Computational Biology

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Research Output 1987 2019

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Article
2006
57 Citations (Scopus)
43 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
iron
accretion
K lines
relativistic effects
accretion disks
45 Citations (Scopus)
48 Downloads (Pure)

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
X Ray Timing Explorer
sky
monitors
luminosity
outburst
2005
49 Citations (Scopus)

GRS 1915+105: The distance, radiative processes and energy-dependent variability

Zdziarski, A. A., Gierliński, M., Rao, A. R., Vadawale, S. V. & Mikolajewska, J., 1 Jul 2005, In : Monthly Notices of the Royal Astronomical Society. 360, 3, p. 825-838 14 p.

Research output: Contribution to journalArticle

proportional counters
energy
Gamma Ray Observatory
X Ray Timing Explorer
detectors
52 Citations (Scopus)
47 Downloads (Pure)

Patterns of energy-dependent variability from Comptonization

Gierliński, M. & Zdziarski, A. A., 11 Nov 2005, In : Monthly Notices of the Royal Astronomical Society. 363, 4, p. 1349-1360 12 p.

Research output: Contribution to journalArticle

Open Access
File
energy
seeds
proportional counters
electron distribution
seed
67 Citations (Scopus)

Physics of accretion in the millisecond pulsar XTE J1751 - 305

Gierliński, M. & Poutanen, J., 1 Jun 2005, In : Monthly Notices of the Royal Astronomical Society. 359, 4, p. 1261-1276 16 p.

Research output: Contribution to journalArticle

pulsars
physics
accretion
accretion disks
optical thickness
46 Citations (Scopus)
46 Downloads (Pure)

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
active galactic nuclei
scaling
radiant flux density
power spectra
luminosity
2004
120 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
182 Citations (Scopus)
23 Downloads (Pure)

GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes

Martin, D. M. A., Berriman, M. & Barton, G. J., 18 Nov 2004, In : BMC Bioinformatics. 5, 17 p., 178.

Research output: Contribution to journalArticle

Open Access
File
Gene Ontology
Annotation
Genome
Genes
Proteins
98 Citations (Scopus)

GRS 1915+105: The brightest Galactic black hole

Done, C., Wardziński, G. & Gierliński, M., 1 Apr 2004, In : Monthly Notices of the Royal Astronomical Society. 349, 2, p. 393-403 11 p.

Research output: Contribution to journalArticle

luminosity
cycles
200 Citations (Scopus)

GX 339-4: The distance, state transitions, hysteresis and spectral correlations

Zdziarski, A. A., Gierlinski, M., Mikołajewska, J., Wardziński, G., Smith, D. M., Harmon, B. A. & Kitamoto, S., 1 Jul 2004, In : Monthly Notices of the Royal Astronomical Society. 351, 3, p. 791-807 17 p.

Research output: Contribution to journalArticle

spectral correlation
hysteresis
sky
monitors
X Ray Timing Explorer
283 Citations (Scopus)

Is the soft excess in active galactic nuclei real?

Gierliński, M. & Done, C., 21 Mar 2004, In : Monthly Notices of the Royal Astronomical Society. 349, 1, p. L7-L11 5 p.

Research output: Contribution to journalArticle

active galactic nuclei
iron
XMM-Newton telescope
opacity
quasars
5 Citations (Scopus)

Modelling the pulse profiles of accreting millisecond pulsars and X-ray bursters

Poutanen, J. & Gierliński, M., 1 Jun 2004, In : Nuclear Physics B - Proceedings Supplements. 132, p. 640-643 4 p.

Research output: Contribution to journalArticle

pulsars
slabs
time lag
profiles
pulses
11 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

event horizon
ingredients
accretion disks
neutron stars
power spectra
1103 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

Multiple Sequence Alignment
Sequence Alignment
Java
Alignment
Protein Sequence
2003
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
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
4 Citations (Scopus)

Increased coverage obtained by combination of methods for protein sequence database searching

Webber, C. & Barton, G. J., 22 Jul 2003, In : Bioinformatics. 19, 11, p. 1397-1403 7 p.

Research output: Contribution to journalArticle

Protein Databases
Protein Sequence
Dynamic programming
Coverage
Proteins
107 Citations (Scopus)

Observing the effects of the event horizon in black holes

Done, C. & Gierliński, M., 11 Jul 2003, In : Monthly Notices of the Royal Astronomical Society. 342, 4, p. 1041-1055 15 p.

Research output: Contribution to journalArticle

event horizon
neutron stars
solid surfaces
x rays
luminosity
153 Citations (Scopus)

On the nature of the X-ray emission from the accreting millisecond pulsar SAX J1808.4-3658

Poutanen, J. & Gierliński, M., 21 Aug 2003, In : Monthly Notices of the Royal Astronomical Society. 343, 4, p. 1301-1311 11 p.

Research output: Contribution to journalArticle

pulsars
slab
slabs
neutron stars
x rays
52 Citations (Scopus)

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

rays
electron distribution
electron
scattering
x rays
1 Citation (Scopus)

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

Servers
Software
Visualization
Databases
Data Mining
2002
69 Citations (Scopus)

Phase-resolved X-ray spectroscopy of the millisecond pulsar SAX J1808.4-3658

Gierliński, M., Done, C. & Barret, D., 21 Mar 2002, In : Monthly Notices of the Royal Astronomical Society. 331, 1, p. 141-153 13 p.

Research output: Contribution to journalArticle

Open Access
pulsars
X-ray spectroscopy
neutron stars
spectroscopy
accretion
67 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
atoll
accretion
neutron stars
boundary layers
accretion disks
55 Citations (Scopus)

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
rays
X Ray Timing Explorer
electron
erg
synchrotrons
2001
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
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
26 Citations (Scopus)

Protein structural domains: analysis of the 3Dee domains database

Dengler, U., Siddiqui, A. S. & Barton, G. J., 15 Feb 2001, In : Proteins: Structure, Function, and Bioinformatics. 42, 3, p. 332-344 13 p.

Research output: Contribution to journalArticle

Databases
Proteins
Protein Domains
Internet
World Wide Web
2000
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
11 Citations (Scopus)

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

Multiple Sequence Alignment
Sequence Alignment
Expressed Sequence Tags
Proteins
Protein
1999

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

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
343 Citations (Scopus)

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
coronas
corona
accretion
accretion disks
geometry

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

1998
149 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)

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

877 Citations (Scopus)

JPred: a consensus secondary structure prediction server

Cuff, J. A., Clamp, M. E., Siddiqui, A. S., Finlay, M. & Barton, G. J., 1998, In : Bioinformatics. 14, 10, p. 892-3 2 p.

Research output: Contribution to journalArticle

Structure Prediction
Secondary Structure
Servers
Server
Secondary Protein Structure
10 Citations (Scopus)

Protein sequence alignment techniques

Barton, G. J., 1 Nov 1998, In : Acta Crystallographica Section D: Biological Crystallography. 54, 6, no. 1, p. 1139-1146 8 p.

Research output: Contribution to journalArticle

Sequence Alignment
Protein Sequence Analysis
Proteins
Research Design
1997

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

Proportional counters
X Ray Timing Explorer
proportional counters
active galaxies
Galaxies
224 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

rays
plasma
x rays
high temperature plasmas
coronas
17 Citations (Scopus)

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

x ray binaries
Gamma rays
accretion
gamma rays
X rays
1996
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
60 Citations (Scopus)

Identification of functional residues and secondary structure from protein multiple sequence alignment

Livingstone, C. D. & Barton, G. J., 1996, In : Methods in Enzymology. 266, p. 497-512 16 p.

Research output: Contribution to journalArticle

Secondary Protein Structure
Sequence Alignment
Proteins
Conservation
114 Citations (Scopus)

Protein fold recognition by mapping predicted secondary structures

Russell, R. B., Copley, R. R. & Barton, G. J., 14 Jun 1996, In : Journal of Molecular Biology. 259, 3, p. 349-365 17 p.

Research output: Contribution to journalArticle

Proteins
Imino Acids
Phosphotyrosine
Sequence Alignment
von Willebrand Factor
24 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

gamma ray spectra
rays
x rays
cut-off
plasma temperature
1995
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
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
72 Citations (Scopus)

Protein secondary structure prediction

Barton, G. J., Jun 1995, In : Current Opinion in Structural Biology. 5, 3, p. 372-376 5 p.

Research output: Contribution to journalArticle

Secondary Protein Structure
Discriminant Analysis
X-Rays
Proteins
Machine Learning
1994
149 Citations (Scopus)
bis(5'-nucleosyl)tetraphosphatase (asymmetrical)
Phosphoprotein Phosphatases
Escherichia coli
Conservation
Consensus Sequence
54 Citations (Scopus)

Mutational analysis of human papillomavirus E4 proteins: identification of structural features important in the formation of cytoplasmic E4/cytokeratin networks in epithelial cells

Roberts, S., Ashmole, I., Gibson, L. J., Rookes, S. M., Barton, G. J. & Gallimore, P. H., Oct 1994, In : Journal of Virology. 68, 10, p. 6432-6445 14 p.

Research output: Contribution to journalArticle

Papillomaviridae
Keratins
epithelial cells
Epithelial Cells
Human papillomavirus 1
12 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