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Publications from the Kohlbacher lab, sorted by year and author.
[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.
[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.
[189] de la Garza, L, Krüger, J, Schärfe, C, Röttig, M, Aiche, S, Reinert, K, and Kohlbacher, O (2013). From the desktop to the grid: conversion of KNIME Workflows to gUSE In: Proc. IWSG 2013, vol. 993, pp. 9. CEUR-WS.
[188] Gifford, CA, Ziller, MJ, Gu, H, Trapnell, C, Donaghey, J, Tsankov, A, Shalek, AK, Shishkin, AA, Issner, R, Zhang, X, Fostel, JL, Holmes, L, Meldrim, J, Guttman, M, Epstein, C, Park, H, Kohlbacher, O, Rinn, J, Gnirke, A, Lander, ES, Bernstein, BE, and Meissner, A (2013). Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells Cell, 153(5):1149-1163.
[187] Kyzirakos, C, Pflueckhahn, U, Sturm, M, Schroeder, C, Bauer, P, Walter, M, Feldhahn, M, Walzer, M, Mohr, C, Szolek, A, Bonin, M, Kohlbacher, O, Ebinger, M, Handgretinger, R, Rammensee, H, and Lang, P (2013). iVacALL: utilizing next-generation sequencing for the establishment of an individual peptide vaccination approach for paediatric acute lymphoblastic leukaemia Bone Marrow Transplant., 48(3):S401.
[186] Nahnsen, S, Bielow, C, Reinert, K, and Kohlbacher, O (2013). Tools for label-free peptide quantification Mol. Cell. Prot., 12(3):549-56.
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