Abdullah Kahraman
  • FENS
  • Abdullah Kahraman

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E-Mail
abdullahksabanciunivedu
Phone
Personal Web
Title
Faculty Member
Areas of Interest
Computational cancer genomics, Alternative splicing in cancer, Non-coding cancer driver mutations, Interaction network prediction, Structural proteomics, Data-driven molecular modeling.
Publications
  • Before SU Publications

    22. Leuenberger P, Ganscha S, Kahraman A. et al. (2017). Cell-wide analysis of protein thermal unfolding across species reveals the determinants of proteome thermostability. Science (in press).

    21. SIB Swiss Institute of Bioinformatics Members. (2016) The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases. Nucleic Acids Res 44, D27–D37.

    20. Grimm, M., Zimniak, T., Kahraman, A., Herzog, F. (2015). xVis: a webserver for the schematic visualization and interpretation of crosslink-derived spatial restraints, Nucleic Acids Res. 43, W362–9.

    19. Valleliana, F., Garcia-Rubiod, I., Pugliaa, M., Kahraman, A., Deuel, J.W., Engelsberger, W.R., Mason, R.P., Buehlerg, P.W., Schaer, D.J. (2015). Spin trapping combined with quantitative mass spectrometry defines free radical redistribution within the oxidized hemoglobin:haptoglobin complex. Free Radic. Biol. Med. 85, 259–268.

    18. Boersema, P., Kahraman, A., Picotti, P. (2015). Proteomics beyond large-scale protein expression analysis. Current Opinion in Biotechnology 34, 162-170.

    17. Robinson, M.D., Kahraman, A. , Law, C.W., Lindsay, H., Nowicka, M., Weber, L.M., Zhou, X., (2014). Statistical methods for detecting differentially methylated loci and regions. Front Genet. (5) 324.

    16. Feng, Y.*, De Franceschi, G.*, Kahraman, A.*, Soste, M., Melnik, A., Boersema, P., Polverino de Laureto, P., Nikoaev, Y., Oliveira, A.P., Picotti, P. (2014). Global analysis of protein structural changes in complex proteomes. Nature Biotech 32, 1036–1044.

    15. Merkley, E.D., Rysavy, S., Kahraman, A., Hafen, R.P., Daggett, V. and Adkins, J.N. (2014). Distance restraints from cross-linking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine-lysine distances Protein Science 23 (6), 747-759.

    14. Kahraman, A.*, Herzog, F.*, Leitner, A., Rosenberger, G., Aebersold, R., Malmström, L. (2013). Cross-Link Guided Molecular Modeling with ROSETTA. PLoS ONE 8(9): e73411.

    13. Herzog, F.*, Kahraman, A.*, Bohringer, D.*, Mak, R., Bracher, A., Walzthoeni, T., Leitner, A., Beck, M., Hartl, F. U., Ban, N, Malmstroem, L., Aebersold, R. (2012). Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry. Science 337, 1348–1352.

    12. Kahraman, A., Malmström, L., Aebersold, R. (2011). Xwalk: Computing and Visualizing Distances in Cross-linking Experiments. Bioinformatics 27, 2163-2164.

    11. Leitner, A., Kahraman, A.*, , Walzthoeni, T.*, Herzog, F., Rinner, O., Beck, M. and Aebersold, R. (2010). Probing native protein structures by chemical cross-linking, mass spectrometry and bioinformatics. Mol Cell Proteomics 9, 1634-1649.

    10. Smith, L., Kahraman, A., & Thornton, J. M. (2010). Heme proteins - diversity in structural characteristics, function and folding. Proteins 78, 2349-68PMID: 20544970.

    9. Kahraman, A., Morris, R. J., Laskowski, R.M., Favia, A.D. & Thornton, J. M. (2010). On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins. Proteins 78, 1120-36PMID: 19927322.

    8. Kahraman, A. (2009). The Geometry and Physicochemistry of Protein Binding Sites and Ligands and their Detection in Electron Density Maps. University of Cambridge. PhD Thesis.

    7. Kahraman, A., Thornton, J. M. (2008). Methods for the analysis of enzyme binding site. Computational Structural Biology: Methods and Applications, Editors: Torsten Schwede, Manuel C. Peitsch. (Amazon).

    6. Kahraman, A., Morris, R. J., Laskowski, R. A. & Thornton, J. M. (2007). Variation of geometrical and physicochemical properties in protein binding pockets and their ligands. BMC Bioinformatics 8, S1.

    5. Kahraman, A., Morris, R. J., Laskowski, R. A. & Thornton, J. M. (2007). Shape variation in protein binding pockets and their ligands. J Mol Biol 368, 283-301PMID: 17337005.

    4. Morris, R. J., Kahraman, A., Funkhouser, T., Stockwell, G., Glaser, F., Laskowski, R. & Thornton, J. M. (2005). Binding pocket shape analysis for protein function prediction. Quantitative Biology, Shape Analysis, and Wavelets, Leeds University Press, Leeds, 91–94.

    3. Morris, R. J., Kahraman, A. & Thornton, J. M. (2005). Binding Pocket Shape Analysis for Protein Function Prediction. Acta Crystallographica Section A 61, C156–157.

    2. Morris, R. J., Najmanovich, R. J., Kahraman, A. & Thornton, J. M. (2005). Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics 21, 2347-55PMID: 15728116.

    1. Kahraman, A., Avramov, A., Nashev. L., Popov, D., Ternes, R., Pohlenz, H.D., and Weiss, B. (2005). PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics. Bioinformatics 21, 418-420PMID: 15374875.