Computational Biology

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Research Output 1987 2019

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44 Citations (Scopus)
244 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
46 Citations (Scopus)

3Dee: a database of protein structural domains

Siddiqui, A. S., Dengler, U. & Barton, G. J., Feb 2001, In : Bioinformatics. 17, 2, p. 200-1 2 p.

Research output: Contribution to journalArticle

Databases
Proteins
Protein
World Wide Web
Internet
12 Citations (Scopus)

3D MRI Analysis of the Lower Legs of Treated Idiopathic Congenital Talipes Equinovarus (Clubfoot)

Duce, S. L., D'Alessandro, M., Du, Y., Jagpal, B., Gilbert, F. J., Crichton, L., Barker, S., Collinson, J. M. & Miedzybrodzka, Z., 30 Jan 2013, In : PLoS ONE. 8, 1, 10 p., e54100.

Research output: Contribution to journalArticle

Open Access
Clubfoot
Magnetic resonance
magnetic resonance imaging
Muscle
Leg
7 Citations (Scopus)
111 Downloads (Pure)
Open Access
File
phylogeny
genome
protein
proteins
Dictyostelium
3 Citations (Scopus)
119 Downloads (Pure)
Open Access
File
Dictyostelium
Adenylyl Cyclases
Genes
Cell Movement
bis(3',5')-cyclic diguanylic acid
9 Citations (Scopus)

A knowledge-based architecture for protein sequence analysis and structure prediction

Clark, D. A., Barton, G. J. & Rawlings, C. J., Jun 1990, In : Journal of Molecular Graphics. 8, 2, p. 94-107 14 p.

Research output: Contribution to journalArticle

Protein Sequence Analysis
Knowledge based systems
Knowledge engineering
Proteins
Molecular biology
2 Citations (Scopus)
36 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
1083 Citations (Scopus)

ALSCRIPT: a tool to format multiple sequence alignments

Barton, G. J., Jan 1993, In : Protein Science. 6, 1, p. 37-40 4 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)
134 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
131 Citations (Scopus)

Amino acid sequence analysis of the annexin super-gene family of proteins

Barton, G. J., Newman, R. H., Freemont, P. S. & Crumpton, M. J., Jun 1991, In : European Journal of Biochemistry. 198, 3, p. 749-760 12 p.

Research output: Contribution to journalArticle

Annexins
Protein Sequence Analysis
Genes
Amino Acids
Uteroglobin
45 Citations (Scopus)
42 Downloads (Pure)

An absorption origin for the soft excess in Seyfert 1 active galactic nuclei

Middleton, M., Done, C. & Gierliński, M., 17 Oct 2007, In : Monthly Notices of the Royal Astronomical Society. 381, 4, p. 1426-1436 11 p.

Research output: Contribution to journalArticle

Open Access
File
active galactic nuclei
accretion
accretion disks
galaxies
outflow
69 Citations (Scopus)
39 Downloads (Pure)

Analysing the atolls: X-ray spectral transitions of accreting neutron stars

Gladstone, J., Done, C. & Gierliński, M., 11 Jun 2007, In : Monthly Notices of the Royal Astronomical Society. 378, 1, p. 13-22 10 p.

Research output: Contribution to journalArticle

Open Access
File
atolls
neutron stars
accretion
x rays
hysteresis
47 Citations (Scopus)
Sequence Deletion
Insertional Mutagenesis
Databases
45 Citations (Scopus)

A normalised scale for structural genomics target ranking: the OB-Score

Overton, I. M. & Barton, G. J., 10 Jul 2006, In : FEBS Letters. 580, 16, p. 4005-4009 5 p.

Research output: Contribution to journalArticle

Isoelectric Point
Hydrophobicity
Genomics
Hydrophobic and Hydrophilic Interactions
Diffraction
157 Citations (Scopus)

A periodicity of ∼1 hour in X-ray emission from the active galaxy RE J1034+396

Gierliński, M., Middleton, M., Ward, M. & Done, C., 18 Sep 2008, In : Nature. 455, 7211, p. 369-371 3 p.

Research output: Contribution to journalArticle

active galaxies
periodic variations
active galactic nuclei
x rays
oscillations

Application of a relativistic accretion disc model to GRO J1655-40 ASCA spectrum

Gierliński, M., Maciołek-Niedźwiecki, A., Magdziarz, P. & Ebisawa, K., 1 Dec 1999, In : Astronomische Nachrichten. 320, 4-5, p. 350 1 p.

Research output: Contribution to journalArticle

65 Citations (Scopus)

Application of a relativistic accretion disc model to X-ray spectra of LMC X-1 and GRO J1655-40

Gierliński, M., Maciołek-Niedźwiecki, A. & Ebisawa, K., 11 Aug 2001, In : Monthly Notices of the Royal Astronomical Society. 325, 3, p. 1253-1265 13 p.

Research output: Contribution to journalArticle

Open Access
accretion disks
accretion
x rays
inclination
radiation pressure
603 Citations (Scopus)

Application of multiple sequence alignment profiles to improve protein secondary structure prediction

Cuff, J. A. & Barton, G. J., 15 Aug 2000, In : Proteins: Structure, Function, and Bioinformatics. 40, 3, p. 502-511 10 p.

Research output: Contribution to journalArticle

Secondary Protein Structure
Sequence Alignment
Proteins
Computer program listings
Servers
3 Citations (Scopus)

A PROLOG approach to analysing protein structure

Barton, G. J. & Rawlings, C. J., 1 Jan 1990, In : Tetrahedron Computer Methodology. 3, 6 PART C, p. 739-756 18 p.

Research output: Contribution to journalArticle

Proteins
Computer programming languages
PROLOG (programming language)
Sanders
Logic programming
16 Citations (Scopus)
116 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
387 Citations (Scopus)

A strategy for the rapid multiple alignment of protein sequences: confidence levels from tertiary structure comparisons

Barton, G. J. & Sternberg, M. J. E., 20 Nov 1987, In : Journal of Molecular Biology. 198, 2, p. 327-337 11 p.

Research output: Contribution to journalArticle

Sequence Alignment
Proteins
Globins
Transferrin
Disulfides
118 Citations (Scopus)

Black hole accretion discs: Reality confronts theory

Gierliński, M. & Done, C., 21 Jan 2004, In : Monthly Notices of the Royal Astronomical Society. 347, 3, p. 885-894 10 p.

Research output: Contribution to journalArticle

accretion disks
accretion
prediction
corona
viscosity
70 Citations (Scopus)

Black hole spin in GRS 1915+105

Middleton, M., Done, C., Gierliński, M. & Davis, S. W., 11 Dec 2006, In : Monthly Notices of the Royal Astronomical Society. 373, 3, p. 1004-1012 9 p.

Research output: Contribution to journalArticle

Open Access
radiative transfer
accretion
radio
gravity
X Ray Timing Explorer
148 Citations (Scopus)

Broad-band X-ray/γ-ray spectra and binary parameters of GX 339-4 and their astrophysical implications

Zdziarski, A. A., Poutanen, J., Mikołajewska, J., Gierliński, M., Ebisawa, K. & Johnson, W. N., 1 Dec 1998, In : Monthly Notices of the Royal Astronomical Society. 301, 2, p. 435-450 16 p.

Research output: Contribution to journalArticle

rays
astrophysics
broadband
x rays
power law
12 Citations (Scopus)
71 Downloads (Pure)

Cohort comparison study of cardiac disease and atherosclerotic burden in type 2 diabetic adults using whole body cardiovascular magnetic resonance imaging

Duce, S. L., Weir-McCall, J. R., Gandy, S. J., Matthew, S. Z., Cassidy, D. B., McCormick, L., Rauchhaus, P., Looker, H., Colhoun, H. M. & Houston, J. G., 18 Sep 2015, In : Cardiovascular Diabetology. 14, 11 p., 122.

Research output: Contribution to journalArticle

Open Access
File
Atherosclerotic Plaques
Heart Diseases
Cohort Studies
Cardiovascular Diseases
Type 2 Diabetes Mellitus
149 Citations (Scopus)
bis(5'-nucleosyl)tetraphosphatase (asymmetrical)
Phosphoprotein Phosphatases
Escherichia coli
Conservation
Consensus Sequence
88 Citations (Scopus)

Conservation analysis and structure prediction of the SH2 family of phosphotyrosine binding domains

Russell, R. B., Breed, J. & Barton, G. J., 8 Jun 1992, In : FEBS Letters. 304, 1, p. 15-20 6 p.

Research output: Contribution to journalArticle

Phosphotyrosine
src Homology Domains
Conservation
Intercellular Signaling Peptides and Proteins
Amino Acids
20 Citations (Scopus)

Conservation of amino acids in multiple alignments: aspartic acid has unexpected conservation

Fiser, A., Simon, I. & Barton, G. J., 18 Nov 1996, In : FEBS Letters. 397, 2-3, p. 225-229 5 p.

Research output: Contribution to journalArticle

Aspartic Acid
Conservation
Amino Acids
Sequence Alignment
Viperidae
27 Citations (Scopus)

Consistency of the black hole mass determination in AGN from the reverberation and the X-ray excess variance method

Nikołajuk, M., Czerny, B., Ziółkowski, J. & Gierliński, M., 11 Aug 2006, In : Monthly Notices of the Royal Astronomical Society. 370, 3, p. 1534-1540 7 p.

Research output: Contribution to journalArticle

Open Access
reverberation
x rays
inclination
galaxies
orbits
143 Citations (Scopus)

Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions

Siddiqui, A. S. & Barton, G. J., May 1995, In : Protein Science. 4, 5, p. 872-84 13 p.

Research output: Contribution to journalArticle

Proteins
Protein Databases
Molecular graphics
Databases
Protein Domains
28 Citations (Scopus)

Correlated timing and spectral behavior of 4U 1705-44

Olive, J. F., Barret, D. & Gierliński, M., 20 Jan 2003, In : Astrophysical Journal. 583, 1 I, p. 416-423 8 p.

Research output: Contribution to journalArticle

time measurement
neutron stars
accretion
geometry
radii
43 Citations (Scopus)

Correlation between the photon index and X-ray luminosity of black hole X-ray binaries and active galactic nuclei: Observations and interpretation

Yang, Q. X., Xie, F. G., Yuan, F., Zdziarski, A. A., Gierliński, M., Ho, L. C. & Yu, Z., 21 Feb 2015, In : Monthly Notices of the Royal Astronomical Society. 447, 2, p. 1692-1704 13 p.

Research output: Contribution to journalArticle

active galactic nuclei
accretion
luminosity
photons
x rays
355 Citations (Scopus)

Crystal structure of isopenicillin N synthase is the first from a new structural family of enzymes

Roach, P. L., Clifton, I. J., Fülöp, V., Harlos, K., Barton, G. J., Hajdu, J., Andersson, I., Schofield, C. & Baldwin, J. E., 22 Jun 1995, In : Nature. 375, 6533, p. 700-704 5 p.

Research output: Contribution to journalArticle

Penicillins
Enzymes
Thiazolidines
Oxygen
Keto Acids
21 Citations (Scopus)

Dependence of the orbital modulation of X-rays from 4U 1820-303 on the accretion rate

Zdziarski, A. A., Gierliński, M., Wen, L. & Kostrzewa, Z., 21 May 2007, In : Monthly Notices of the Royal Astronomical Society. 377, 3, p. 1017-1023 7 p.

Research output: Contribution to journalArticle

Open Access
accretion
modulation
orbitals
X Ray Timing Explorer
x rays
12 Citations (Scopus)

Deposition of macromolecular structures

Keller, P. A., Henrick, K., McNeil, P., Moodie, S. & Barton, G. J., 1 Nov 1998, In : Acta Crystallographica Section D: Biological Crystallography. 54, 6, no. 1, p. 1105-1108 4 p.

Research output: Contribution to journalArticle

39 Downloads (Pure)

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

Mourao, K., Schurch, N., Lukoszek, R., Froussios, K., Mackinnon, K., Duc, C., Simpson, G. & Barton, G., 10 Jun 2019, In : F1000 Research. 8, 7 p., 819.

Research output: Contribution to journalArticle

Open Access
File
Antisense RNA
RNA
Gene Expression
Genes
Arabidopsis
30 Citations (Scopus)

Discovery of powerful millisecond flares from Cygnus X-1

Gierliński, M. & Zdziarski, A. A., 11 Aug 2003, In : Monthly Notices of the Royal Astronomical Society. 343, 3, p. L84-L88 5 p.

Research output: Contribution to journalArticle

flares
folding
energy flux
hardness
accretion
Open Access
Point Mutation
Proteins
Intellectual Disability
Mutation
Protein Folding

Distinct signals and immune cells drive liver pathology and glomerulonephritis in ABIN1[D485N] mice

Nanda, S. K., Petrova, T., Marchesi, F., Gierlinski, M., Razsolkov, M., Lee, K. L., Wright, S. W., Rao, V. R., Cohen, P. & Arthur, J. S. C., 6 Nov 2019, In : Life Science Alliance. 2, 6, p. 1-19 19 p., e201900533.

Research output: Contribution to journalArticle

Open Access
File
glomerulonephritis
Pathology
pathology
Glomerulonephritis
Liver
12 Citations (Scopus)
88 Downloads (Pure)

Dynamically generated patterns in dense suspensions of active filaments

Kokkoorakunnel Ramankutty, P., Henkes, S. & Sknepnek, R., 12 Feb 2018, In : Physical Review E: Statistical, Nonlinear, and Soft Matter Physics. 97, 2, 022606.

Research output: Contribution to journalArticle

Open Access
File
Filament
filaments
Active Particles
Langevin Dynamics
bundles
4 Citations (Scopus)

Dynamical Patterns of Coexisting Strategies in a Hybrid Discrete-continuum Spatial Evolutionary Game Model

Burgess, A. E. F., Schofield, P. G., Hubbard, S. F., Chaplain, M. A. J. & Lorenzi, T., 7 Dec 2016, In : Mathematical Modelling of Natural Phenomena. 11, 5, p. 49-64 16 p.

Research output: Contribution to journalArticle

Evolutionary Game
Continuum
Motion
Game
Individual-based Model

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
481 Citations (Scopus)

Evaluation and improvement of multiple sequence methods for protein secondary structure prediction

Cuff, J. A. & Barton, G. J., 1 Mar 1999, In : Proteins: Structure, Function, and Bioinformatics. 34, 4, p. 508-19 12 p.

Research output: Contribution to journalArticle

Secondary Protein Structure
Proteins
World Wide Web
Web services
Sequence Alignment
107 Citations (Scopus)

Evaluation and improvements in the automatic alignment of protein sequences

Barton, G. J. & Sternberg, M. J., 1 Feb 1987, In : Protein Science. 1, 2, p. 89-94 6 p.

Research output: Contribution to journalArticle

Sequence Alignment
Secondary Protein Structure
Sequence Homology
Proteins
Testing
22 Citations (Scopus)
92 Downloads (Pure)

Evaluation of the diagnostic accuracy of prototype rapid tests for human African trypanosomiasis

Sternberg, J. M., Gierlinski, M., Biéler, S., Ferguson, M. A. J. & Ndung'u, J. M., Dec 2014, In : PLoS Neglected Tropical Diseases. 8, 12, p. e3373 8 p.

Research output: Contribution to journalArticle

Open Access
File
African Trypanosomiasis
Antigens
Routine Diagnostic Tests
Equipment and Supplies
Sensitivity and Specificity
4 Citations (Scopus)

Examining the role of individual movement in promoting coexistence in a spatially explicit prisoner's dilemma

Burgess, A. E. F., Lorenzi, T., Schofield, P. G., Hubbard, S. F. & Chaplain, M. A. J., 21 Apr 2017, In : Journal of Theoretical Biology. 419, p. 323-332 10 p.

Research output: Contribution to journalArticle

Prisoners' Dilemma
semiochemicals
Pheromones
Coexistence
Individual-based Model
8 Citations (Scopus)
90 Downloads (Pure)

Expanding the clinical spectrum of hereditary fibrosing poikiloderma with tendon contractures, myopathy and pulmonary fibrosis due to FAM111B mutations

Mercier, S., Küry, S., Salort-Campana, E., Magot, A., Agbim, U., Besnard, T., Bodak, N., Bou-Hanna, C., Bréhéret, F., Brunelle, P., Caillon, F., Chabrol, B., Cormier-Daire, V., David, A., Eymard, B., Faivre, L., Figarella-Branger, D., Fleurence, E., Ganapathi, M., Gherardi, R. & 34 others, Goldenberg, A., Hamel, A., Igual, J., Irvine, A. D., Israël-Biet, D., Kannengiesser, C., Laboisse, C., Le Caignec, C., Mahé, J. Y., Mallet, S., MacGowan, S., McAleer, M. A., McLean, I., Méni, C., Munnich, A., Mussini, J. M., Nagy, P. L., Odel, J., O'Regan, G. M., Péréon, Y., Perrier, J., Piard, J., Puzenat, E., Sampson, J. B., Smith, F., Soufir, N., Tanji, K., Thauvin, C., Ulane, C., Watson, R. M., Khumalo, N. P., Mayosi, B. M., Barbarot, S. & Bézieau, S., 15 Oct 2015, In : Orphanet Journal of Rare Diseases. 10, 16 p., 135.

Research output: Contribution to journalArticle

Open Access
File
Pulmonary Fibrosis
Contracture
Muscular Diseases
Tendons
Mutation
1 Citation (Scopus)
83 Downloads (Pure)

Faster growth with shorter antigens can explain a VSG hierarchy during African trypanosome infections: a feint attack by parasites

Liu, D., Albergante, L., Newman, T. & Horn, D., 2018, In : Scientific Reports. 8, p. 1-10 10 p., 10922.

Research output: Contribution to journalArticle

Open Access
File
Trypanosomiasis
Membrane Glycoproteins
Parasites
Antigens
Growth
114 Citations (Scopus)

Flexible protein sequence patterns: a sensitive method to detect weak structural similarities

Barton, G. J. & Sternberg, M. J. E., 20 Mar 1990, In : Journal of Molecular Biology. 212, 2, p. 389-402 14 p.

Research output: Contribution to journalArticle

Globins
Proteins
Sequence Alignment
Hemoglobins
Databases

Generation and interpretation of protein sequence and structural multiple alignments

Barton, G. J., Russell, R. B. & Livingstone, C. D., 1 Aug 1992, In : Journal of Protein Chemistry. 11, 4, p. 389-389 1 p.

Research output: Contribution to journalArticle