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Publications

Publications from the Kohlbacher lab, sorted by year and author.

2015

[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.

2014

[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.

[198] Krüger, J, Grunzke, R, Herres-Pawlies, S, de la Garza, L, Kohlbacher, O, Nagel, WE, and Gesing, S (2014).
Performance Studies on Distributed Virtual Screening
Biomed Res Int, 2014:624024.

[197] Menzel, M, Meckbach, D, Weide, B, Toussaint, NC, Schilbach, K, Noor, S, Eigentler, T, Ikenberg, K, Busch, C, Qunitanilla-Martinez, L, Göke, A, Göke, F, Handgretinger, R, Ottmann, C, Bastian, B, Garbe, C, Röcken, M, Perner, S, Kohlbacher, O, and Bauer, J (2014).
In melanoma, Hippo signaling is affected by copy number alterations and YAP1 overexpression impairs patient survival
Pigment Cell Melanoma Res., 23(3):E45.

[196] Roberts, JC, Yang, J, Kohlbacher, O, Ward, MO, and Zhou, MX (2014).
Novel Visual Metaphors for Multivariate Networks
In: Multivariate Network Visualization 2013, ed. by Andreas Kerren et al.. Springer, chap. 7, pp. 127-147.