Dr Simon Rogers

Honorary (School of Computing Science)

Room S123, School of Computing Science, Sir Alwyn Williams Bldg, Glasgow G12 8QQ

Biography

Dr. Rogers is a Senior Lecturer in the School of Computing Science and a member of the Inference, Dynamics and Interaction group. He did his undergraduate degree in Electrical and Electronic Engineering at the University of Bristol before staying in Bristol to do his PhD (Machine Learning Techniques for Microarray Analysis; 2001-2004), supervised byDr. Colin Campbell. He moved to Glasgow in 2004 to work with Prof. Mark Girolami on the application of Machine Learning to Computational Biology. In 2009 he became a Lecturer in the School and has since (August 2015) been promoted to Senior Lecturer.

Research Interests

Metabolomics: the development of Machine Learning and Statistical methods for the analysis of data from LC/MS metabolomics experiments.
Human-Computer Interaction: the use of Machine Learning and probabilistic modelling to develop new, and improve current interface technology.
Machine Learning: particularly kernel methods and non-parametric Bayesian approaches.

More details are available at his personal page:http://www.dcs.gla.ac.uk/~srogers.

For more details on the textbook "A First Course in Machine Learning".

Other online profiles:

Publications

Selected publications

van Der Hooft, J. J. J. , Wandy, J. , Barrett, M. P. , Burgess, K. E.V. and Rogers, S. (2016) Topic modeling for untargeted substructure exploration in metabolomics. Proceedings of the National Academy of Sciences of the United States of America, 113(48), pp. 13738-13743. (doi: 10.1073/pnas.1608041113) (PMID:27856765) (PMCID:PMC5137707)

van der Hooft, J. J.J. , Wandy, J. , Young, F., Padmanabhan, S. , Gerasimidis, K. , Burgess, K. E.V., Barrett, M. P. and Rogers, S. (2017) Unsupervised discovery and comparison of structural families across multiple samples in untargeted metabolomics. Analytical Chemistry, 89(14), pp. 7569-7577. (doi: 10.1021/acs.analchem.7b01391) (PMID:28621528) (PMCID:PMC5524435)

Weir, D., Pohl, H., Rogers, S. , Vertanen, K. and Kristensson, P. O. (2014) Uncertain text entry on mobile devices. In: CHI 2014: ACM CHI Conference on Human Factors in Computing Systems, Toronto, Canada, 26 April - 1 May 2014, pp. 2307-2316. ISBN 9781450324731 (doi: 10.1145/2556288.2557412)

Daly, R. , Rogers, S. , Wandy, J., Jankevics, A., Burgess, K. E.V. and Breitling, R. (2014) MetAssign: probabilistic annotation of metabolites from LC–MS data using a Bayesian clustering approach. Bioinformatics, 30(19), pp. 2764-2771. (doi: 10.1093/bioinformatics/btu370) (PMID:24916385) (PMCID:PMC4173012)

Rogers, S. and Girolami, M. (2011) A First Course in Machine Learning. Chapman & Hall / CRC. ISBN 9781439824146

All publications

List by: Type | Date

Jump to: 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005

Number of items: 98.

2023

McBride, R., Wandy, J. , Weidt, S., Rogers, S. , Davies, V. , Daly, R. and Bryson, K. (2023) TopNEXt: automatic DDA exclusion framework for multi-sample mass spectrometry experiments. Bioinformatics, 39(7), btad406. (doi: 10.1093/bioinformatics/btad406) (PMID:37364005)

Năstase, A.-M. et al. (2023) Alignment of multiple metabolomics LC-MS datasets from disparate diseases to reveal fever-associated metabolites. PLoS Neglected Tropical Diseases, 17(7), e0011133. (doi: 10.1371/journal.pntd.0011133) (PMID:37486920) (PMCID:PMC10399774)

Mansouri-Benssassi, E., Rogers, S. , Reel, S., Malone, M., Smith, J., Ritchie, F. and Jefferson, E. (2023) Disclosure control of machine learning models from trusted research environments (TRE): new challenges and opportunities. Heliyon, 9(4), e15143. (doi: 10.1016/j.heliyon.2023.e15143) (PMID:37123891) (PMCID:PMC10130764)

Wandy, J. , Mcbride, R., Rogers, S. , Terzis, N., Weidt, S., van der Hooft, J. J.J. , Bryson, K. , Daly, R. and Davies, V. (2023) Simulated-to-real benchmarking of acquisition methods in untargeted metabolomics. Frontiers in Molecular Biosciences, 10, 1130781. (doi: 10.3389/fmolb.2023.1130781) (PMID:36959982) (PMCID:PMC10027714)

2022

Gómez-Castañeda, E., Hopcroft, L. E.M. , Rogers, S. , Munje, C., Bittencourt-Silvestre, J., Copland, M. , Vetrie, D. , Holyoake, T. and Jørgensen, H. G. (2022) Tyrosine kinase inhibitor independent gene expression signature in CML offers new targets for LSPC eradication therapy. Cancers, 14(21), 5253. (doi: 10.3390/cancers14215253) (PMID:36358672) (PMCID:PMC9655972)

Pancheva, A., Wheadon, H. , Rogers, S. and Otto, T. D. (2022) Using topic modeling to detect cellular crosstalk in scRNA-seq. PLoS Computational Biology, 18(4), e1009975. (doi: 10.1371/journal.pcbi.1009975) (PMID:35395014) (PMCID:PMC9064087)

Wandy, J. , Davies, V. , McBride, R., Weidt, S., Rogers, S. and Daly, R. (2022) ViMMS 2.0: A framework to develop, test and optimise fragmentation strategies in LC-MS metabolomics. Journal of Open Source Software, 7(71), 3990. (doi: 10.21105/joss.03990)

2021

Churakov, M., Katholm, J., Rogers, S. , Kao, R. R. and Zadoks, R. N. (2021) Assessing potential routes of Streptococcus agalactiae transmission between dairy herds using national surveillance, animal movement data and molecular typing. Preventive Veterinary Medicine, 197, 105501. (doi: 10.1016/j.prevetmed.2021.105501) (PMID:34624567)

Beniddir, M. A., Kang, K. B., Genta-Jouve, G., Huber, F., Rogers, S. and Van Der Hooft, J. J.J. (2021) Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches. Natural Product Reports, 38(11), pp. 1967-1993. (doi: 10.1039/D1NP00023C)

Bach, E., Rogers, S. , Williamson, J. and Rousu, J. (2021) Probabilistic framework for integration of mass spectrum and retention time information in small molecule identification. Bioinformatics, 37(12), pp. 1724-1731. (doi: 10.1093/bioinformatics/btaa998) (PMID:33244585)

Ernst, M. et al. (2021) Gestational age-dependent development of the neonatal metabolome. Pediatric Research, 89(6), pp. 1396-1404. (doi: 10.1038/s41390-020-01149-z) (PMID:32942288)

Davies, V. , Wandy, J. , Weidt, S., van der Hooft, J. J.J. , Miller, A. , Daly, R. and Rogers, S. (2021) Rapid development of improved data-dependent acquisition strategies. Analytical Chemistry, 93(14), pp. 5676-5683. (doi: 10.1021/acs.analchem.0c03895) (PMID:33784814) (PMCID:PMC8047769)

Schorn, M. A. et al. (2021) A community resource for paired genomic and metabolomic data mining. Nature Chemical Biology, 17(4), pp. 363-368. (doi: 10.1038/s41589-020-00724-z) (PMID:33589842) (PMCID:PMC7987574)

Rogers, S. and Lew, V. L. (2021) PIEZO1 and the mechanism of the long circulatory longevity of human red blood cells. PLoS Computational Biology, 17(3), e1008496. (doi: 10.1371/journal.pcbi.1008496)

Rogers, S. and Lew, V. L. (2021) Up-down biphasic volume response of human red blood cells to PIEZO1 activation during capillary transits. PLoS Computational Biology, 17(3), e1008706. (doi: 10.1371/journal.pcbi.1008706)

Niu, M., Wandy, J. , Daly, R. , Rogers, S. and Husmeier, D. (2021) R package for statistical inference in dynamical systems using kernel based gradient matching: KGode. Computational Statistics, 36(1), pp. 715-747. (doi: 10.1007/s00180-020-01014-x)

Soldatou, S., Eldjárn, G. H., Ramsay, A. , Van Der Hooft, J. J.J. , Hughes, A. H., Rogers, S. and Duncan, K. R. (2021) Comparative metabologenomics analysis of polar actinomycetes. Marine Drugs, 19(2), 103. (doi: 10.3390/md19020103) (PMID:33578887) (PMCID:PMC7916644)

Jensen, L. J., Huber, F., Ridder, L., Verhoeven, S., Spaaks, J. H., Diblen, F., Rogers, S. and van der Hooft, J. J. J. (2021) Spec2Vec: improved mass spectral similarity scoring through learning of structural relationships. PLoS Computational Biology, 17(2), e1008724. (doi: 10.1371/journal.pcbi.1008724) (PMID:33591968) (PMCID:PMC7909622)

McLuskey, K., Wandy, J. , Vincent, I. , Van Der Hooft, J. J.J. , Rogers, S. , Burgess, K. and Daly, R. (2021) Ranking metabolite sets by their activity levels. Metabolites, 11(2), 103. (doi: 10.3390/metabo11020103) (PMID:33670102) (PMCID:PMC7916825)

Hjorleifsson Eldjarn, G., Ramsay, A. , Van Der Hooft, J. , Duncan, K. R., Soldatou, S., Rousu, J., Daly, R. , Wandy, J. and Rogers, S. (2021) Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions. PLoS Computational Biology, 17(5), e1008920. (doi: 10.1371/journal.pcbi.1008920) (PMID:33945539) (PMCID:PMC8130963)

Leighton, S. P. et al. (2021) Development and validation of a non-remission risk prediction model in first episode psychosis: an analysis of two longitudinal studies. Schizophrenia Bulletin Open, 2(1), sgab041. (doi: 10.1093/schizbullopen/sgab041) (PMID:34568827) (PMCID:PMC8458108)

2020

Huber, F. et al. (2020) matchms - processing and similarity evaluation of mass spectrometry data. Journal of Open Source Software, 5(52), 2411. (doi: 10.21105/joss.02411)

Nothias, L.-F. et al. (2020) Feature-based molecular networking in the GNPS analysis environment. Nature Methods, 17, pp. 905-908. (doi: 10.1038/s41592-020-0933-6) (PMID:32839597)

Young, F., Rogers, S. and Robertson, D. L. (2020) Predicting host taxonomic information from viral genomes: a comparison of feature representations. PLoS Computational Biology, 16(5), e1007894. (doi: 10.1371/journal.pcbi.1007894) (PMID:32453718) (PMCID:PMC7307784)

Kurkiewicz, A. et al. (2020) Towards development of a statistical framework to evaluate myotonic dystrophy type 1 mRNA biomarkers in the context of a clinical trial. PLoS ONE, 15(4), e0231000. (doi: 10.1371/journal.pone.0231000) (PMID:32287265) (PMCID:PMC7156058)

Simpson, K. A. , Rogers, S. and Pezaros, D. P. (2020) Per-host DDoS mitigation by direct-control reinforcement learning. IEEE Transactions on Network and Service Management, 17(1), pp. 103-117. (doi: 10.1109/TNSM.2019.2960202)

2019

Del Carratore, F., Schmidt, K., Vinaixa, M., Hollywood, K. A., Greenland-Bews, C., Takano, E., Rogers, S. and Breitling, R. (2019) Integrated Probabilistic Annotation: a Bayesian-based annotation method for metabolomic profiles integrating biochemical connections, isotope patterns and adduct relationships. Analytical Chemistry, 91(20), pp. 12799-12807. (doi: 10.1021/acs.analchem.9b02354) (PMID:31509381)

Wandy, J. , Davies, V. , van der Hooft, J. J.J. , Weidt, S., Daly, R. and Rogers, S. (2019) In silico optimization of mass spectrometry fragmentation strategies in metabolomics. Metabolites, 9(10), 219. (doi: 10.3390/metabo9100219) (PMID:31600991)

Afonso, C. et al. (2019) Data mining and visualisation: general discussion. Faraday Discussions, 218, pp. 354-371. (doi: 10.1039/c9fd90044f) (PMID:31373341)

Rogers, S. , Ong, C. W., Wandy, J. , Ernst, M., Ridder, L. and Van Der Hooft, J. J.J. (2019) Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra. Faraday Discussions, 218, pp. 284-302. (doi: 10.1039/C8FD00235E) (PMID:31120050)

Ernst, M. et al. (2019) MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools. Metabolites, 9(7), 144. (doi: 10.3390/metabo9070144) (PMID:31315242)

Soldatou, S., Hjorleifsson Eldjarn, G., Huerta Uribe, A. , Rogers, S. and Duncan, K. R. (2019) Linking biosynthetic and chemical space to accelerate microbial secondary metabolite discovery. FEMS Microbiology Letters, 366(13), fnz142. (doi: 10.1093/femsle/fnz142) (PMID:31252431) (PMCID:PMC6697067)

2018

Sun, L., Aragon-Camarasa, G. , Rogers, S. and Siebert, J. P. (2018) Autonomous clothes manipulation using a hierarchical vision architecture. IEEE Access, 6, pp. 76646-76662. (doi: 10.1109/ACCESS.2018.2883072)

Shahzad, Z., Kellermeier, F., Armstrong, E. M., Rogers, S. , Lobet, G., Amtmann, A. and Hills, A. (2018) EZ-Root-VIS: A software pipeline for the rapid analysis and visual reconstruction of root system architecture. Plant Physiology, 177(4), pp. 1368-1381. (doi: 10.1104/pp.18.00217) (PMID:29895611)

Newton, J., Ramage, G. , Gadegaard, N. , Zachs, W., Rogers, S. , Barrett, M. P. , Carruthers, G. and Burgess, K. (2018) Minimally-destructive atmospheric ionisation mass spectrometry authenticates authorship of historical manuscripts. Scientific Reports, 8, 10944. (doi: 10.1038/s41598-018-28810-2) (PMID:30050048) (PMCID:PMC6062563)

Wandy, J. , Niu, M., Giurghita, D., Daly, R. , Rogers, S. and Husmeier, D. (2018) ShinyKGode: an interactive application for ODE parameter inference using gradient matching. Bioinformatics, 34(13), pp. 2314-2315. (doi: 10.1093/bioinformatics/bty089) (PMID:29490021) (PMCID:PMC6022662)

Niu, M., Macdonald, B. , Rogers, S. , Filippone, M. and Husmeier, D. (2018) Statistical inference in mechanistic models: time warping for improved gradient matching. Computational Statistics, 33(2), pp. 1091-1123. (doi: 10.1007/s00180-017-0753-z)

Wandy, J. , Zhu, Y., van der Hooft, J. J.J. , Daly, R. , Barrett, M. P. and Rogers, S. (2018) Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry. Bioinformatics, 34(2), pp. 317-318. (doi: 10.1093/bioinformatics/btx582) (PMID:28968802) (PMCID:PMC5860206)

2017

Gloaguen, Y. , Morton, F. , Daly, R. , Gurden, R., Rogers, S. , Wandy, J. , Wilson, D., Barrett, M. and Burgess, K. (2017) PiMP my metabolome: An integrated, web-based tool for LC-MS metabolomics data. Bioinformatics, 33(24), pp. 4007-4009. (doi: 10.1093/bioinformatics/btx499) (PMID:28961954) (PMCID:PMC5860087)

Wang, Y., Hills, A., Vialet-Chabrand, S., Papanatsiou, M., Griffiths, H., Rogers, S. , Lawson, T., Lew, V. L. and Blatt, M. R. (2017) Unexpected connections between humidity and ion transport discovered using a model to bridge guard cell-to-leaf scales. Plant Cell, 29(11), pp. 2921-2939. (doi: 10.1105/tpc.17.00694) (PMID:29093213)

Niu, M., Rogers, S. , Filippone, M. and Husmeier, D. (2017) Parameter Inference in Differential Equation Models Using Time Warped Gradient Matching. RSS 2017 Annual Conference, Glasgow, Scotland, 04-07 Sep 2017.

Vialet-Chabrand, S., Hills, A., Wang, Y., Griffiths, H., Lew, V. L., Lawson, T., Blatt, M. R. and Rogers, S. (2017) Global sensitivity analysis of OnGuard models identifies key hubs for transport interaction in stomatal dynamics. Plant Physiology, 174(2), pp. 680-688. (doi: 10.1104/pp.17.00170) (PMID:28432256)

Jackson, L. , Gómez-Castañeda, E., Jørgensen, H. G. , Hopcroft, L. E.M. , Rogers, S. , Holyoake, T. L. and Huang, X. (2017) Oncogene addiction in chronic myeloid leukaemia. In: eLS. John Wiley & Sons, Ltd, pp. 1-9. ISBN 9780470015902 (doi: 10.1002/9780470015902.a0024464)

Niu, M., Rogers, S. , Filippone, M. and Husmeier, D. (2017) Parameter Inference in Differential Equation Models of Biopathways using Time Warped Gradient Matching. In: 13th International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics, Stirling, UK, 01-03 Sep 2016, pp. 145-159. ISBN 9783319678337 (doi: 10.1007/978-3-319-67834-4_12)

Noor, M. F. M., Rogers, S. and Williamson, J. (2017) Pre-Interaction Identification by Dynamic Grip Classification. In: 11th International Conference on Ubiquitous Information Management and Communication, Beppu, Japan, 5-7 Jan 2017, pp. 1-7. ISBN 9781450348881 (doi: 10.1145/3022227.3022320)

Sun, L., Aragon-Camarasa, G. , Rogers, S. , Stolkin, R. and Siebert, J. P. (2017) Single-Shot Clothing Category Recognition in Free-Configurations with Application to Autonomous Clothes Sorting. In: IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2017), Vancouver, British Columbia, Canada, 24-28 Sept 2017, pp. 6699-6706. ISBN 9781538626825 (doi: 10.1109/IROS.2017.8206586)

2016

Vialet-Chabrand, S., Matthews, J. S. A., Brendel, O., Blatt, M.R. , Wang, Y., Hills, A., Griffiths, H., Rogers, S. and Lawson, T. (2016) Modelling water use efficiency in a dynamic environment: an example using Arabidopsis thaliana. Plant Science, 251, pp. 65-74. (doi: 10.1016/j.plantsci.2016.06.016) (PMID:27593464) (PMCID:PMC5038844)

Macdonald, B., Niu, M., Rogers, S. , Filippone, M. and Husmeier, D. (2016) Approximate parameter inference in systems biology using gradient matching: a comparative evaluation. BioMedical Engineering OnLine, 15, 80. (doi: 10.1186/s12938-016-0186-x) (PMID:27454253) (PMCID:PMC4959362)

Niu, M., Rogers, S. , Filippone, M. and Husmeier, D. (2016) Fast inference in nonlinear dynamical systems using gradient matching. Proceedings of Machine Learning Research, 48, pp. 1699-1707.

Sun, L., Rogers, S. , Aragon-Camarasa, G. and Siebert, J. P. (2016) Recognising the Clothing Categories from Free-Configuration Using Gaussian-Process-Based Interactive Perception. In: IEEE International Conference on Robotics and Automation (ICRA), Stockholm, Sweden, 16-21 May 2016, 2464 -2470. (doi: 10.1109/ICRA.2016.7487399)

Gómez-Castañeda, E., Hopcroft, L.E.M. , Rogers, S. , Jorgensen, H.G. , Pellicano, F., Vetrie, D. , Copland, M. , Grimmond, S. and Holyoake, T.L. (2016) Uncovering the BCR-ABL1 Tyrosine Kinase Independent Signature in Chronic Myeloid Leukaemia Stem Cells. 36th World Congress of the International Society of Hematology, Glasgow, Scotland, 18-21 Apr 2016. (doi: 10.1111/bjh.14019)

Jackson, L., Hopcroft, L.E.M. , Rogers, S. , Jorgensen, H., Pellicano, F., Wells, C., Mosbergen, R., Chen, T., Vetrie, D. and Holyoake, T.L. (2016) Identifying Genes and Pathways Deregulated in Chronic Myeloid Leukaemia Stem Cells Through Meta-Analysis of Transcriptomic Data. 36th World Congress of the International Society of Hematology, Glasgow, Scotland, 18-21 Apr 2016. (doi: 10.1111/bjh.14019)

Musić, J., Weir, D., Murray-Smith, R. and Rogers, S. (2016) Modelling and correcting for the impact of the gait cycle on touch screen typing accuracy. mUX: The Journal of Mobile User Experience, 5, 1. (doi: 10.1186/s13678-016-0002-3)

Sun, L., Aragon Camarasa, G. , Khan, A., Rogers, S. and Siebert, P. (2016) A precise method for cloth configuration parsing applied to single-arm flattening. International Journal of Advanced Robotic Systems, 13, 70. (doi: 10.5772/62513)

Noor, M. F. M., Rogers, S. and Williamson, J. (2016) Detecting Swipe Errors on Touchscreens Using Grip Modulation. In: CHI 2016, San Jose, CA, USA, 7-12 May 2016, pp. 1909-1920. ISBN 9781450333627 (doi: 10.1145/2858036.2858474)

2015

Niu, M., Filippone, M., Husmeier, D. and Rogers, S. (2015) Inference in Nonlinear Differential Equations. In: 30th International Workshop on Statistical Modelling, Linz, Austria, 06-10 Jul 2015, pp. 187-190.

Wandy, J., Daly, R. , Breitling, R. and Rogers, S. (2015) Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets. Bioinformatics, 31(12), pp. 1999-2006. (doi: 10.1093/bioinformatics/btv072) (PMID:25649621) (PMCID:PMC4760236)

Sun, L., Aragon-Camarasa, G. , Rogers, S. and Siebert, J. P. (2015) Accurate Garment Surface Analysis using an Active Stereo Robot Head with Application to Dual-Arm Flattening. In: IEEE International Conference in Robotics and Automation, Seattle, WA., USA, 26-30 May 2015, pp. 185-192. (doi: 10.1109/ICRA.2015.7138998)

2014

Suvitaival, T., Rogers, S. and Kaski, S. (2014) Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations. Bioinformatics, 30(17), i461-i467. (doi: 10.1093/bioinformatics/btu455) (PMID:25161234) (PMCID:PMC4147908)

Noor, M. F. M., Ramsay, A. , Hughes, S., Rogers, S. , Williamson, J. and Murray-Smith, R. (2014) 28 frames later: predicting screen touches from back-of-device grip changes. In: CHI 2014: ACM CHI Conference on Human Factors in Computing Systems, Toronto, Canada, 26 April - 1 May 2014, pp. 2005-2008. ISBN 9781450324731 (doi: 10.1145/2556288.2557148)

Suvitaival, T., Rogers, S. and Kaski, S. (2014) Stronger findings from mass spectral data through multi-peak modeling. BMC Bioinformatics, 15, p. 208. (doi: 10.1186/1471-2105-15-208) (PMID:24947013) (PMCID:PMC4080774)

Thuma, E., Rogers, S. and Ounis, I. (2014) Detecting missing content queries in an SMS-Based HIV/AIDS FAQ retrieval system. In: 36th European Conference on Information Retrieval, Amsterdam, The Netherlands, 13-16 April 2014, pp. 247-259. (doi: 10.1007/978-3-319-06028-6_21)

2013

Rogers, S. , Sleeman, D. and Kinsella, J. (2013) Investigating the disagreement between clinicians’ ratings of patients in ICUs. IEEE Journal of Biomedical and Health Informatics, 17(4), pp. 843-852. (doi: 10.1109/JBHI.2013.2252182)

Mancy, R. , Prosser, P. and Rogers, S. (2013) Discrete and continuous time simulations of spatial ecological processes predict different final population sizes and interspecific competition outcomes. Ecological Modelling, 259, pp. 50-61. (doi: 10.1016/j.ecolmodel.2013.03.013)

Buschek, D., Rogers, S. and Murray-Smith, R. (2013) User-specific touch models in a cross-device context. In: MobileHCI 2013, Munich, Germany, 27-30 Aug 2013,

Chanialidis, C. , Craigmile, P., Davies, V. , Dean, N. , Evers, L. , Filiippone, M., Gupta, M. , Ray, S. and Rogers, S. (2013) Discussion of Henning and Liao: How to find an appropriate clustering for mixed type variables with application to socio-economic stratification. Journal of the Royal Statistical Society: Series C. 62, 309-369. Discussion Paper. Springer. (doi: 10.1111/j.1467-9876.2012.01066.x).

Dondelinger, F., Filippone, M., Rogers, S. and Husmeier, D. (2013) ODE parameter inference using adaptive gradient matching with Gaussian processes. Proceedings of Machine Learning Research, 31, pp. 216-228.

Sun, L., Aragon-Camarasa, G. , Siebert, J.P. and Rogers, S. (2013) A heuristic-based approach for flattening wrinkled clothes. In: Towards Autonomous Robotic Systems, TAROS 2013, Oxford, UK, 28-30 Aug 2013,

Thuma, E., Rogers, S. and Ounis, I. (2013) Evaluating Bad Query Abandonment in an Iterative SMS-Based FAQ Retrieval System. In: OAIR 2013, Lisbon, Portugal, 15-17 May 2013, pp. 117-120. ISBN 9782905450098

Thuma, E., Rogers, S. and Ounis, I. (2013) Exploiting query logs and field-based models to address term mismatch in an HIV/AIDS FAQ retrieval system. In: Métais, E., Meziane, F., Saraee, M., Sugumaran, V. and Vadera, S. (eds.) Natural Language Processing and Information Systems: 18th International Conference on Application of Natural Language to Information Systems, NLDB2013, Salford, UK, June 2013, Proceedings. Series: Lecture Notes in Computer Science (7934). Springer: Berlin, pp. 77-89. ISBN 9783642388231

Weir, D., Rogers, S. and Buschek, D. (2013) Sparse selection of training data for touch correction systems. In: MobileHCI 2013, Munich, Germany, 27-30 Aug 2013, pp. 1-4.

2012

Dondelinger, F., Rogers, S. , Filippone, M., Cretella, R., Palmer, T., Smith, R., Millar, A. and Husmeier, D. (2012) Parameter inference in mechanistic models of cellular regulation and signalling pathways using gradient matching. In: WCSB2012 - 9th International Workshop on Computational Systems Biology, Ulm, Germany, 4-6 Jun 2012,

Rogers, S. , Daly, R. and Breitling, R. (2012) Mixture model clustering for peak filtering in metabolomics. In: WCSB2012 - 9th International Workshop on Computational Systems Biology, Ulm, Germany, 4-6 Jun 2012,

Sleeman, D., Rogers, S. , Moss, L. , Aitken, A. and Kinsella, J. (2012) INSIGHT: Helping domain experts make their knowledge more consistent. K-MED 2012 - International Workshop on Capturing and Refining Knowledge in the Medical Domain, Galway City, Ireland, 08-12 Oct 2012. pp. 22-35.

Weir, D., Rogers, S. , Murray-Smith, R. and Löchtefeld, M. (2012) A user-specific Machine Learning approach for improving touch accuracy on mobile devices. In: 25th ACM Symposium on User Interface Software and Technology, Cambridge, MA, 7-10 Oct 2012, (doi: 10.1145/2380116.2380175)

2011

Rogers, S. and Girolami, M. (2011) A First Course in Machine Learning. Chapman & Hall / CRC. ISBN 9781439824146

Polajnar, T., Rogers, S. and Girolami, M. (2011) Protein interaction detection in sentences via gaussian processes: a preliminary evaluation. International Journal of Data Mining and Bioinformatics, 5(1), pp. 52-72. (doi: 10.1504/IJDMB.2011.038577)

Rogers, S. (2011) Statistical methods and models for bridging omics data levels. In: Mayer, B. (ed.) Bioinformatics for Omics Data: Methods and Protocols. Series: Methods in molecular biology (719). Humana Press: New York, NY, USA, pp. 133-151. ISBN 9781617790263 (doi: 10.1007/978-1-61779-027-0_6)

Rogers, S. , Scheltema, R.A., Barrett, M. and Breitling, R. (2011) Bayesian approaches for mass spectrometry-based metabolomics. In: Stumpf, M.P.H., Balding, D.J. and Girolami, M. (eds.) Handbook of Statistical Systems Biology. John Wiley & Sons: Chichester, UK, pp. 467-476. ISBN 9780470710869 (doi: 10.1002/9781119970606.ch24)

Rogers, S. , Williamson, J. , Stewart, C. and Murray-Smith, R. (2011) AnglePose: robust, precise capacitive touch tracking via 3d orientation estimation. In: CHI 2011 : ACM CHI Conference on Human Factors in Computing Systems, Vancouver, B.C., 7-12 May 2011, pp. 2575-2584. (doi: 10.1145/1978942.1979318)

2010

Rogers, S. , Klami, A., Sinkkonen, J., Girolami, M. and Kaski, S. (2010) Infinite factorization of multiple non-parametric views. Machine Learning, 79(1-2), pp. 201-226. (doi: 10.1007/s10994-009-5155-1)

Rogers, S. , Williamson, J. , Stewart, C. and Murray-Smith, R. (2010) FingerCloud: uncertainty and autonomy handover incapacitive sensing. In: Mynatt, E. and Schoner, D. (eds.) CHI '10: Proceedings of the 28th International Conference on Human Factors in Computing Systems, 12-15 April 2010, Atlanta, USA. Association for Computing Machinery: New York, NY, USA, pp. 577-580. ISBN 9781605589299 (doi: 10.1145/1753326.1753412)

2009

Rogers, S., Scheltema, R. A., Girolami, M. and Breitling, R. (2009) Probabilistic assignment of formulas to mass peaks in metabolomics experiments. Bioinformatics, 25(4), pp. 512-518. (doi: 10.1093/bioinformatics/btn642)

Polajnar, T., Rogers, S. and Girolami, M. (2009) Classification of protein interaction sentences via gaussian processes. Lecture Notes in Computer Science, 5780, pp. 282-292. (doi: 10.1007/978-3-642-04031-3_25)

Rogers, S. , Girolami, M. and Polajnar, T. (2009) Semi-parametric analysis of multi-rater data. Statistics and Computing, 20(3), pp. 317-334. (doi: 10.1007/s11222-009-9125-z)

2008

Rogers, S., Girolami, M., Kolch, W., Waters, K. M., Liu, T., Thrall, B. and Wiley, H. S. (2008) Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models. Bioinformatics, 24(24), pp. 2894-2900. (doi: 10.1093/bioinformatics/btn553)

2007

Rogers, S., Khanin, R. and Girolami, M. (2007) Bayesian model-based inference of transcription factor activity. BMC Bioinformatics, 8(Suppl), (doi: 10.1186/1471-2105-8-S2-S2)

Rogers, S. and Girolami, M. (2007) Multi-class semi-supervised learning with the e-truncated multinomial probit Gaussian process. Journal of Machine Learning Research: Proceedings Track, 1, pp. 17-32.

2006

Carrivick, L., Rogers, S. , Clark, J., Campbell, C., Girolami, M. and Cooper, C. (2006) Identification of prognostic signatures in breast cancer microarray data using bayesian techniques. Journal of the Royal Society: Interface, 3(8), pp. 367-381. (doi: 10.1098/rsif.2005.0093)

Girolami, M. and Rogers, S. (2006) Variational Bayesian multinomial probit regression with Gaussian process priors. Neural Computation, 18(8), pp. 1790-1817.

2005

Rogers, S., Girolami, M., Campbell, C. and Breitling, R. (2005) The latent process decomposition of cDNA microarray data sets. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2(2), pp. 143-156. (doi: 10.1109/TCBB.2005.29)

Girolami, M. and Rogers, S. (2005) Hierarchic Bayesian models for kernel learning. In: Proceedings of the 22nd International Conference on Machine Learning, Bonn, Germany, 7-11 August 2005., pp. 241-248. ISBN 1595931805 (doi: 10.1145/1102351.1102382)

Rogers, S. and Girolami, M. (2005) A Bayesian regression approach to the inference of regulatory networks from gene expression data. Bioinformatics, 21, pp. 3131-3137. (doi: 10.1093/bioinformatics/bti487)

Rogers, S., Girolami, M., Krebs, R. and Mischak, H. (2005) Disease classification from capillary electrophoresis: mass spectrometry. Lecture Notes in Computer Science, 3686, pp. 183-191. (doi: 10.1007/11551188_20)

This list was generated on Tue Apr 23 08:09:07 2024 BST.

Number of items: 98.

Articles

Ernst, M. et al. (2021) Gestational age-dependent development of the neonatal metabolome. Pediatric Research, 89(6), pp. 1396-1404. (doi: 10.1038/s41390-020-01149-z) (PMID:32942288)

Huber, F. et al. (2020) matchms - processing and similarity evaluation of mass spectrometry data. Journal of Open Source Software, 5(52), 2411. (doi: 10.21105/joss.02411)

Nothias, L.-F. et al. (2020) Feature-based molecular networking in the GNPS analysis environment. Nature Methods, 17, pp. 905-908. (doi: 10.1038/s41592-020-0933-6) (PMID:32839597)

Afonso, C. et al. (2019) Data mining and visualisation: general discussion. Faraday Discussions, 218, pp. 354-371. (doi: 10.1039/c9fd90044f) (PMID:31373341)

Ernst, M. et al. (2019) MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools. Metabolites, 9(7), 144. (doi: 10.3390/metabo9070144) (PMID:31315242)

Niu, M., Rogers, S. , Filippone, M. and Husmeier, D. (2016) Fast inference in nonlinear dynamical systems using gradient matching. Proceedings of Machine Learning Research, 48, pp. 1699-1707.

Rogers, S. , Girolami, M. and Polajnar, T. (2009) Semi-parametric analysis of multi-rater data. Statistics and Computing, 20(3), pp. 317-334. (doi: 10.1007/s11222-009-9125-z)

Rogers, S., Khanin, R. and Girolami, M. (2007) Bayesian model-based inference of transcription factor activity. BMC Bioinformatics, 8(Suppl), (doi: 10.1186/1471-2105-8-S2-S2)

Girolami, M. and Rogers, S. (2006) Variational Bayesian multinomial probit regression with Gaussian process priors. Neural Computation, 18(8), pp. 1790-1817.

Books

Rogers, S. and Girolami, M. (2011) A First Course in Machine Learning. Chapman & Hall / CRC. ISBN 9781439824146

Book Sections

Research Reports or Papers

Conference or Workshop Item

Conference Proceedings

Buschek, D., Rogers, S. and Murray-Smith, R. (2013) User-specific touch models in a cross-device context. In: MobileHCI 2013, Munich, Germany, 27-30 Aug 2013,

Weir, D., Rogers, S. and Buschek, D. (2013) Sparse selection of training data for touch correction systems. In: MobileHCI 2013, Munich, Germany, 27-30 Aug 2013, pp. 1-4.

This list was generated on Tue Apr 23 08:09:07 2024 BST.

Grants

Current Funding

Stomatal-based systems analysis of water use efficiency (BBSRC [BB/L001276/1], £416,746) (with Prof. Michael Blatt)
Computational inference of biopathway dynamics and structures (EPSRC [EP/L020319/1], £341,825) (with Prof. Dirk Husmeier and Dr. Maurizio Filippone)
Enhanced interpretation of metabolomics data to accelerate microbial engineering (Innovate UK, £155,628) (with Dr. Karl Burgess, Dr. Rónán Daly and Prof. Michael Barrett)
In-silico integration of primary CML stem cell polyomic datasets to identify kinase-independent networks and novel prognostic biomarkers (Bloodwise, £138,724) (with Prof. Tessa Holyoake)

Previous Funding

Unifying metabolome and proteome informatics (BBSRC [BB/L018616/1], £144,291) (with Dr. Andy Dowsey, (University of Bristol) and Prof. Rainer Breitling (University of Manchester))

Supervision

Current Students

Joe Wandy
Faizuddin M. Noor
Li Sun
Lorna Jackson
Eduardo Gómez Castañeda

Previous Students

Daryl Weir: Modelling Uncertainty in Touch Interaction
Rebecca Mancy: Modelling Persistence in Spatially-Explicit Ecological and Epidemiological Systems (with Dr. Patrick Prosser)
Edwin Thuma: A semi-automated FAQ retrieval system for HIV/AIDS (with Prof. Iadh Ounis)
Mikhail Churakov: Spatial and network aspects of the spread of infectious diseases in livestock populations (with Prof. Rowloand Kao and Prof. Ruth Zadoks)

Teaching

2016/2017

Professional activities & recognition

Grant committees & research advisory boards

2010 - 2011: Academy of Finland,

Editorial boards

2012 - 2017: PLoS One

Research datasets

Jump to: 2022 | 2021 | 2019 | 2017 | 2016

Number of items: 10.

2022

Wandy, J. , McBride, R., Weidt, S., Rogers, S. , Terzis, N., van der Hooft, J. J. J., Bryson, K. , Daly, R. and Davies, V. (2022) DDA and DIA data for ViMMS 2.0. [Data Collection]

2021

Davies, V. , Wandy, J., Weidt, S., van der Hooft, J., Miller, A. , Daly, R. and Rogers, S. (2021) Rapid Development of Improved Data-Dependent Acquisition Strategies. [Data Collection]

2019

Wandy, J., Davies, V. , van der Hooft, J., Weidt, S., Daly, R. and Rogers, S. (2019) In-silico Optimisation of Mass Spectrometry Fragmentation Strategies in Metabolomics. [Data Collection]

2017

Niu, M., Rogers, S. , Filippone, M. and Husmeier, D. (2017) Parameter Inference in Differential Equation Models of Biopathways using Time Warped Gradient Matching. [Data Collection] (Unpublished)

2016

Niu, M., Rogers, S. , Filippone, M. and Husmeier, D. (2016) Fast Parameter Inference in Nonlinear Dynamical Systems using Iterative Gradient Matching. [Data Collection]

Noor, M. F. M., Rogers, S. and Williamson, J. (2016) Detecting swipe errors on touchscreens using touch modulation. [Data Collection]

Van Der Hooft, J., Rogers, S. , Wandy, J., Barrett, M. and Burgess, K. (2016) Topic Modeling for Untargeted Substructure Exploration in Metabolomics. [Data Collection]

Wandy, J., van der Hooft, J. and Rogers, S. (2016) Ionisation Product Clustering to Improve Peak Alignment in LC-MS-based Metabolomics. [Data Collection]

Macdonald, B., Niu, M., Rogers, S. , Filippone, M. and Husmeier, D. (2016) Approximate parameter inference in systems biology using gradient matching: a comparative evaluation. [Data Collection]

Niu, M., Filippone, M., Husmeier, D. and Rogers, S. (2016) Inference in nonlinear differential equations. [Data Collection]

This list was generated on Wed Apr 24 00:41:35 2024 BST.

Simon Rogers

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Dr Simon Rogers

Biography

Research Interests

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2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

Articles

Books

Book Sections

Research Reports or Papers

Conference or Workshop Item

Conference Proceedings

Grants

Current Funding

Previous Funding

Supervision

Current Students

Previous Students

Teaching

2016/2017

Professional activities & recognition

Grant committees & research advisory boards

Editorial boards

Research datasets

2022

2021

2019

2017

2016