Publications

301 entries « 3 of 7 »

Wagner, Robert; Li, Jia; Kenar, Erhan; Kohlbacher, Oliver; Machicao, Fausto; Häring, Hans-Ulrich; Fritsche, Andreas; Xu, Guowang; Lehmann, Rainer

Clinical and non-targeted metabolomic profiling of homozygous carriers of Transcription Factor 7-like 2 variant rs7903146

Sci. Rep., 4 , pp. 5296, 2014.

(Abstract | Links | BibTeX)

Krüger, Jens; Grunzke, Richard; Herres-Pawlies, Sonja; de la Garza, Luis; Kohlbacher, Oliver; Nagel, Wolfgang E; Gesing, Sandra

Performance Studies on Distributed Virtual Screening

Biomed Res Int, 2014 , pp. 624024, 2014.

(Abstract | Links | BibTeX)

Griss, Johannes; Jones, Andrew R; Sachsenberg, Timo; Walzer, Mathias; Gatto, Laurent; Hartler, Jürgen; Thallinger, Gerhard G; Salek, Reza M; Steinbeck, Christhop; Neuhauser, Nadin; Cox, Jürgen; Neumann, Steffen; Fan, Jun; Reisinger, Florian; Xu, Qing-Wei; Bandeira, Nuno; Xenarios, Ioannis; Kohlbacher, Oliver; Vizcaino, Juan Antonio; Hermjakob, Henning

The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience

Mol. Cell. Prot., pp. mcp.O113.036681, 2014.

(Abstract | Links | BibTeX)

Kramer, Katharina; Sachsenberg, Timo; Beckmann, Benedict M; Qamar, Saadia; Boon, Kum-Loong; Hentze, Matthias W; Kohlbacher, Oliver; Urlaub, Henning

Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins

Nat. Methods, 11 (10), pp. 1064-70, 2014.

(Abstract | Links | BibTeX)

Szolek, Andras; Schubert, Benjamin; Mohr, Christopher; Sturm, Marc; Feldhahn, Magdalena; Kohlbacher, Oliver

OptiType: precision HLA typing from next-generation sequencing data

Bioinformatics, 30 (23), pp. 3310-6, 2014.

(Abstract | Links | BibTeX)

Thiel, Philipp; Sach-Peltason, Lisa; Ottmann, Christian; Kohlbacher, Oliver

Blocked Inverted Indices for Exact Clustering of Large Chemical Spaces

J. Chem. Inf. Model., 54 (9), pp. 2395-401, 2014.

(Abstract | Links | BibTeX)

Jordan, Elena; Roosen-Runge, Felix; Leibfarth, Sara; Zhang, Fajun; Sztucki, Michael; Hildebrandt, Andreas; Kohlbacher, Oliver; Schreiber, Frank

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), pp. 11365-74, 2014.

(Abstract | Links | BibTeX)

Hopf, Thomas A; Schärfe, Charlotta P I; Rodrigues, João P G L M; Green, Anna G; Kohlbacher, Oliver; Sander, Chris; Bonvin, Alexandre M J J; Marks, Debora S

Sequence co-evolution gives 3D contacts and structures of protein complexes

eLife, pp. 10.7554/eLife.03430, 2014.

(Abstract | Links | BibTeX)

Avbelj, Monika; Wolz, Olaf-Oliver; Fekonja, Ota; Bencina, Mojca; Repič, Matej; Mavri, Janez; Krüger, Jens; Schärfe, Charlotta; Delmiro-Garcia, Magno; Panter, Gabriela; Kohlbacher, Oliver; Weber, Alexander N R; Jerala, Roman

Activation of lymphoma-associated MyD88 mutations via allostery-induced TIR domain oligomerization

Blood, 124 (26), pp. 3896-904, 2014.

(Abstract | Links | BibTeX)

Römer, Michael; Backert, Linus; Eichner, Johannes; Zell, Andreas

ToxDBScan: Large-Scale Similarity Screening of Toxicological Databases for Drug Candidates

International Journal of Molecular Sciences, 15 (10), pp. 19037–19055, 2014.

(Abstract | Links | BibTeX)

Nahnsen, Sven; Bielow, Chris; Reinert, Knut; Kohlbacher, Oliver

Tools for label-free peptide quantification

Mol. Cell. Prot., 12 (3), pp. 549-56, 2013.

(Abstract | Links | BibTeX)

Nahnsen, Sven; Sachsenberg, Timo; Kohlbacher, Oliver

PTMeta: Increasing Identification Rates of Modified Peptides Using Modification Pre-scanning and Meta-analysis

Proteomics, 13 (6), pp. 1042-51, 2013.

(Abstract | Links | BibTeX)

Perez-Riverol, Yasset; Hermjakob, Henning; Kohlbacher, Oliver; Martens, Lennart; Creasy, David; Cox, Jürgen; Leprevost, Felipe; Shan, Baozhen Paul; Cabrera, Gleysin; Guillen, Gerardo; Padron, Gabriel; Gonzalez, Luis Xavier; Besada, Vladimir

Computational Proteomics Pitfalls and Challenges: HavanaBioinfo 2012 Workshop Report

J. Proteomics, 87 , pp. 134-8, 2013.

(Abstract | Links | BibTeX)

Weisser, Hendrik; Nahnsen, Sven; Grossmann, Jonas; Nilse, Lars; Quandt, Andreas; Brauer, Hendrik; Sturm, Marc; Kenar, Erhan; Kohlbacher, Oliver; Aebersold, Ruedi; Malmström, Lars

An automated pipeline for high-throughput label-free quantitative proteomics

J. Proteome Res., 12 (4), pp. 1824-1644, 2013.

(Abstract | Links | BibTeX)

Brand, Luise; Fischer, Nina; Harter, Klaus; Kohlbacher, Oliver; Wanke, Dierk

Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays

Nucl. Acids Res., 41 (21), pp. 9764-78, 2013.

(Abstract | Links | BibTeX)

Wanke, Dierk; Brand, Luise H; Fischer, Nina M; Peschke, Florian; Kilian, Joachim; Berendzen, K W

Implications of DNA-nanostructures by Hoogsteen-dinucleotides on transcription factor binding

Quantum Bio-Informatics V: From Quantum Information to Bio-Informatics, 30 , Chapter 30, pp. 351-362, World Scientific, 2013, ISBN: 978-981-4460-01-9, (ISBN: 978-981-4460-01-9).

(Links | BibTeX)

Sturm, T; Leinders-Zufall, T; Maček, Boris; Walzer, Mathias; Jung, S; Pömmerl, B; Stevanović, Stefan; Zufall, F; Overath, P; Rammensee, Hans-Georg

Mouse urinary peptides provide a molecular basis for genotype discrimination by nasal sensory neurons.

Nat. Commun., 19 (4), pp. 1616, 2013.

(Abstract | Links | BibTeX)

Roosen-Runge, Felix; Heck, Benjamin; Zhang, Fajun; Kohlbacher, Oliver; Schreiber, Frank

Interplay of pH and Binding of Multivalent Metal Ions: Charge Inversion and Reentrant Condensation in Protein Solutions

J. Phys. Chem. B, 117 (18), pp. 5777-87, 2013.

(Abstract | Links | BibTeX)

Walzer, Mathias; Qi, Da; Mayer, Gerhard; Uszkoreit, Julian; Eisenacher, Martin; Sachsenberg, Timo; Gonzalez-Galarza, Faviel F; Fan, Jun; Bessant, Conrad; Deutsch, Eric W; Reisinger, Florian; Vizcaíno, Juan Antonio; Medina-Aunon, Alberto J; Albar, Juan Pablo; Kohlbacher, Oliver; Jones, Andrew R

The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics

Mol. Cell. Prot., 12 (8), pp. 2332-40, 2013.

(Abstract | Links | BibTeX)

de la Garza, Luis; Krüger, Jens; Schärfe, Charlotta; Röttig, Marc; Aiche, Stephan; Reinert, Knut; Kohlbacher, Oliver

From the desktop to the grid: conversion of KNIME Workflows to gUSE

Proc. IWSG 2013, 993 , CEUR-WS 2013.

(Abstract | Links | BibTeX)

Novák, Jirí; Sachsenberg, Timo; Hoksza, David; Skopal, Tomás; Kohlbacher, Oliver

A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools

7th International Conference on Practical Applications of Computational Biology & Bioinformatics, pp. 101–109, Springer 2013.

(Links | BibTeX)

Gifford, Casey A; Ziller, Michael J; Gu, Hongcang; Trapnell, Cole; Donaghey, Julie; Tsankov, Alexander; Shalek, Alex K; Shishkin, Alexander A; Issner, Robbyn; Zhang, Xiaolan; Fostel, Jennifer L; Holmes, Laurie; Meldrim, Jim; Guttman, Mitchell; Epstein, Charles; Park, Hongkun; Kohlbacher, Oliver; Rinn, John; Gnirke, Andreas; Lander, Eric S; Bernstein, Bradley E; Meissner, Alexander

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

Cell, 153 (5), pp. 1149-1163, 2013.

(Abstract | Links | BibTeX)

Ziller, Michael J; Gu, Hongcang; Müller, Fabian; Donaghey, Julian; Kohlbacher, Oliver; Bernstein, Bradley E; Gnirke, Andreas; Meissner, Alexander

Charting a dynamic DNA methylation landscape of the human genome

Nature, 500 , pp. 477–481, 2013.

(Abstract | Links | BibTeX)

Kyzirakos, C; Pflueckhahn, U; Sturm, M; Schroeder, C; Bauer, P; Walter, M; Feldhahn, M; Walzer, M; Mohr, C; Szolek, A; Bonin, M; Kohlbacher, O; Ebinger, M; Handgretinger, R; Rammensee, H -G; Lang, P

iVacALL: utilizing next-generation sequencing for the establishment of an individual peptide vaccination approach for paediatric acute lymphoblastic leukaemia

Bone Marrow Transplant., 48 (3), pp. S401, 2013, (39th Annual Meeting of the European-Group-for-Blood-and-Marrow-Transplantation (EBMT), London, ENGLAND, APR 07-10, 2013).

(Links | BibTeX)

Thiel, Philipp; Röglin, Lars; Meissner, Nicole; Hennig, Sven; Kohlbacher, Oliver; Ottmann, Christian

Virtual Screening and Experimental Validation Reveal Novel Small-Molecule Inhibitors of 14-3-3 Protein-Protein Interactions

Chem. Commun., 49 (76), pp. 8468-70, 2013.

(Abstract | Links | BibTeX)

Novak, Jiri; Sachsenberg, Timo; Hoksza, David; Skopal, Tomas; Kohlbacher, Oliver

On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications

J. Integrative Bioinformatics, 10 (3), pp. 228, 2013.

(Abstract | Links | BibTeX)

Schubert, Benjamin; Lund, Ole; Nielsen, Morten

Evaluation of peptide selection approaches for epitope-based vaccine design

Tissue Antigens, 82 (4), pp. 243–251, 2013.

(Abstract | Links | BibTeX)

Michta, Ewelina; Schad, Klaus; Blin, Kai; Ort-Winklbauer, Regina; Röttig, Marc; Kohlbacher, Oliver; Wohlleben, Wolfgang; Schinko, Eva; Mast, Yvonne

The bifunctional role of aconitase in Streptomyces viridochromogenes Tü494

Env. Microbiol., 2012.

(Abstract | Links | BibTeX)

Briesemeister, Sebastian; Rahnenführer, Jörg; Kohlbacher, Oliver

No longer confidential: Estimating the Confidence of Individual Regression Predictions

PLoS One, 7 (11), pp. e48723, 2012.

(Abstract | Links | BibTeX)

Kenar, Erhan; Franken, Holger; Rosenbaum, Lars; Lehmann, Rainer; Forcisi, S; Wörmann, Kilian; Lucio, M; König, Andre; Rahnenführer, Jörg; Schmidt-Kopplin, Philippe; Haering, Hans-Ulrich; Zell, Andreas; Kohlbacher, Oliver

Mit Bioinformatik zu Biomarkern

Med. Welt, 63 (5), pp. 245-50, 2012.

(Abstract | BibTeX)

Nahnsen, Sven; Kohlbacher, Oliver

In silico design of targeted SRM-based experiments

BMC Bioinformatics, 13 , pp. S8, 2012.

(Abstract | Links | BibTeX)

Malisi, Christoph U; Toussaint, Nora C; Kohlbacher, Oliver; Höcker, Birte

Binding pocket optimization by computational protein design

PLoS One, 7 (12), pp. e52505, 2012.

(Abstract | Links | BibTeX)

Gesing, Sandra; Herres-Pawlis, Sonja; Birkenheuer, Georg; Brinkmann, André; Grunzke, Richard; Kacsuk, Peter; Kohlbacher, Oliver; Kozlovszky, Miklos; Krüger, Jens; Müller-Pfefferkorn, Ralph; Schäfer, Patrick; Steinke, Thomas

A Science Gateway Getting Ready for Serving the International Molecular Simulation Community

Proceedings of Science, PoS(EGICF12-EMITC2)050 , 2012.

(Abstract | Links | BibTeX)

Birkenheuer, Georg; Blunk, Dirk; Breuers, Sebastian; Brinkmann, Andre; Fels, Gregor; Gesing, Sandra; Grunzke, Richard; Herres-Pawlis, Sonja; Kohlbacher, Oliver; Krüger, Jens; Lang, Ulrich; Packschies, Lars; Müller-Pfefferkorn, Ralf; Schäfer, Patrick; Schuster, Johannes; Steinke, Thomas; Warzecha, Klaus; Wewior, Martin

MoSGrid: Progress of Workflow driven Chemical Simulations

Proc. of Grid Workflow Workshop 2011, Cologne, Germany, 826 , CEUR Workshop Proceedings, 2012.

(Abstract | Links | BibTeX)

Wörman, Kilian; Lucio, M; Forcisi, S; Heinzmann, S S; Kenar, E; Franken, H; Rosenbaum, L; Schmitt-Kopplin, P; Kohlbacher, O; Zell, A; Häring, H -U; Lehmann, R

„Metabolomics“ in der Diabetesforschung

Der Diabetologe, (1), pp. 42-48, 2012.

(Abstract | Links | BibTeX)

Gesing, Sandra; Herres-Pawlis, Sonja; Birkenheuer, Georg; Brinkmann, André; Grunzke, Richard; Kacsuk, Peter; Kohlbacher, Oliver; Kozlovszky, Miklos; Krüger, Jens; Müller-Pfe fferkorn, Ralf; Schäfer, Patrick; Steinke, Thomas

The MoSGrid Community – From National to International Scale

EGI Community Forum 2012, 2012.

(Abstract | BibTeX)

Jones, Andrew R; Eisenacher, Martin; Mayer, Gerhard; Kohlbacher, Oliver; Siepen, Jennifer; Hubbard, Simon J; Selley, Julian N; Searle, Brian C; Shofstahl, James; Seymour, Sean L; Julian, Randall; Binz, Pierre-Alain; Deutsch, Eric W; Hermjakob, Henning; Reisinger, Florian; Griss, Johannes; Vizcaino, Juan Antonio; Chambers, Matthew; Pizarro, Angel; Creasy, David

The mzIdentML data standard for mass spectrometry-based proteomics results

Mol. Cell. Prot., 11 (7), pp. M111.014381, 2012.

(Abstract | Links | BibTeX)

Trusch, Maria; Tillack, Kati; Kwiatkowski, Marcel; Bertsch, Andreas; Ahrends, Robert; Kohlbacher, Oliver; Martin, Roland; Sospedra, Mirieia; Schlüter, Hartmut

Displacement chromatography as first separating step in online two-dimensional liquid chromatography coupled to mass spectrometry analysis of a complex protein sample—The proteome of neutrophils

J. Chromatogr. A, 1232 , pp. 288-94, 2012.

(Abstract | Links | BibTeX)

Röglin, Lars; Thiel, Philipp; Kohlbacher, Oliver; Ottmann, Christian

Covalent attachment of pyridoxal-phosphate derivatives to 14-3-3 proteins

Proc. Natl. Acad. Sci. USA, 109 (18), pp. E1051-3, 2012.

(Links | BibTeX)

Junker, Johannes; Bielow, Chris; Bertsch, Andreas; Sturm, Marc; Reinert, Knut; Kohlbacher, Oliver

TOPPAS: A graphical workflow editor for the analysis of high-throughput proteomics data

J. Proteome Res., 11 (7), pp. 3914-20, 2012.

(Abstract | Links | BibTeX)

Ahrends, Robert; Lichtner, Björn; Buck, Friedrich; Hildebrand, Diana; Kotasinska, Marta; Kohlbacher, Oliver; Kwiatkowski, Marcel; Wagner, Moritz; Trusch, Maria; Schlüter, Hartmut

Comparison of displacement versus gradient mode for separation of a complex protein mixture by anion-exchange chromatography

J. Chromatogr. B, 901 , pp. 34-40, 2012.

(Abstract | Links | BibTeX)

Herres-Pawlis, Sonja; Birkenheuer, Georg; Brinkmann, André; Gesing, Sandra; Grunzke, Richard; Jäkel, René; Kohlbacher, Oliver; Krüger, Jens; dos Vieira, Ines Santos

Workflow-enhanced conformational analysis of guanidine zinc complexes via a science gateway

HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences, pp. 142-151, IOS Press, 2012.

(Abstract | Links | BibTeX)

Birkenheuer, Georg; Blunk, Dirk; Breuers, Sebastian; Brinkmann, André; dos Vieira, Ines Santos; Fels, Gregor; Gesing, Sandra; Grunzke, Richard; Herres-Pawlis, Sonja; Kohlbacher, Oliver; Krüger, Jens; Lang, Ulrich; Packschies, Lars; Müller-Pfefferkorn, Ralph; Schäfer, Patrick; Steinke, Thomas; Warzecha, Klaus; Wewior, Martin

MoSGrid: Efficient Data Management and a Standardized Data Exchange Format for Molecular Simulations in a Grid Environment

Journal of Cheminformatics, 4 (Suppl 1), pp. P21, 2012.

(Abstract | Links | BibTeX)

Gesing, Sandra; Glatard, Tristan; Krüger, Jens; Olabarriaga, Silvia Delgado; Solomonides, Tony; Silverstein, Jonathan; Montagnat, Johan; Gaignard, Alban; Krefting, Dagmar (Ed.)

HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences

IOS Press, 175 , 2012.

(Abstract | Links | BibTeX)

Schlemmer, Tobias; Grunzke, Richard; Gesing, Sandra; Krüger, Jens; Birkenheuer, Georg; Müller-Pfefferkorn, Ralph; Kohlbacher, Oliver

Generic User Management for Science Gateways via Virtual Organizations

EGI Technical Forum 2012, 2012.

(Abstract | Links | BibTeX)

Feldhahn, Magdalena; Dönne, Pierre; Schubert, Benjamin; Schilbach, Karin; Rammensee, Hans-Georg; Kohlbacher, Oliver

miHA-Match: computational detection of tissue-specific minor histocompatibility antigens

J. Immunol. Meth., 386 (1-2), pp. 94-100, 2012.

(Abstract | Links | BibTeX)

Gesing, Sandra; Grunzke, Richard; Krüger, Jens; Birkenheuer, Georg; Wewior, Martin; Schäfer, Patrick; Schuller, Bernd; Schuster, Johannes; Herres-Pawlis, Sonja; Breuers, Sebastian; Balasko, Akos; Kozlovszky, Miklos; Fabri, Anna Szikszay; Packschies, Lars; Kacsuk, Peter; Blunk, Dirk; Steinke, Thomas; Brinkmann, André; Fels, Gregor; Müller-Pfefferkorn, Ralph; Jäkel, René; Kohlbacher, Oliver

A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics

Journal of Grid Computing, 10 (4), pp. 769-790., 2012.

(Abstract | Links | BibTeX)

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

Exact Algorithms for Cluster Editing: Evaluation and Experiments

Algorithmica, 60 (2), pp. 316-334, 2011, (A preliminary version of this paper appeared under the title 'Exact algorithms for cluster editing: Evaluation and experiments' in the Proceedings of the 7th Workshop on Experimental Algorithms, WEA 2008, in: LNCS, vol. 5038, Springer, pp. 289-302).

(Abstract | Links | BibTeX)

Martens, Lennart; Chambers, Matthew; Sturm, Marc; Kessner, Darren; Levander, Fredrik; Shofstahl, Jim; Tang, Wilfried H; Römpp, Andreas; Neumann, Steffen; Pizarro, Angel D; Montecchi-Palazzi, Luisa; Tasman, Natalie; Coleman, Mike; Reisinger, Florian; Souda, Puneet; Hermjakob, Henning; Binz, Pierre-Alain; Deutsch, Eric W

mzML – a Community Standard for Mass Spectrometry Data

Mol. Cell. Prot., 10 (1), pp. R110.000133, 2011.

(Abstract | Links | BibTeX)

Gesing, Sandra; van Hemert, Jano; Kacsuk, Peter; Kohlbacher, Oliver

Special Issue: Portals for life sciences—Providing intuitive access to bioinformatic tools

Concurrency and Computation: Practice and Experience, 23 (3), pp. 223–234, 2011.

(Abstract | Links | BibTeX)

301 entries « 3 of 7 »

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