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

Import to contacts

ORCID iDhttps://orcid.org/0000-0002-1163-6368

Biography

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

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 to bioinformatics.

After my postdoc position at Warwick, I got an EU Individual Marie Curie Fellowship at INRA in Paris where we developed another cooperative distributed system for annotating the genomes of fermented sausage, cheese and yogurt bacteria.

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 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

We use machine learning, and in particular deep learning, to tackle challenges in the area of bioscience. A lot of our research has been in the area of cancer and we are grateful to the clinical research groups that have allowed us to work with them on these problems.

We work with -omics data including gene expression, genomic methylation, proteomics and metabolics data. We employ supervised and unsupervised machine learning approaches to make predictions and reveal patterns in the data. We use biological network information to integrate data and gain holistic understanding of biological mechanisms. We also analyze image data including fluorescent labelled images of E. coli and H&E microscope slide images of cancer tissues sections. The long-term goal is to integrate molecular information, imaging data and clinical data to gain holistic understanding of diseases, particularly targeted at cancer.

Projects involving clinical prediction from -omics data have included:
  • Breast cancer subtypes.
  • Psychiatric conditions such as depression and autism.

We have also developed a number of machine learning tools to:

  • Find patterns within large heterogeneous gene expression data collections (MCbiclust based on R).
  • Create realistic synthetic gene expression datasets (GANs using TensorFlow).

We have recently started projects doing traditional image analysis (scikit-image) and CNN image prediction (PyTorch/Tensorflow) including:

  • Phenotype analysis of fluorescent C. elegans worms.
  • Nucleus image analysis using PCA, t-SNE and TensorFlow.
  • Classification between liposarcoma and lipoma using H&E whole slide images.
  • Classification between synovial sarcoma and singular fibrous tumour using H&E images.

We also analyze protein sequences using machine learning approaches to predict both structural and functional aspects of proteins including:

  • Secondary structure.
  • Protein disorder.
  • Amyloid propensity.
  • B-cell epitopes.
 

Publications

List by: Type | Date

Jump to: 2023 | 2022 | 2021 | 2020 | 2019 | 2017 | 2016 | 2015 | 2013 | 2012 | 2010 | 2008 | 2007 | 2006 | 2005 | 2004 | 2001 | 2000 | 1999 | 1996
Number of items: 42.

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 Sun Dec 3 02:08:06 2023 GMT.
Jump to: Articles | Book Sections | Conference or Workshop Item | Conference Proceedings
Number of items: 42.

Articles

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)

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)

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)

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)

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. (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)

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)

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)

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)

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)

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)

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)

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)

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)

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.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)

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)

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)

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. (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)

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)

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

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)

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)

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)

Conference or Workshop Item

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)

Conference Proceedings

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)

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)

This list was generated on Sun Dec 3 02:08:06 2023 GMT.

Teaching

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

I currently teach the following courses:

  • COMPSCI5103 Deep Learning for MSc
  • COMPSCI4084 Programming and Development

Previously I have taught at Glasgow:

  • 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 Sat Dec 2 20:59:55 2023 GMT.