridge (MA),2009 publisher's page

A. Ruttor, G. Sanguinetti and M. Opper, Approximate inference for stochastic reaction systems, in Lawrence et al, Learning in Computational Systems Biology, MIT press (2009)

Journal papers

2014

David Schnoerr, Guido Sanguinetti and Ramon Grima, The Complex Chemical Langevin Equation, Journal of Chemical Physics, in press, 2014.

2013

Gabriele Schweikert, Botond Cseke, Thomas Clouaire, Adrian Bird and Guido Sanguinetti, MMDiff: quantitative testing for shape changes in ChIP-Seq data sets, BMC Genomics 14:826, 2013, link

Robert I. Menzies, Andrew Zammit-Mangion, Lyam M. Hollis, Ross J. Lennen, Maurits A Jansen, David J. Webb, John J. Mullins, James W Dear, Guido Sanguinetti and Matthew Bailey, An antatomically-unbiased approach for analysis of renal BOLD magnetic resonance images, American Journal of Physiology, in press (2013)

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.

2012

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.

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

Grigorios Skolidis, Katja Hansen, Guido Sanguinetti and Matthias Rupp, Multi-task Learning for pKA prediction, Journal of Computer Aided Modelling and Design, 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.

Grigorios Skolidis and Guido Sanguinetti, A Case Study on Meta-Generalising: A Gaussian Processes Approach, Journal of Machine Learning Research 13 (Mar), 691-721, (2012), journal link

Alison I Graham, Guido Sanguinetti, Neil Bramall, Cameron W McLeod and Robert K Poole, Dynamics of a starvation-to-surfeit shift: A transcriptomic and modelling analysis of the bacterial response to zinc reveals transient behaviour of the Fur and SoxS regulators, Microbiology, 158(1), 284-292 journal link.

2011

Grigorios Skolidis and Guido Sanguinetti, Bayesian Multitask Classification with Gaussian Process Priors, IEEE Transaction on Neural Networks, 22(12), 2011-2021 (2011), journal link.

Eleanor W. Trotter, Matthew D. Rolfe, Andrea M. Hounslow, C. Jeremy Craven, Michael P. Williamson, Guido Sanguinetti, Robert K. Poole and Jeffrey Green, Reprogramming of Escherichia coli K-12 Metabolism during the Initial Phase of Transition from an Anaerobic to a Micro-Aerobic Environment, PLoS One 6(9) (2011) journal link

Andrea Ocone and Guido Sanguinetti, Reconstructing transcription factor activities in hierarchical transcription network motifs, Bioinformatics 27(20):2873-9 (2011), journal link.

Ilaria Bellantuono, Guido Sanguinetti and W. Nicol Keith, Progeroid syndromes: models for stem cell aging?, Biogerontology, to appear (2011) journal link.

Maurizio Filippone and Guido Sanguinetti, Approximate Inference of the Bandwidth in Multivariate Kernel Density Estimation, Computational Statistics and Data Analysis, to appear (2011) advance access.

Asuka Kuwabara, Andreas Backhaus, Robert Malinowski, Marion Bauch, Lee Hunt, Toshijuki Nagata, Nick Monk, Guido Sanguinetti, and Andrew Fleming, A shift towards smaller cell size via manipulation of cell cycle gene expression acts to smoothen Arabidopsis leaf shape , Plant Physiology, in press (2011) advance access.

A. Zammit-Mangion, K. Yuan, V. Kadirkamanathan, M. Niranjan and G. Sanguinetti, Online Variational Inference for State-Space Models with Point-Process Observations, Neural Computation 23(8), 1967-1999 (2011) journal link

H.M. Shahzad Asif and Guido Sanguinetti, Large-scale learning of combinatorial transcriptional dynamics from gene expression, Bioinformatics, 27(9), 1277-1283 (2011), journal link

Matthew D. Rolfe, Alex Ter Beek, Alison I. Graham, Eleanor W. Trotter, H. M. Shahzad Asif, SysMO SUMO, Guido Sanguinetti, Joost Teixeira de Mattos, Robert K. Poole, and Jeffrey Green, Transcript profiling and inference of Escherichia coli K-12 ArcA activity across the range of physiologically relevant oxygen concentrations, Journal of Biological Chemistry, 286, 10147-10154 (2011) advance access

Maurizio Filippone and Guido Sanguinetti, A Perturbative Approach to Novelty Detection in Autoregressive Models, IEEE Transactions on Signal Processing, 59(3), 1027-1036 (2011) journal link

2010

H.M. Shahzad Asif, Matthew Rolfe, Jeff Green, Neil D. Lawrence, Magnus Rattray and Guido Sanguinetti, TFInfer: A Tool for Probabilistic Inference of Transcription Factor Activities, Bioinformatics, 26(20), 2635-2636 (2010) journal link

Manfred Opper and Guido Sanguinetti, Learning combinatorial transcriptional dynamics from gene expression data, Bioinformatics, 26(13) 1623-1629 (2010) journal link

Samantha McLean, Lesley A. H. Bowman, Guido Sanguinetti, Robert C. Read and Robert K. Poole, Peroxynitrite toxicity in Escherichia coli K-12 elicits expression of oxidative stress responses, and protein nitration and nitrosylation, Journal of Biological Chemistry, 285: 20724-20731 (2010) journal link,

Mark Shepherd, Guido Sanguinetti, Gregory M. Cook and Robert K. Poole, Compensations for diminished terminal oxidase activity in Escherichia coli: cytochrome bd-II-mediated respiration and glutamate metabolism, Journal of Biological Chemistry, 285: 18464-18472 (2010)journal link

Michael A Dewar, Visakan Kadirkamanathan, Manfred Opper and Guido Sanguinetti, Parameter estimation and inference for stochastic reaction-diffusion systems: application to morphogenesis in D. melanogaster, BMC Systems Biology 4:21 (2010), journal linkAndreas Backhaus, Asuka Kuwabara, Marion Bauch, Nick Monk, Guido Sanguinetti and Andrew Fleming, LEAFPROCESSOR: a new leaf phenotyping tool using contour bending energy and shape cluster analysis, New Phytologist, 187: 251-261 journal link

Maurizio Filippone and Guido Sanguinetti, Information theoretic novelty detection, Pattern recognition 43(3) 805-814 (2010)journal link

2009

Richard D Pearson, Xuejun Liu, Guido Sanguinetti, Marta Milo, Neil D Lawrence and Magnus Rattray, puma: a Bioconductor package for Propagating Uncertainty in Microarray Analysis, BMC Bioinformatics 10:211 (2009) journal link.

Josselin Noirel, Saw Yen Ow, Guido Sanguinetti and Phillip C. Wright, Systems biology meets synthetic biology: a case study of the metabolic effects of synthetic rewiring, Molecular Biosystems, 5(10),1214-1224 journal link

Guido Sanguinetti, Andreas Ruttor, Manfred Opper and Cedric Archambeau, Switching Regulatory Models of Cellular Stress Response, Bioinformatics, 25(10):1280-1286 (2009) journal link

C.J. Cairney, G. Sanguinetti, E. Ranghini, A.D. Chantry, M.C. Nostro, A. Bhattacharyya, C.N. Svendsen, W.N. Keith and I. Bellantuono, A systems biology approach to Down syndrome: Identification of Notch/Wnt dysregulation in a model of stem cells aging, Biochimica and Biophysica Acta, Molecular Basis of Disease, 1792(4), 353-363 (2009) journal link

K.S. Davidge, G. Sanguinetti, C.H. Yee, A.G. Cox, C.W. McLeod, C.E. Monk, B.E. Mann, R. Motterlini and R.K. Poole, Carbon Monoxide-releasing Antibacterial Molecules Target Respiration and Global Transcriptional Regulators, Journal of Biological Chemistry, 284: 4516-4524 (2009) journal link.

2008

J. Noirel, G. Sanguinetti and P.C. Wright, Identifying differentially expressed subnetworks with MMG, Bioinformatics 24(23) 2792-2793 (2008)journal link

G. Sanguinetti, J. Noirel and P.C. Wright, MMG: a probabilistic tool to identify submodules of metabolic pathways, Bioinformatics 24(8), 1078-1084 (2008), journal link

J. Noirel, S.Y. Ow, G. Sanguinetti, A. Jaramillo and P.C. Wright, Automated extraction of meaningful pathways from quantitative proteomics data, Briefings in Functional Genomics and Proteomics 7(2), 136-146 (2008), journal linkG. Sanguinetti, Dimensionality reduction of clustered data sets, IEEE Trans. Pattern Analysis and Machine Intelligence (PAMI) 30(3), 535-540 (2008), preprint version

2007

J.D. Partridge, G. Sanguinetti, D. Dibden, R.E. Roberts, R.K. Poole and J. Green, Transition of Escherichia coli from aerobic to micro-aerobic conditions involves fast and slow reacting regulatory components, Journal of Biological Chemistry, 282(15), 11230-11237 (2007) journal link.

2006

G. Sanguinetti, N.D. Lawrence and M. Rattray, Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities, Bioinformatics 22(22):2775-2781 (2006) journal link.

G. Sanguinetti, M. Rattray and N.D. Lawrence, A probabilistic dynamical model for quantitative inference of the regulatory mechanism of transcription, Bioinformatics 22(14):1753-1759(2006) journal link

M. Rattray, X. Liu, G. Sanguinetti, M.Milo and N.D. Lawrence, Propagating Uncertainty in Microarray Data Analysis, Briefings in Bioinformatics 7(1):37-47 (2006) journal link

2005

G. Sanguinetti, M. Milo, M. Rattray and N.D. Lawrence, Accounting for Probe-level Noise in Principal Component Analysis of Microarray Data, Bioinformatics,21(19) pp.3748-3754 (2005) journal link

Early Mathematical Physics work

G. Sanguinetti and N.M.J Woodhouse, The Geometry of Dual Isomonodromic Deformations, J.Geom.Phys. 52 (2004), no. 1, 44-56 pdfdownload.

G. Sanguinetti and N.M.J. Woodhouse, ASD Four Manifolds from Frobenius Manifolds, Twistor Newsletter 45 (2000).

C. Bartocci, U.Bruzzo and G. Sanguinetti, Categorial Mirror Symmetry for K3 Surfaces, Comm.Math Phys. 206 (1999), no.2, 265-272 pdfdownload.

U. Bruzzo and G. Sanguinetti, Mirror Symmetry on K3 Surfaces as a Hyper-Kaehler Rotation, Lett.Math.Phys., 45 (1998), no.4, 295-301 pdfdownload.

Refereed conference papers

Ezio Bartocci, Luca Bortolussi and Guido Sanguinetti, Data-driven Statistical Learning of Temporal Logic Properties, FORMATS 2014

Luca Bortolussi and Guido Sanguinetti, A statistical approach for computing reachability of non-linear and stochastic dynamical systems, QEST 2014

Anastasis Georgoulas, Jane Hillston and Guido Sanguinetti, Probabilistic Programming Process Algebra, QEST 2014

Botond Cseke, Manfred Opper and Guido Sanguinetti, Approximate Inference in Latent Diffusion Processes from Continuous Time Observations, to appear at NIPS 2013 camera-ready version and supplementary material

Anastasis Georgoulas, Jane Hillston and Guido Sanguinetti, ABC-Fun: A Probabilistic Programming Language for Biology, in Computational Methods for Systems Biology (CMSB) 13

Luca Bortolussi and Guido Sanguinetti, Learning and designing stochastic processes from logical constraints, in Quantitative Evaluation of Systems (QEST) 13 pdf

Florian Stimberg, Andreas Ruttor, Manfred Opper and Guido Sanguinetti, Inference in continuous-time change-point models, Advances in Neural Information Processing Systems 2011 pdf.

Andrew Zammit-Mangion, Guido Sanguinetti and Visakan Kadirkamanathan,A Variational Approach for the Online Dual Estimation of Spatiotemporal Systems Governed by the IDE, IFAC World Congress 2011, link.

M. Opper, Andreas Ruttor and G Sanguinetti, Approximate inference in continuous time Gaussian-Jump processes, to appear in Advances in Neural Information Processing Systems (NIPS) 2010 pdf.

P. Lecca, A. Palmisano, C. Priami and G. Sanguinetti, A new probabilistic generative model of parameter inference in biochemical networks, Proceedings of the 2009 ACM Symposium on Applied Computing

J. Noirel, G. Sanguinetti and P.C. Wright, Network-based integration of transcriptomic and proteomic data, to appear at MGED 11 (oral presentation) abstract.

G. Skolidis, R.H. Clayton and G. Sanguinetti, Automatic Classification of Normal and Ventricular Beats Using Gaussian Processes, to appear in Computers in Cardiology 2008 (oral presentation).

M. Opper and G Sanguinetti, Variational inference for Markov Jump Processes, Advances in Neural Information Processing Systems (NIPS) 2007 pdf.

N.D. Lawrence, G. Sanguinetti and M. Rattray, Modelling transcriptional regulation using Gaussian processes, Advances in Neural Information Processing Systems (NIPS) 2006 pdf.

G. Sanguinetti and N.D. Lawrence, Missing Data in Kernel PCA, to appear in Proceedings of ECML 2006 (2006). Longer techreport version available here

G. Sanguinetti, M. Rattray and N.D. Lawrence, Identifying submodules of cellular regulatory networks, Proceedings of Computational Methods in Systems Biology (CMSB) 2006 slides

G. Sanguinetti, J. Laidler and N.D. Lawrence, Automatic determination of the number of clusters using spectral algorithms, in Proc. MLSP 2005 55-60 (2005)pdfdownload

Technical reports

G. Sanguinetti, Dimensional Reduction of Clustered Data Sets, Technical Report CS-07-02, available here

G. Sanguinetti and N.D. Lawrence, Missing Data in Kernel PCA, Technical Report CS-06-08 pdf

G. Sanguinetti, N.D. Lawrence and M. Rattray, Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities, Technical Report CS-06-06, University of Sheffield, 2006 pdf

G. Sanguinetti, M. Rattray and N.D. Lawrence, A probabilistic model to integrate chip and microarray data, Technical Report CS-06-02, University of Sheffield, 2006. pdf

N.D. Lawrence and G. Sanguinetti, Matching kernels through Kullback-Leibler divergence minimisation, Technical Report no CS-04-12, The university of Sheffield, Department of Computer Science.

Workshop contributions etc

N.D. Lawrence , G. Sanguinetti and M. Rattray, Gaussian process model for inferring the regulatory activity of transcription factor proteins, talk given at GPIP 2006, Bletchley Park abstract.

G. Sanguinetti, A probabilistic dynamical model for quantitative inference of the regulatory mechanism of transcription, talk given at MASAMB 2006, Dublin slides

G. Sanguinetti, M. Milo, M. Rattray and N.D. Lawrence, Accounting for Probe-level Noise in Principal Component Analysis of Microarray Data, Poster presented at ECCB 2005, Madrid

M. Rattray, X. Liu, G. Sanguinetti, M.Milo and N.D. Lawrence, Novel Probabilistic Models for Propagating Uncertainty in Microarray Data Analysis, slides of a talk given at MASAMB 2005.

G. Sanguinetti, J. Laidler and N.D. Lawrence, A probabilistic approach to spectral clustering: using KL divergence to find good clusters, in Statistics and Optimization of Clustering Workshop, London, 2005.