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ORCIDOliver Kohlbacher
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- affiliation: University of Tübingen, Germany
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2020 – today
- 2023
[j75]Mirjam Figaschewski
, Bilge Sürün, Thorsten Tiede, Oliver Kohlbacher:
The personalized cancer network explorer (PeCaX) as a visual analytics tool to support molecular tumor boards. BMC Bioinform. 24(1): 88 (2023)- [j74]Eleftheria Kontou, Axel Walter, Oliver Alka, Julianus Pfeuffer, Timo Sachsenberg, Omkar S. Mohite, Matin Nuhamunada, Oliver Kohlbacher, Tilmann Weber:
UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis. J. Cheminformatics 15(1): 52 (2023) - [c42]Nils Hoffmann, Irena Maus, Sebastian Beier, Peter Belmann, Jan Krüger, Andreas Tauch, Alexander Goesmann, Roland Eils, Peer Bork, Oliver Kohlbacher, Ursula Kummer, Rolf Backofen, Ivo Buchhalter, Alexander Sczyrba:
Embedding the de.NBI Cloud in the National Research Data Infrastructure Activities. CoRDI 2023 - 2022
- [j73]Mete Akgün, Nico Pfeifer, Oliver Kohlbacher:
Efficient privacy-preserving whole-genome variant queries. Bioinform. 38(8): 2202-2210 (2022) - [j72]Sebastian Winkler, Ivana Winkler, Mirjam Figaschewski, Thorsten Tiede, Alfred Nordheim, Oliver Kohlbacher:
De novo identification of maximally deregulated subnetworks based on multi-omics data with DeRegNet. BMC Bioinform. 23(1): 139 (2022) - [c41]Hans-Ulrich Prokosch, Thomas Bahls, Martin Bialke, Jürgen Eils, Christian Fegeler, Julian Gründner, Birger Haarbrandt, Christopher Hampf, Wolfgang Hoffmann, Hauke Hund, Marvin O. Kampf, Lorenz A. Kapsner, Piotr Kasprzak, Oliver Kohlbacher, Dagmar Krefting, Jonathan Mang, Michael Marschollek, Sebastian Mate, Armin Müller, Fabian Prasser, Julian Sass, Sebastian C. Semler, Holger Stenzhorn, Sylvia Thun, Sven Zenker, Roland Eils:
The COVID-19 Data Exchange Platform of the German University Medicine. MIE 2022: 674-678 - [i18]Marius de Arruda Botelho Herr, Michael Graf, Peter Placzek, Florian König, Felix Bötte, Tyra Stickel, David Hieber, Lukas Zimmermann, Michael Slupina, Christopher Mohr, Stephanie Biergans, Mete Akgün, Nico Pfeifer, Oliver Kohlbacher:
Bringing the Algorithms to the Data - Secure Distributed Medical Analytics using the Personal Health Train (PHT-meDIC). CoRR abs/2212.03481 (2022) - 2021
- [j71]Mete Akgün, Ali Burak Ünal, Bekir Ergüner, Nico Pfeifer, Oliver Kohlbacher:
Identifying disease-causing mutations with privacy protection. Bioinform. 36(21): 5205-5213 (2021) - 2020
- [j70]Bilge Sürün, Charlotta P. I. Schärfe, Mathew R. Divine, Julian Heinrich, Nora C. Toussaint, Lukas Zimmermann, Janina Beha, Oliver Kohlbacher:
ClinVAP: a reporting strategy from variants to therapeutic options. Bioinform. 36(7): 2316-2317 (2020) - [j69]Lars Christoph Gleim, Md. Rezaul Karim, Lukas Zimmermann, Oliver Kohlbacher, Holger Stenzhorn, Stefan Decker, Oya Beyan:
Enabling ad-hoc reuse of private data repositories through schema extraction. J. Biomed. Semant. 11(1): 6 (2020) - [j68]Oya Beyan, Ananya Choudhury, Johan van Soest, Oliver Kohlbacher, Lukas Zimmermann, Holger Stenzhorn, Md. Rezaul Karim, Michel Dumontier, Stefan Decker, Luiz Olavo Bonino da Silva Santos, Andre Dekker:
Distributed Analytics on Sensitive Medical Data: The Personal Health Train. Data Intell. 2(1-2): 96-107 (2020)
2010 – 2019
- 2019
- [j67]Lara Schneider, Tim Kehl, Kristina Thedinga, Nadja Liddy Grammes, Christina Backes, Christopher Mohr, Benjamin Schubert, Kerstin Lenhof, Nico Gerstner, Andreas Daniel Hartkopf, Markus Wallwiener, Oliver Kohlbacher, Andreas Keller, Eckart Meese, Norbert M. Graf, Hans-Peter Lenhof:
ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification. Bioinform. 35(24): 5171-5181 (2019) - [c40]Thorsten Tiede, Oliver Kohlbacher:
Biological Network Knowledge in Molecular Tumor Boards. AMIA 2019 - [c39]Maximilian Hanussek, Felix Bartusch, Jens Krüger, Oliver Kohlbacher:
BOOTABLE: Bioinformatics Benchmark Tool Suite. CCGRID 2019: 157-160 - [c38]Felix Bartusch, Maximilian Hanussek, Jens Krüger, Oliver Kohlbacher:
Reproducible Scientific Workflows for High Performance and Cloud Computing. CCGRID 2019: 161-164 - [i17]Daniel Wibberg, Bérénice Batut, Peter Belmann, Jochen Blom, Frank Oliver Glöckner, Björn A. Grüning, Nils Hoffmann, Nils Kleinbölting, René Rahn, Maja Rey, Uwe Scholz, Malvika Sharan, Andreas Tauch, Ulrike Trojahn, Björn Usadel, Oliver Kohlbacher:
The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR. F1000Research 8: 1877 (2019) - 2018
- [j66]Benjamin Schubert, Charlotta Schärfe, Pierre Dönnes, Thomas A. Hopf, Debora S. Marks, Oliver Kohlbacher:
Population-specific design of de-immunized protein biotherapeutics. PLoS Comput. Biol. 14(3) (2018) - [c37]Andreas Friedrich, Luis de la Garza, Oliver Kohlbacher, Sven Nahnsen:
Interactive Visualization for Large-Scale Multi-factorial Research Designs. DILS 2018: 75-84 - [c36]Marc Halfmann, Holger Stenzhorn, Peter Gerjets, Oliver Kohlbacher, Uwe Oestermeier:
User-Driven Development of a Novel Molecular Tumor Board Support Tool. DILS 2018: 195-199 - [c35]Md. Rezaul Karim, Binh-Phi Nguyen, Lukas Zimmermann, Toralf Kirsten, Matthias Löbe, Frank A. Meineke, Holger Stenzhorn, Oliver Kohlbacher, Stefan Decker, Oya Beyan:
A distributed analytics platform to execute FHIR based phenotyping algorithms. SWAT4LS 2018 - 2017
- [j65]Marc G. Chevrette, Fabian Aicheler, Oliver Kohlbacher, Cameron R. Currie, Marnix H. Medema:
SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria. Bioinform. 33(20): 3202-3210 (2017) - [j64]Benjamin Schubert, Luis de la Garza, Christopher Mohr, Mathias Walzer, Oliver Kohlbacher:
ImmunoNodes - graphical development of complex immunoinformatics workflows. BMC Bioinform. 18(1): 242:1-242:7 (2017) - [c34]Florian Heimgaertner, Stefan Hettich, Oliver Kohlbacher, Michael Menth:
Scaling home automation to public buildings: A distributed multiuser setup for OpenHAB 2. GIoTS 2017: 1-6 - [c33]Maximilian Hanussek, Felix Bartusch, Jens Krüger, Oliver Kohlbacher:
Efficient Mass Spectra Prediction through Container Orchestration with a Scientific Workflow. IWSG 2017 - [i16]Benjamin Schubert, Charlotta Schärfe, Pierre Dönnes, Thomas A. Hopf, Debora S. Marks, Oliver Kohlbacher:
Population-specific design of de-immunized protein biotherapeutics. CoRR abs/1706.09083 (2017) - [i15]Merlijn N. van Rijswijk, Charlie Beirnaert, Christophe Caron, Marta Cascante, Victoria Dominguez Del Angel, Warwick B. Dunn, Timothy M. D. Ebbels, Franck Giacomoni, Alejandra N. González-Beltrán, Thomas Hankemeier, Kenneth Haug, Jose L. Izquierdo-García, Rafael C. Jiménez, Fabien Jourdan, Namrata Kale, Maria I. Klapa, Oliver Kohlbacher, Kairi Koort, Kim Kultima, Gildas Le Corguillé, Nicholas K. Moschonas, Steffen Neumann, Claire O'Donovan, Martin Reczko, Philippe Rocca-Serra, Antonio Rosato, Reza M. Salek, Susanna-Assunta Sansone, Venkata P. Satagopam, Daniel Schober, Ruth Shimmo, Rachel A. Spicer, Ola Spjuth, Etienne A. Thévenot, Mark R. Viant, Ralf J. M. Weber, Egon L. Willighagen, Gianluigi Zanetti, Christoph Steinbeck:
The future of metabolomics in ELIXIR. F1000Research 6: 1649- (2017) - [i14]Christopher Mohr, Andreas Friedrich, David Wojnar, Erhan Kenar, Aydin Can Polatkan, Marius Cosmin Codrea, Stefan Czemmel, Oliver Kohlbacher, Sven Nahnsen:
qPortal - A science gateway for biomedical applications. PeerJ Prepr. 5: e2839 (2017) - [i13]Luis de la Garza, Fabian Aicheler, Oliver Kohlbacher:
From the desktop to the grid and cloud: conversion of KNIME workflows to WS-PGRADE. PeerJ Prepr. 5: e2849 (2017) - 2016
- [j63]Sabine C. Mueller, Christina Backes, Alexander Greß, Nina Baumgarten, Olga V. Kalinina, Andreas Moll, Oliver Kohlbacher, Eckart Meese, Andreas Keller:
BALL-SNPgp - from genetic variants toward computational diagnostics. Bioinform. 32(12): 1888-1890 (2016) - [j62]Benjamin Schubert, Mathias Walzer, Hans-Philipp Brachvogel, András Szolek, Christopher Mohr, Oliver Kohlbacher:
FRED 2: an immunoinformatics framework for Python. Bioinform. 32(13): 2044-2046 (2016) - [j61]Luis de la Garza, Johannes Veit, András Szolek, Marc Röttig, Stephan Aiche, Sandra Gesing, Knut Reinert, Oliver Kohlbacher:
From the desktop to the grid: scalable bioinformatics via workflow conversion. BMC Bioinform. 17: 127 (2016) - [j60]Lisa M. Breckels, Sean B. Holden, David Wojnar, Claire M. Mulvey, Andy Christoforou, Arnoud Groen, Matthew W. B. Trotter, Oliver Kohlbacher, Kathryn S. Lilley, Laurent Gatto:
Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics. PLoS Comput. Biol. 12(5) (2016) - [c32]Luis de la Garza, Fabian Aicheler, Oliver Kohlbacher:
From the Desktop to the Grid and Cloud: Conversion of KNIME Workflows to WS-PGRADE. IWSG 2016 - [i12]Jens Krüger, Oliver Kohlbacher:
Containerization and wrapping of a mass spectra prediction workflow. PeerJ Prepr. 4: e2528 (2016) - 2015
- [j59]Anna Katharina Hildebrandt, Daniel Stöckel, Nina M. Fischer, Luis de la Garza, Jens Krüger, Stefan Nickels, Marc Röttig, Charlotta Schärfe, Marcel Schumann, Philipp Thiel, Hans-Peter Lenhof, Oliver Kohlbacher, Andreas Hildebrandt:
ballaxy: web services for structural bioinformatics. Bioinform. 31(1): 121-122 (2015) - [j58]Ramanuja Simha, Sebastian Briesemeister, Oliver Kohlbacher, Hagit Shatkay:
Protein (multi-)location prediction: utilizing interdependencies via a generative model. Bioinform. 31(12): 365-374 (2015) - [j57]Benjamin Schubert, Hans-Philipp Brachvogel, Christopher Jürges, Oliver Kohlbacher:
EpiToolKit - a web-based workbench for vaccine design. Bioinform. 31(13): 2211-2213 (2015) - [j56]Andreas Gerasch, Jan Küntzer, Peter Niermann, Daniel Stöckel, Michael Kaufmann, Oliver Kohlbacher, Hans-Peter Lenhof:
Network-based interactive navigation and analysis of large biological datasets. it Inf. Technol. 57(1): 37-48 (2015) - [i11]Rudolf Aebersold, Oliver Kohlbacher, Olga Vitek:
Computational Mass Spectrometry (Dagstuhl Seminar 15351). Dagstuhl Reports 5(8): 9-33 (2015) - 2014
- [j55]András Szolek, Benjamin Schubert, Christopher Mohr, Marc Sturm, Magdalena Feldhahn, Oliver Kohlbacher:
OptiType: precision HLA typing from next-generation sequencing data. Bioinform. 30(23): 3310-3316 (2014) - [j54]Philipp Thiel, Lisa Sach-Peltason, Christian Ottmann, Oliver Kohlbacher:
Blocked Inverted Indices for Exact Clustering of Large Chemical Spaces. J. Chem. Inf. Model. 54(9): 2395-2401 (2014) - [c31]Andreas Gerasch, Michael Kaufmann, Oliver Kohlbacher:
Rebuilding KEGG Maps: Algorithms and Benefits. PacificVis 2014: 97-104 - 2013
- [j53]Lars Packschies, Georg Birkenheuer, Dirk Blunk, Sebastian Breuers, André Brinkmann, Ines dos Santos Vieira, Gregor Fels, Sandra Gesing, Richard Grunzke, Sonja Herres-Pawlis, Oliver Kohlbacher, Jens Krüger, Martin Kruse, Ulrich Lang, Ralph Müller-Pfefferkorn, Patrick Schäfer, Tobias Schlemmer, Thomas Steinke, Klaus-Dieter Warzecha, Andreas Zink:
The MoSGrid - e-science gateway: molecular simulations in a distributed computing environment. J. Cheminformatics 5(S-1): 3 (2013) - [j52]Charlotta Schärfe, Joachim Taeger, Peggy Reuter, Nina M. Fischer, Jens Krüger, Bernd Wissinger, Oliver Kohlbacher:
Development of a pharmacorphore model for pharmacological chaperones targeting mutant trafficking-deficient CNG channels. J. Cheminformatics 5(S-1): 18 (2013) - [j51]Philipp Thiel, Lisa Peltason, Christian Ottmann, Oliver Kohlbacher:
Deterministic clustering of the available chemical space. J. Cheminformatics 5(S-1): 53 (2013) - [j50]Jirí Novák, Timo Sachsenberg, David Hoksza, Tomás Skopal, Oliver Kohlbacher:
On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications. J. Integr. Bioinform. 10(3) (2013) - [c30]Oliver Kohlbacher, Falk Schreiber, Matthew O. Ward:
Multivariate Networks in the Life Sciences. Multivariate Network Visualization 2013: 61-73 - [c29]Jonathan C. Roberts, Jing Yang, Oliver Kohlbacher, Matthew O. Ward, Michelle X. Zhou:
Novel Visual Metaphors for Multivariate Networks. Multivariate Network Visualization 2013: 127-150 - [c28]Luis de la Garza, Jens Krüger, Charlotta Schärfe, Marc Röttig, Stephan Aiche, Knut Reinert, Oliver Kohlbacher:
From the Desktop to the Grid: conversion of KNIME Workflows to gUSE. IWSG 2013 - [c27]Jirí Novák, Timo Sachsenberg, David Hoksza, Tomás Skopal, Oliver Kohlbacher:
A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools. PACBB 2013: 101-109 - [i10]Ruedi Aebersold, Oliver Kohlbacher, Olga Vitek:
Computational Mass Spectrometry (Dagstuhl Seminar 13491). Dagstuhl Reports 3(12): 1-16 (2013) - 2012
- [j49]Sven Nahnsen, Oliver Kohlbacher:
In silico design of targeted SRM-based experiments. BMC Bioinform. 13(S-16): S8 (2012) - [j48]Sandra Gesing, Richard Grunzke, Jens Krüger, Georg Birkenheuer, Martin Wewior, Patrick Schäfer, Bernd Schuller, Johannes Schuster, Sonja Herres-Pawlis, Sebastian Breuers, Ákos Balaskó, Miklos Kozlovszky, Anna Szikszay Fabri, Lars Packschies, Péter Kacsuk, Dirk Blunk, Thomas Steinke, André Brinkmann, Gregor Fels, Ralph Müller-Pfefferkorn, René Jäkel, Oliver Kohlbacher:
A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics. J. Grid Comput. 10(4): 769-790 (2012) - [j47]Oliver Kohlbacher:
CADDSuite - a workflow-enabled suite of open-source tools for drug discovery. J. Cheminformatics 4(S-1): 2 (2012) - [j46]Georg Birkenheuer, Dirk Blunk, Sebastian Breuers, André Brinkmann, Ines dos Santos Vieira, Gregor Fels, Sandra Gesing, Richard Grunzke, Sonja Herres-Pawlis, Oliver Kohlbacher, Jens Krüger, Ulrich Lang, Lars Packschies, Ralph Müller-Pfefferkorn, Patrick Schäfer, Thomas Steinke, Klaus-Dieter Warzecha, Martin Wewior:
MoSGrid: efficient data management and a standardized data exchange format for molecular simulations in a grid environment. J. Cheminformatics 4(S-1): 21 (2012) - [c26]Magdalena Feldhahn, Karin Schilbach, Pierre Dönnes, Hans-Georg Rammensee, Benjamin Schubert, Oliver Kohlbacher:
miHA-match: computational detection of tissue-specific minor histocompatibility antigens. BCB 2012: 625-626 - [c25]Sonja Herres-Pawlis, Georg Birkenheuer, André Brinkmann, Sandra Gesing, Richard Grunzke, René Jäkel, Oliver Kohlbacher, Jens Krüger, Ines dos Santos Vieira:
Workflow-enhanced conformational analysis of guanidine zinc complexes via a science gateway. HealthGrid 2012: 142-151 - 2011
- [j45]Chun-Wei Tung, Matthias Ziehm, Andreas Kämper, Oliver Kohlbacher, Shinn-Ying Ho:
POPISK: T-cell reactivity prediction using support vector machines and string kernels. BMC Bioinform. 12: 446 (2011) - [j44]Sandra Gesing, Jano I. van Hemert, Péter Kacsuk, Oliver Kohlbacher:
Special Issue: Portals for life sciences - Providing intuitive access to bioinformatic tools. Concurr. Comput. Pract. Exp. 23(3): 223-234 (2011) - [j43]Georg Birkenheuer, Dirk Blunk, Sebastian Breuers, André Brinkmann, Ines dos Santos Vieira, Gregor Fels, Sandra Gesing, Richard Grunzke, Sonja Herres-Pawlis, Oliver Kohlbacher, Nico Kruber, Jens Krüger, Ulrich Lang, Lars Packschies, Ralph Müller-Pfefferkorn, Patrick Schäfer, Hans-Günther Schmalz, Thomas Steinke, Klaus-Dieter Warzecha, Martin Wewior:
MoSGrid - a molecular simulation grid as a new tool in computational chemistry, biology and material science. J. Cheminformatics 3(S-1): 14 (2011) - [j42]Marcel Schumann, Marc Röttig, Nina M. Fischer, Oliver Kohlbacher:
A framework and workflow system for virtual screening and molecular docking. J. Cheminformatics 3(S-1): 15 (2011) - [j41]Jens Krüger, Georg Birkenheuer, Dirk Blunk, Sebastian Breuers, André Brinkmann, Gregor Fels, Sandra Gesing, Richard Grunzke, Oliver Kohlbacher, Nico Kruber, Ulrich Lang, Lars Packschies, Ralph Müller-Pfefferkorn, Sonja Herres-Pawlis, Patrick Schäfer, Hans-Günther Schmalz, Thomas Steinke, Klaus-Dieter Warzecha, Martin Wewior:
Molecular simulation grid. J. Cheminformatics 3(S-1): 17 (2011) - [j40]Marc Röttig, Marnix H. Medema, Kai Blin, Tilmann Weber, Christian Rausch, Oliver Kohlbacher:
NRPSpredictor2 - a web server for predicting NRPS adenylation domain specificity. Nucleic Acids Res. 39(Web-Server-Issue): 362-367 (2011) - [c24]Nora C. Toussaint, Magdalena Feldhahn, Matthias Ziehm, Stefan Stevanovic, Oliver Kohlbacher:
T-cell epitope prediction based on self-tolerance. BCB 2011: 584-588 - [c23]Sandra Gesing, Richard Grunzke, Ákos Balaskó, Georg Birkenheuer, Dirk Blunk, Sebastian Breuers, André Brinkmann, Gregor Fels, Sonja Herres-Pawlis, Péter Kacsuk, Miklos Kozlovszky, Jens Krüger, Lars Packschies, Patrick Schäfer, Bernd Schuller, Johannes Schuster, Thomas Steinke, Anna Szikszay Fabri, Martin Wewior, Ralph Müller-Pfefferkorn, Oliver Kohlbacher:
Granular Security for a Science Gateway in Structural Bioinformatics. IWSG-Life 2011 - 2010
- [j39]Sebastian Briesemeister, Jörg Rahnenführer, Oliver Kohlbacher:
Going from where to why - interpretable prediction of protein subcellular localization. Bioinform. 26(9): 1232-1238 (2010) - [j38]Andreas Hildebrandt, Anna Katharina Dehof, Alexander Rurainski, Andreas Bertsch, Marcel Schumann, Nora C. Toussaint, Andreas Moll, Daniel Stöckel, Stefan Nickels, Sabine C. Mueller, Hans-Peter Lenhof, Oliver Kohlbacher:
BALL - biochemical algorithms library 1.3. BMC Bioinform. 11: 531 (2010) - [j37]Nora C. Toussaint, Christian Widmer, Oliver Kohlbacher, Gunnar Rätsch:
Exploiting physico-chemical properties in string kernels. BMC Bioinform. 11(S-8): S7 (2010) - [j36]Nina M. Fischer, Wolfgang M. Schneider, Oliver Kohlbacher:
Rescoring of docking poses using force field-based methods. J. Cheminformatics 2(S-1): 52 (2010) - [j35]Sebastian Briesemeister, Jörg Rahnenführer, Oliver Kohlbacher:
YLoc - an interpretable web server for predicting subcellular localization. Nucleic Acids Res. 38(Web-Server-Issue): 497-502 (2010) - [j34]Marc Röttig, Christian Rausch, Oliver Kohlbacher:
Combining Structure and Sequence Information Allows Automated Prediction of Substrate Specificities within Enzyme Families. PLoS Comput. Biol. 6(1) (2010) - [c22]Sandra Gesing, Jano I. van Hemert, Jos Koetsier, Andreas Bertsch, Oliver Kohlbacher:
TOPP goes Rapid The OpenMS Proteomics Pipeline in a Grid-Enabled Web Portal. CCGRID 2010: 598-599 - [c21]Carsten Henneges, Marc Röttig, Oliver Kohlbacher, Andreas Zell:
Graphlet Data Mining of Energetical Interaction Patterns in Protein 3D Structures. IJCCI (ICFC-ICNC) 2010: 190-195 - [c20]Christian Widmer, Nora C. Toussaint, Yasemin Altun, Oliver Kohlbacher, Gunnar Rätsch:
Novel Machine Learning Methods for MHC Class I Binding Prediction. PRIB 2010: 98-109 - [c19]Georg Birkenheuer, Sebastian Breuers, André Brinkmann, Dirk Blunk, Gregor Fels, Sandra Gesing, Sonja Herres-Pawlis, Oliver Kohlbacher, Jens Krüger, Lars Packschies:
Grid-Workflows in Molecular Science. Software Engineering (Workshops) 2010: 177-184 - [p1]Knut Reinert, Oliver Kohlbacher:
OpenMS and TOPP: Open Source Software for LC-MS Data Analysis. Proteome Bioinformatics 2010: 201-211
2000 – 2009
- 2009
- [j33]Sebastian J. Schultheiß, Wolfgang Busch, Jan U. Lohmann, Oliver Kohlbacher, Gunnar Rätsch:
KIRMES: kernel-based identification of regulatory modules in euchromatic sequences. Bioinform. 25(16): 2126-2133 (2009) - [j32]Magdalena Feldhahn, Pierre Dönnes, Philipp Thiel, Oliver Kohlbacher:
FRED - a framework for T-cell epitope detection. Bioinform. 25(20): 2758-2759 (2009) - [j31]Andreas Keller, Christina Backes, Andreas Gerasch, Michael Kaufmann, Oliver Kohlbacher, Eckart Meese, Hans-Peter Lenhof:
A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis. Bioinform. 25(21): 2787-2794 (2009) - [j30]Sebastian J. Schultheiß, Wolfgang Busch, Jan U. Lohmann, Oliver Kohlbacher, Gunnar Rätsch:
KIRMES: kernel-based identification of regulatory modules in euchromatic sequences. BMC Bioinform. 10(S-13): 0 (2009) - [j29]Torsten Blum, Sebastian Briesemeister, Oliver Kohlbacher:
MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. BMC Bioinform. 10: 274 (2009) - [j28]Andreas Dräger, Marcel Kronfeld, Michael J. Ziller, Jochen Supper, Hannes Planatscher, Jørgen B. Magnus, Marco Oldiges, Oliver Kohlbacher, Andreas Zell:
Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. BMC Syst. Biol. 3: 5 (2009) - [j27]Nora C. Toussaint, Oliver Kohlbacher:
OptiTope - a web server for the selection of an optimal set of peptides for epitope-based vaccines. Nucleic Acids Res. 37(Web-Server-Issue): 617-622 (2009) - [c18]Ernst Althaus, Gunnar W. Klau, Oliver Kohlbacher, Hans-Peter Lenhof, Knut Reinert:
Integer Linear Programming in Computational Biology. Efficient Algorithms 2009: 199-218 - [c17]Mario Albrecht, Andreas Kerren, Karsten Klein, Oliver Kohlbacher, Petra Mutzel, Wolfgang Paul, Falk Schreiber, Michael Wybrow:
On Open Problems in Biological Network Visualization. GD 2009: 256-267 - [c16]Sandra Gesing, Oliver Kohlbacher, Jano I. van Hemert:
Portals for Life Sciences - a Brief Introduction. IWPLS 2009 - 2008
- [j26]Torsten Blum, Oliver Kohlbacher:
MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization. Bioinform. 24(18): 2108-2109 (2008) - [j25]Andreas Keller, Christina Backes, Maher Al-Awadhi, Andreas Gerasch, Jan Küntzer, Oliver Kohlbacher, Michael Kaufmann, Hans-Peter Lenhof:
GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments. BMC Bioinform. 9 (2008) - [j24]Ole Schulz-Trieglaff, Nico Pfeifer, Clemens Gröpl, Oliver Kohlbacher, Knut Reinert:
LC-MSsim - a simulation software for liquid chromatography mass spectrometry data. BMC Bioinform. 9 (2008) - [j23]Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, Oliver Kohlbacher:
OpenMS - An open-source software framework for mass spectrometry. BMC Bioinform. 9 (2008) - [j22]Wiebke Timm, Alexandra Scherbart, Sebastian Böcker, Oliver Kohlbacher, Tim W. Nattkemper:
Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics. BMC Bioinform. 9 (2008) - [j21]Torsten Blum, Oliver Kohlbacher:
Using Atom Mapping Rules for an Improved Detection of Relevant Routes in Weighted Metabolic Networks. J. Comput. Biol. 15(6): 565-576 (2008) - [j20]Andreas Kerzmann, Jan Fuhrmann, Oliver Kohlbacher, Dirk Neumann:
BALLDock/SLICK: A New Method for Protein-Carbohydrate Docking. J. Chem. Inf. Model. 48(8): 1616-1625 (2008) - [j19]Magdalena Feldhahn, Philipp Thiel, Mathias M. Schuler, Nina Hillen, Stefan Stevanovic, Hans-Georg Rammensee, Oliver Kohlbacher:
EpiToolKit - a web server for computational immunomics. Nucleic Acids Res. 36(Web-Server-Issue): 519-522 (2008) - [j18]Nora C. Toussaint, Pierre Dönnes, Oliver Kohlbacher:
A Mathematical Framework for the Selection of an Optimal Set of Peptides for Epitope-Based Vaccines. PLoS Comput. Biol. 4(12) (2008) - [c15]Sebastian J. Schultheiß, Wolfgang Busch, Jan U. Lohmann, Oliver Kohlbacher, Gunnar Rätsch:
KIRMES: Kernel-based Identification of Regulatory Modules in Euchromatic Sequences. German Conference on Bioinformatics 2008: 158-167 - [c14]Nico Pfeifer, Oliver Kohlbacher:
Multiple Instance Learning Allows MHC Class II Epitope Predictions Across Alleles. WABI 2008: 210-221 - [e5]Christian G. Huber, Oliver Kohlbacher, Michal Linial, Kathrin Marcus, Knut Reinert:
Computational Proteomics, 02.03. - 07.03.2008. Dagstuhl Seminar Proceedings 08101, Internationales Begegnungs- und Forschungszentrum für Informatik (IBFI), Schloss Dagstuhl, Germany 2008 [contents] - [e4]Stephen P. Borgatti, Stephen G. Kobourov, Oliver Kohlbacher, Petra Mutzel:
Graph Drawing with Applications to Bioinformatics and Social Sciences, 04.05. - 09.05.2008. Dagstuhl Seminar Proceedings 08191, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, Germany 2008 [contents] - [i9]Mario Albrecht, Alejandro Estrella-Balderrama, Markus Geyer, Carsten Gutwenger, Karsten Klein, Oliver Kohlbacher, Michael Schulz:
08191 Working Group Summary - Visually Comparing a Set of Graphs. Graph Drawing with Applications to Bioinformatics and Social Sciences 2008 - [i8]Stephen P. Borgatti, Stephen G. Kobourov, Oliver Kohlbacher, Petra Mutzel:
08191 Abstracts Collection - Graph Drawing with Applications to Bioinformatics and Social Sciences. Graph Drawing with Applications to Bioinformatics and Social Sciences 2008 - [i7]Stephen P. Borgatti, Stephen G. Kobourov, Oliver Kohlbacher, Petra Mutzel:
08191 Executive Summary - Graph Drawing with Applications to Bioinformatics and Social Sciences. Graph Drawing with Applications to Bioinformatics and Social Sciences 2008 - [i6]Knut Reinert, Christian G. Huber, Kathrin Marcus, Michal Linial, Oliver Kohlbacher:
08101 Abstracts Collection - Computational Proteomics. Computational Proteomics 2008 - 2007
- [j17]Andreas Hildebrandt, Ralf Blossey, Sergej Rjasanow, Oliver Kohlbacher, Hans-Peter Lenhof:
Electrostatic potentials of proteins in water: a structured continuum approach. Bioinform. 23(2): 99-103 (2007) - [j16]Oliver Kohlbacher, Knut Reinert, Clemens Gröpl, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Marc Sturm:
TOPP - the OpenMS proteomics pipeline. Bioinform. 23(2): 191-197 (2007) - [j15]Hagit Shatkay, Annette Höglund, Scott Brady, Torsten Blum, Pierre Dönnes, Oliver Kohlbacher:
SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data. Bioinform. 23(11): 1410-1417 (2007) - [j14]Jan Küntzer, Christina Backes, Torsten Blum, Andreas Gerasch, Michael Kaufmann, Oliver Kohlbacher, Hans-Peter Lenhof:
BNDB - The Biochemical Network Database. BMC Bioinform. 8 (2007) - [j13]Nico Pfeifer, Andreas Leinenbach, Christian G. Huber, Oliver Kohlbacher:
Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics. BMC Bioinform. 8 (2007) - [j12]Jan Küntzer, Benny Kneissl, Oliver Kohlbacher, Hans-Peter Lenhof:
Abstract analysis of pathways using the BN++ software framework. BMC Syst. Biol. 1(S-1): P24 (2007) - [c13]Torsten Blum, Oliver Kohlbacher:
Finding Relevant Biotransformation Routes in Weighted Metabolic Networks. German Conference on Bioinformatics 2007: 30-44 - 2006
- [j11]Andreas Moll, Andreas Hildebrandt, Hans-Peter Lenhof, Oliver Kohlbacher:
BALLView: a tool for research and education in molecular modeling. Bioinform. 22(3): 365-366 (2006) - [j10]Annette Höglund, Pierre Dönnes, Torsten Blum, Hans-Werner Adolph, Oliver Kohlbacher:
MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition. Bioinform. 22(10): 1158-1165 (2006) - [j9]Dirk Neumann, Oliver Kohlbacher, Christian Merkwirth, Thomas Lengauer:
A Fully Computational Model for Predicting Percutaneous Drug Absorption. J. Chem. Inf. Model. 46(1): 424-429 (2006) - [j8]Andreas Kerzmann, Dirk Neumann, Oliver Kohlbacher:
SLICK - Scoring and Energy Functions for Protein-Carbohydrate Interactions. J. Chem. Inf. Model. 46(4): 1635-1642 (2006) - [j7]Jan Küntzer, Torsten Blum, Andreas Gerasch, Christina Backes, Andreas Hildebrandt, Michael Kaufmann, Oliver Kohlbacher, Hans-Peter Lenhof:
BN++ - A Biological Information System. J. Integr. Bioinform. 3(2) (2006) - [j6]Pierre Dönnes, Oliver Kohlbacher:
SVMHC: a server for prediction of MHC-binding peptides. Nucleic Acids Res. 34(Web-Server-Issue): 194-197 (2006) - [c12]Annette Höglund, Torsten Blum, Scott Brady, Pierre Dönnes, John San Miguel, Matthew Rocheford, Oliver Kohlbacher, Hagit Shatkay:
Significantly Improved Prediction of Subcellular Localization by Integrating Text and Protein Sequence Data . Pacific Symposium on Biocomputing 2006: 16-27 - [c11]Eva Lange, Clemens Gröpl, Knut Reinert, Oliver Kohlbacher, Andreas Hildebrandt:
High-Accuracy Peak Picking of Proteomics Data Using Wavelet Techniques. Pacific Symposium on Biocomputing 2006: 243-254 - [e3]Christian G. Huber, Oliver Kohlbacher, Knut Reinert:
Computational Proteomics, 20.-25. November 2005. Dagstuhl Seminar Proceedings 05471, Internationales Begegnungs- und Forschungszentrum für Informatik (IBFI), Schloss Dagstuhl, Germany 2006 [contents] - [e2]Daniel H. Huson, Oliver Kohlbacher, Andrei N. Lupas, Kay Nieselt, Andreas Zell:
German Conference on Bioinformatics GCB 2006, 19.09. 2006 - 22.09. 2006 in Tübingen, Germany. LNI P-83, GI 2006, ISBN 978-3-88579-177-5 [contents] - 2005
- [j5]Andreas Moll, Andreas Hildebrandt, Hans-Peter Lenhof, Oliver Kohlbacher:
BALLView: An object-oriented molecular visualization and modeling framework. J. Comput. Aided Mol. Des. 19(11): 791-800 (2005) - [c10]Clemens Gröpl, Eva Lange, Knut Reinert, Oliver Kohlbacher, Marc Sturm, Christian G. Huber, Bettina M. Mayr, Christoph L. Klein:
Algorithms for the Automated Absolute Quantification of Diagnostic Markers in Complex Proteomics Samples. CompLife 2005: 151-162 - [c9]Annette Höglund, Pierre Dönnes, Torsten Blum, Hans-Werner Adolph, Oliver Kohlbacher:
Using N-terminal targeting sequences, amino acid composition, and sequence motifs for predicting protein subcellular localizations. German Conference on Bioinformatics 2005: 45-59 - [c8]Jochen Supper, Pierre Dönnes, Oliver Kohlbacher:
Analysis of MHC-Peptide Binding Using Amino Acid Property-Based Decision Rules. ICAPR (1) 2005: 446-453 - [e1]Michael R. Berthold, Robert C. Glen, Kay Diederichs, Oliver Kohlbacher, Ingrid Fischer:
Computational Life Sciences, First International Symposium, CompLife 2005, Konstanz, Germany, September 25-27, 2005, Proceedings. Lecture Notes in Computer Science 3695, Springer 2005, ISBN 3-540-29104-0 [contents] - [i5]Nathanaël Delmotte, Bettina M. Mayr, Andreas Leinenbach, Knut Reinert, Oliver Kohlbacher, Christoph L. Klein, Christian G. Huber:
Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins. Computational Proteomics 2005 - [i4]Christian G. Huber, Oliver Kohlbacher, Knut Reinert:
05471 Executive Summary - Computational Proteomics. Computational Proteomics 2005 - [i3]Christian G. Huber, Oliver Kohlbacher, Knut Reinert:
05471 Abstract Collection - Computational Proteomics. Computational Proteomics 2005 - [i2]Eva Lange, Clemens Gröpl, Oliver Kohlbacher, Andreas Hildebrandt:
High-accuracy peak picking of proteomics data. Computational Proteomics 2005 - [i1]Marc Sturm, Sascha Quinten, Christian G. Huber, Oliver Kohlbacher:
A machine learning approach for prediction of DNA and peptide retention times. Computational Proteomics 2005 - 2004
- [j4]Oliver Kohlbacher, Knut Reinert:
Differenzielle Proteomanalyse - Experimentelle Methoden, algorithmische Herausforderungen (Differential Analysis in Proteomics: Experimental Methods, Algorithmic Challenges). it Inf. Technol. 46(1): 31-38 (2004) - 2003
- [c7]Liliana Florea, Bjarni V. Halldórsson, Oliver Kohlbacher, Russell Schwartz, Stephen Hoffman, Sorin Istrail:
Epitope Prediction Algorithms for Peptide based Vaccine Design. CSB 2003: 17-26 - 2002
- [j3]Ernst Althaus, Oliver Kohlbacher, Hans-Peter Lenhof, Peter Müller:
A Combinatorial Approach to Protein Docking with Flexible Side Chains. J. Comput. Biol. 9(4): 597-612 (2002) - [c6]Marite Sirava, T. Schäfer, Markus Eiglsperger, Michael Kaufmann, Oliver Kohlbacher, Erich Bornberg-Bauer, Hans-Peter Lenhof:
BioMiner - modeling, analyzing, and visualizing biochemical pathways and networks. ECCB 2002: 219-230 - 2001
- [b1]Oliver Kohlbacher:
New approaches to protein docking. Saarland University, Germany, 2001 - [c5]Russell J. Turner, Kabir Chaturvedi, Nathan Edwards, Daniel P. Fasulo, Aaron L. Halpern, Daniel H. Huson, Oliver Kohlbacher, Jason R. Miller, Knut Reinert, Karin A. Remington, Russell Schwartz, Brian Walenz, Shibu Yooseph, Sorin Istrail:
Visualization challenges for a new cyberpharmaceutical computing paradigm. IEEE Symposium on Parallel and Large-Data Visualization and Graphics 2001: 7-18 - [c4]Oliver Kohlbacher, Andreas Burchardt, Andreas Moll, Andreas Hildebrandt, Peter Bayer, Hans-Peter Lenhof:
A NMR-spectra-based scoring function for protein docking. RECOMB 2001: 184-192 - 2000
- [j2]Oliver Kohlbacher, Hans-Peter Lenhof:
BALL-rapid software prototyping in computational molecular biology. Bioinform. 16(9): 815-824 (2000) - [j1]Nicolas Boghossian, Oliver Kohlbacher, Hans-Peter Lenhof:
Rapid Software Prototyping in Molecular Modeling Using the Biochemical Algorithms Library (BALL). ACM J. Exp. Algorithmics 5: 16 (2000) - [c3]Ernst Althaus, Oliver Kohlbacher, Hans-Peter Lenhof, Peter Müller:
A combinatorial approach to protein docking with flexible side-chains. RECOMB 2000: 15-24
1990 – 1999
- 1999
- [c2]Oliver Kohlbacher, Hans-Peter Lenhof:
Rapid Software Prototyping in Computational Molecular Biology. German Conference on Bioinformatics 1999: 81-92 - [c1]Nicolas Boghossian, Oliver Kohlbacher, Hans-Peter Lenhof:
BALL: Biochemical Algorithms Library. WAE 1999: 331-345
Coauthor Index
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