Computational Biology

  • United Kingdom

Research Output 1987 2019

2008
102 Citations (Scopus)
38 Downloads (Pure)

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
irradiation
radii
plasma
x rays
outburst
2007
45 Citations (Scopus)
37 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
68 Citations (Scopus)
32 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
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
590 Citations (Scopus)
accretion
modeling
x rays
luminosity
radio
4 Citations (Scopus)

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

pantothenate synthetase
Methicillin
staphylococcus
Methicillin-Resistant Staphylococcus aureus
Crystallization
29 Citations (Scopus)

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
ionization
galaxies
iron
profiles
K lines
70 Citations (Scopus)

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

Serine C-Palmitoyltransferase
Sphingolipids
Glycosphingolipids
Catalytic Domain
Enzymes
36 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
eccentricity
oscillation
x rays
oscillations
light curve
2006
44 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
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
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
42 Citations (Scopus)
37 Downloads (Pure)
Open Access
File
active galactic nuclei
opacity
constancy
luminosity
continuums
56 Citations (Scopus)
36 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)
42 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

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

gravitation
accretion disks
templates
scaling
physics
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)
42 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)
41 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
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
181 Citations (Scopus)
19 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
97 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
198 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
279 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
184 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

scattering
synchrotrons
electrons
x rays
hysteresis
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
1102 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
106 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
50 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
51 Citations (Scopus)

A comment on the colour-colour diagrams of low-mass X-ray binaries

Gierliński, M. & Done, C., 21 Apr 2002, In : Monthly Notices of the Royal Astronomical Society. 331, 4, p. L47-L50 4 p.

Research output: Contribution to journalReview article

Open Access
color-color diagram
diagram
atolls
atoll
x rays
4 Citations (Scopus)

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

Sequence Alignment
Proteins
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
602 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

478 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
342 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