Dr Kevin Bryson

Senior Lecturer (School of Computing Science)

telephone: 0141 330 4934
email: Kevin.Bryson@glasgow.ac.uk

Room S113, Sir Alwyn Williams Building, Glasgow, Scotland, United Kingdom, G12 8QN

Biography

I joined the School in 2021 as a Senior Lecturer in Bioinformatics and AI.

I received a BSc honours degree (1st class) in Mathematics and Computer Science from Heriot-Watt University in 1991 and a DPhil in Physics from the University of York in 1996, and then spent 3 years in industry working at Oxford Molecular Ltd. developing bioinformatics software before taking up a BBSRC Fellowship at University of Warwick, studying the application of multi-agent systems for data integration in bioinformatics.

After my postdoc position at Warwick, I was awarded an EU Individual Marie Curie Fellowship at INRA in Paris to further develop the idea of autonomous multi-agent systems for bioinformatics data analysis. A system was developed that allowed different labs at INRA to collaboratively annotate evolutionary related species of lactobacillus (lactis, debrukei and sakei - used for cheese, yogurt and fermented sausage!). Each lab had control over its own annotation processes while the systems collaborated with each other on shared annotation when this was relevant.

I then moved to the Department of Computer Science at UCL to take up a Fellowship position analyzing gene expression profiles of stem cells; leading onto a lectureship position, senior lecturer and associate professor in bioinformatics and systems biology where we applied machine learning techniques to protein structure, biological networks, -omics data and histopathology images, collaborating with bioscience groups mostly in the area of cancer.

Research interests

I direct the BioAI Research Group where more information about my research interests can be found.

Our overarching goal is to use computational biology approaches to gain a better understanding of biological systems. One focus is to develop deep neural network architectures to analyse high-throughput cancer data and push forward the area of precision medicine. We are interested in integrative approaches that combine high-throughput data (genomics, transcriptomics, proteomics, metabolomics) with existing biological knowledge from knowledge-bases such as KEGG and Reactome. We are also investigating the use of multi-agent systems (MAS) to facilitate flexible and goal-driven bioinformatics data analysis.

Publications

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Number of items: 44.

2024

Li, W., Anagnostopoulos, C. , Puthiya Parambath, S. and Bryson, K. (2024) LIFE: Leader-driven Hierarchical & Inclusive Federated Learning. In: 2024 IEEE International Conference on Big Data (IEEE BigData 2024), Washington D.C., USA, 15-18 Dec 2024, (Accepted for Publication)

Menegollo, M. et al. (2024) Multi-state gene cluster switches determine the adaptive mitochondrial and metabolic landscape of breast cancer. Cancer Research, (doi: 10.1158/0008-5472.can-23-3172) (PMID:38924467) (Early Online Publication)

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)

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

Viñas, R., Andrés-Terré, H., Liò, P. and Bryson, K. (2022) Adversarial generation of gene expression data. Bioinformatics, 38(3), pp. 730-737. (doi: 10.1093/bioinformatics/btab035) (PMID:33471074) (PMCID:PMC8756177)

2021

Park, G. W. (W.) and Bryson, K. (2021) LDEncoder: Reference deep learning-based feature detector for transfer learning in the field of epigenomics. In: 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB '21), Gainesville, Florida, 1-4 August 2021, p. 58. ISBN 9781450384506 (doi: 10.1145/3459930.3469487)

Yan, Y. et al. (2021) A continuously benchmarked and crowdsourced challenge for rapid development and evaluation of models to predict COVID-19 diagnosis and hospitalization. JAMA Network Open, 4(10), e2124946. (doi: 10.1001/jamanetworkopen.2021.24946) (PMID:34633425) (PMCID:PMC8506231)

2020

Xu, R. et al. (2020) The breast cancer oncogene IKKε coordinates mitochondrial function and serine metabolism. EMBO Reports, 21(9), e48260. (doi: 10.15252/embr.201948260) (PMID:32783398) (PMCID:PMC7116048)

2019

Pryor, R. et al. (2019) Host-microbe-drug-nutrient screen identifies bacterial effectors of metformin therapy. Cell, 178(6), 1299-1312.e29. (doi: 10.1016/j.cell.2019.08.003) (PMID:31474368) (PMCID:PMC6736778)

Bentham, R. B., Bryson, K. and Szabadkai, G. (2019) Biclustering analysis of co-regulation patterns in nuclear-encoded mitochondrial genes and metabolic pathways. In: Haznadar, M. (ed.) Cancer Metabolism: Methods and Protocols. Series: Methods in Molecular Biology, 1928. Springer: New York, pp. 469-478. ISBN 9781493990276 (doi: 10.1007/978-1-4939-9027-6_24)

2017

Bentham, R. B., Bryson, K. and Szabadkai, G. (2017) MCbiclust: A novel algorithm to discover large-scale functionally related gene sets from massive transcriptomics data collections. Nucleic Acids Research, 45(15), pp. 8712-8730. (doi: 10.1093/nar/gkx590) (PMID:28911113) (PMCID:PMC5587796)

Scott, T. A. et al. (2017) Host-microbe co-metabolism dictates cancer drug efficacy in C. elegans. Cell, 169(3), 442-456.e18. (doi: 10.1016/j.cell.2017.03.040) (PMID:28431245) (PMCID:PMC5406385)

Malki, K. et al. (2017) Highly polygenic architecture of antidepressant treatment response: comparative analysis of SSRI and NRI treatment in an animal model of depression. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics, 174(3), pp. 235-250. (doi: 10.1002/ajmg.b.32494) (PMID:27696737) (PMCID:PMC5434854)

2016

Jiang, Y. et al. (2016) An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology, 17, 184. (doi: 10.1186/s13059-016-1037-6) (PMID:27604469) (PMCID:PMC5015320)

Malki, K., Koritskaya, E., Harris, F., Bryson, K. , Herbster, M. and Tosto, M.G. (2016) Epigenetic differences in monozygotic twins discordant for major depressive disorder. Translational Psychiatry, 6, e839. (doi: 10.1038/tp.2016.101) (PMID:27300265) (PMCID:PMC4931599)

2015

Karr, J. R. et al. (2015) Summary of the DREAM8 parameter estimation challenge: toward parameter identification for whole-cell models. PLoS Computational Biology, 11(5), e1004096. (doi: 10.1371/journal.pcbi.1004096) (PMID:26020786) (PMCID:PMC4447414)

2013

Buchan, D. W.A., Minneci, F., Nugent, T. C.O., Bryson, K. and Jones, D. T. (2013) Scalable web services for the PSIPRED Protein Analysis Workbench. Nucleic Acids Research, 41(W1), W349-W357. (doi: 10.1093/nar/gkt381) (PMID:23748958) (PMCID:PMC3692098)

Radivojac, P. et al. (2013) A large-scale evaluation of computational protein function prediction. Nature Methods, 10(3), pp. 221-227. (doi: 10.1038/nmeth.2340) (PMID:23353650) (PMCID:PMC3584181)

Cozzetto, D., Buchan, D. W.A., Bryson, K. and Jones, D. T. (2013) Protein function prediction by massive integration of evolutionary analyses and multiple data sources. BMC Bioinformatics, 14(Sup 3), S1. (doi: 10.1186/1471-2105-14-S3-S1) (PMID:23514099) (PMCID:PMC3584902)

Medlar, A., Głowacka, D., Stanescu, H., Bryson, K. and Kleta, R. (2013) SwiftLink: parallel MCMC linkage analysis using multicore CPU and GPU. Bioinformatics, 29(4), pp. 413-419. (doi: 10.1093/bioinformatics/bts704) (PMID:23239673)

Ellul, C., Gupta, S., Haklay, M. M. and Bryson, K. (2013) A platform for location based app development for citizen science and community mapping. In: Krisp, J. M. (ed.) Progress in Location-Based Services. Series: Lecture Notes in Geoinformation and Cartography. Springer, pp. 71-90. ISBN 9783642342035 (doi: 10.1007/978-3-642-34203-5_5)

2012

Leung, M. H., Bryson, K. , Freystatter, K., Pichon, B., Edwards, G., Charalambous, B. M. and Gillespie, S. H. (2012) Sequetyping: serotyping Streptococcus pneumoniae by a single PCR sequencing strategy. Journal of Clinical Microbiology, 50(7), pp. 2419-2427. (doi: 10.1128/JCM.06384-11) (PMID:22553238) (PMCID:PMC3405617)

2010

Itan, Y., Bryson, K. and Thomas, M. G. (2010) Detecting gene duplications in the human lineage. Annals of Human Genetics, 74(6), pp. 555-565. (doi: 10.1111/j.1469-1809.2010.00609.x) (PMID:20946257)

Buchan, D.W.A., Ward, S.M., Lobley, A.E., Nugent, T.C.O., Bryson, K. and Jones, D.T. (2010) Protein annotation and modelling servers at University College London. Nucleic Acids Research, 38(Suppl2), W563-W568. (doi: 10.1093/nar/gkq427) (PMID:20507913) (PMCID:PMC2896093)

2008

Edwards, Y. J.K., Bryson, K. and Jones, D. T. (2008) A meta-analysis of microarray gene expression in mouse stem cells: redefining stemness. PLoS ONE, 3(7), e2712. (doi: 10.1371/journal.pone.0002712) (PMID:18628962) (PMCID:PMC2444034)

2007

Bryson, K. , Cozzetto, D. and Jones, D. T. (2007) Computer-assisted protein domain boundary prediction using the dom-pred server. Current Protein and Peptide Science, 8(2), pp. 181-188. (doi: 10.2174/138920307780363415) (PMID:17430199)

2006

Van De Guchte, M. et al. (2006) The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. Proceedings of the National Academy of Sciences of the United States of America, 103(24), pp. 9274-9279. (doi: 10.1073/pnas.0603024103) (PMID:16754859) (PMCID:PMC1482600)

McGuffin, L. J., Smith, R. T., Bryson, K. , Sørensen, S.-A. and Jones, D. T. (2006) High throughput profile-profile based fold recognition for the entire human proteome. BMC Bioinformatics, 7, 288. (doi: 10.1186/1471-2105-7-288) (PMID:16759376) (PMCID:PMC1513610)

Bryson, K. et al. (2006) AGMIAL: Implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Research, 34(12), pp. 3533-3545. (doi: 10.1093/nar/gkl471) (PMID:16855290) (PMCID:PMC1524909)

2005

Bryson, K. , McGuffin, L. J., Marsden, R. L., Ward, J. J., Sodhi, J. S. and Jones, D. T. (2005) Protein structure prediction servers at University College London. Nucleic Acids Research, 33(suppl2), W36-W38. (doi: 10.1093/nar/gki410) (PMID:15980489) (PMCID:PMC1160171)

Jones, D., Sodhi, J., Lise, S., McGuffin, L. and Bryson, K. (2005) Prediction of protein-protein and protein-ligand interactions from protein structures. 30th FEBS Congress and the 9th IUBMB Conference, Budapest, Hungary, 2-7 Jul 2005. pp. 397-398. (doi: 10.1111/j.1742-4658.2005.4739_9.x)

Jones, D.T., Bryson, K. , Coleman, A., McGuffin, L.J., Sadowski, M.I., Sodhi, J.S. and Ward, J.J. (2005) Prediction of novel and analogous folds using fragment assembly and fold recognition. Proteins: Structure Function and Bioinformatics, 61(S7), pp. 143-151. (doi: 10.1002/prot.20731) (PMID:16187356)

2004

Sodhi, J. S., Bryson, K. , McGuffin, L. J., Ward, J. J., Wernisch, L. and Jones, D. T. (2004) Predicting metal-binding site residues in low-resolution structural models. Journal of Molecular Biology, 342(1), pp. 307-320. (doi: 10.1016/j.jmb.2004.07.019) (PMID:15313626)

Ward, J. J., McGuffin, J. J., Bryson, K. , Buxton, B. F. and Jones, D. T. (2004) The DISOPRED server for the prediction of protein disorder. Bioinformatics, 20(13), pp. 2138-2139. (doi: 10.1093/bioinformatics/bth195) (PMID:15044227)

Sodhi, J. S., McGuffin, L.J., Bryson, K. , Ward, J.J., Wernisch, L. and Jones, D.T. (2004) Automatic prediction of functional site regions in low-resolution protein structures. In: 2004 IEEE Computational Systems Bioinformatics Conference, Stanford, California, USA, 19 Aug 2004, pp. 702-703. ISBN 0769521940 (doi: 10.1109/CSB.2004.1332551)

McGuffin, L. J., Street, S. A., Bryson, K. , Sørensen, S.‐A. and Jones, D. T. (2004) The Genomic Threading Database: A comprehensive resource for structural annotations of the genomes from key organisms. Nucleic Acids Research, 32(suppl1), D196-D199. (doi: 10.1093/nar/gkh043) (PMID:14681393) (PMCID:PMC308777)

2001

McGuffin, L. J., Bryson, K. and Jones, D. T. (2001) What are the baselines for protein fold recognition? Bioinformatics, 17(1), pp. 63-72. (doi: 10.1093/bioinformatics/17.1.63) (PMID:11222263)

Bryson, K. , Luck, M., Joy, M. and Jones, D.T. (2001) Agent interaction for bioinformatics data management. Applied Artificial Intelligence, 15(10), pp. 917-947. (doi: 10.1080/088395101753242688)

2000

McGuffin, L. J., Bryson, K. and Jones, D. T. (2000) The PSIPRED protein structure prediction server. Bioinformatics, 16(4), pp. 404-405. (doi: 10.1093/bioinformatics/16.4.404) (PMID:10869041)

Bryson, K. and Greenall, R.J. (2000) Binding sites of the polyamines putrescine, cadaverine, spermidine and spermine on A- and B-DNA located by simulated annealing. Journal of Biomolecular Structure and Dynamics, 18(3), pp. 393-412. (doi: 10.1080/07391102.2000.10506676) (PMID:11149516)

Bryson, K. , Luck, M., Joy, M. and Jones, D.T. (2000) Applying agents to bioinformatics in geneweaver. In: Klusch, M. and Kerschberg, L. (eds.) Cooperative Information Agents IV - The Future of Information Agents in Cyberspace. Series: Lecture Notes in Artificial Intelligence, 1860. Springer: Boston, MA, pp. 60-71. ISBN 9783540450122 (doi: 10.1007/978-3-540-45012-2_7)

1999

Fischer, D. et al. (1999) CAFASP-1: Critical assessment of fully automated structure prediction methods. Proteins: Structure Function and Bioinformatics, 37(S3), pp. 209-217. (doi: 10.1002/(SICI)1097-0134(1999)37:3+<209::AID-PROT27>3.0.CO;2-Y)

Jones, D. T., Tress, M., Bryson, K. and Hadley, C. (1999) Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure. Proteins: Structure Function and Bioinformatics, 37(S3), pp. 104-111. (doi: 10.1002/(SICI)1097-0134(1999)37:3+<104::AID-PROT14>3.0.CO;2-P)

1996

Bryson, K. and Greenall, R. J. (1996) Molecular dynamics of putrescine. Journal of the Chemical Society: Faraday Transactions, 92(6), pp. 913-919. (doi: 10.1039/FT9969200913)

This list was generated on Wed Nov 20 17:06:58 2024 GMT.

Jump to: Articles | Book Sections | Conference or Workshop Item | Conference Proceedings

Number of items: 44.

Articles

Scott, T. A. et al. (2017) Host-microbe co-metabolism dictates cancer drug efficacy in C. elegans. Cell, 169(3), 442-456.e18. (doi: 10.1016/j.cell.2017.03.040) (PMID:28431245) (PMCID:PMC5406385)

Radivojac, P. et al. (2013) A large-scale evaluation of computational protein function prediction. Nature Methods, 10(3), pp. 221-227. (doi: 10.1038/nmeth.2340) (PMID:23353650) (PMCID:PMC3584181)

Itan, Y., Bryson, K. and Thomas, M. G. (2010) Detecting gene duplications in the human lineage. Annals of Human Genetics, 74(6), pp. 555-565. (doi: 10.1111/j.1469-1809.2010.00609.x) (PMID:20946257)

McGuffin, L. J., Bryson, K. and Jones, D. T. (2001) What are the baselines for protein fold recognition? Bioinformatics, 17(1), pp. 63-72. (doi: 10.1093/bioinformatics/17.1.63) (PMID:11222263)

Bryson, K. , Luck, M., Joy, M. and Jones, D.T. (2001) Agent interaction for bioinformatics data management. Applied Artificial Intelligence, 15(10), pp. 917-947. (doi: 10.1080/088395101753242688)

McGuffin, L. J., Bryson, K. and Jones, D. T. (2000) The PSIPRED protein structure prediction server. Bioinformatics, 16(4), pp. 404-405. (doi: 10.1093/bioinformatics/16.4.404) (PMID:10869041)

Bryson, K. and Greenall, R. J. (1996) Molecular dynamics of putrescine. Journal of the Chemical Society: Faraday Transactions, 92(6), pp. 913-919. (doi: 10.1039/FT9969200913)

Book Sections

Conference or Workshop Item

Conference Proceedings

This list was generated on Wed Nov 20 17:06:58 2024 GMT.

Supervision

Alsharif, Ghadeer Obaid F
Security-by-Design Framework for the IoT
LI, WENHAO
Mini-batch Gradient-parallel Heterogeneous Ensembles for Large-scale Multi-feature Data Learning Optimization
Xiao, Ke
Resilient Learning in Edge Computing
Zhiwei, Zheng
DNA methylation detection through the development of masked autoencoders and contrastive learning methods

Teaching

Currently I'm the Director of the MSc in Data Science.

I currently teach the following courses:

COMPSCI5103 Deep Learning for MSc
COMPSCI4084 Programming and Development

At Glasgow I have previously taught:

COMPSCI4039 Programming (IT)

Previously, at UCL, I was the Undergraduate Programme Director and also the Director of the MSc in Computer Science. I have taught in the past the following subjects:

BIOC0016 (3rd year Computational and Systems Biology within the Department of Structural and Molecular Biology, UCL)
COMP0008 (2nd year Computer Architecture and Concurrency)
COMP0082 (Bioinformatics module as part of the MSc in Machine Learning)
COMP1001 (1st year Computer Architecture) using assembly language programming to explain the underlying working of the MIPS processor (and processors in general).
COMP2007 (2nd year Networking and Concurrency) teaching Java Concurrent Programming and introduces the concepts of computer networking by developing concurrent Java simulators demonstrating the key principles.
COMP3006 (Advanced Mathematics) where I taught advanced linear algebra and vector calculus.
CPLXG001 (MRes Advanced Biological Modelling and Bioinformatics within CoMPLEX) teaching bioinformatics.
CPLXG003 (MRes Transferrable Skills Module within CoMPLEX) teaching the application of SQL relational databases within bioinformatics.
INFN3004 (MSc and Intercalating Medical BSc in Immunology and Cell Pathology and Infection) taught introductory bioinformatics to medical students.
WIBRG001 (MSc Drug Design within the Wolfson Institute of Medical Research) teaching introductory bioinformatics.

I was also an Honorary Teaching Fellow at Birkbeck College where I taught:

Birkbeck MSc in Bioinformatics and Systems Biology teaching biological networks and mathematical modelling.

Research datasets

Jump to: 2022

Number of items: 1.

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]

This list was generated on Wed Nov 20 17:07:00 2024 GMT.

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Clarity

Dr Kevin Bryson

Biography

Research interests

Publications

2024

2023

2022

2021

2020

2019

2017

2016

2015

2013

2012

2010

2008

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1996

Articles

Book Sections

Conference or Workshop Item

Conference Proceedings

Supervision

Teaching

Research datasets

2022