Publications

325 entries « 3 of 7 »

Aicheler, Fabian; Li, Jia; Lehmann, Rainer; Xu, Guowang; Kohlbacher, Oliver

Retention Time Prediction Improves Identification in Non-Targeted Lipidomics Approaches

Anal. Chem., 87 (15), pp. 7698-704, 2015.

(Abstract | Links | BibTeX)

de Lange, Orlando; Wolf, Christina; Thiel, Philipp; Krüger, Jens; Kleusch, Christian; Kohlbacher, Oliver; Lahaye, Thomas

DNA-binding proteins from marine bacteria expand the sequence diversity of known TALE-like repeats

Nucl. Acids Res, 43 (20), pp. 10065-80, 2015.

(Abstract | Links | BibTeX)

Venturelli, Sascha; Belz, Regina G; Kämper, Andreas; Berger, Alexandra; von Horn, Kyra; Wegner, André; Böcker, Alexander; Zabulon, Gérald; Langenecker, Tobias; Kohlbacher, Oliver; Barneche, Fredy; Weigel, Detlef; Lauer, Ulrich M; Bitzer, Michael; Becker, Claude

Plants release precursors of potent histone deacetylase inhibitors to suppress growth of competitors

Plant Cell, 27 (11), pp. 3175-89., 2015.

(Abstract | Links | BibTeX)

Zaman, Uzma; Richter, Florian M; Hofele, Romina; Kramer, Katharina; Sachsenberg, Timo; Lenz, Christof; Urlaub, Henning

Dithiothreitol (DTT) acts as a specific, UV-inducible cross-linker in elucidation of protein-RNA interactions

Mol. Cell. Prot., 14 (12), pp. 3196-210, 2015.

(Abstract | Links | BibTeX)

Backert, Linus; Kohlbacher, Oliver

Immunoinformatics and epitope prediction in the age of genomic medicine

Genome Med., 7 (1), pp. 119, 2015.

(Abstract | Links | BibTeX)

Kowalewski, Daniel J; Schuster, Heiko; Backert, Linus; Berlin, Claudia; Kahn, Stefan; Kanz, Lothar; Salih, Helmut R; Rammensee, Hans-Georg; Stevanovic, Stefan; Stickel, Juliane Sarah

HLA ligandome analysis identifies the underlying specificities of spontaneous antileukemia immune responses in chronic lymphocytic leukemia (CLL)

Proceedings of the National Academy of Sciences of the United States of America, 112 (2), pp. E166–E175, 2015.

(Abstract | Links | BibTeX)

Bier, David; Thiel, Philipp; Briels, Jeroen; Ottmann, Christian

Stabilization of Protein-Protein Interactions in chemical biology and drug discovery.

Prog Biophys Mol Biol, 119 (1), pp. 10-9, 2015, (automatic medline import).

(Abstract | Links | BibTeX)

Nicoludis, John M; Lau, Sze-Yi; Schärfe, Charlotta P.I; Marks, Debora S; Weihofen, Wilhelm A; Gaudet, Rachelle

Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity

Structure, 23 (11), pp. 2087 - 2098, 2015.

(Abstract | Links | BibTeX)

Kenar, Erhan; Franken, Holger; Forcisi, Sara; Wörmann, Kilian; Häring, Hans-Ulrich; Lehmann, Rainer; Schmitt-Kopplin, Philippe; Zell, Andreas; Kohlbacher, Oliver

Automated Label-Free Quantification of Metabolites from LC-MS Data

Mol. Cell. Prot., 13 (1), pp. 348-59, 2014.

(Abstract | Links | BibTeX)

Beck, Florian; Geiger, Jörg; Gambaryan, Stepan; Veit, Johannes; Vaudel, Marc; Nollau, Peter; Kohlbacher, Oliver; Martens, Lennart; Walter, Ulrich; Sickmann, Albert; Zahedi, René P

Time-resolved characterization of cAMP/PKA-dependant signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways

Blood, 123 (4), pp. e1-e10, 2014.

(Abstract | Links | BibTeX)

Gerasch, Andreas; Kaufmann, Michael; Kohlbacher, Oliver

Rebuilding KEGG Maps - An integrative approach for visual analytics of metabolic networks

Pacific Visualization Symposium (PacificVis), 2014 IEEE, pp. 97-104, IEEE 2014.

(Abstract | Links | BibTeX)

Gerasch, Andreas; Faber, Daniel; Küntzer, Jan; Niermann, Peter; Kohlbacher, Oliver; Lenhof, Hans-Peter; Kaufmann, Michael

BiNA: a visual analytics tool for biological network data

PLoS ONE, 9 (2), pp. e87397, 2014.

(Abstract | Links | BibTeX)

Kohlbacher, Oliver; Schreiber, Falk; Ward, Matthew O

Multivariate Networks in the Life Sciences

Multivariate Network Visualization 2013, Chapter 4, pp. 61-73, Springer, 2014.

(Links | BibTeX)

Roberts, Jonathan C; Yang, Jing; Kohlbacher, Oliver; Ward, Matthew O; Zhou, Michelle X

Novel Visual Metaphors for Multivariate Networks

Multivariate Network Visualization 2013, Chapter 7, pp. 127-147, Springer, 2014.

(Links | BibTeX)

Aebersold, Rudolph; Kohlbacher, Oliver; Vitek, Olga (Ed.)

Report from Dagstuhl Seminar 13491 Computational Mass Spectrometry

Dagstuhl Publishing, Dagstuhl, Germany, 3 (12), 2014.

(Abstract | Links | BibTeX)

Menzel, Moritz; Meckbach, Diana; Weide, Benjamin; Toussaint, Nora C; Schilbach, Karin; Noor, Seema; Eigentler, Thomas; Ikenberg, Kristian; Busch, Christian; Qunitanilla-Martinez, Leticia; Göke, Antonia; Göke, Friederike; Handgretinger, Rupert; Ottmann, Christian; Bastian, Boris; Garbe, Claus; Röcken, Martin; Perner, Sven; Kohlbacher, Oliver; Bauer, Jürgen

In melanoma, Hippo signaling is affected by copy number alterations and YAP1 overexpression impairs patient survival

Pigment Cell Melanoma Res., 23 (3), pp. E45, 2014.

(Abstract | Links | BibTeX)

Walzer, Mathias; Pernas, Lucia Espona; Nasso, Sara; Bittremieux, Wout; Nahnsen, Sven; Kelchtermans, Pieter; Pichler, Peter; van den Toorn, Henk W P; Staes, An; Vandenbussche, Jonathan; Mazanek, Michael; Taus, Thomas; Scheltema, Richard A; Kelstrup, Christian D; Gatto, Laurent; van Breukelen, Bas; Aiche, Stephan; Valkenborg, Dirk; Laukens, Kris; Lilley, Kathryn S; Olsen, Jesper Velgaard; Heck, Albert J R; Mechtler, Karl; Aebersold, Ruedi; Gevaert, Kris; Vizcaino, Juan Antonio; Hermjakob, Henning; Kohlbacher, Oliver; Martens, Lennart

qcML: an exchange format for quality control metrics from mass spectrometry experiments

Mol. Cell. Prot., 13 (8), pp. 1905-13, 2014.

(Abstract | Links | BibTeX)

Krüger, Jens; Grunzke, Richard; Gesing, Sandra; Breuers, Sebastian; Brinkmann, André; de la Garza, Luis; Kohlbacher, Oliver; Kruse, Martin; Nagel, Wolfgang; Packschies, Lars; Müller-Pfefferkorn, Ralph; Schärfe, Charlotta; Steinke, Thomas; Schlemmer, Tobias; Warzecha, Klaus; Zink, Andreas; Herres-Pawlis, Sonja

The MoSGrid Science Gateway – A Complete Solution for Molecular Simulations

J. Chem. Theor. Comput., 10 (6), pp. 2232-2245, 2014.

(Abstract | Links | BibTeX)

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)

325 entries « 3 of 7 »

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