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PUBLICATIONS
Here are the links to the publications in which members of SABLab have been participated as co-autors.
The contents of all on-line information are protected by copyright law. No portion of these publications, whether in original or in altered form, may be duplicated, distributed, transmitted in any form, or included in other documents without explicit approval of the copyright holder.
Notation:
 journal article,
 conference proccedings,
 thesis
2011
Moussay E., Wangb K., Chob J.-H., van Moera K., Piersona S., Paggettia J., Nazarov P.V., Palissot V., Hoodb L.E., Berchem G., Galasb D.J.,
MicroRNA as biomarkers and regulators in B-cell chronic lymphocytic leukemia.
PNAS, 2011, v.7:7, in press
Moussay E., Kaoma T., Baginska J., Muller A., Van Moer K., Nicot N., Nazarov P.V., Vallar L., Chouaib S., Berchem G., Janji B.
The acquisition of resistance to TNFa in breast cancer cells is associated with constitutive activation of autophagy as revealed by a transcriptome analysis using a custom microarray.
Autophagy, 2011, in press
Nepomuceno I., Azuaje F., Devaux Y, Nazarov P.V., Muller A., Aguilar-Ruiz J.S., Wagner D.R.,
Prognostic transcriptional association networks: a new supervised approach based on regression trees.
Bioinformatics, 2011, v.27:2, 252-8.
2010
Philippidou D., Schmitt M., Moser D., Margue C., Nazarov P.V., Muller A., Vallar L., Nashan D., Behrmann I., Kreis S.
Signatures of microRNAs and selected microRNA target genes in human melanoma.
Cancer Research, 2010, v.70:10, 4163-73.
Halavatyi A.A., Nazarov P.V., Al Tanoury Z., Apanasovich V.V., Yatskou M., Friederich E.,
A mathematical model of actin filament turnover for fitting FRAP data.
Eur. Biophys. J., 2010, v. 39:4, 669-77.
Hemminga M.A., Vos W.L., Nazarov P.V., Koehorst R.B.M., Wolfs C.J.A.M., Spruijt R.B., Stopar D.,
Viruses: incredible nanomachines. New advances with filamentous phages.
Eur. Biophys. J., 2010, v. 39:4, 541-50.
2009
Kavalenka A.A.,
Modeling membrane protein structure using site-directed ESR spectroscopy,
PhD Thesis, 2009 , ISBN: 978-90-8585-424-1.
Vos W.L., Nazarov P.V., Koehorst R.B.M., Spruijt R.B., Hemminga M.A.,
From ‘I’ to ‘L’ and back again: the odyssey of membrane-bound M13 protein
Trends Biochem. Sci., 2009, v. 34, p. 249-255.
Halavatyi A.A., Nazarov P.V., Medves S., van Troys M., Ampe C., Yatskou M., Friederich E.,
An Integrative Simulation Model Linking Major Biochemical reactions of actin-polymerization to structural properties of actin filaments.
Biophys. Chem., 2009, v. 140, p. 24-34.
2008
Yatskou M., Novikov E., Vetter G., Muller A., Barillot E., Vallar L., and Friederich E.
Advanced spot quality analysis in two-colour microarray experiments.
BMC Res Notes., 2008, 1:80.
Halavatyi A., Medves S., Hoffman C., Apanasovich V., Yatskou M., Friederich E.
Mathematical model and software FRAPAnalyser for analysis of actin-cytoskeleton dynamics with FRAP experiments.
Proceedings of FEBS/ECF Workshop "Mechanics and dynamics of the cytoskeleton". 22nd -26th June, 2008, Potsdam, Germany, p.50.
Yatskou M., Halavatyi A., Nazarov P., Medves S., van Troys M., Ampe C., Friederich E.
An automated integrative computer simulation approach for stochastic modelling of actin-polymerization.
Proceedings of FEBS/ECF Workshop "Mechanics and dynamics of the cytoskeleton". 22nd -26th June, 2008, Potsdam, Germany, p.100.
2007
Halavatyi A.A., Nazarov, P.V., Yatskou M.M., Apanasovich V.V. and Friederich E.
Simulation and analytical models for the analysis of in vitro actin polimerization.
Proceedings of the 8th International Conference "Computer Data Analysis and Modeling: Complex Stochastic Data and Systems", 2007, v.2, p. 184-187.
Nazarov P.V., Koehorst R.B.M., Vos W.L., Apanasovich V.V. and Hemminga M.A.
FRET study of membrane proteins: determination of the tilt and orientation of the N-terminal domain of M13 major coat protein.
Biophys. J., 2007, v. 92, p. 1296-1305.
Vos W.L., Schor M., Nazarov P.V., Koehorst R.B.M., Spruijt R.B. and Hemminga M.A.,
Structure of membrane-embedded M13 major coat protein is insensitive to hydrophobic stress,
Biophys. J., 2007, v. 93, p. 3541-3547.
2006
Nazarov P.V.,
Simulation and analysis of FRET in the study of membrane proteins,
PhD Thesis, 2006, ISBN: 90-8504-553-3.
Nazarov P.V., Koehorst R.B.M., Vos W.L., Apanasovich V.V. and Hemminga M.A.
FRET study of membrane proteins: simulation-based fitting for analysis of protein structure, membrane embedment and association.
Biophys. J., 2006, v. 91, p. 454-466.
Nazarov P.V., Yatskou M.M., Barsukov E.A., Ivashkevich E.V., Golovaty A.A., Apanasovich V.V., Friederich E.
Developing mathematical models, algorithms and programming tools for analysis of actin-based motility.
Proceedings of the 3rd Wolfgang Pauli International Workshop on Mathematical Modelling of Actin-Based Motility, Vienna, Austria, 2006, p. 13-14.
2005
Hesselink R.W., Koehorst R.B.M., Nazarov P.V., Hemminga M.A.
Membrane-bound peptides mimicking transmembrane Vph1p helix 7 of yeast V-ATPase: A spectroscowpic and polarity mismatch study.
Biochim. et Biophys. Acta, 2005, v. 1716:2, p. 137-145.
Sparr E., Ash W.L., Nazarov P.V., Rijkers D.T.S., Hemminga M.A., Tieleman D.P., Killian J.A.
Self-association of transmembrane a-helices in model membranes: importance of helix orientation and role of hydrophobic mismatch.
J. Biol. Chem., 2005, v. 280:47, p. 39324-39331.
Kavalenka A.A., Filiwpic B., Hemminga M.A., Strancar J.
Speeding up a genetic algorithm for EPR-based spin label characterization of biosystem complexity.
J. Chem. Inf. Model., 2005, v. 45, p. 1628-1635.
2004
Nazarov P.V., Apanasovich V.V., Lutkovski V.M., Yatskou M.M., Koehorst R.B.M., Hemminga M.A.
Artificial neural network modification of simulation-based fitting: application to a protein-lipid system.
J. Chem. Inf. Comput. Sci. (present J. Chem. Inf. Model), 2004, v. 44, p. 568-574.
Nazarova I., Hemminga M.A.
Analytical analysis of multi-pulse NMR.
J. Magn. Res., 2004, v. 170, p. 284-289.
2003
Yatskou M.M., Meyer M., Huber S., Pfenniger M., Calzaferri G.
Electronic excitation energy migration in a photonic dye-zeolite antenna.
Chem. Phys. Chem., 2003, v. 4, p. 567-587.
Nazarov P.V., Apanasovich V.V., Lutkovski V.M., Hemminga M.A., Koehorst R.B.M.
Neural network simulation of energy transfer processes in a membrane protein system.
Advances in Soft Computing: Neural Networks and Soft Computing, 2003, p. 873-878.
Nazarov P.V., Apanasovich V.V., Lutkovskaya K.U., Lutkovski V.M., Misakov P.Ya.
Neural network data analysis for intracavity laser spectroscopy.
Proc. SPIE: Optical Information, Data Processing and Storage, and Laser Communication Technologies, 2003, v. 5135, p. 61-69.
Isaevich A.V., Lutkovski V.M., Misakov P.Ya., Nazarov P.V.
Determination of small amounts of elements by the atomic emission method with preliminary concentration of a sample.
J. Appl. Spec., 2003, v. 70:5, p. 672-676.
2001
Yatskou M.M., Koehorst R.B.M., van Hoek A., Donker H., Schaafsma T.J., Gobets B., van Stokkum I., van Grondelle R.
Spectroscowpic properties of a self-assembled zinc porphyrin tetramer II. Time-resolved fluorescence spectroscopy.
J. Phys. Chem. A, 2001, v. 105, p. 11432-11440.
Yatskou M.M., Koehorst R.B.M., Donker H., Schaafsma T.J.
Spectroscowpic properties of a self-assembled zinc porphyrin tetramer I. Steady state optical spectroscopy.
J. Phys. Chem. A, 2001, v. 105, p. 11425-11431.
Yatskou M.M., Donker H., Novikov E.G., Koehorst R.B.M., van Hoek A., Apanasovich V.V., Schaafsma T.J.
Nonisotrowpic excitation energy transport in organized molecular systems: Monte Carlo simulation-based analysis of fluorescence and fluorescence anisotropy decay.
J. Phys. Chem. A, 2001, v. 105, p. 9498-9508.
Burakov V.S., Isaevich A.V., Misakov P.Ya., Apanasovich V.V., Lutkovski V.M., Nazarov P.V.
Data processing and estimation of measurement errors in intracavity laser spectroscopy.
Proc. SPIE: Novel Trends in Nonlinear Laser Spectroscopy and Optical Diagnostics and Lasers in Chemistry, Biophysics, and Biomedicine, 2001, v. 4749, p. 172-177.
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