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Author

  • Geoffrey Barton
2016

Improved Annotation with de novo Transcriptome Assembly in Four Social Amoeba Species

Singh, R., Lawal, H. M., Schilde, C., Gloeckner, G., Barton, G., Schaap, P. & Cole, C., 24 May 2016, 34 p. BioRxiv.

Research output: Other contribution

File
85 Downloads (Pure)
2011

Computational approaches to selecting and optimising targets for structural biology

Overton, I. M. & Barton, G. J., Sep 2011, In : Journal of Neuroscience Methods. 55, 1, p. 311 9 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)

NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins

Scott, M. S., Troshin, P. V. & Barton, G. J., 3 Aug 2011, In : BMC Bioinformatics. 12, p. - 7 p., 317.

Research output: Contribution to journalArticle

69 Citations (Scopus)
2014

Filaggrin-stratified transcriptomic analysis of pediatric skin identifies mechanistic pathways in patients with atopic dermatitis

Cole, C., Kroboth, K., Schurch, N. J., Sandilands, A., Sherstnev, A., O'Regan, G. M., Watson, R. M., McLean, W. H. I., Barton, G. J., Irvine, A. D. & Brown, S. J., Jul 2014, In : Journal of Allergy and Clinical Immunology. 134, 1, p. 82-91 10 p.

Research output: Contribution to journalArticle

Open Access
File
75 Citations (Scopus)
184 Downloads (Pure)
2015

14-3-3-Pred: Improved methods to predict 14-3-3-binding phosphopeptides

Madeira, F., Tinti, M., Murugesan, G., Berrett, E., Stafford, M., Toth, R., Cole, C., MacKintosh, C. & Barton, G. J., 2015, In : Bioinformatics.

Research output: Contribution to journalArticle

Open Access
File
58 Citations (Scopus)
315 Downloads (Pure)
2019
Open Access
File
75 Downloads (Pure)
2013

Transcription Termination and Chimeric RNA Formation Controlled by Arabidopsis thaliana FPA

Duc, C., Sherstnev, A., Cole, C., Barton, G. & Simpson, G. G., 31 Oct 2013, In : PLoS Genetics. 9, 10, e1003867.

Research output: Contribution to journalArticle

40 Citations (Scopus)

Tmem79/Matt is the matted mouse gene and is a predisposing gene for atopic dermatitis in human subjects

Saunders, S. P., Goh, C. S. M., Brown, S. J., Palmer, C. N. A., Porter, R. M., Cole, C., Campbell, L. E., Gierlinski, M., Barton, G. J., Schneider, G., Balmain, A., Prescott, A. R., Weidinger, S., Baurecht, H., Kabesch, M., Gieger, C., Lee, Y-A., Tavendale, R., Mukhopadhyay, S., Turner, S. W. & 14 others, Madhok, V. B., Sullivan, F. M., Relton, C., Burn, J., Meggitt, S., Smith, C. H., Allen, M. A., Barker, J. N. W. N., Reynolds, N. J., Cordell, H. J., Irvine, A. D., McLean, W. H. I., Sandilands, A. & Fallon, P. G., Nov 2013, In : Journal of Allergy and Clinical Immunology. 132, 5, p. 1121-1129 9 p.

Research output: Contribution to journalArticle

78 Citations (Scopus)
2019

Detection and Mitigation of Spurious Antisense RNA-seq Reads with RoSA

Mourão, K., Schurch, N. J., Lukoszek, R., Froussios, K., Mackinnon, K., Duc, C., Simpson, G. & Barton, G., 7 Jun 2019, In : F1000 Research. 8, p. 1-7 7 p., 819.

Research output: Contribution to journalArticle

Open Access
File
100 Downloads (Pure)
2015

JPred4: a protein secondary structure prediction server

Drozdetskiy, A., Cole, C., Procter, J. & Barton, G. J., 1 Jul 2015, In : Nucleic Acids Research. 43, W1, p. W389-W394 6 p.

Research output: Contribution to journalArticle

Open Access
File
671 Citations (Scopus)
293 Downloads (Pure)
2020

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

Parker, M. T., Knop, K., Sherwood, A. V., Schurch, N. J., Mackinnon, K., Gould, P. D., Hall, A. J. W., Barton, G. J. & Simpson, G. G., 14 Jan 2020, In : eLife. 9, p. 1-35 35 p., e49658.

Research output: Contribution to journalArticle

Open Access
File
10 Citations (Scopus)
65 Downloads (Pure)
2011

Java bioinformatics analysis web services for multiple sequence alignment-JABAWS:MSA

Troshin, P. V., Procter, J. B. & Barton, G. J., 15 Jul 2011, In : BMC Bioinformatics. 27, 14, p. 2001-2002 2 p.

Research output: Contribution to journalArticle

44 Citations (Scopus)
2012

Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation

Muramoto, T., Cannon, D., Gierlinski, M., Corrigan, A., Barton, G. J. & Chubb, J. R., 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 19, p. 7350-7355 6 p.

Research output: Contribution to journalArticle

76 Citations (Scopus)
2011

A Dictyostelium SH2 adaptor protein required for correct DIF-1 signaling and pattern formation

Sugden, C., Ross, S., Annesley, S. J., Cole, C., Bloomfield, G., Ivens, A., Skelton, J., Fisher, P. R., Barton, G. & Williams, J. G., 15 May 2011, In : Developmental Biology. 353, 2, p. 290-301 12 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)
2017

Correction: A study of the structural properties of sites modified by the O-linked 6-N-acetylglucosamine transferase

Britto Borges, T. & Barton, G., 27 Dec 2017, In : PLoS ONE. 12, 12, p. 1 1 p., e0190461.

Research output: Contribution to journalComment/debate

Open Access
File
114 Downloads (Pure)

Human Missense Variation is Constrained by Domain Structure and Highlights Functional and Pathogenic Residues

MacGowan, S., Madeira, F., Britto Borges, T., Schmittner, M. S., Cole, C. & Barton, G., 13 Apr 2017, In : BioRxiv. 35 p.

Research output: Contribution to journalArticle

File
93 Downloads (Pure)
Open Access
File
5 Citations (Scopus)
191 Downloads (Pure)
2012

The kinomes of apicomplexan parasites

Miranda-Saavedra, D., Gabaldón, T., Barton, G. J., Langsley, G. & Doerig, C., 2012, In : Microbes and Infection. 14, 10, p. 796-810 15 p.

Research output: Contribution to journalArticle

35 Citations (Scopus)
2011

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities

Troshin, P. V., Postis, V. L. G., Ashworth, D., Baldwin, S. A., McPherson, M. J. & Barton, G. J., 7 Mar 2011, In : BMC Research Notes. 4, 9 p., 48.

Research output: Contribution to journalArticle

5 Citations (Scopus)
2012

Transcriptome analysis of skin reveals differences between atopic eczema cases stratified for filaggrin genotype

Brown, S., Cole, C., Irvine, A., Barton, G. & McLean, I., Apr 2012, In : British Journal of Dermatology. 166, 4, p. e26-e27 2 p., O-30.

Research output: Contribution to journalArticle

2013

PGE2 induces macrophage IL-10 production and a regulatory-like phenotype via a protein kinase A-SIK-CRTC3 pathway

Mackenzie, K. F., Clark, K., Naqvi, S., McGuire, V. A., Nöehren, G., Kristariyanto, Y., van den Bosch, M., Mudaliar, M., McCarthy, P. C., Pattison, M. J., Pedrioli, P. G. A., Barton, G. J., Toth, R., Prescott, A. & Arthur, J. S. C., 15 Jan 2013, In : Journal of Immunology. 190, 2, p. 565-577 13 p.

Research output: Contribution to journalArticle

122 Citations (Scopus)

The RNA-binding protein FPA regulates flg22-triggered defense responses and transcription factor activity by alternative polyadenylation

Lyons, R., Iwase, A., Gänsewig, T., Sherstnev, A., Duc, C., Barton, G. J., Hanada, K., Higuchi-Takeuchi, M., Matsui, M., Sugimoto, K., Kazan, K., Simpson, G. G. & Shirasu, K., 9 Oct 2013, In : Scientific Reports. 3, 10 p., 2866.

Research output: Contribution to journalArticle

25 Citations (Scopus)
2020
Open Access
File
57 Downloads (Pure)
2016

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

Schurch, N. J., Schofield, P., Gierliński, M., Cole, C., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G. G., Owen-Hughes, T., Blaxter, M. & Barton, G. J., Jun 2016, In : RNA: a Publication of the RNA Society. 22, 6, p. 839-851 13 p.

Research output: Contribution to journalArticle

Open Access
File
205 Citations (Scopus)
196 Downloads (Pure)
2011

The SWI/SNF complex acts to constrain distribution of the centromeric histone variant Cse4

Gkikopoulos, T., Singh, V., Tsui, K., Awad, S., Renshaw, M. J., Scholfield, P., Barton, G. J., Nislow, C., Tanaka, T. U. & Owen-Hughes, T., 18 May 2011, In : EMBO Journal. 30, 10, p. 1919-1927 9 p.

Research output: Contribution to journalArticle

Open Access
File
33 Citations (Scopus)
144 Downloads (Pure)
2014

Quantitative proteomics in resected renal cancer tissue for biomarker discovery and profiling

Atrih, A., Mudaliar, M. A. V., Zakikhani, P., Lamont, D. J., Huang, J. T-J., Bray, S. E., Barton, G., Fleming, S. & Nabi, G., 2014, In : British Journal of Cancer. 110, 6, p. 1622-1633 12 p.

Research output: Contribution to journalArticle

Open Access
File
39 Citations (Scopus)
165 Downloads (Pure)
2012

Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation

Sherstnev, A., Duc, C., Cole, C., Zacharaki, V., Hornyik, C., Ozsolak, F., Milos, P. M., Barton, G. J. & Simpson, G. G., Aug 2012, In : Nature Structural & Molecular Biology. 19, 8, p. 845-852 8 p.

Research output: Contribution to journalArticle

94 Citations (Scopus)
2017

Improved annotation with de novo transcriptome assembly in four social amoeba species

Singh, R., Lawal, H. M., Schilde, C., Glöckner, G., Barton, G. J., Schaap, P. & Cole, C., 31 Jan 2017, In : BMC Genomics. 18, p. 1-17 17 p., 120.

Research output: Contribution to journalArticle

Open Access
File
1 Citation (Scopus)
108 Downloads (Pure)
2016

AlmostSignificant: Simplifying quality control of high-throughput sequencing data

Ward, J., Cole, C., Febrer, M. & Barton, G., 16 May 2016, 2 p. BioRxiv.

Research output: Other contribution

File
76 Downloads (Pure)
2015

Proteotoxic stress reprograms the chromatin landscape of SUMO modification

Seifert, A., Schofield, P., Barton, G. & Hay, R., 7 Jul 2015, In : Science Signaling. 8, 384, p. rs7 14 p.

Research output: Contribution to journalArticle

Open Access
File
36 Citations (Scopus)
212 Downloads (Pure)
2019
Open Access
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2 Citations (Scopus)
93 Downloads (Pure)
2014
Open Access
File
16 Citations (Scopus)
376 Downloads (Pure)
2011

A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization

Gkikopoulos, T., Schofield, P., Singh, V., Pinskaya, M., Mellor, J., Smolle, M., Workman, J. L., Barton, G. J. & Owen-Hughes, T., 23 Sep 2011, In : Science. 333, 6050, p. 1758-1760 3 p.

Research output: Contribution to journalArticle

175 Citations (Scopus)
2015

Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment

Gierlinski, M., Cole, C., Schofield, P., Schurch, N. J., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G., Owen-Hughes, T., Blaxter, M. & Barton, G. J., 15 Nov 2015, In : Bioinformatics. 31, 22, p. 3625-3630 6 p.

Research output: Contribution to journalArticle

Open Access
File
33 Citations (Scopus)
165 Downloads (Pure)
2018

Proteus: an R package for downstream analysis of MaxQuant output

Gierlinski, M., Gastaldello, F., Cole, C. & Barton, G., 20 Sep 2018, In : BioRxiv. 10 p.

Research output: Contribution to journalArticle

Open Access
File
405 Downloads (Pure)
2012

Haploinsufficiency for AAGAB causes clinically heterogeneous forms of punctate palmoplantar keratoderma

Pohler, E., Mamai, O., Hirst, J., Zamiri, M., Horn, H., Nomura, T., Irvine, A. D., Moran, B., Wilson, N. J., Smith, F. J. D., Goh, C. S. M., Sandilands, A., Cole, C., Barton, G. J., Evans, A. T., Shimizu, H., Akiyama, M., Suehiro, M., Konohana, I., Shboul, M. & 12 others, Teissier, S., Boussofara, L., Denguezli, M., Saad, A., Gribaa, M., Dopping-Hepenstal, P. J., McGrath, J. A., Brown, S. J., Goudie, D. R., Reversade, B., Munro, C. S. & McLean, W. H. I., Nov 2012, In : Nature Genetics. 44, 11, p. 1272-1276 5 p.

Research output: Contribution to journalArticle

47 Citations (Scopus)
2016

AlmostSignificant: simplifying quality control of high-throughput sequencing data

Ward, J., Cole, C., Febrer, M. & Barton, G. J., 15 Dec 2016, In : Bioinformatics. 32, 24, p. 3850-3851 2 p.

Research output: Contribution to journalArticle

Open Access
File
2 Citations (Scopus)
90 Downloads (Pure)
2018

JABAWS 2.2 Distributed Web Services for Bioinformatics: Protein Disorder, Conservation and RNA Secondary Structure

Troshin, P. V., Procter, J. B., Sherstnev, A., Barton, D. L., Madeira, F. & Barton, G. J., 1 Jun 2018, In : Bioinformatics. 34, 11, p. 1939-1940 2 p., byt045.

Research output: Contribution to journalArticle

Open Access
File
5 Citations (Scopus)
173 Downloads (Pure)
2012

PTEN protein phosphatase activity correlates with control of gene expression and invasion, a tumor-suppressing phenotype, but not with AKT activity

Tibarewal, P., Zilidis, G., Spinelli, L., Schurch, N., Maccario, H., Gray, A., Perera, N. M., Davidson, L., Barton, G. J. & Leslie, N. R., 2012, In : Science Signaling. 5, 213, p. ra18

Research output: Contribution to journalArticle

74 Citations (Scopus)
2011

Identification of human miRNA precursors that resemble box C/D snoRNAs

Ono, M., Scott, M. S., Yamada, K., Avolio, F., Barton, G. J. & Lamond, A. I., May 2011, In : Nucleic Acids Research. 39, 9, p. 3879-3891 13 p.

Research output: Contribution to journalArticle

95 Citations (Scopus)

XANNpred: Neural nets that predict the propensity of a protein to yield diffraction-quality crystals

Overton, I. M., van Niekerk, C. A. J. & Barton, G. J., Apr 2011, In : Proteins: Structure, Function, and Bioinformatics. 79, 4, p. 1027-1033 7 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)
2014

Major transcriptome re-organisation and abrupt changes in signalling, cell cycle and chromatin regulation at neural differentiation in vivo

Olivera-Martinez, I., Schurch, N., Li, R., Song, J., Halley, P. A., Das, R. M., Burt, D. W., Barton, G. J. & Storey, K. G., Aug 2014, In : Development. 141, 16, p. 3266-3276 11 p.

Research output: Contribution to journalArticle

Open Access
File
23 Citations (Scopus)
143 Downloads (Pure)
2012

Human box C/D snoRNA processing conservation across multiple cell types

Scott, M. S., Ono, M., Yamada, K., Endo, A., Barton, G. J. & Lamond, A. I., Apr 2012, In : Nucleic Acids Research. 40, 8, p. 3676-3688 13 p.

Research output: Contribution to journalArticle

45 Citations (Scopus)

A quantitative spatial proteomics analysis of proteome turnover in human cells

Boisvert, F-M., Ahmad, Y., Gierlinski, M., Charrière, F., Lamont, D., Scott, M., Barton, G. & Lamond, A. I., 1 Mar 2012, In : Molecular & Cellular Proteomics. 11, 3, M111.011429.

Research output: Contribution to journalArticle

214 Citations (Scopus)
2011

Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus

Overton, I. M., Graham, S., Gould, K. A., Hinds, J., Botting, C. H., Shirran, S., Barton, G. J. & Coote, P. J., 12 May 2011, In : BMC Systems Biology. 5, p. - 16 p., 68.

Research output: Contribution to journalArticle

26 Citations (Scopus)

PNAC: a protein nucleolar association classifier

Scott, M. S., Boisvert, F-M., Lamond, A. I. & Barton, G. J., 27 Jan 2011, In : BMC Genomics. 12, p. - 14 p., 74.

Research output: Contribution to journalArticle

7 Citations (Scopus)
2014

Elevated O-GlcNAc levels activate epigenetically repressed genes and delay mouse ES cell differentiation without affecting naive to primed cell transition

Speakman, C. M., Domke, T. C. E., Wongpaiboonwattana, W., Sanders, K., Mudaliar, M., van Aalten, D. M. F., Barton, G. J. & Stavridis, M. P., Oct 2014, In : Stem Cells. 32, 10, p. 2605-2615

Research output: Contribution to journalArticle

Open Access
File
25 Citations (Scopus)
421 Downloads (Pure)
2019

The Dundee Resource for Sequence Analysis and Structure Prediction

MacGowan, S., Madeira, F., Britto-Borges, T., Warowny, M., Drozdetskiy, A., Procter, J. & Barton, G., 28 Nov 2019, In : Protein Science. 29, 1, p. 277-297 21 p.

Research output: Contribution to journalArticle

Open Access
File
2 Citations (Scopus)
64 Downloads (Pure)
2017

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: A proposed framework

Glusman, G., Rose, P. W., Prlić, A., Dougherty, J., Duarte, J. M., Hoffman, A. S., Barton, G. J., Bendixen, E., Bergquist, T., Bock, C., Brunk, E., Buljan, M., Burley, S. K., Cai, B., Carter, H., Gao, J. J., Godzik, A., Heuer, M., Hicks, M., Hrabe, T. & 17 others, Karchin, R., Leman, J. K., Lane, L., Masica, D. L., Mooney, S. D., Moult, J., Omenn, G. S., Pearl, F., Pejaver, V., Reynolds, S. M., Rokem, A., Schwede, T., Song, S., Tilgner, H., Valasatava, Y., Zhang, Y. & Deutsch, E. W., 18 Dec 2017, In : Genome Medicine. 9, 1, p. 1-10 10 p., 113.

Research output: Contribution to journalArticle

Open Access
File
18 Citations (Scopus)
139 Downloads (Pure)