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Publications

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

accepted

[271] Chevrette, MG, Aicheler, F, Kohlbacher, O, Currie, CR, and Medema, MH (accepted).
SANDPUMA: Ensemble Predictions of Nonribosomal Peptide Chemistry Reveals Biosynthetic Diversity across Actinobacteria
Bioinformatics.

[270] Heimgärtner, F, Hettich, S, Kohlbacher, O, and Menth, M (accepted).
Scaling Home Automation to Public Buildings: A Distributed Multiuser Setup for OpenHAB 2
In: Proc. GIoTS 2017.

[269] Nelde, A, Kowalewski, DJ, Backert, L, Schuster, H, Werner, J, Klein, R, Kohlbacher, O, Kanz, L, Salih, HR, Rammensee, H, Stevanović, S, and Stickel, JS (accepted).
HLA ligandome analysis of primary chronic lymphocytic leukemia (CLL) cells under lenalidomide treatment confirms the suitability of lenalidomide for combination with T-cell based immunotherapy
OncoImmunol..

[268] Vizcaino, JA, Mayer, G, Perkins, SR, Barnsnes, H, Vaudel, M, Perez-Riverol, Y, Ternent, T, Uszkoreit, J, Eisenacher, M, Fischer, L, Rappsilber, J, Netz, E, Walzer, M, Kohlbacher, O, Leitner, A, Chalkley, RJ, Ghali, F, Martínez-Bartolomé, S, Deutsch, EW, and Jones, AR (accepted).
The mzIdentML data standard version 1.2, supporting advances in proteome informatics
Mol. Cell. Prot..

2017

[267] Alberer, M, Gnad-Vogt, U, Hong, HS, Mehr, KT, Backert, L, Finak, G, Gottardo, R, Bica, MA, Garofano, A, Koch, SD, Fotin-Mleczek, M, Hoerr, I, Clemens, R, and von Sonnenburg, F (2017).
Safety and immunogenicity of a mRNA rabies vaccine in healthy adults: an open-label, non-randomised, prospective, first-in-human phase 1 clinical trial
The Lancet.

[266] Audain, E, Uszkoreit, J, Sachsenberg, T, Pfeuffer, J, Liang, X, Hermjakob, H, Sanchez, A, Eisenacher, M, Reinert, K, Tabb, DL, Kohlbacher, O, and Perez-Riverol, Y (2017).
In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics
J. Proteomics, 150:170–182.

[265] Backert, L, Kowalewski, D, Walz, S, Schuster, H, Berlin, C, Neidert, M, Schemionek, M, Brümmendorf, TH, Vicinic, V, Niederwieser, D, Kanz, L, Salih, HR, Kohlbacher, O, Weisel, K, Rammensee, H, Stevanovic, S, and Walz, JS (2017).
A meta-analysis of HLA peptidome composition in different hematological entities: Entity-specific dividing lines and "pan-leukemia" antigens
Oncotarget.

[264] Haen, SP, Groh, C, Schumm, M, Backert, L, Löffler, MW, Federmann, B, Faul, C, Dörfel, D, Vogel, W, Handgretinger, R, Kanz, L, and Bethge, WA (2017).
Haploidentical hematopoietic cell transplantation using in vitro T cell depleted grafts as salvage therapy in patients with disease relapse after prior allogeneic transplantation
Annals of Hematology:1-11.

[263] Pfeuffer, JU, Sachsenberg, T, Alka, O, Walzer, M, Fillbrunn, A, Nilse, L, Schilling, O, Reinert, K, and Kohlbacher, O (2017).
OpenMS - A platform for reproducible analysis of mass spectrometry data
J. Biotechnol.:S0168-1656(17)30251-1.

[262] Schubert, B, de la Garza, L, Mohr, C, Walzer, M, and Kohlbacher, O (2017).
ImmunoNodes - Graphical Development of Complex Immunoinformatics Workflows
BMC Bioinformatics.

[261] Schärfe, CPI, Tremmel, R, Schwab, M, Kohlbacher, O, and Marks, DS (2017).
Genetic variation in human drug-related genes
Preprint at arXiv.

[260] Vizcaíno, JA, Walzer, M, Jiménez, RC, Bittremieux, W, Bouyssie, D, Carapito, C, Corrales, F, Ferro, M, Heck, AJR, Horvatovich, P, Hubalek, M, Lane, L, Laukens, K, Levander, F, Lisacek, F, Novak, P, Palmblad, M, Piovesan, D, Pühler, A, Schwämmle, V, Valkenborg, D, van Rijswijk, M, Vondrasek, J, Eisenacher, M, Martens, L, and Kohlbacher, O (2017).
A community proposal to integrate proteomics activities in ELIXIR
F1000Research, 6:875.

2016

[259] Aebersold, R, Kohlbacher, O, and Vitek, O (2016).
Computational Mass Spectrometry (Dagstuhl Seminar 15351)
Dagstuhl Reports, 5(8):9–33.

[258] Boyles, M, Ranninger, C, Reischl, R, Rurik, M, Tessadri, R, Kohlbacher, O, Duschl, A, and Huber, C (2016).
Copper oxide nanoparticle toxicity profiling using untargeted metabolomics
Part. Fiber Toxicol., 13:49.

[257] Breckels, LM, Holden, S, Wojnar, D, Mulvey, CM, Christoforou, A, Groen, A, Kohlbacher, O, Lilley, KS, and Gatto, L (2016).
Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics
PLoS Comput. Biol., 12(5):e1004920.

[256] Dammeier, S, Nahnsen, S, Veit, J, Wehner, F, Ueffing, M, and Kohlbacher, O (2016).
Mass Spectrometry-based Proteomics Reveals Organspecific Expression Patterns To Be Used as Forensic Evidence
J. Proteome Res., 15(1):182-92.

[255] de la Garza, L, Aicheler, F, and Kohlbacher, O (2016).
From the Desktop to the Grid and Cloud: Conversion of KNIME Workflows to gUSE
Proc. Int. Workshop Science Gateways (IWSG 2016).

[254] de la Garza, L, Veit, J, Szolek, A, Röttig, M, Aiche, S, Gesing, S, Reinert, K, and Kohlbacher, O (2016).
From the Desktop to the Grid: scalable Bioinformatics via Workflow Conversion
BMC Bioinformatics, 17(1):127.

[253] Dietsche, T, Mebrhatu, MT, Brunner, MJ, Abrusci, P, Yan, J, Franz-Wachtel, M, Schärfe, C, Zilkenat, S, Grin, I, Galán, JE, Kohlbacher, O, Lea, S, Macek, B, Marlovits, TC, Robinson, C, and Wagner, S (2016).
Structural and functional characterization of the bacterial type III secretion export apparatus
PLoS Pathogens, 12(12):e1006071. .

[252] Gatto, L, Hansen, K, Hoopmann, M, Hermjakob, H, Kohlbacher, O, and Beyer, A (2016).
Testing and validation of computational methods for mass spectrometry
J. Proteome Res., 15(3):809-14.

[251] Griss, J, Perez-Riverol, Y, Lewis, S, Tabb, DL, Dianes, JA, del-Toro, N, Rurik, M, Walzer, MM, Kohlbacher, O, Hermjakob, H, Wang, R, and Vizcaíno, JA (2016).
Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets
Nat. Methods, 13(8):651-656.

[250] Hong, HS, Koch, SD, Scheel, B, Gnad-Vogt, U, Schröder, A, Kallen, K, Wiegand, V, Backert, L, Kohlbacher, O, Hoerr, I, Fotin-Mleczek, M, and Billingsley, JM (2016).
Distinct transcriptional changes in non-small cell lung cancer patients associated with multi-antigenic RNActive® CV9201 immunotherapy
Oncoimmunol., 5(12):e1249560..

[249] Junker, J, Sachsenberg, T, Chernev, A, Aicheler, F, Urlaub, H, and Kohlbacher, O (2016).
LFQProfiler and RNPxl: Open-Source Tools for Label-Free Quantification and Protein-RNA Cross-Linking Integrated into Proteome Discoverer
J. Proteome Res., 15(9):3441-8..

[248] Kohlbacher, O, Vitek, O, and Weintraub, ST (2016).
Challenges in Large-Scale Computational Mass Spectrometry and Multiomics
J. Proteome Res., 15(3):681-2.

[247] Krüger, J and Kohlbacher, O (2016).
Containerization and wrapping of a mass spectra prediction workflow
Preprint.