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Publications

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

2015

[227] Gerasch, A, Küntzer, J, Niermann, P, Stöckel, D, Kohlbacher, O, and Lenhof, H (2015).
Network-based interactive navigation and analysis of large biological datasets
it - Information Technology, 57(1):37-48.

[226] Hildebrandt, AK, Stöckel, D, Fischer, N, de la Garza Trevino, L, Krüger, J, Nickels, S, Röttig, M, Schärfe, C, Schumann, M, Thiel, P, Lenhof, H, Kohlbacher, O, and Hildebrandt, A (2015).
ballaxy: web services for structural bioinformatics
Bioinformatics, 31(1):121-2.

[225] Kowalewski, DJ, Schuster, H, Backert, L, Berlin, C, Kahn, S, Kanz, L, Salih, HR, Rammensee, H, Stevanovic, S, and Stickel, JS (2015).
HLA ligandome analysis identifies the underlying specificities of spontaneous antileukemia immune responses in chronic lymphocytic leukemia (CLL)
Proceedings of the National Academy of Sciences of the United States of America, 112(2):E166–E175.

[224] Martens, L, Kohlbacher, O, and Weintraub, ST (2015).
Managing Expectations when Publishing Tools and Methods for Computational Proteomics
J. Proteome Res., 14(5):2002-4.

[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.

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.