Computational Biology

  • United Kingdom

Research Output

Article

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
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33 Citations (Scopus)
167 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
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7 Citations (Scopus)
151 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
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49 Citations (Scopus)
186 Downloads (Pure)

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
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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
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2 Citations (Scopus)
64 Downloads (Pure)

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

1127 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
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6 Citations (Scopus)
107 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
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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
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26 Citations (Scopus)
222 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., 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
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51 Citations (Scopus)
208 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
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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
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62 Citations (Scopus)
110 Downloads (Pure)

Universal attenuators and their interactions with feedback loops in gene regulatory networks

Liu, D., Albergante, L. & Newman, T. J., 7 Jul 2017, In : Nucleic Acids Research. 45, 12, p. 7078-7093 16 p.

Research output: Contribution to journalArticle

Open Access
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1 Citation (Scopus)
196 Downloads (Pure)

Unreplicated DNA remaining from unperturbed S phases passes through mitosis for resolution in daughter cells

Moreno, A., Carrington, J. T., Albergante, L., Al Mamun, M., Haagensen, E. J., Komseli, E-S., Gorgoulis, V. G., Newman, T. J. & Blow, J., 27 Sep 2016, In : Proceedings of the National Academy of Sciences. 113, 39, p. E5757-E5764 8 p.

Research output: Contribution to journalArticle

Open Access
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48 Citations (Scopus)
366 Downloads (Pure)

Visualization of Biomedical Data

O'Donoghue, S. I., Baldi, B. F., Clark, S. J., Darling, A. E., Hogan, J. M., Kaur, S., Maier-Hein, L., McCarthy, D. J., Moore, W., Stenau, E., Swedlow, J., Vuong, J. & Procter, J., 20 Jul 2018, In : Annual Review of Biomedical Data Science. 1

Research output: Contribution to journalArticle

Open Access

Visual representation of database search results: the RHIMS Plot

Martin, D. M. A., Hill, P., Barton, G. J. & Flavell, A. J., 22 May 2003, In : Bioinformatics. 19, 8, p. 1037-1038 2 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

What's in a name? Word inflation, punctuation, abbreviation and cloud formation

Schofield, S. J. & Schofield, P. G., Dec 2016, In : Medical Education. 50, 12, p. 1264-1268 5 p.

Research output: Contribution to journalArticle

Open Access
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4 Citations (Scopus)
178 Downloads (Pure)

Wnt regulates amino-acid transporter Slc7a5 and so constrains the integrated stress response in mouse embryos

Poncet, N., Halley, P., Lipina, C., Gierlinski, M., Dady, A., Singer, G., Febrer, M., Shi, Y-B., Yamaguchi, T. P., Taylor, P. & Storey, K., 7 Jan 2020, In : EMBO Reports. 21, 1, p. 1-20 20 p., e48469.

Research output: Contribution to journalArticle

Open Access
File
1 Citation (Scopus)
62 Downloads (Pure)

X-ray and γ-ray spectra and variability of the black hole candidate GX 339-4

Wardziński, G., Zdziarski, A. A., Gierliński, M., Grove, J. E., Jahoda, K. & Johnson, W. N., 11 Dec 2002, In : Monthly Notices of the Royal Astronomical Society. 337, 3, p. 829-839 11 p.

Research output: Contribution to journalArticle

Open Access
57 Citations (Scopus)

X-ray irradiation in XTE J1817-330 and the inner radius of the truncated disc in the hard state

Gierliński, M., Done, C. & Page, K., 1 Aug 2008, In : Monthly Notices of the Royal Astronomical Society. 388, 2, p. 753-760 8 p.

Research output: Contribution to journalArticle

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

X-rays and gamma-rays from accretion flows onto black holes in Seyferts and x-ray binaries

Zdziarski, A. A., Johnson, W. N., Poutanen, J., Magdziarz, P. & Gierliński, M., 1 Dec 1997, In : European Space Agency, (Special Publication) ESA SP. 382, p. 373-380 8 p.

Research output: Contribution to journalArticle

17 Citations (Scopus)

X-ray spectral transitions of black holes from RXTE all-sky monitor

Gierliński, M. & Newton, J., 1 Aug 2006, In : Monthly Notices of the Royal Astronomical Society. 370, 2, p. 837-844 8 p.

Research output: Contribution to journalArticle

Open Access
File
49 Citations (Scopus)
106 Downloads (Pure)
Book
Chapter

Accretion in strong gravity: From galactic to supermassive black holes

Done, C. & Gierliński, M., 1 Dec 2005, Astrophysics and Space Science: From X-Ray Binaries to Quasars: Black Holes on all Mass Scales. Springer Netherlands, p. 167-175 9 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Creation and analysis of protein multiple sequence alignments

Barton, G. J., 11 Jan 2002, Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. Second ed. Wiley, Vol. 43. p. 215-32 18 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

4 Citations (Scopus)

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)
Chapter (peer-reviewed)

Insights into biological complexity from simple foundations

Albergante, L., Liu, D., Palmer, S. & Newman, T. J., 19 May 2016, Biophysics of infection. Leake, M. C. (ed.). Switzerland: Springer International Publishing, p. 295-305 11 p. (Advances in experimental medicine and biology; vol. 915).

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

3 Citations (Scopus)
Comment/debate

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
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114 Downloads (Pure)

Erratum: Visualization of image data from cells to organisms (Nature Methods (2010) 7 (S26-S41))

Walter, T., Shattuck, D. W., Baldock, R., Bastin, M. E., Carpenter, A. E., Duce, S., Ellenberg, J., Fraser, A., Hamilton, N., Pieper, S., Ragan, M. A., Schneider, J. E., Tomancak, P. & Hériché, J. K., 1 Jun 2010, In : Nature Methods. 7, 6, 1 p.

Research output: Contribution to journalComment/debate

Open Access
5 Citations (Scopus)

Publisher Correction: GPCRmd uncovers the dynamics of the 3D-GPCRome

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., Aug 2020, In : Nature Methods. 17, p. 861-862 2 p.

Research output: Contribution to journalComment/debate

Conference article

Large knowledge based applications in molecular biology and genetics

Rawlings, C. J., Clark, D. A., Barton, G. J., Archer, L. & Saldanha, J. W., 1 Dec 1990, In : IEE Colloquium (Digest). 96, p. 6/1-6/5 5 p.

Research output: Contribution to journalConference article

1 Citation (Scopus)
Conference contribution

Protein fold recognition from secondary structure assignments

Russell, R. B., Copley, R. R. & Barton, G. J., 1995, Proceedings of the 28th Annual Hawaii International Conference on System Sciences (HICSS 1995). IEEE, p. 302-311 10 p. 375326. (Proceedings of the Annual Hawaii International Conference on System Sciences; vol. 5).

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

10 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

Letter

AIDS vaccine predictions

Coates, A. R. M., Cookson, J., Barton, G. J., Zvelebil, M. J. & Sternberg, M. J. E., 9 Apr 1987, In : Nature. 326, 6113, p. 549-550 2 p.

Research output: Contribution to journalLetter

37 Citations (Scopus)

An SH2-SH3 domain hybrid

Russell, R. B. & Barton, G. J., 26 Aug 1993, In : Nature. 364, 6440, p. 765 1 p.

Research output: Contribution to journalLetter

26 Citations (Scopus)
132 Citations (Scopus)

Computer speed and sequence comparison

Barton, G. J., 18 Sep 1992, In : Science. 257, 5077, p. 1609-1610 2 p.

Research output: Contribution to journalLetter

4 Citations (Scopus)
Open Access
File
45 Citations (Scopus)
105 Downloads (Pure)

Expanding the phenotypic spectrum of Olmsted syndrome

Wilson, N. J., Cole, C., Milstone, L. M., Kiszewski, A. E., Hansen, C. D., O'Toole, E. A., Schwartz, M. E., McLean, W. H. I. & Smith, F. J. D., Nov 2015, In : Journal of Investigative Dermatology. 135, 11, p. 2879-2883 5 p.

Research output: Contribution to journalLetter

13 Citations (Scopus)