Publications

380 entries « 6 of 8 »

Briesemeister, Sebastian; Rahnenführer, Jörg; Kohlbacher, Oliver

Going from where to why - interpretable prediction of protein subcellular localization

Bioinformatics, 26 (9), pp. 1232-1238, 2010.

(Abstract | Links | BibTeX)

Briesemeister, Sebastian; Rahnenführer, Jörg; Kohlbacher, Oliver

YLoc – an interpretable web server for predicting subcellular localization

Nucl. Acids Res., 38 , pp. W497-W502, 2010.

(Abstract | Links | BibTeX)

Widmer, Christian; Toussaint, Nora C; Altun, Yasemin; Kohlbacher, Oliver; Rätsch, Gunnar

Novel Machine Learning Methods for MHC Class I Binding Prediction

Pattern Recognition in Bioinformatics 5th IAPR International Conference, PRIB 2010, Nijmegen, The Netherlands, September 22-24, 2010. Proceedings, pp. 98-109, Springer, 2010.

(Abstract | Links | BibTeX)

Widmer, Christian; Altun, Yasemin; Toussaint, Nora C; Rätsch, Gunnar

Inferring Latent Task Structure for Multi-Task Learning via Multiple Kernel Learning

BMC Bioinformatics, 11 (Suppl 8), pp. S5, 2010.

(Abstract | Links | BibTeX)

Toussaint, Nora C; Widmer, Christian; Kohlbacher, Oliver; Rätsch, Gunnar

Exploiting Physico-Chemical Properties in String Kernels

BMC Bioinformatics, 11 (Suppl 8), pp. S7, 2010.

(Abstract | Links | BibTeX)

Gesing, Sandra; van Hemert, Jano; Koetsier, Jos; Bertsch, Andreas; Kohlbacher, Oliver

TOPP goes Rapid—The OpenMS Proteomics Pipeline in a Grid-enabled Web Portal

10th IEEE/ACM Internactional Conference on Cluster, Cloud, and Grid Computing (ccgrid 2010), pp. 598-599, IEEE/ACM ACM, 2010.

(Abstract | Links | BibTeX)

Zhang, Fajun; Weggler, Sophie; Ziller, Michael J; Ianeselli, Luca; Heck, B S; Hildebrandt, Andreas; Kohlbacher, Oliver; Skoda, Maxwell W A; Jacobs, Robert M J; Schreiber, Frank

On the Universality of Protein Reentrant Condensation in Solution Induced by Multivalent Metal Ions

PROTEINS: Structure, Function, Bioinformatics, 78 (16), pp. 3450–3457, 2010.

(Abstract | Links | BibTeX)

Birkenheuer, Georg; Breuers, Sebastian; Brinkmann, Andre; Blunk, Dirk; Fels, Gregor; Gesing, Sandra; Herres-Pawlis, Sonja; Kohlbacher, Oliver; Krüger, Jens; Packschies, Lars

Grid-Workflows in Molecular Science

Lecture Notes in Informatics, pp. 177-184, 2010.

(Abstract | Links | BibTeX)

Gesing, Sandra; Marton, Istvan; Birkenheuer, Georg; Schuller, Bernd; Grunzke, Richard; Krüger, Jens; Breuers, Sebastian; Blunk, Dirk; Fels, Gregor; Packschies, Lars; Brinkmann, Andre; Kohlbacher, Oliver; Kozlovszky, Miklos

Workflow Interoperability in a Grid Portal for Molecular Simulations

Proceedings of the International Worshop on Science Gateways (IWSG2010), pp. 44-48, Consorzio COMETA 2010.

(Abstract | BibTeX)

Wewior, Martin; Packschies, Lars; Blunk, Dirk; Wickeroth, Daniel; Warzecha, Klaus; Herres-Pawlis, Sonja; Gesing, Sandra; Breuers, Sebastian; Krüger, Jens; Birkenheuer, Georg; Lang, Ulrich

The MoSGrid Gaussian portlet -- Technologies for Implementation of Portlets for Molecular Simulations

Proceedings of the International Worshop on Science Gateways (IWSG2010), pp. 39-43, Consorzio COMETA 2010.

(Abstract | BibTeX)

Hildebrandt, Andreas; Dehof, Anna Katharina; Rurainski, Alexander; Bertsch, Andreas; Schumann, Marcel; Toussaint, Nora C; Moll, Andreas; Stöckel, Daniel; Nickels, Stefan; Mueller, Sabine C; Lenhof, Hans-Peter; Kohlbacher, Oliver

BALL - Biochemical Algorithms Library 1.3

BMC Bioinformatics, 11 , pp. 531, 2010.

(Abstract | Links | BibTeX)

Henneges, Carsten; Röttig, Marc; Kohlbacher, Oliver; Zell, Andreas

Graphlet Data Mining of Energetical Interaction Patterns in Protein 3D Structures

Proceedings of the International Conference on Fuzzy Computation and 2nd International Conference on Neural Computation, SciTePress, 2010.

(Abstract | Links | BibTeX)

Trusch, A; Ehlert, S; Bertsch, A; Kohlbacher, O; Hildebrand, D; Schlüter, H; Tallarek, U

Improved particle-packed HPLC/MS microchips for proteomic analysis

J. Pep. Sci, 33 (21), pp. 3283-91, 2010.

(Abstract | Links | BibTeX)

Neumann, Dirk; Kohlbacher, Oliver

Structural Glycomics – Molecular Details of Protein-Carbohydrate Interactions and their Prediction

Hicks, Martin G; Kettner, Carsten (Ed.): Proceedings of the International Beilstein Symposium on Glyco-Bioinformatics, Beilstein-Institut, Frankfurt, Germany, 2010.

(Abstract | Links | BibTeX)

Venturelli, S; von Horn, K; Berger, A; Weiland, T; Smirnow, I; Schenk, A; Weiss, T S; Kämper, A; Kohlbacher, O; Gregor, M; Lauer, U M; Bitzer, M

Identifikation und präklinische Charakterisierung neuartiger epigenetischer Wirkstoffe zur Behandlung therapieresistenter Tumore am Beispiel des Hepatozellulären Karzinoms

Z Gastroenterol, 47 (06), pp. P1_13, 2009.

(Abstract | BibTeX)

Rätsch, Gunnar; Lohmann, Jan U; Kohlbacher, Oliver; Schultheiss, Sebastian J; Busch, Wolfgang

KIRMES: kernel-based identification of regulatory modules in euchromatic sequences

Bioinformatics, 25 (16), pp. 2126-2133, 2009, ISSN: 1367-4803.

(Abstract | Links | BibTeX)

Dräger, Andreas; Kronfeld, Marcel; Ziller, Michael J; Supper, Jochen; Planatscher, Hannes; Magnus, Jørgen B; Oldiges, Marco; Kohlbacher, Oliver; Zell, Andreas

Modeling Metabolic Networks in C. glutamicum: A Comparison of Rate Laws in Combination with Various Parameter Optimization Strategies

BMC Systems Biology, 3 , pp. 5, 2009.

(Abstract | Links | BibTeX)

Mitschke, Jan; Fuss, Janina; Blum, Torsten; Höglund, Annette; Reski, Ralf; Kohlbacher, Oliver; Rensing, Stefan

Prediction of dual protein targeting to plant organelles

New Phytologist, 183 (1), pp. 224-236, 2009.

(Abstract | Links | BibTeX)

Malisi, Christoph; Kohlbacher, Oliver; Höcker, Birte

Automated scaffold selection for enzyme design

PROTEINS: Structure, Function, and Bioinformatics, 77 (1), pp. 74-83, 2009.

(Abstract | Links | BibTeX)

Toussaint, Nora C; Kohlbacher, Oliver

OptiTope - A Web Server for the Selection of an Optimal Set of Peptides for Epitope-based Vaccines

Nucl. Acids Res., 37 , pp. W617-22, 2009.

(Abstract | Links | BibTeX)

Schultheiss, Sebastian J; Busch, Wolfgang; Lohmann, Jan U; Kohlbacher, Oliver; Rätsch, Gunnar

KIRMES: Kernel-based identification of regulatory modules in euchromatic sequences

Bioinformatics, 25 (16), pp. 2126-33, 2009.

(Links | BibTeX)

Nahnsen, Sven; Nordheim, Alfred; Kohlbacher, Oliver

A geometric matching approach improves throughput and accurary in DIGE based proteomics

Proceedings of the sixth International Workshop on Computational Systems Biology (WCSB 2009), pp. 123-126, Tampere International Center for Signal Processing WCSB 2009, 2009.

(Abstract | Links | BibTeX)

Sturm, Marc; Kohlbacher, Oliver

TOPPView: An Open-Source Viewer for Mass Spectrometry Data

J. Proteome Res., 8 (7), pp. 3760-3, 2009.

(Abstract | Links | BibTeX)

Pfeifer, Nico; Leinenbach, Andreas; Huber, Christian G; Kohlbacher, Oliver

Improving Peptide Identification in Proteome Analysis by a Two-Dimensional Retention Time Filtering Approach

J. Proteome Res., 8 (8), pp. 4109-15, 2009.

(Abstract | Links | BibTeX)

Feldhahn, Magdalena; Dönnes, Pierre; Thiel, Philipp; Kohlbacher, Oliver

FRED - A Framework for T-cell Epitope Detection

Bioinformatics, 25 (20), pp. 2758-9, 2009.

(Abstract | Links | BibTeX)

Bertsch, Andreas; Leinenbach, Andreas; Pervukhin, Anton; Lubeck, Markus; Hartmer, Ralf; Baessmann, Carsten; Elnakady, Yasser Abbas; Müller, Rolf; Böcker, Sebastian; Huber, Christian G; Kohlbacher, Oliver

De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation

Electrophoresis, 30 (21), pp. 3736-3747, 2009.

(Abstract | Links | BibTeX)

Keller, Andreas; Backes, Christina; Gerasch, Andreas; Kaufmann, Michael; Kohlbacher, Oliver; Lenhof, Hans-Peter

A novel algorithm for detecting differentially regulated paths based on Gene Set Enrichment Analysis

Bioinformatics, 25 (21), pp. 2787-94, 2009.

(Abstract | Links | BibTeX)

Blum, Torsten; Briesemeister, Sebastian; Kohlbacher, Oliver

MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction

BMC Bioinformatics, 10 , pp. 274, 2009.

(Abstract | Links | BibTeX)

Schneeberger, Korbinian; Hagmann, Jörg; Ossowski, Stephan; Warthmann, Norman; Gesing, Sandra; Kohlbacher, Oliver; Weigel, Detlef

Simultaneous alignment of short reads against multiple genomes

Genome Biology, 10 (9), pp. R98, 2009.

(Abstract | Links | BibTeX)

Böcker, Sebastian; Briesemeister, Sebastian; Klau, Gunnar W

On Optimal Comparability Editing with Applications to Molecular Diagnostics

BMC Bioinformatics, 10 (Suppl 1), pp. S61, 2009.

(Abstract | Links | BibTeX)

Böcker, Sebastian; Briesemeister, Sebastian; Bui, Quang BaoAnh; Truss, Anke

Going Weighted: Parameterized Algorithms for Cluster Editing

Theoretical Computer Science, 410 (52), pp. 5467-5480, 2009, (This is an extended version of two articles published in the Proc. of the 6th Asia Pacific Bioinformatics Conference, APBC 2008, in: Series on Advances in Bioinformatics and Computational Biology, vol. 5, Imperial College Press, pp. 211–220; and Proc. of the 2nd Conference on Combinatorial Optimization and Applications, COCOA 2008, in: LNCS, vol. 5038, Springer, pp. 289–302.).

(Abstract | Links | BibTeX)

Toussaint, Nora C; Kohlbacher, Oliver

Towards in silico design of epitope-based vaccines

Expert Opinion on Drug Discovery, 4 (10), pp. 1047-1060, 2009.

(Abstract | Links | BibTeX)

Althaus, Ernst; Klau, Gunnar W; Kohlbacher, Oliver; Lenhof, Hans-Peter; Reinert, Knut

Integer Linear Programming in Computational Biology

Efficient Algorithms, pp. 199-218, Springer, 2009.

(Abstract | Links | BibTeX)

Briesemeister, Sebastian; Blum, Torsten; Brady, Scott; Lam, Yin; Kohlbacher, Oliver; Shatkay, Hagit

SherLoc2: a high-accuracy hybrid method for predicting subcellular localization of proteins

J. Proteome Res., 8 (11), pp. 5363–5366, 2009.

(Abstract | Links | BibTeX)

Ahrends, Robert; Lichtner, Björn; Bertsch, Andreas; Kohlbacher, Oliver; Trusch, Maria; Schlüter, Hartmut

Application of displacement chromatography for the proteome analysis of a human plasma protein fraction

J. Chromatogr. A, 1217 (19), pp. 3321-9, 2009.

(Abstract | Links | BibTeX)

Toussaint, Nora; Kohlbacher, Oliver; Rätsch, Gunnar

Exploiting Physico-Chemical Properties in String-Kernels

MLCB 2009 (accepted), 2009.

(BibTeX)

Kohlbacher, Oliver; Reinert, Knut

OpenMS and TOPP: Open Source Software for LC-MS Data Analysis

Hubbard, Simon J; Jones, Andrew R (Ed.): Proteome Bioinformatics, 604 , pp. 201-11, Humana Press, 2009.

(Abstract | Links | BibTeX)

Peifer, Christian; Urich, Robert; Schattel, Verena; Abdaleh, Mohammed; Röttig, Marc; Kohlbacher, Oliver; Laufer, Stefan

Implications for selectivity of 3,4-diarylquinolinones as p38aMAP kinase inhibitors

Bioorg. Med. Chem. Lett., 18 (4), pp. 1431-1435, 2008.

(Links | BibTeX)

Sturm, Marc; Bertsch, Andreas; Gröpl, Clemens; Hildebrandt, Andreas; Hussong, Rene; Lange, Eva; Pfeifer, Nico; Schulz-Trieglaff, Ole; Zerck, Alexandra; Reinert, Knut; Kohlbacher, Oliver

OpenMS - An open-source software framework for mass spectrometry

BMC Bioinformatics, 9 , pp. 163, 2008.

(Links | BibTeX)

Feldhahn, Magdalena; Thiel, Philipp; Schuler, Mathias; Hillen, Nina; Stevanovic, Stefan; Rammensee, Hans-Georg; Kohlbacher, Oliver

EpiToolKit - A web server for computational immunomics

Nucleic Acids Res., 36 , pp. W519-22, 2008.

(Abstract | Links | BibTeX)

Blum, Torsten; Kohlbacher, Oliver

Using atom mapping rules for an improved detection of relevant routes in weighted metabolic networks

J. Comput. Biol., 15 (6), pp. 565-576, 2008.

(Links | BibTeX)

Kerzmann, Andreas; Fuhrmann, Jan; Kohlbacher, Oliver; Neumann, Dirk

BALLDock/SLICK: A new Method for Protein-Carbohydrate Docking

J. Chem. Inf. Model., 48 (8), pp. 1616-1625, 2008.

(Links | BibTeX)

Schultheiss, Sebastian J; Busch, Wolfgang; Lohmann, Jan U; Kohlbacher, Oliver; Rätsch, Gunnar

KIRMES: Kernel-based Identification of Regulatory Modules in Euchromatic Sequences

Beyer, A; Schroeder, M (Ed.): Proc. German Conference Bioinformatikcs (GCB 2008), pp. 158-167, GI, 2008.

(Links | BibTeX)

Borgatti, Stephen; Kobourov, Stephen; Kohlbacher, Oliver; Mutzel, Petra

08191 Abstracts Collection -- Graph Drawing with Applications to Bioinformatics and Social Sciences

Borgatti, Stephen P; Kobourov, Stephen; Kohlbacher, Oliver; Mutzel, Petra (Ed.): Graph Drawing with Applications to Bioinformatics and Social Sciences, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany, Dagstuhl, Germany, 2008.

(Links | BibTeX)

Borgatti, Stephen; Kobourov, Stephen; Kohlbacher, Oliver; Mutzel, Petra

08191 Executive Summary -- Graph Drawing with Applications to Bioinformatics and Social Sciences

Borgatti, Stephen P; Kobourov, Stephen; Kohlbacher, Oliver; Mutzel, Petra (Ed.): Graph Drawing with Applications to Bioinformatics and Social Sciences, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany, Dagstuhl, Germany, 2008.

(Links | BibTeX)

Albrecht, Mario; Estrella-Balderrama, Alejandro; Geyer, Markus; Gutwenger, Carsten; Klein, Karsten; Kohlbacher, Oliver; Schulz, Michael

08191 Working Group Summary -- Visually Comparing a Set of Graphs

Borgatti, Stephen P; Kobourov, Stephen; Kohlbacher, Oliver; Mutzel, Petra (Ed.): Graph Drawing with Applications to Bioinformatics and Social Sciences, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany, Dagstuhl, Germany, 2008.

(Links | BibTeX)

Pfeifer, Nico; Kohlbacher, Oliver

Multiple Instance Learning Allows MHC Class II Epitope Predictions across Alleles

Crandall, K A; Lagergren, J (Ed.): Proceedings of the 8th Workshop on Algorithms in Bioinformatics (WABI 2008), Lecture Note in Bioinformatics vol. 5251, pp. 210-221, Springer, 2008.

(Links | BibTeX)

Zhang, Fajun; Skoda, Maximilian W A; Jacobs, Robert M J; Zorn, S; Martin, R A; Martin, C M; Clark, G F; Weggler, Sophie; Hildebrandt, Andreas; Kohlbacher, Oliver; Schreiber, Frank

Reentrant Condensation of Proteins ins Solution Induced by Multivalent Counterions

Phys. Rev. Lett., 101 (14), pp. 148101, 2008.

(Links | BibTeX)

Schulz-Trieglaff, Ole; Pfeifer, Nico; Gröpl, Clemens; Kohlbacher, Oliver; Reinert, Knut

LC-MSsim - a simulation software for Liquid ChromatographyMass Spectrometry data

BMC Bioinformatics, 9 , pp. 423, 2008.

(Abstract | Links | BibTeX)

Toussaint, Nora C; Dönnes, Pierre; Kohlbacher, Oliver

A Mathematical Framework for the Selection of an Optimal Set of Peptides for Epitope-based Vaccines

PLoS Comput. Biol., 4 (12), pp. e1000246, 2008.

(Links | BibTeX)

380 entries « 6 of 8 »

You hereby assure to have read and agree to our GDPR Disclaimer (Datenschutzerklärung).

GDPR Disclaimer

The cookie settings on this website are set to "allow cookies" to give you the best browsing experience possible. If you continue to use this website without changing your cookie settings or you click "Accept" below then you are consenting to this.

Close