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Publications from the Kohlbacher lab, sorted by year and author.
[223] Nicoludis, J, Lau, S, Schärfe, C, Marks, D, Weihofen, W, and Gaudet, R (2015). Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity Structure , 23(11):2087 - 2098.
[222] Proikas-Cezanne, T, Takacs, Z, Dönnes, P, and Kohlbacher, O (2015). WIPI proteins: essential PtdIns3P effectors at the nascent autophagosome J. Cell Sci., 128(2):207-217.
[221] Ranninger, C, Rurik, M, Limonciel, A, Ruzek, S, Reischl, R, Wilmes, A, Jennings, P, Hewitt, P, Dekant, W, Kohlbacher, O, and Huber, CG (2015). Nephron Toxicity Profiling via Untargeted Metabolome Analysis Employing a High-Performance Liquid Chromatography-Mass Spectrometry-Based Experimental and Computational Pipeline J. Biol. Chem., 290(31):19121-32.
[220] Sachsenberg, T, Herbst, F, Taubert, M, Kermer, R, Jehmlich, N, von Bergen, M, Seifert, J, and Kohlbacher, O (2015). MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics J. Proteome Res., 14(2):619-27.
[219] Schubert, B, Brachvogel, H, Jürges, C, and Kohlbacher, O (2015). EpiToolKit – A Web-based Workbench for Vaccine Design Bioinformatics, 31(13):2211-3.
[218] Sharma, K, Hrle, A, Kramer, K, Sachsenberg, T, Staals, RH, Randau, L, Marchfelder, A, van der Oost, J, Kohlbacher, O, Conti, E, and Urlaub, H (2015). Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry Methods: S1046-2023(15)00246-7.
[217] Simha, R, Briesemeister, S, Kohlbacher, O, and Shatkay, H (2015). Protein (Multi-)Location Prediction: Utilizing Interdependencies via a Generative Model Bioinformatics, 31(12):i365-i374.
[216] Thost, A, Dönnes, P, Kohlbacher, O, and Proikas-Cezanne, T (2015). Fluorescence-based imaging of autophagy progression by human WIPI beta-propeller protein detection in single cells Methods, 75:69-78.
[215] Uszkoreit, J, Maerkens, A, Perez-Riverol, Y, Meyer, HE, Marcus, K, Stephan, C, Kohlbacher, O, and Eisenacher, M (2015). PIA - An intuitive protein inference engine with a web-based user interface J. Proteome Res., 14(7):2988-97.
[214] Venturelli, S, Belz, RG, Kämper, A, Berger, A, von Horn, K, Wegner, A, Böcker, A, Zabulon, G, Langenecker, T, Kohlbacher, O, Barneche, F, Weigel, D, Lauer, UM, Bitzer, M, and Becker, C (2015). Plants release precursors of potent histone deacetylase inhibitors to suppress growth of competitors Plant Cell, 27(11):3175-89..
[213] Walz, S, Stickel, JS, Kowalewski, DJ, Schuster, H, Weisel, K, Backert, L, Kahn, S, Nelde, A, Stroh, T, Handel, M, Kohlbacher, O, Kanz, L, Salih, HR, Rammensee, H, and Stevanovic, S (2015). The antigenic landscape of multiple myeloma: mass spectrometry (re-)defines targets for T-cell based immunotherapy Blood, 126(10):1203-13.
[212] Zaman, U, Richter, FM, Hofele, R, Kramer, K, Sachsenberg, T, Lenz, C, and Urlaub, H (2015). Dithiothreitol (DTT) acts as a specific, UV-inducible cross-linker in elucidation of protein-RNA interactions Mol. Cell. Prot., 14(12):3196-210.
[211] Ziller, MJ, Edri, R, Yaffe, Y, Donaghey, J, Pop, R, Mallard, W, Issner, R, Gifford, CA, Goren, A, Xing, J, Gu, H, Cacchiarelli, D, Tsankov, AM, Epstein, C, Rinn, JL, Mikkelsen, TS, Kohlbacher, O, Gnirke, A, Bernstein, BE, Elkabetz, Y, and Meissner, A (2015). Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature, 518:355-359.
[210] Aebersold, R, Kohlbacher, O, and Vitek, O (2014). Report from Dagstuhl Seminar 13491 Computational Mass Spectrometry Dagstuhl Publishing, Dagstuhl, Germany, vol. 3(12). Dagstuhl Reports.
[209] Avbelj, M, Wolz, O, Fekonja, O, Bencina, M, Repič, M, Mavri, J, Krüger, J, Schärfe, C, Delmiro-Garcia, M, Panter, G, Kohlbacher, O, Weber, AN, and Jerala, R (2014). Activation of lymphoma-associated MyD88 mutations via allostery-induced TIR domain oligomerization Blood, 124(26):3896-904.
[208] Beck, F, Geiger, J, Gambaryan, S, Veit, J, MV, Nollau, P, Kohlbacher, O, Martens, L, Walter, U, Sickmann, A, and Zahedi, RP (2014). Time-resolved characterization of cAMP/PKA-dependant signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways Blood, 123(4):e1-e10.
[207] Gerasch, A, Faber, D, Küntzer, J, Niermann, P, Kohlbacher, O, Lenhof, H, and Kaufmann, M (2014). BiNA: a visual analytics tool for biological network data PLoS ONE, 9(2):e87397.
[206] Gerasch, A, Kaufmann, M, and Kohlbacher, O (2014). Rebuilding KEGG Maps - An integrative approach for visual analytics of metabolic networks In: Pacific Visualization Symposium (PacificVis), 2014 IEEE, pp. 97-104, IEEE.
[205] Griss, J, Jones, AR, Sachsenberg, T, Walzer, M, Gatto, L, Hartler, J, Thallinger, GG, Salek, RM, Steinbeck, C, Neuhauser, N, Cox, J, Neumann, S, Fan, J, Reisinger, F, Xu, Q, Bandeira, N, Xenarios, I, Kohlbacher, O, Vizcaino, JA, and Hermjakob, H (2014). The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience Mol. Cell. Prot.:mcp.O113.036681.
[204] Hopf, TA, Schärfe, CPI, Rodrigues, JP, Green, AG, Kohlbacher, O, Sander, C, Bonvin, AM, and Marks, DS (2014). Sequence co-evolution gives 3D contacts and structures of protein complexes eLife:10.7554/eLife.03430.
[203] Jordan, E, Roosen-Runge, F, Leibfarth, S, Zhang, F, Sztucki, M, Hildebrandt, A, Kohlbacher, O, and Schreiber, F (2014). Competing Salt Effects on Phase Behavior of Protein Solutions: Tailoring of Protein Interaction by the Binding of Multivalent Ions and Charge Screening J. Phys. Chem. B, 118(38):11365-74.
[202] Kenar, E, Franken, H, Forcisi, S, Wörmann, K, Häring, H, Lehmann, R, Schmitt-Kopplin, P, Zell, A, and Kohlbacher, O (2014). Automated Label-Free Quantification of Metabolites from LC-MS Data Mol. Cell. Prot., 13(1):348-59.
[201] Kohlbacher, O, Schreiber, F, and Ward, MO (2014). Multivariate Networks in the Life Sciences In: Multivariate Network Visualization 2013, ed. by Andreas Kerren et al.. Springer, chap. 4, pp. 61-73.
[200] Kramer, K, Sachsenberg, T, Beckmann, BM, Qamar, S, Boon, K, Hentze, MW, Kohlbacher, O, and Urlaub, H (2014). Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins Nat. Methods, 11(10):1064-70.
[199] Krüger, J, Grunzke, R, Gesing, S, Breuers, S, Brinkmann, A, de la Garza, L, Kohlbacher, O, Kruse, M, Nagel, W, Packschies, L, Müller-Pfefferkorn, R, Schärfe, C, Steinke, T, Schlemmer, T, Warzecha, K, Zink, A, and Herres-Pawlis, S (2014). The MoSGrid Science Gateway – A Complete Solution for Molecular Simulations J. Chem. Theor. Comput., 10(6):2232-2245.
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