Computational Biology

  • United Kingdom

Research Output

ProtEST: protein multiple sequence alignments from expressed sequence tags

Cuff, J. A., Birney, E., Clamp, M. E. & Barton, G. J., Feb 2000, In : Bioinformatics. 16, 2, p. 111-6 6 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)

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
400 Downloads (Pure)

Publisher Correction: GPCRmd uncovers the dynamics of the 3D-GPCRome (Nature Methods, (2020), 10.1038/s41592-020-0884-y)

Rodríguez-Espigares, I., Torrens-Fontanals, M., Tiemann, J. K. S., Aranda-García, D., Ramírez-Anguita, J. M., Stepniewski, T. M., Worp, N., Varela-Rial, A., Morales-Pastor, A., Medel-Lacruz, B., Pándy-Szekeres, G., Mayol, E., Giorgino, T., Carlsson, J., Deupi, X., Filipek, S., Filizola, M., Gómez-Tamayo, J. C., Gonzalez, A., Gutiérrez-de-Terán, H. & 27 others, Jiménez-Rosés, M., Jespers, W., Kapla, J., Khelashvili, G., Kolb, P., Latek, D., Marti-Solano, M., Matricon, P., Matsoukas, M. T., Miszta, P., Olivella, M., Perez-Benito, L., Provasi, D., Ríos, S., Torrecillas, I. R., Sallander, J., Sztyler, A., Vasile, S., Weinstein, H., Zachariae, U., Hildebrand, P. W., De Fabritiis, G., Sanz, F., Gloriam, D. E., Cordomi, A., Guixà-González, R. & Selent, J., 23 Jul 2020, In : Nature Methods. p. 861-862 2 p.

Research output: Contribution to journalComment/debate

Open Access

Pulcherrimin formation controls growth arrest of the Bacillus subtilis biofilm

Arnaouteli, S., Matoz Fernandez, D., Porter, M., Kalamara, M., Abbott, J., MacPhee, C. E., Davidson, F. & Stanley-Wall, N., 2 Jul 2019, In : Proceedings of the National Academy of Sciences. 116, 27, p. 13553-13562 10 p.

Research output: Contribution to journalArticle

Open Access
File
3 Citations (Scopus)
108 Downloads (Pure)

Purification, crystallization and data collection of methicillin-resistant Staphylococcus aureus Sar2676, a pantothenate synthetase

Seetharamappa, J., Oke, M., Liu, H., McMahon, S. A., Johnson, K. A., Carter, L., Dorward, M., Zawadzki, M., Overton, I. M., Van Niekirk, C. A. J., Graham, S., Botting, C. H., Taylor, G. L., White, M. F., Barton, G. J., Coote, P. J. & Naismith, J. H., 5 May 2007, In : Acta Crystallographica Section F: Structural Biology and Crystallization Communications. 63, 6, p. 488-491 4 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Quantitative MRI establishes the efficacy of PI3K inhibitor (GDC-0941) multi-treatments in PTEN-deficient mice lymphoma

Wullschleger, S., García-Martínez, J. M. & Duce, S. L., 1 Feb 2012, In : Anticancer Research. 32, 2, p. 415-420 6 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Quantitative proteome analysis of temporally-resolved phagosomes following uptake via key phagocytic receptors

Dill, B., Gierliński, M., Härtlova, A., González Arandilla, A., Guo, M., Clarke, R. G. & Trost, M., 1 May 2015, In : Molecular & Cellular Proteomics. 14, 5, p. 1334 1349 p., 16.

Research output: Contribution to journalArticle

Open Access
28 Citations (Scopus)

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)
164 Downloads (Pure)

Radiation mechanisms and geometry of cygnus X-1 in the soft state

Gierliński, M., Zdziarski, A. A., Poutanen, J., Coppi, P. S., Ebisawa, K. & Johnson, W. N., 21 Oct 1999, In : Monthly Notices of the Royal Astronomical Society. 309, 2, p. 496-512 17 p.

Research output: Contribution to journalArticle

Open Access
352 Citations (Scopus)

Radiative processes, spectral states and variability of black-hole binaries

Zdziarski, A. A. & Gierliński, M., 1 May 2004, In : Progress of Theoretical Physics Supplements. 155, p. 99-119 21 p.

Research output: Contribution to journalReview article

191 Citations (Scopus)

RE J1034+396: the origin of the soft X-ray excess and quasi-periodic oscillation

Middleton, M., Done, C., Ward, M., Gierliński, M. & Schurch, N., 21 Mar 2009, In : Monthly Notices of the Royal Astronomical Society. 394, 1, p. 250-260 11 p.

Research output: Contribution to journalArticle

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

Reply to Jiménez-Alonso et al., Schooling and Zhao, and Mortazavi: Further discussion on the immunological model of carcinogenesis

Palmer, S., Albergante, L., Blackburn, C. C. & Newman, T. J., 8 May 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 19, p. E4319-E4321 3 p.

Research output: Contribution to journalLetter

Open Access

Reprocessing of X-rays in the outer accretion disc of the black hole binary XTE J1817-330

Gierliński, M., Done, C. & Page, K., 21 Jan 2009, In : Monthly Notices of the Royal Astronomical Society. 392, 3, p. 1106-1114 9 p.

Research output: Contribution to journalArticle

80 Citations (Scopus)

Role of structural dynamics at the receptor G protein interface for signal transduction

Rose, A. S., Zachariae, U., Grubmüller, H., Hofmann, K. P., Scheerer, P. & Hildebrand, P. W., 25 Nov 2015, In : PLoS ONE. 10, 11, 13 p., e0143399.

Research output: Contribution to journalArticle

Open Access
File
6 Citations (Scopus)
142 Downloads (Pure)

RXTE observations of AGN

Rothschild, R. E., Heindl, W. A., Blanco, P. R., Gruber, D. E., Marsden, D. C., Pelling, M. R., Jahoda, K., Madejski, G., Swank, J. H., Zdziarski, A. A., Gierliński, M. & Hink, P. L., 1 Dec 1997, In : European Space Agency, (Special Publication) ESA SP. 382, p. 393-395 3 p.

Research output: Contribution to journalArticle

Scaling variability from stellar to supermassive black holes

Done, C. & Gierliński, M., 21 Nov 2005, In : Monthly Notices of the Royal Astronomical Society. 364, 1, p. 208-216 9 p.

Research output: Contribution to journalArticle

Open Access
File
47 Citations (Scopus)
106 Downloads (Pure)
8 Citations (Scopus)

scop: structural classification of proteins

Barton, G. J., Dec 1994, In : Trends in Biochemical Sciences. 19, 12, p. 554-555 2 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Secondary structure prediction for modelling by homology

Boscott, P. E., Barton, G. J. & Richards, W. G., Apr 1993, In : Protein Science. 6, 3, p. 261-266 6 p.

Research output: Contribution to journalArticle

18 Citations (Scopus)
16 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

61 Citations (Scopus)

Simultaneous X-ray and γ-ray observations of Cyg X-1 in the hard state by Ginga and OSSE

Gierliński, M., Zdziarski, A. A., Done, C., Neil Johnson, W., Ebisawa, K., Ueda, Y., Haardt, F. & Phlips, B. F., 1 Dec 1997, In : Monthly Notices of the Royal Astronomical Society. 288, 4, p. 958-964 7 p.

Research output: Contribution to journalArticle

226 Citations (Scopus)

Spectral transitions in X-ray binaries

Done, C. & Gierliński, M., 1 May 2004, In : Progress of Theoretical Physics Supplements. 155, p. 9-18 10 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)

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)

Stepwise Simulation of 3,5-Dihydro-5-methylidene-4H-imidazol-4-one (MIO) Biogenesis in Histidine Ammonia-lyase

Sánchez-Murcia, P. A., Bueren-Calabuig, J. A., Camacho-Artacho, M., Cortés-Cabrera, Á. & Gago, F., 18 Oct 2016, In : Biochemistry. 55, 41, p. 5854-5864 11 p.

Research output: Contribution to journalArticle

Open Access
File
7 Citations (Scopus)
149 Downloads (Pure)
158 Citations (Scopus)

Structural similarity between the p17 matrix protein of HIV-1 and interferon-γ

Matthews, S., Barlow, P., Boyd, J., Barton, G., Russell, R., Mills, H., Cunningham, M., Meyers, N., Burns, N., Clark, N., Kingsman, S., Kingsman, A. & Campbell, I., 25 Aug 1994, In : Nature. 370, 6491, p. 666-668 3 p.

Research output: Contribution to journalArticle

127 Citations (Scopus)

Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump

Fitzpatrick, A. W. P., Llabres, S., Neuberger, A., Blaza, J. N., Bai, X-C., Okada, U., Murakami, S., van Veen, H. W., Zachariae, U., Scheres, S. H. W., Luisi, B. F. & Du, D., 15 May 2017, In : Nature Microbiology. 2, p. 1-8 8 p., 17070.

Research output: Contribution to journalArticle

Open Access
File
48 Citations (Scopus)
183 Downloads (Pure)

The AMPS package for multiple protein sequence alignment

Barton, G. J., 1994, Computer Analysis of Sequence Data Part II . Springer Verlag, Vol. 25. p. 327-47 21 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

10 Citations (Scopus)

The canonical X-ray/gamma-ray spectrum of Seyfert Is and low-state Galactic black hole candidates

Zdziarski, A. A., Gierlinski, M., Gondek, D. & Magdziarz, P., 1 Dec 1996, In : Astronomy and Astrophysics: Supplement Series. 120, 4, p. 553-558 6 p.

Research output: Contribution to journalArticle

24 Citations (Scopus)

The chromatin remodelling enzymes SNF2H and SNF2L position nucleosomes adjacent to CTCF and other transcription

Wiechens, N., Singh, V., Gkikopoulos, T., Schofield, P., Rocha, S. & Owen-Hughes, T., 28 Mar 2016, In : PLoS Genetics. 12, 3, e1005940.

Research output: Contribution to journalArticle

Open Access
File
30 Citations (Scopus)
149 Downloads (Pure)

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)

The iron K feature in narrow line Seyfert 1 galaxies: Evidence for a P Cygni profile?

Done, C., Sobolewska, M. A., Gierliński, M. & Schurch, N. J., 1 Jan 2007, In : Monthly Notices of the Royal Astronomical Society: Letters. 374, 1, p. L15-L19 5 p.

Research output: Contribution to journalLetter

Open Access
32 Citations (Scopus)

The Jalview Java alignment editor

Clamp, M., Cuff, J., Searle, S. M. & Barton, G. J., 12 Feb 2004, In : Bioinformatics. 20, 3, p. 426-427 2 p.

Research output: Contribution to journalArticle

1125 Citations (Scopus)

The limits of protein secondary structure prediction accuracy from multiple sequence alignment

Russell, R. B. & Barton, G. J., 20 Dec 1993, In : Journal of Molecular Biology. 234, 4, p. 951-957 7 p.

Research output: Contribution to journalLetter

70 Citations (Scopus)

The lipid environment determines the activity of the Escherichia coli ammonium transporter AmtB

Mirandela, G. D., Tamburrino, G., Hoskisson, P. A., Zachariae, U. & Javelle, A., Feb 2019, In : FASEB Journal. 33, 2, p. 1989-1999 11 p.

Research output: Contribution to journalArticle

Open Access
File
6 Citations (Scopus)
106 Downloads (Pure)

The O-GlcNAc Transferase Intellectual Disability Mutation L254F Distorts the TPR Helix

Gundogdu, M., Llabres, S., Gorelik, A., Ferenbach, A., Zachariae, U. & Van Aalten, D., 17 May 2018, In : Cell Chemical Biology. 25, 5, p. 513-518.e4 10 p.

Research output: Contribution to journalArticle

Open Access
File
11 Citations (Scopus)
160 Downloads (Pure)

Thermal/non-thermal model of Cyg X-1 in the soft state

Gierliński, M., Zdziarski, A. A., Coppi, P. S., Poutanen, J., Ebisawa, K. & Johnson, W. N., 1 Jan 1999, In : Nuclear Physics B - Proceedings Supplements. 69, 1-3, p. 312-315 4 p.

Research output: Contribution to journalArticle

Thermal proteome profiling of breast cancer cells reveals proteasomal activation by CDK4/6 inhibitor palbociclib

Miettinen, T. P., Peltier, J., Härtlova, A., Gierliński, M., Jansen, V. M., Trost, M. & Björklund, M., 15 May 2018, In : EMBO Journal. 37, 10, p. 1-19 19 p., e98359.

Research output: Contribution to journalArticle

Open Access
File
26 Citations (Scopus)
221 Downloads (Pure)

The Structure of Serine Palmitoyltransferase; Gateway to Sphingolipid Biosynthesis

Yard, B. A., Carter, L. G., Johnson, K. A., Overton, I. M., Dorward, M., Liu, H., McMahon, S. A., Oke, M., Puech, D., Barton, G. J., Naismith, J. H. & Campopiano, D. J., 27 Jul 2007, In : Journal of Molecular Biology. 370, 5, p. 870-886 17 p.

Research output: Contribution to journalArticle

79 Citations (Scopus)

The superorbital variability and triple nature of the X-ray source 4U 1820-303

Zdziarski, A. A., Wen, L. & Gierliński, M., 1 Dec 2008, Astrophysics of Compact Objects - International Conference on Astrophysics of Compact Objects. Vol. 968. 1 p. 244. (AIP Conference Proceedings; vol. 968).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

The superorbital variability and triple nature of the X-ray source 4U 1820-303

Zdziarski, A. A., Wen, L. & Gierliński, M., 21 May 2007, In : Monthly Notices of the Royal Astronomical Society. 377, 3, p. 1006-1016 11 p.

Research output: Contribution to journalArticle

Open Access
39 Citations (Scopus)

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)

The X-ray/γ-ray spectrum of XTE J1550-564 in the very high state

Gierliński, M. & Done, C., 11 Jul 2003, In : Monthly Notices of the Royal Astronomical Society. 342, 4, p. 1083-1092 10 p.

Research output: Contribution to journalArticle

53 Citations (Scopus)

The X-ray spectrum of the atoll source 4U 1608-52

Gierliński, M. & Done, C., 21 Dec 2002, In : Monthly Notices of the Royal Astronomical Society. 337, 4, p. 1373-1380 8 p.

Research output: Contribution to journalArticle

Open Access
69 Citations (Scopus)

Thymic involution and rising disease incidence with age

Palmer, S., Albergante, L., Blackburn, C. C. & Newman, T. J., 20 Feb 2018, In : Proceedings of the National Academy of Sciences. 115, 8, p. 1883-1888 6 p.

Research output: Contribution to journalArticle

Open Access
File
50 Citations (Scopus)
207 Downloads (Pure)

Triggering MSR1 promotes JNK-mediated inflammation in IL-4 activated macrophages

Guo, M., Härtlova, A., Gierlinski, M., Prescott, A., Castellvi, J., Hernandez Losa, J., Petersen, S. K., Wenzel, U. A., Dill, B. D., Emmerich, C. H., Ramon Y Cajal, S., Russell, D. G. & Trost, M., 3 Jun 2019, In : EMBO Journal. 38, 11, p. 1-15 15 p., e100299.

Research output: Contribution to journalArticle

Open Access
File
5 Citations (Scopus)
187 Downloads (Pure)

Truncated disc versus extremely broad iron line in XTE J1650-500

Done, C. & Gierliński, M., 1 Apr 2006, In : Monthly Notices of the Royal Astronomical Society. 367, 2, p. 659-668 10 p.

Research output: Contribution to journalArticle

Open Access
File
62 Citations (Scopus)
110 Downloads (Pure)