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Publications

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

2015

[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.

[195] Römer, M, Backert, L, Eichner, J, and Zell, A (2014).
ToxDBScan: Large-Scale Similarity Screening of Toxicological Databases for Drug Candidates
International Journal of Molecular Sciences, 15(10):19037–19055.

[194] Szolek, A, Schubert, B, Mohr, C, Sturm, M, Feldhahn, M, and Kohlbacher, O (2014).
OptiType: precision HLA typing from next-generation sequencing data
Bioinformatics, 30(23):3310-6.

[193] Thiel, P, Sach-Peltason, L, Ottmann, C, and Kohlbacher, O (2014).
Blocked Inverted Indices for Exact Clustering of Large Chemical Spaces
J. Chem. Inf. Model., 54(9):2395-401.

[192] Wagner, R, Li, J, Kenar, E, Kohlbacher, O, Machicao, F, Häring, H, Fritsche, A, Xu, G, and Lehmann, R (2014).
Clinical and non-targeted metabolomic profiling of homozygous carriers of Transcription Factor 7-like 2 variant rs7903146
Sci. Rep., 4:5296.

[191] Walzer, M, Pernas, LE, Nasso, S, Bittremieux, W, Nahnsen, S, Kelchtermans, P, Pichler, P, van den Toorn, HW, Staes, A, Vandenbussche, J, Mazanek, M, Taus, T, Scheltema, RA, Kelstrup, CD, Gatto, L, van Breukelen, B, Aiche, S, Valkenborg, D, Laukens, K, Lilley, KS, Olsen, JV, Heck, AJ, Mechtler, K, Aebersold, R, Gevaert, K, Vizcaino, JA, Hermjakob, H, Kohlbacher, O, and Martens, L (2014).
qcML: an exchange format for quality control metrics from mass spectrometry experiments
Mol. Cell. Prot., 13(8):1905-13.

2013

[190] Brand, L, Fischer, N, Harter, K, Kohlbacher, O, and Wanke, D (2013).
Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays
Nucl. Acids Res., 41(21):9764-78.