Publications

336 entries « 2 of 7 »

Halfmann, Marc; Stenzhorn, Holger; Gerjets, Peter; Kohlbacher, Oliver; Oestermeier, Uwe

User-Driven Development of a Novel Molecular Tumor Board Support Tool

Vidal, Sören AuerMaria-Esther (Ed.): DILS 2018: Data Integration in the Life Sciences, pp. 195-199, Springer, 2018.

(Abstract | Links | BibTeX)

Friedrich, Andreas; de la Garza, Luis; Kohlbacher, Oliver; Nahnsen, Sven

Interactive Visualization for Large-Scale Multi-factorial Research Designs

Auer, Maria-Esther Vidal Sören (Ed.): DILS 2018: Data Integration in the Life Sciences, pp. 75-84, 2018.

(Abstract | Links | BibTeX)

Audain, Enrique; Uszkoreit, Julian; Sachsenberg, Timo; Pfeuffer, Julianus; Liang, Xiao; Hermjakob, Henning; Sanchez, Aniel; Eisenacher, Martin; Reinert, Knut; Tabb, David L; Kohlbacher, Oliver; Perez-Riverol, Yasset

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics

J. Proteomics, 150 , pp. 170–182, 2017.

(Abstract | Links | BibTeX)

Backert, Linus; Kowalewski, Daniel; Walz, Simon; Schuster, Heiko; Berlin, Claudia; Neidert, Marian; Schemionek, Mirle; Brümmendorf, Tim Hendrik; Vicinic, Vladan; Niederwieser, Dietger; Kanz, Lothar; Salih, Helmut Rainer; Kohlbacher, Oliver; Weisel, Katja; Rammensee, Hans-Georg; Stevanovic, Stefan; Walz, Juliana Sarah

A meta-analysis of HLA peptidome composition in different hematological entities: Entity-specific dividing lines and

Oncotarget, 8 (27), pp. 43915-43924., 2017.

(Abstract | Links | BibTeX)

Haen, Sebastian P; Groh, Christiane; Schumm, Michael; Backert, Linus; Löffler, Markus W; Federmann, Birgit; Faul, Christoph; Dörfel, Daniela; Vogel, Wichard; Handgretinger, Rupert; Kanz, Lothar; Bethge, Wolfgang A

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, pp. 1-11, 2017.

(Abstract | Links | BibTeX)

Nelde, Annika; Kowalewski, Daniel J; Backert, Linus; Schuster, Heiko; Werner, Jan-Ole; Klein, Reinhild; Kohlbacher, Oliver; Kanz, Lothar; Salih, Helmut R; Rammensee, Hans-Georg; Stevanović, Stefan; Stickel, Juliane S

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., 5 (12), pp. e1249560, 2017.

(Abstract | Links | BibTeX)

Heimgärtner, Florian; Hettich, Stefan; Kohlbacher, Oliver; Menth, Michael

Scaling Home Automation to Public Buildings: A Distributed Multiuser Setup for OpenHAB 2

Global Internet of Things Summit (GIoTS) 2017, 2017.

(Abstract | Links | BibTeX)

Schubert, Benjamin; de la Garza, Luis; Mohr, Christopher; Walzer, Mathias; Kohlbacher, Oliver

ImmunoNodes - Graphical Development of Complex Immunoinformatics Workflows

BMC Bioinformatics, 18 (1), pp. 242, 2017.

(Abstract | Links | BibTeX)

Vizcaino, Juan Antonio; Mayer, Gerhard; Perkins, Simon R; Barnsnes, Harald; Vaudel, Marc; Perez-Riverol, Yasset; Ternent, Tobias; Uszkoreit, Julian; Eisenacher, Martin; Fischer, Lutz; Rappsilber, Juri; Netz, Eugen; Walzer, Mathias; Kohlbacher, Oliver; Leitner, Alexander; Chalkley, Robert J; Ghali, Fawaz; Martínez-Bartolomé, Salvador; Deutsch, Eric W; Jones, Andrew R

The mzIdentML data standard version 1.2, supporting advances in proteome informatics

Mol. Cell. Prot., 16 (7), pp. 1275-1285, 2017.

(Abstract | Links | BibTeX)

Pfeuffer, Julianus U; Sachsenberg, Timo; Alka, Oliver; Walzer, Mathias; Fillbrunn, Alexander; Nilse, Lars; Schilling, Oliver; Reinert, Knut; Kohlbacher, Oliver

OpenMS - A platform for reproducible analysis of mass spectrometry data

J. Biotechnol., pp. S0168-1656(17)30251-1, 2017.

(Abstract | Links | BibTeX)

Chevrette, Marc G; Aicheler, Fabian; Kohlbacher, Oliver; Currie, Cameron R; Medema, Marnix H

SANDPUMA: Ensemble Predictions of Nonribosomal Peptide Chemistry Reveals Biosynthetic Diversity across Actinobacteria

Bioinformatics, 33 (20), pp. 3202-3210, 2017.

(Abstract | Links | BibTeX)

Vizcaíno, Juan Antonio; Walzer, Mathias; Jiménez, Rafael C; Bittremieux, Wout; Bouyssie, David; Carapito, Christine; Corrales, Fernando; Ferro, Myriam; Heck, Albert J R; Horvatovich, Peter; Hubalek, Martin; Lane, Lydia; Laukens, Kris; Levander, Fredrik; Lisacek, Frederique; Novak, Petr; Palmblad, Magnus; Piovesan, Damiano; Pühler, Alfred; Schwämmle, Veit; Valkenborg, Dirk; van Rijswijk, Merlijn; Vondrasek, Jiri; Eisenacher, Martin; Martens, Lennart; Kohlbacher, Oliver

A community proposal to integrate proteomics activities in ELIXIR

F1000Research, 6 , pp. 875, 2017.

(Abstract | Links | BibTeX)

Alberer, Martin; Gnad-Vogt, Ulrike; Hong, Henoch Sangjoon; Mehr, Keyvan Tadjalli; Backert, Linus; Finak, Greg; Gottardo, Raphael; Bica, Mihai Alexandru; Garofano, Aurelio; Koch, Sven Dominik; Fotin-Mleczek, Mariola; Hoerr, Ingmar; Clemens, Ralf; von Sonnenburg, Frank

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, 390 (10101), pp. 1511-1520, 2017.

(Abstract | Links | BibTeX)

van Rijswijk, M; Beirnaert, C; Caron, C; Cascante, M; Dominguez, V; Dunn, WB; Ebbels, TMD; Giacomoni, F; Gonzalez-Beltran, A; Hankemeier, T; Haug, K; Izquierdo-Garcia, JL; Jimenez, RC; Jourdan, F; Kale, N; Klapa, MI; Kohlbacher, O; Koort, K; Kultima, K; Corguillé, Le G; Moschonas, NK; Neumann, S; O?Donovan, C; Reczko, M; Rocca-Serra, P; Rosato, A; Salek, RM; Sansone, SA; Satagopam, V; Schober, D; Shimmo, R; Spicer, RA; Spjuth, O; Thévenot, EA; Viant, MR; Weber, RJM; Willighagen, EL; Zanetti, G; Steinbeck, C

The future of metabolomics in ELIXIR [version 1; referees: awaiting peer review]

F1000Research, 6 (1649), 2017.

(Links | BibTeX)

Flett, Fiona J; Sachsenberg, Timo; Kohlbacher, Oliver; Mackay, Logan C; Interthal, Heidrun

Differential Enzymatic 16O/18O Labelling for the Detection of Cross-Linked Nucleic Acid-Protein Heteroconjugates

Anal. Chem., 89 (21), pp. 11208-11213, 2017.

(Abstract | Links | BibTeX)

Marco, Moreno Di; Schuster, Heiko; Backert, Linus; Ghosh, Michael; Rammensee, Hans-Georg; Stevanovic, Stefan

Unveiling the Peptide Motifs of HLA-C and HLA-G from Naturally Presented Peptides and Generation of Binding Prediction Matrices

J. Immunol., 199 (8), pp. 2639-2651, 2017.

(Abstract | Links | BibTeX)

Schuster, Heiko; Peper, Janet Kerstin; Bösmüller, Hans-Christian; Röhle, Kevin; Backert, Linus; Bilich, Tatjana; Ney, Britta; Löffler, Markus W; Kowalewski, Daniel J; Trautwein, Nico; Rabsteyn, Armin; Engler, Tobias; Braun, Sabine; Haen, Sebastian P; Walz, Juliane Sarah; Schmid-Horch, Barbara; Brucker, Sara; Wallwiener, Diethelm; Kohlbacher, Oliver; Fend, Falko; Rammensee, Hans-Georg; Stevanovic, Stefan; Staebler, Annette; Wagner, Philipp

The immunopeptidomic landscape of ovarian carcinomas

Proc. Natl. Acad. Sci. USA, 114 (46), pp. E9942-E9951, 2017.

(Abstract | Links | BibTeX)

Schärfe, Charlotta P I; Tremmel, Roman; Schwab, Matthias; Kohlbacher, Oliver; Marks, Debora S

Genetic variation in human drug-related genes

Genome Med., 9 , pp. 117, 2017.

(Abstract | Links | BibTeX)

Schneider, Lara; Stöckel, Daniel; Kehl, Tim; Gerasch, Andreas; Ludwig, Nicole; Leidinger, Petra; Huwer, Hanno; Tenzer, Stefan; Kohlbacher, Oliver; Hildebrandt, Andreas; Kaufmann, Michael; Gessler, Manfred; Keller, Andreas; Meese, Eckart; Graf, Norbert; Lenhof, Hans-Peter

DrugTargetInspector: An assistance tool for patient treatment stratification

Int. J. Cancer, 138 (7), pp. 1765-76, 2016.

(Abstract | Links | BibTeX)

Gatto, Laurent; Hansen, Kasper; Hoopmann, Michael; Hermjakob, Henning; Kohlbacher, Oliver; Beyer, Andreas

Testing and validation of computational methods for mass spectrometry

J. Proteome Res., 15 (3), pp. 809-14, 2016.

(Abstract | Links | BibTeX)

Dammeier, Sascha; Nahnsen, Sven; Veit, Johannes; Wehner, Frank; Ueffing, Marius; Kohlbacher, Oliver

Mass Spectrometry-based Proteomics Reveals Organspecific Expression Patterns To Be Used as Forensic Evidence

J. Proteome Res., 15 (1), pp. 182-92, 2016.

(Abstract | Links | BibTeX)

Schubert, Benjamin; Kohlbacher, Oliver

Designing string-of-beads vaccines with optimal spacers

Genome Med., 8 (1), pp. 9, 2016.

(Abstract | Links | BibTeX)

Stickel, Juliane; Kowalewski, Daniel; Walz, Simon; Backert, Linus; Schuster, Heiko; Kohlbacher, Oliver; Weisel, Katja; Rittig, Susanne; Kanz, Lothar; Salih, Helmut; Rammensee, Hans-Georg; Stevanovic, Stefan

Carfilzomib alters the HLA-presented peptidome of myeloma cells and impairs presentation of peptides with aromatic C-termini

Blood Cancer J., 6 , pp. e411, 2016.

(Abstract | Links | BibTeX)

Kohlbacher, Oliver; Vitek, Olga; Weintraub, Susan T

Challenges in Large-Scale Computational Mass Spectrometry and Multiomics

J. Proteome Res., 15 (3), pp. 681-2, 2016.

(Links | BibTeX)

Müller, Sabine C; Backes, Christina; Gress, Alexander; Baumgarten, Nina; Kalinina, Olga V; Moll, Andreas; Kohlbacher, Oliver; Meese, Eckart; Keller, Andreas

BALL-SNPgp – from genetic variants towards computational diagnostics

Bioinformatics, 2016.

(Abstract | Links | BibTeX)

Schubert, Benjamin; Walzer, Mathias; Brachvogel, Hans-Philipp; Szolek, Andras; Mohr, Christopher; Kohlbacher, Oliver

FRED 2 – An Immunoinformatics Framework for Python

Bioinformatics, 32 (13), pp. 2044-6, 2016.

(Abstract | Links | BibTeX)

de la Garza, Luis; Veit, Johannes; Szolek, Andras; Röttig, Marc; Aiche, Stephan; Gesing, Sandra; Reinert, Knut; Kohlbacher, Oliver

From the Desktop to the Grid: scalable Bioinformatics via Workflow Conversion

BMC Bioinformatics, 17 (1), pp. 127, 2016.

(Abstract | Links | BibTeX)

Breckels, Lisa M; Holden, Sean; Wojnar, David; Mulvey, Claire M; Christoforou, Adny; Groen, Arnoud; Kohlbacher, Oliver; Lilley, Kathryn S; Gatto, Laurent

Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics

PLoS Comput. Biol., 12 (5), pp. e1004920, 2016.

(Abstract | Links | BibTeX)

Mohr, Christopher; Friedrich, Andreas; Wojnar, David; Kenar, Erhan; Polatkan, Aydin Can; Codrea, Marius Cosmin; Czemmel, Stefan; Kohlbacher, Oliver; Nahnsen, Sven

qPortal – A Science Gateway for Biomedical Applications

Proc. Int. Workshop Science Gateways (IWSG 2016), 2016.

(BibTeX)

de la Garza, Luis; Aicheler, Fabian; Kohlbacher, Oliver

From the Desktop to the Grid and Cloud: Conversion of KNIME Workflows to gUSE

Proc. Int. Workshop Science Gateways (IWSG 2016), 2016.

(BibTeX)

Griss, Johannes; Perez-Riverol, Yasset; Lewis, Steve; Tabb, David L; Dianes, José A; del-Toro, Noemi; Rurik, Marc; Walzer, Mathias M; Kohlbacher, Oliver; Hermjakob, Henning; Wang, Rui; Vizcaíno, Juan Antonio

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets

Nat. Methods, 13 (8), pp. 651-656, 2016.

(Abstract | Links | BibTeX)

Ranninger, Christina; Schmidt, Lukas E; Rurik, Marc; Limonciel, Alice; Jennings, Paul; Kohlbacher, Oliver; Huber, Christian G

Improving global feature detectabilities through scan range splitting for untargeted metabolomics by high-performance liquid chromatography-Orbitrap mass spectrometry

Anal. Chim. Acta, 930 , pp. 13-22, 2016.

(Abstract | Links | BibTeX)

Perez-Riverol, Yasset; Gatto, Laurent; Wang, Rui; Sachsenberg, Timo; Uszkoreit, Julian; Leprevost, Felipe; Fufezan, Christian; Ternent, Tobias; Eglen, Stephen J; Katz, Daniel S S; Pollard, Tom J; Konovalov, Alexander; Flight, Robert M; Blin, Kai; Vizcaino, Juan Antonio

Ten Simple Rules for Taking Advantage of git and GitHub

bioRxiv, 2016.

(Abstract | Links | BibTeX)

Löffler, Markus; Chandra, Anoop P; Laske, Karoline; Schroeder, Christopher; Bonzheim, Irina; Hilke, Franz J; Kowalewski, Daniel J; Trautwein, Nico; Schuster, Heiko; Gründer, Marc; Walzer, Mathias; Mohr, Christopher; Nguyen, Huu-Phuc; Riess, Olaf; Bauer, Peter; Nahnsen, Sven; Königsrainer, Alfred; Nadalina, Silvio; Zieker, Derek; Glatzle, Jörg; Thiel, Karolin; Clasen, Stephan; Bösmüller, Hans; Fend, Falko; Kohlbacher, Oliver; Gouttefangeas, Cecile; Stevanovic, Stefan; Rammensee, Hans-Georg

Personalized peptide vaccine induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient

J. Hepatol., 65 (4), pp. 849-55, 2016.

(Abstract | Links | BibTeX)

Röst, Hannes L; Sachsenberg, Timo; Aiche, Stephan; Bielow, Chris; Weisser, Hendrik; Aicheler, Fabian; Andreotti, Sandro; Ehrlich, Hans-Christian; Gutenbrunner, Petra; Kenar, Erhan; Liang, Xiao; Nahnsen, Sven; Nilse, Lars; Pfeuffer, Julianus; Rosenberger, George; Rurik, Marc; Schmitt, Uwe; Veit, Johannes; Walzer, Mathias; Wojnar, David; Wolski, Witold E; Schilling, Oliver; Choudhary, Jyoti S; Malmström, Lars; Aebersold, Ruedi; Reinert, Knut; Kohlbacher, Oliver

OpenMS: A flexible open-source software platform for mass spectrometry data analysis

Nat. Methods, 13 (9), pp. 741-748, 2016.

(Abstract | Links | BibTeX)

Veit, Johannes; Sachsenberg, Timo; Chernev, Alexsandr; Aicheler, Fabian; Urlaub, Henning; Kohlbacher, Oliver

LFQProfiler and RNPxl: Open-Source Tools for Label-Free Quantification and Protein-RNA Cross-Linking Integrated into Proteome Discoverer

J. Proteome Res., 15 (9), pp. 3441-8., 2016.

(Abstract | Links | BibTeX)

Boyles, Matthe; Ranninger, Christina; Reischl, Roland; Rurik, Marc; Tessadri, Richard; Kohlbacher, Oliver; Duschl, Albert; Huber, Christian

Copper oxide nanoparticle toxicity profiling using untargeted metabolomics

Part. Fiber Toxicol., 13 , pp. 49, 2016.

(Abstract | Links | BibTeX)

Nicoludis, John M; Vogt, Bennett E; Green, Anna G; Schärfe, Charlotta PI; Marks, Debora S; Gaudet, Rachelle

Antiparallel protocadherin homodimers use distinct affinity- and specificity-mediating regions in cadherin repeats 1-4

eLife, 5 , pp. e18449, 2016.

(Abstract | Links | BibTeX)

Krüger, Jens; Thiel, Philipp; Merelli, Ivan; Grunzke, Richard; Gesing, Sandra

Portals and Web-based Resources for Virtual Screening.

Curr Drug Targets, 2016, (automatic medline import).

(Abstract | Links | BibTeX)

Hong, Henoch S; Koch, Sven D; Scheel, Birgit; Gnad-Vogt, Ulrike; Schröder, Andreas; Kallen, Karl-Josef; Wiegand, Volker; Backert, Linus; Kohlbacher, Oliver; Hoerr, Ingmar; Fotin-Mleczek, Mariola; Billingsley, James M

Distinct transcriptional changes in non-small cell lung cancer patients associated with multi-antigenic RNActive® CV9201 immunotherapy

Oncoimmunol., 5 (12), pp. e1249560., 2016.

(Abstract | Links | BibTeX)

Thijssen, Bram; Dijkstra, Tjeerd; Heskes, Tom; Wessels, Lodewyk

BCM: toolkit for Bayesian analysis of Computational Models using samplers

BMC Systems Biology, 10:100 , 2016.

(Abstract | Links | BibTeX)

Dietsche, Tobias; Mebrhatu, Mehari Tesfazgi; Brunner, Matthias J; Abrusci, Patrizia; Yan, Jun; Franz-Wachtel, Mirita; Schärfe, Charlotta; Zilkenat, Susann; Grin, Iwan; Galán, Jorge E; Kohlbacher, Oliver; Lea, Susan; Macek, Boris; Marlovits, Thomas C; Robinson, Carol; Wagner, Samuel

Structural and functional characterization of the bacterial type III secretion export apparatus

PLoS Pathogens, 12 (12), pp. e1006071., 2016.

(Abstract | Links | BibTeX)

Krüger, Jens; Kohlbacher, Oliver

Containerization and wrapping of a mass spectra prediction workflow

2016.

(Abstract | Links | BibTeX)

Aebersold, Rudolf; Kohlbacher, Oliver; Vitek, Olga

Computational Mass Spectrometry (Dagstuhl Seminar 15351)

Dagstuhl Reports, 5 (8), pp. 9–33, 2016, ISSN: 2192-5283.

(Links | BibTeX)

Hildebrandt, Anna Katharina; Stöckel, Daniel; Fischer, Nina; de la Trevino, Luis Garza; Krüger, Jens; Nickels, Stefan; Röttig, Marc; Schärfe, Charlotta; Schumann, Marcel; Thiel, Philipp; Lenhof, Hans-Peter; Kohlbacher, Oliver; Hildebrandt, Andreas

ballaxy: web services for structural bioinformatics

Bioinformatics, 31 (1), pp. 121-2, 2015.

(Abstract | Links | BibTeX)

Proikas-Cezanne, Tassula; Takacs, Zsuzsanna; Dönnes, Pierre; Kohlbacher, Oliver

WIPI proteins: essential PtdIns3P effectors at the nascent autophagosome

J. Cell Sci., 128 (2), pp. 207-217, 2015.

(Abstract | Links | BibTeX)

Thost, Ann-Kathrin; Dönnes, Pierre; Kohlbacher, Oliver; Proikas-Cezanne, Tassula

Fluorescence-based imaging of autophagy progression by human WIPI beta-propeller protein detection in single cells

Methods, 75 , pp. 69-78, 2015.

(Abstract | Links | BibTeX)

Sachsenberg, Timo; Herbst, Florian-Alexander; Taubert, Martin; Kermer, René; Jehmlich, Nico; von Bergen, Martin; Seifert, Jana; Kohlbacher, Oliver

MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics

J. Proteome Res., 14 (2), pp. 619-27, 2015.

(Abstract | Links | BibTeX)

Gerasch, Andreas; Küntzer, Jan; Niermann, Peter; Stöckel, Daniel; Kohlbacher, Oliver; Lenhof, Hans-Peter

Network-based interactive navigation and analysis of large biological datasets

it - Information Technology, 57 (1), pp. 37-48, 2015.

(Abstract | Links | BibTeX)

Ziller, Michael J; Edri, Reuven; Yaffe, Yakey; Donaghey, Julie; Pop, Ramona; Mallard, William; Issner, Robbyn; Gifford, Casey A; Goren, Alon; Xing, Jeffrey; Gu, Hongcang; Cacchiarelli, Davide; Tsankov, Alexander M; Epstein, Charles; Rinn, John L; Mikkelsen, Tarjei S; Kohlbacher, Oliver; Gnirke, Andreas; Bernstein, Bradley E; Elkabetz, Yechiel; Meissner, Alexander

Dissecting neural differentiation regulatory networks through epigenetic footprinting.

Nature, 518 , pp. 355-359, 2015.

(Abstract | Links | BibTeX)

336 entries « 2 of 7 »

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