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 Oct 30 20:28:00 2024 GMT.