• 3248 Citations
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20082019
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Research Output 2008 2019

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Article
2019

EMSY expression affects multiple components of the skin barrier with relevance to atopic dermatitis

Elias, M. S., Wright, S. C., Remenyi, J., Abbott, J. C., Bray, S. E., Cole, C., Edwards, S., Gierlinski, M., Glok, M., McGrath, J. A., Nicholson, W. V., Paternoster, L., Prescott, A. R., Have, S. T., Whitfield, P. D., Lamond, A. I. & Brown, S. J., Aug 2019, In : Journal of Allergy and Clinical Immunology. 144, 2, p. 470-481 12 p.

Research output: Contribution to journalArticle

Open Access
Atopic Dermatitis
Skin
Genome-Wide Association Study
Keratinocytes
Skin Diseases
2018
170 Downloads (Pure)

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
Proteus
Peptides
Mass Spectrometry
Proteins
2017
3 Citations (Scopus)
112 Downloads (Pure)
Open Access
File
Dictyostelium
Adenylyl Cyclases
Genes
Cell Movement
bis(3',5')-cyclic diguanylic acid
5 Citations (Scopus)
131 Downloads (Pure)

A mechanistic target of rapamycin complex 1/2 (mTORC1)/V-Akt murine thymoma viral oncogene homolog 1 (AKT1)/cathepsin H axis controls filaggrin expression and processing in skin, a novel mechanism for skin barrier disruption in patients with atopic dermatitis

Naeem, A. S., Tommasi, C., Cole, C., Brown, S. J., Zhu, Y., Way, B., Willis Owen, S. A. G., Moffatt, M., Cookson, W. O., Harper, J. I., Di, W. L., Brown, S. J., Reinheckel, T. & O'Shaughnessy, R. F. L., Apr 2017, In : Journal of Allergy and Clinical Immunology. 139, 4, p. 1228-1241 14 p.

Research output: Contribution to journalArticle

Open Access
File
Cathepsin H
Thymoma
Atopic Dermatitis
Oncogenes
Skin
14 Citations (Scopus)
109 Downloads (Pure)

A Proteomic Approach to Analyze the Aspirin-mediated Lysine Acetylome

Tatham, M. H., Cole, C., Scullion, P., Wilkie, R., Westwood, N. J., Stark, L. A. & Hay, R. T., 1 Feb 2017, In : Molecular & Cellular Proteomics. 16, 2, p. 310-326 17 p.

Research output: Contribution to journalArticle

Open Access
File
Acetylation
Proteomics
Aspirin
Lysine
acetylsalicylic acid lysinate
17 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
RNA Splice Sites
Ligands
Proteins
Sequence Alignment
DNA-Binding Proteins
1 Citation (Scopus)
37 Downloads (Pure)

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
Amoeba
Transcriptome
Genome
RNA Sequence Analysis
Molecular Sequence Annotation
10 Citations (Scopus)
78 Downloads (Pure)

Mutations in desmoglein-1 cause diverse inherited palmoplantar keratoderma phenotypes: implications for genetic screening

Lovgren, M-L., McAleer, M. A., Irvine, A. D., Wilson, N. J., Tavadia, S., Schwartz, M. E., Cole, C., Sandilands, A., Smith, F. J. D. & Zamiri, M., 2 Apr 2017, In : British Journal of Dermatology.

Research output: Contribution to journalArticle

Open Access
File
Desmoglein 1
Palmoplantar Keratoderma
Genetic Testing
Phenotype
Mutation
2016
2 Citations (Scopus)
30 Downloads (Pure)

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
Quality Control
DNA Sequence Analysis
Sequencing
High Throughput
Quality control
151 Citations (Scopus)
113 Downloads (Pure)

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
RNA
Genes
Research Design
Genome
Guidelines
3 Citations (Scopus)
54 Downloads (Pure)

Isolated recessive nail dysplasia caused by FZD6 mutations: report of three families and review of the literature

Kasparis, C., Reid, D., Wilson, N. J., Okur, V., Cole, C., Hansen, C. D., Bosse, K., Betz, R. C., Khan, M. & Smith, F. J. D., Dec 2016, In : Clinical and Experimental Dermatology. 41, 8, p. 884-889 6 p.

Research output: Contribution to journalArticle

Open Access
File
Nails
Mutation
Malformed Nails
Skin
Hair
2 Citations (Scopus)
76 Downloads (Pure)

Keratin 12 missense mutation induces the unfolded protein response and apoptosis in meesmann epithelial corneal dystrophy

Allen, E. H. A., Courtney, D. G., Atkinson, S. D., Moore, J. E., Mairs, L., Poulsen, E. T., Schiroli, D., Maurizi, E., Cole, C., Hickerson, R. P., James, J., Murgatroyd, H., Smith, F. J. D., MacEwen, C., Enghild, J. J., Nesbit, M. A., Leslie Pedrioli, D. M., McLean, W. H. I. & Moore, C. B. T., 15 Mar 2016, In : Human Molecular Genetics. 25, 6, p. 1176-1191 16 p., ddw001.

Research output: Contribution to journalArticle

Open Access
File
Juvenile Epithelial of Meesmann Corneal Dystrophy
Keratin-12
Unfolded Protein Response
Missense Mutation
Apoptosis
2015
40 Citations (Scopus)
238 Downloads (Pure)

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
Phosphopeptides
Predict
Position-Specific Scoring Matrices
Prediction
Scoring
506 Citations (Scopus)
219 Downloads (Pure)

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
Secondary Protein Structure
Sequence Alignment
Equipment and Supplies
11 Citations (Scopus)

Loss-of-function mutations in CAST cause peeling skin, leukonychia, acral punctate keratoses, cheilitis, and knuckle pads

Lin, Z., Zhao, J., Nitoiu, D., Scott, C. A., Plagnol, V., Smith, F. J. D., Wilson, N. J., Cole, C., Schwartz, M. E., McLean, W. H. I., Wang, H., Feng, C., Duo, L., Zhou, E. Y., Ren, Y., Dai, L., Chen, Y., Zhang, J., Xu, X., O'Toole, E. A. & 2 others, Kelsell, D. P. & Yang, Y., 5 Mar 2015, In : American Journal of Human Genetics. 96, 3, p. 440-447 8 p.

Research output: Contribution to journalArticle

Cheilitis
Keratosis
Extremities
Skin
Mutation
51 Citations (Scopus)

Severe dermatitis, multiple allergies, and metabolic wasting syndrome caused by a novel mutation in the N-terminal plakin domain of desmoplakin

McAleer, M. A., Pohler, E., Smith, F. J. D., Wilson, N. J., Cole, C., MacGowan, S., Koetsier, J. L., Godsel, L. M., Harmon, R. M., Gruber, R., Crumrine, D., Elias, P. M., McDermott, M., Butler, K., Broderick, A., Sarig, O., Sprecher, E., Green, K. J., McLean, W. H. I. & Irvine, A. D., Nov 2015, In : Journal of Allergy and Clinical Immunology. 136, 5, p. 1268-1276 9 p.

Research output: Contribution to journalArticle

Desmoplakins
Wasting Syndrome
Dermatitis
Hypersensitivity
Desmoglein 1
27 Citations (Scopus)
91 Downloads (Pure)

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
2014
64 Citations (Scopus)
103 Downloads (Pure)

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
Atopic Dermatitis
Pediatrics
Skin
Genotype
Extracellular Space
12 Citations (Scopus)
289 Downloads (Pure)
Open Access
File
RNA Sequence Analysis
Expressed Sequence Tags
3' Untranslated Regions
3' untranslated regions
sequence analysis
2013
69 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

Atopic Dermatitis
Skin
Genes
Mutation
Single Nucleotide Polymorphism
32 Citations (Scopus)

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

Arabidopsis
RNA
Arabidopsis thaliana
transcription (genetics)
mutants
2012
82 Citations (Scopus)

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

Polyadenylation
Arabidopsis
Genome
RNA
RNA Sequence Analysis
42 Citations (Scopus)

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

Palmoplantar Keratoderma
Haploinsufficiency
Epidermal Growth Factor Receptor
Carrier Proteins
Vesicular Transport Adaptor Proteins

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

2011
1 Citation (Scopus)

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

2010
146 Citations (Scopus)

Regulation of the miR-212/132 locus by MSK1 and CREB in response to neurotrophins

Remenyi, J., Hunter, C. J., Cole, C., Ando, H., Impey, S., Monk, C. E., Martin, K. J., Barton, G. J., Hutvagner, G. & Arthur, J. S. C., 1 Jun 2010, In : Biochemical Journal. 428, 2, p. 281-291 11 p.

Research output: Contribution to journalArticle

2009
309 Citations (Scopus)

Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs

Cole, C., Sobala, A., Lu, C., Thatcher, S. R., Bowman, A., Brown, J. W. S., Green, P. J., Barton, G. J. & Hutvagner, G., Dec 2009, In : RNA: a Publication of the RNA Society. 15, 12, p. 2147-2160 14 p.

Research output: Contribution to journalArticle

311 Citations (Scopus)

System-wide changes to SUMO modifications in response to heat shock

Golebiowski, F., Matic, I., Tatham, M. H., Cole, C., Yin, Y., Nakamura, A., Cox, J., Barton, G. J., Mann, M. & Hay, R. T., 26 May 2009, In : Science Signaling. 2, 72, 12 p., ra24.

Research output: Contribution to journalArticle

2008
1151 Citations (Scopus)

The Jpred 3 secondary structure prediction server

Cole, C., Barber, J. D. & Barton, G. J., Jul 2008, In : Nucleic Acids Research. 36, S2, p. W197-W201 5 p.

Research output: Contribution to journalArticle