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Publications

Sharma K, Hrle A, Kramer K, Sachsenberg T, Staals RHJ, Randau L, Marchfelder A, van der Oost J, Kohlbacher O, Conti E, Urlaub H (accepted) Analysis of protein-RNA interactions by UV-induced cross-linking and mass spectrometry. Methods
 
de Lange O, Wolf C, Thiel P, Krüger J, Kleusch C, Kohlbacher O, Lahaye T (accepted) DNA-binding proteins from marine bacteria expand the sequence diversity of known TALE-like repeats Nucl Acids Res
 
Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cacchiarelli D, Tsankov AM, Epstein C, Rinn JL, Mikkelsen TS, Kohlbacher O, Gnirke A, Bernstein BE, Elkabetz Y, Meissner A (2015) Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature 518: 355-359
 
Walz S, Stickel JS, Kowalewski DJ, Schuster H, Weisel K, Backert L, Kahn S, Nelde A, Stroh T, Handel M, Kohlbacher O, Kanz L, Salih HR, Rammensee H-G, Stevanovic S (2015) The antigenic landscape of multiple myeloma: mass spectrometry (re-)defines targets for T-cell based immunotherapy. Blood 126: 1203-1213
 
Uszkoreit J, Maerkens A, Perez-Riverol Y, Meyer HE, Marcus K, Stephan C, Kohlbacher O, Eisenacher M (2015) PIA - An intuitive protein inference engine with a web-based user interface. J Proteome Res 14: 2988-2997
 
Thost A-K, Dönnes P, Kohlbacher O, Proikas-Cezanne T (2015) Fluorescence-based imaging of autophagy progression by human WIPI beta-propeller protein detection in single cells. Methods 75: 69-78
 
Simha R, Briesemeister S, Kohlbacher O, Shatkay H (2015) Protein (Multi-)Location Prediction: Utilizing Interdependencies via a Generative Model Bioinformatics 31: i365-i374
 
Schubert B, Brachvogel H-P, Jürges C, Kohlbacher O (2015) EpiToolKit – A Web-based Workbench for Vaccine Design. Bioinformatics 31: 2211-2213
 
Sachsenberg T, Herbst F-A, Taubert M, Kermer R, Jehmlich N, von Bergen M, Seifert J, Kohlbacher O (2015) MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics. J Proteome Res 14: 619-627
 
Ranninger C, Rurik M, Limonciel A, Ruzek S, Reischl R, Wilmes A, Jennings P, Hewitt P, Dekant W, Kohlbacher O, Huber CG (2015) Nephron Toxicity Profiling via Untargeted Metabolome Analysis Employing a High-Performance Liquid Chromatography-Mass Spectrometry-Based Experimental and Computational Pipeline. J Biol Chem 290: 19121-19132
 
Proikas-Cezanne T, Takacs Z, Dönnes P, Kohlbacher O (2015) WIPI proteins: essential PtdIns3P effectors at the nascent autophagosome. J Cell Sci 128: 207-217
 
Martens L, Kohlbacher O, Weintraub ST (2015) Managing Expectations when Publishing Tools and Methods for Computational Proteomics. J Proteome Res 14: 2002-2004
 
Hildebrandt AK, Stöckel D, Fischer N, de la Garza Trevino L, Krüger J, Nickels S, Röttig M, Schärfe C, Schumann M, Thiel P, Lenhof H-P, Kohlbacher O, Hildebrandt A (2015) ballaxy: web services for structural bioinformatics. Bioinformatics 31: 121-122
 
Gerasch A, Küntzer J, Niermann P, Stöckel D, Kohlbacher O, Lenhof H-P (2015) Network-based interactive navigation and analysis of large biological datasets. it - Information Technology 57: 37-48
 
Friedrich A, Kenar E, Kohlbacher O, Nahnsen S (2015) Intuitive Web-based Experimental Design for High-throughput Biomedical Data. BioMed Res Int 2015: 958302
 
Breckels LM, Holden S, Wojnar D, Mulvey CM, Christoforou A, Groen AJ, Kohlbacher O, Lilley KS, Gatto L (2015) Learning from heterogeneous data sources: an application in spatial proteomics. bioRxiv
 
Aicheler F, Li J, Lehmann R, Xu G, Kohlbacher O (2015) Retention Time Prediction Improves Identification in Non-Targeted Lipidomics Approaches. Anal Chem 87: 7698-7704
 
Aiche S, Sachsenberg T, Kenar E, Walzer M, Wiswedel B, Kristl T, Boyles M, Duschl A, Huber C, Berthold M, Reinert K, Kohlbacher O (2015) Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry. Proteomics 15: 1443-1447
 
Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HWP, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJR, Mechtler K, Aebersold R, Gevaert K, Vizcaino JA, Hermjakob H, Kohlbacher O, Martens L (2014) qcML: an exchange format for quality control metrics from mass spectrometry experiments. Mol Cell Prot 13: 1905-1913
 
Wagner R, Li J, Kenar E, Kohlbacher O, Machicao F, Häring H-U, Fritsche A, Xu G, Lehmann R (2014) Clinical and non-targeted metabolomic profiling of homozygous carriers of Transcription Factor 7-like 2 variant rs7903146 Sci Rep 4: 5296
 
Thiel P, Sach-Peltason L, Ottmann C, Kohlbacher O (2014) Blocked Inverted Indices for Exact Clustering of Large Chemical Spaces. J Chem Inf Model 54: 2395-2401
 
Szolek A, Schubert B, Mohr C, Sturm M, Feldhahn M, Kohlbacher O (2014) OptiType: precision HLA typing from next-generation sequencing data. Bioinformatics 30: 3310-3316
 
Roberts JC, Yang J, Kohlbacher O, Ward MO, Zhou MX (2014) Novel Visual Metaphors for Multivariate Networks. In Multivariate Network Visualization 2013, pp 127-147.
 
Menzel M, Meckbach D, Weide B, Toussaint NC, Schilbach K, Noor S, Eigentler T, Ikenberg K, Busch C, Qunitanilla-Martinez L, Göke A, Göke F, Handgretinger R, Ottmann C, Bastian B, Garbe C, Röcken M, Perner S, Kohlbacher O, Bauer J (2014) In melanoma, Hippo signaling is affected by copy number alterations and YAP1 overexpression impairs patient survival. Pigment Cell Melanoma Res 23: E45
 
Krüger J, Grunzke R, Herres-Pawlies S, de la Garza L, Kohlbacher O, Nagel WE, Gesing S (2014) Performance Studies on Distributed Virtual Screening. Biomed Res Int 2014: 624024
 
Krüger J, Grunzke R, Gesing S, Breuers S, Brinkmann A, de la Garza L, Kohlbacher O, Kruse M, Nagel W, Packschies L, Müller-Pfefferkorn R, Schärfe C, Steinke T, Schlemmer T, Warzecha K, Zink A, Herres-Pawlis S (2014) The MoSGrid Science Gateway – A Complete Solution for Molecular Simulations. J Chem Theor Comput 10: 2232-2245
 
Kramer K, Sachsenberg T, Beckmann BM, Qamar S, Boon K-L, Hentze MW, Kohlbacher O, Urlaub H (2014) Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins. Nat Methods 11: 1064-1070
 
Kohlbacher O, Schreiber F, Ward MO (2014) Multivariate Networks in the Life Sciences. In Multivariate Network Visualization 2013, pp 61-73.
 
Kenar E, Franken H, Forcisi S, Wörmann K, Häring H-U, Lehmann R, Schmitt-Kopplin P, Zell A, Kohlbacher O (2014) Automated Label-Free Quantification of Metabolites from LC-MS Data. Mol Cell Prot 13: 348-359
 
Jordan E, Roosen-Runge F, Leibfarth S, Zhang F, Sztucki M, Hildebrandt A, Kohlbacher O, Schreiber F (2014) 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: 11365-11374
 
Hopf TA, Schärfe CPI, Rodrigues JPGLM, Green AG, Kohlbacher O, Sander C, Bonvin AMJJ, Marks DS (2014) Sequence co-evolution gives 3D contacts and structures of protein complexes. eLife: 10.7554/eLife.03430
 
Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu Q-W, Bandeira N, Xenarios I, Kohlbacher O, Vizcaino JA, Hermjakob H (2014) The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience. Mol Cell Prot: mcp.O113.036681
 
Gerasch A, Kaufmann M, Kohlbacher O. (2014) Rebuilding KEGG Maps - An integrative approach for visual analytics of metabolic networks. Pacific Visualization Symposium (PacificVis), 2014 IEEE, pp. 97-104.
 
Gerasch A, Faber D, Küntzer J, Niermann P, Kohlbacher O, Lenhof H-P, Kaufmann M (2014) BiNA: a visual analytics tool for biological network data. PLoS ONE 9: e87397
 
Beck F, Geiger J, Gambaryan S, Veit J, Vaudel M, Nollau P, Kohlbacher O, Martens L, Walter U, Sickmann A, Zahedi RP (2014) Time-resolved characterization of cAMP/PKA-dependant signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways. Blood 123: e1-e10
 
Avbelj M, Wolz O-O, Fekonja O, Bencina M, Repič M, Mavri J, Krüger J, Schärfe C, Delmiro-Garcia M, Panter G, Kohlbacher O, Weber ANR, Jerala R (2014) Activation of lymphoma-associated MyD88 mutations via allostery-induced TIR domain oligomerization. Blood 124: 3896-3904
 
(2014) Report from Dagstuhl Seminar 13491 Computational Mass Spectrometry, Vol. 3. Dagstuhl, Germany
 
Ziller MJ, Gu H, Müller F, Donaghey J, Kohlbacher O, Bernstein BE, Gnirke A, Meissner A (2013) Charting a dynamic DNA methylation landscape of the human genome. Nature 500: 477–481
 
Weisser H, Nahnsen S, Grossmann J, Nilse L, Quandt A, Brauer H, Sturm M, Kenar E, Kohlbacher O, Aebersold R, Malmström L (2013) An automated pipeline for high-throughput label-free quantitative proteomics. J Proteome Res 12: 1824-1644
 
Wanke D, Brand LH, Fischer NM, Peschke F, Kilian J, Berendzen KW (2013) Implications of DNA-nanostructures by Hoogsteen-dinucleotides on transcription factor binding. In Quantum Bio-Informatics V: From Quantum Information to Bio-Informatics, pp 351-362.
 
Walzer M, Qi D, Mayer G, Uszkoreit J, Eisenacher M, Sachsenberg T, Gonzalez-Galarza FF, Fan J, Bessant C, Deutsch EW, Reisinger F, Vizcaíno JA, Medina-Aunon JA, Albar JP, Kohlbacher O, Jones AR (2013) The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Mol Cell Prot 12: 2332-2340
 
Thiel P, Röglin L, Meissner N, Hennig S, Kohlbacher O, Ottmann C (2013) Virtual Screening and Experimental Validation Reveal Novel Small-Molecule Inhibitors of 14-3-3 Protein-Protein Interactions. Chem Commun 49: 8468-8470
 
Sturm T, Leinders-Zufall T, Maček B, Walzer M, Jung S, Pömmerl B, Stevanović S, Zufall F, Overath P, Rammensee H-G (2013) Mouse urinary peptides provide a molecular basis for genotype discrimination by nasal sensory neurons. Nat Commun 19: 1616
 
Roosen-Runge F, Heck B, Zhang F, Kohlbacher O, Schreiber F (2013) Interplay of pH and Binding of Multivalent Metal Ions: Charge Inversion and Reentrant Condensation in Protein Solutions. J Phys Chem B 117: 5777-5787
 
Perez-Riverol Y, Hermjakob H, Kohlbacher O, Martens L, Creasy D, Cox J, Leprevost F, Shan BP, Cabrera G, Guillen G, Padron G, Xavier Gonzalez L, Besada V (2013) Computational Proteomics Pitfalls and Challenges: HavanaBioinfo 2012 Workshop Report. J Proteomics 87: 134-138
 
Novák J, Sachsenberg T, Hoksza D, Skopal T, Kohlbacher O. (2013) 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.
 
Novak J, Sachsenberg T, Hoksza D, Skopal T, Kohlbacher O (2013) 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: 228
 
Nahnsen S, Sachsenberg T, Kohlbacher O (2013) PTMeta: Increasing Identification Rates of Modified Peptides Using Modification Pre-scanning and Meta-analysis. Proteomics 13: 1042-1051
 
Nahnsen S, Bielow C, Reinert K, Kohlbacher O (2013) Tools for label-free peptide quantification. Mol Cell Prot 12: 549-556
 
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 (2013) iVacALL: utilizing next-generation sequencing for the establishment of an individual peptide vaccination approach for paediatric acute lymphoblastic leukaemia. Bone Marrow Transplant 48: S401
 
Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Shishkin AA, Issner R, Zhang X, Fostel JL, Holmes L, Meldrim J, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn J, Gnirke A, Lander ES, Bernstein BE, Meissner A (2013) Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells. Cell 153: 1149-1163
 
de la Garza L, Krüger J, Schärfe C, Röttig M, Aiche S, Reinert K, Kohlbacher O. (2013) From the desktop to the grid: conversion of KNIME Workflows to gUSE. Proc. IWSG 2013, Vol. 993, p. 9.
 
Brand L, Fischer N, Harter K, Kohlbacher O, Wanke D (2013) Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays. Nucl Acids Res 41: 9764-9778
 
Wörman K, Lucio M, Forcisi S, Heinzmann SS, Kenar E, Franken H, Rosenbaum L, Schmitt-Kopplin P, Kohlbacher O, Zell A, Häring H-U, Lehmann R (2012) „Metabolomics“ in der Diabetesforschung. Der Diabetologe: 42-48
 
Trusch M, Tillack K, Kwiatkowski M, Bertsch A, Ahrends R, Kohlbacher O, Martin R, Sospedra M, Schlüter H (2012) 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: 288-294
 
Schlemmer T, Grunzke R, Gesing S, Krüger J, Birkenheuer G, Müller-Pfefferkorn R, Kohlbacher O. (2012) Generic User Management for Science Gateways via Virtual Organizations. EGI Technical Forum 2012.
 
Röglin L, Thiel P, Kohlbacher O, Ottmann C (2012) Covalent attachment of pyridoxal-phosphate derivatives to 14-3-3 proteins. Proc Natl Acad Sci USA 109: E1051-1053
 
Nahnsen S, Kohlbacher O (2012) In silico design of targeted SRM-based experiments. BMC Bioinformatics 13: S8
 
Michta E, Schad K, Blin K, Ort-Winklbauer R, Röttig M, Kohlbacher O, Wohlleben W, Schinko E, Mast Y (2012) The bifunctional role of aconitase in Streptomyces viridochromogenes Tü494. Env Microbiol
 
Malisi CU, Toussaint NC, Kohlbacher O, Höcker B (2012) Binding pocket optimization by computational protein design. PLoS One 7: e52505
 
Kenar E, Franken H, Rosenbaum L, Lehmann R, Forcisi S, Wörmann K, Lucio M, König A, Rahnenführer J, Schmidt-Kopplin P, Haering H-U, Zell A, Kohlbacher O (2012) Mit Bioinformatik zu Biomarkern. Med Welt 63: 245-250
 
Junker J, Bielow C, Bertsch A, Sturm M, Reinert K, Kohlbacher O (2012) TOPPAS: A graphical workflow editor for the analysis of high-throughput proteomics data. J Proteome Res 11: 3914-3920
 
Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz P-A, Deutsch EW, Hermjakob H, Reisinger F, Griss J, Vizcaino JA, Chambers M, Pizarro A, Creasy D (2012) The mzIdentML data standard for mass spectrometry-based proteomics results. Mol Cell Prot 11: M111.014381
 
Herres-Pawlis S, Birkenheuer G, Brinkmann A, Gesing S, Grunzke R, Jäkel R, Kohlbacher O, Krüger J, dos Santos Vieira I. (2012) Workflow-enhanced conformational analysis of guanidine zinc complexes via a science gateway. HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences IOS Press, Vol. 175, pp. 142-151.
 
Gesing S, Herres-Pawlis S, Birkenheuer G, Brinkmann A, Grunzke R, Kacsuk P, Kohlbacher O, Kozlovszky M, Krüger J, Müller-Pfefferkorn R, Schäfer P, Steinke T (2012) A Science Gateway Getting Ready for Serving the International Molecular Simulation Community. Proceedings of Science PoS(EGICF12-EMITC2)050
 
Gesing S, Herres-Pawlis S, Birkenheuer G, Brinkmann A, Grunzke R, Kacsuk P, Kohlbacher O, Kozlovszky M, Krüger J, Müller-Pfe fferkorn R, Schäfer P, Steinke T. (2012) The MoSGrid Community – From National to International Scale. EGI Community Forum 2012.
 
Gesing S, Grunzke R, Krüger J, Birkenheuer G, Wewior M, Schäfer P, Schuller B, Schuster J, Herres-Pawlis S, Breuers S, Balasko A, Kozlovszky M, Szikszay Fabri A, Packschies L, Kacsuk P, Blunk D, Steinke T, Brinkmann A, Fels G, Müller-Pfefferkorn R, Jäkel R, Kohlbacher O (2012) A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics. Journal of Grid Computing 10: 769-790.
 
Feldhahn M, Dönne P, Schubert B, Schilbach K, Rammensee H-G, Kohlbacher O (2012) miHA-Match: computational detection of tissue-specific minor histocompatibility antigens. J Immunol Meth 386: 94-100
 
Briesemeister S, Rahnenführer J, Kohlbacher O (2012) No longer confidential: Estimating the Confidence of Individual Regression Predictions. PLoS One 7: e48723
 
Birkenheuer G, Blunk D, Breuers S, Brinkmann A, Fels G, Gesing S, Grunzke R, Herres-Pawlis S, Kohlbacher O, Krüger J, Lang U, Packschies L, Müller-Pfefferkorn R, Schäfer P, Schuster J, Steinke T, Warzecha K, Wewior M. (2012) MoSGrid: Progress of Workflow driven Chemical Simulations. Proc. of Grid Workflow Workshop 2011, Cologne, Germany. CEUR Workshop Proceedings, Vol. 826.
 
Birkenheuer G, Blunk D, Breuers S, Brinkmann A, dos Santos Vieira I, Fels G, Gesing S, Grunzke R, Herres-Pawlis S, Kohlbacher O, Krüger J, Lang U, Packschies L, Müller-Pfefferkorn R, Schäfer P, Steinke T, Warzecha K, Wewior M (2012) MoSGrid: Efficient Data Management and a Standardized Data Exchange Format for Molecular Simulations in a Grid Environment. Journal of Cheminformatics 4: P21
 
Ahrends R, Lichtner B, Buck F, Hildebrand D, Kotasinska M, Kohlbacher O, Kwiatkowski M, Wagner M, Trusch M, Schlüter H (2012) Comparison of displacement versus gradient mode for separation of a complex protein mixture by anion-exchange chromatography. J Chromatogr B 901: 34-40
 
(2012) HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences Vol. 175.
 
Zhang G, Ansari H, Bradley P, Cawley G, Hertz T, Hu X, Jojic N, Kim Y, Kohlbacher O, Lund O, Lundegaard C, Magaret C, Nielsen M, Papadopoulos H, Raghava G, Tal V, Xue L, Yanover C, Zhu S, Rock M, Crowe , , Jr, Polycarpou M, Duch W, Brusic V (2011) Machine learning competition in immunology - Prediction of HLA class I molecules. J Immunol Meth 375: 1-4
 
Wörmann K, Lucio M, Forcisi S, Schmitt-Kopplin P, Kenar E, Kohlbacher O, Franken H, Rosenbaum L, Zell A, Lehmann R, Häring H (2011) Verbund "BIOMARKERS" - Metabolomics im BMBF Kompetenznetz Diabetes. Diabetes, Stoffwechsel und Herz 20: 178-184
 
Tung C-W, Ziehm M, Kämper A, Kohlbacher O, Ho S-Y (2011) POPISK: T-cell reactivity prediction using support vector machines and string kernels. BMC Bioinformatics 12: 246
 
Toussaint NC, Maman Y, Kohlbacher O, Louzoun Y (2011) Universal peptide vaccines – optimal peptide vaccine based on viral sequence conservation. Vaccine 29: 8745-8753
 
Toussaint NC, Feldhahn M, Ziehm M, Stevanovic S, Kohlbacher O. (2011) T-Cell Epitope Prediction Based on Self-Tolerance. Proc. ICIW 2011.
 
Röttig M, Medema M, Blin K, Weber T, Rausch C, Kohlbacher O (2011) NRPSpredictor2 - a webserver for predicting NRPS adenylation domain specificity. Nucl Acids Res 39: W362-W367
 
Nahnsen S, Bertsch A, Rahnenführer J, Nordheim A, Kohlbacher O (2011) Probabilistic Consensus Scoring Improves Tandem Mass Spectrometry Peptide Identification. J Proteome Res 10: 3332-3343
 
Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Römpp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, Hermjakob H, Binz P-A, Deutsch EW (2011) mzML – a Community Standard for Mass Spectrometry Data. Mol Cell Prot 10: R110.000133
 
Gesing S, van Hemert J, Kacsuk P, Kohlbacher O (2011) Special Issue: Portals for life sciences—Providing intuitive access to bioinformatic tools. Concurrency and Computation: Practice and Experience 23: 223–234
 
Gesing S, Kacsuk P, Kozlovszky M, Birkenheuer G, Blunk D, Breuers S, Brinkmann A, Fels G, Grunzke R, Herres-Pawlis S, Krüger J, Packschies L, Müller-Pfefferkorn R, Schäfer P, Steinke T, Szikszay Fabri A, Warzecha K, Wewior M, Kohlbacher O. (2011) A Science Gateway for Molecular Simulations. EGI (European Grid Infrastructure) User Forum 2011, Book of Abstracts. ISBN 978 90 816927 1 7, pp. 94–95.
 
Gesing S, Grunzke R, Balasko A, Birkenheuer G, Blunk D, Breuers S, Brinkmann A, Fels G, Herres-Pawlis S, Kacsuk P, Kozlovszky M, Krüger J, Packschies L, Schäfer P, Schuller B, Schuster J, Steinke T, Szikszay Fabri A, Wewior M, Müller-Pfefferkorn R, Kohlbacher O. (2011) Granular Security for a Science Gateway in Structural Bioinformatics. Proc. IWSG-Life 2011.
 
Feldhahn M, Menzel M, Weide B, Bauer P, Meckbach D, Garbe C, Kohlbacher O, Bauer J (2011) No evidence of viral genomes in whole-transcriptome sequencings of three melanoma metastases. Exp Dermatol 20: 766-768
 
Canzar S, Toussaint NC, Klau GW (2011) An exact algorithm for side-chain placement in protein design. Optimization Letters: 1-14
 
Birkenheuer G, Blunk D, Breuers S, Brinkmann A, dos Santos Vieira I, Fels G, Gesing S, Grunzke R, Herres-Pawlis S, Kohlbacher O, Krüger J, Lang U, Packschies L, Müller-Pfefferkorn R, Schäfer P, Schmalz H-G, Steinke T, Warzecha K, Wewior M. (2011) A Molecular Simulation Grid as new tool for Computational Chemistry, Biology and Material Science. Journal of Cheminformatics 2011, Vol. 3.
 
Bielow C, Gröpl C, Kohlbacher O, Reinert K (2011) Bioinformatics for Qualitative and Quantitative Proteomics. In Bioinformatics for Omics Data: Methods and Protocols, pp 1-19.
 
Bertsch A, Gröpl C, Reinert K, Kohlbacher O (2011) OpenMS and TOPP: Open Source Software for LC-MS Data Analysis. Methods Mol Biol 696: 353-367
 
Böcker S, Briesemeister S, Klau GW (2011) Exact Algorithms for Cluster Editing: Evaluation and Experiments. Algorithmica 60: 316-334
 
Zhang F, Weggler S, Ziller MJ, Ianeselli L, Heck BS, Hildebrandt A, Kohlbacher O, Skoda MWA, Jacobs RMJ, Schreiber F (2010) On the Universality of Protein Reentrant Condensation in Solution Induced by Multivalent Metal Ions. PROTEINS: Structure, Function, Bioinformatics 78: 3450–3457
 
Widmer C, Toussaint NC, Altun Y, Kohlbacher O, Rätsch G. (2010) 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. Springer, Vol. 6282, pp. 98-109.
 
Widmer C, Altun Y, Toussaint NC, Rätsch G (2010) Inferring Latent Task Structure for Multi-Task Learning via Multiple Kernel Learning. BMC Bioinformatics 11: S5
 
Wewior M, Packschies L, Blunk D, Wickeroth D, Warzecha K, Herres-Pawlis S, Gesing S, Breuers S, Krüger J, Birkenheuer G, Lang U. (2010) The MoSGrid Gaussian portlet - Technologies for Implementation of Portlets for Molecular Simulations. Proceedings of the International Worshop on Science Gateways (IWSG2010), pp. 39-43.
 
Trusch M, Böhlick A, Hildebrand D, Lichtner B, Bertsch A, Kohlbacher O, Bachmann S, Schlüter H (2010) Application of displacement chromatography for the analysis of a lipid raft proteome. J Chromatogr B 878: 309-314
 
Trusch A, Ehlert S, Bertsch A, Kohlbacher O, Hildebrand D, Schlüter H, Tallarek U (2010) Improved particle-packed HPLC/MS microchips for proteomic analysis. J Pep Sci 33: 3283-3291
 
Toussaint NC, Widmer C, Kohlbacher O, Rätsch G (2010) Exploiting Physico-Chemical Properties in String Kernels. BMC Bioinformatics 11: S7
 
Röttig M, Rausch C, Kohlbacher O (2010) Combining Structure and Sequence Information Allows Automated Prediction of Substrate Specificities within Enzyme Families. PLoS Comput Biol 6: e1000636
 
Neumann D, Kohlbacher O. (2010) Structural Glycomics – Molecular Details of Protein-Carbohydrate Interactions and their Prediction. Proceedings of the International Beilstein Symposium on Glyco-Bioinformatics. Beilstein-Institut, Frankfurt, Germany.
 
Kirchler T, Briesemeister S, Singer M, Schütze K, Keinath M, Kohlbacher O, Vicente-Carbajosa J, Teige M, Harter K, Chaban C (2010) The role of phosphorylatable serine residues in the DNA-binding domain of Arabidopsis bZIP transcription factors. Eur J Cell Biol 89: 175-183
 
Hildebrandt A, Dehof AK, Rurainski A, Bertsch A, Schumann M, Toussaint NC, Moll A, Stöckel D, Nickels S, Mueller SC, Lenhof H-P, Kohlbacher O (2010) BALL - Biochemical Algorithms Library 1.3. BMC Bioinformatics 11: 531
 
Henneges C, Röttig M, Kohlbacher O, Zell A. (2010) 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, pp. 190-195.
 
Gesing S, van Hemert J, Koetsier J, Bertsch A, Kohlbacher O. (2010) 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). ACM, pp. 598-599.
 
Gesing S, Marton I, Birkenheuer G, Schuller B, Grunzke R, Krüger J, Breuers S, Blunk D, Fels G, Packschies L, Brinkmann A, Kohlbacher O, Kozlovszky M. (2010) Workflow Interoperability in a Grid Portal for Molecular Simulations. Proceedings of the International Worshop on Science Gateways (IWSG2010), pp. 44-48.
 
Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin A-C (2010) Visualization of omics data for systems biology. Nat Methods 7: S56-68
 
Briesemeister S, Rahnenführer J, Kohlbacher O (2010) Going from where to why - interpretable prediction of protein subcellular localization. Bioinformatics 26: 1232-1238
 
Briesemeister S, Rahnenführer J, Kohlbacher O (2010) YLoc – an interpretable web server for predicting subcellular localization. Nucl Acids Res 38: W497-W502
 
Birkenheuer G, Breuers S, Brinkmann A, Blunk D, Fels G, Gesing S, Herres-Pawlis S, Kohlbacher O, Krüger J, Packschies L. (2010) Grid-Workflows in Molecular Science. Lecture Notes in Informatics, pp. 177-184.
 
Bertsch A, Jung S, Zerck A, Pfeifer N, Nahnsen S, Henneges C, Nordheim A, Kohlbacher O (2010) Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics. J Proteome Res 9: 2696-2704
 
(2010) On open problems in biological network visualization, Vol. 5849.
 
Venturelli S, Horn Kv, Berger A, Weiland T, Smirnow I, Schenk A, Weiss TS, Kämper A, Kohlbacher O, Gregor M, Lauer UM, Bitzer M (2009) Identifikation und präklinische Charakterisierung neuartiger epigenetischer Wirkstoffe zur Behandlung therapieresistenter Tumore am Beispiel des Hepatozellulären Karzinoms. Z Gastroenterol 47: P1\_13
 
Toussaint NC, Kohlbacher O (2009) OptiTope - A Web Server for the Selection of an Optimal Set of Peptides for Epitope-based Vaccines. Nucl Acids Res 37: W617-622
 
Toussaint NC, Kohlbacher O (2009) Towards in silico design of epitope-based vaccines. Expert Opinion on Drug Discovery 4: 1047-1060
 
Toussaint N, Kohlbacher O, Rätsch G. (2009) Exploiting Physico-Chemical Properties in String-Kernels. MLCB 2009 (accepted).
 
Sturm M, Kohlbacher O (2009) TOPPView: An Open-Source Viewer for Mass Spectrometry Data. J Proteome Res 8: 3760-3763
 
Schultheiss SJ, Busch W, Lohmann JU, Kohlbacher O, Rätsch G (2009) KIRMES: Kernel-based identification of regulatory modules in euchromatic sequences. Bioinformatics 25: 2126-2133
 
Schneeberger K, Hagmann J, Ossowski S, Warthmann N, Gesing S, Kohlbacher O, Weigel D (2009) Simultaneous alignment of short reads against multiple genomes. Genome Biology 10: R98
 
Pfeifer N, Leinenbach A, Huber CG, Kohlbacher O (2009) Improving Peptide Identification in Proteome Analysis by a Two-Dimensional Retention Time Filtering Approach. J Proteome Res 8: 4109-4115
 
Nahnsen S, Nordheim A, Kohlbacher O. (2009) A geometric matching approach improves throughput and accurary in DIGE based proteomics. Proceedings of the sixth International Workshop on Computational Systems Biology (WCSB 2009). WCSB 2009, pp. 123-126.
 
Mitschke J, Fuss J, Blum T, Höglund A, Reski R, Kohlbacher O, Rensing S (2009) Prediction of dual protein targeting to plant organelles. New Phytologist 183: 224-236
 
Malisi C, Kohlbacher O, Höcker B (2009) Automated scaffold selection for enzyme design. PROTEINS: Structure, Function, and Bioinformatics 77: 74-83
 
Kohlbacher O, Reinert K. (2009) OpenMS and TOPP: Open Source Software for LC-MS Data Analysis. Proteome Bioinformatics. Humana Press, Vol. 604, pp. 201-211.
 
Keller A, Backes C, Gerasch A, Kaufmann M, Kohlbacher O, Lenhof H-P (2009) A novel algorithm for detecting differentially regulated paths based on Gene Set Enrichment Analysis. Bioinformatics 25: 2787-2794
 
Feldhahn M, Dönnes P, Thiel P, Kohlbacher O (2009) FRED - A Framework for T-cell Epitope Detection. Bioinformatics 25: 2758-2759
 
Dräger A, Kronfeld M, Ziller MJ, Supper J, Planatscher H, Magnus JB, Oldiges M, Kohlbacher O, Zell A (2009) Modeling Metabolic Networks in C. glutamicum: A Comparison of Rate Laws in Combination with Various Parameter Optimization Strategies. BMC Systems Biology 3: 5
 
Briesemeister S, Blum T, Brady S, Lam Y, Kohlbacher O, Shatkay H (2009) SherLoc2: a high-accuracy hybrid method for predicting subcellular localization of proteins. J Proteome Res 8: 5363–5366
 
Böcker S, Briesemeister S, Bui QB, Truss A (2009) Going Weighted: Parameterized Algorithms for Cluster Editing. Theoretical Computer Science 410: 5467-5480
 
Blum T, Briesemeister S, Kohlbacher O (2009) MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. BMC Bioinformatics 10: 274
 
Bertsch A, Leinenbach A, Pervukhin A, Lubeck M, Hartmer R, Baessmann C, Elnakady YA, Müller R, Böcker S, Huber CG, Kohlbacher O (2009) De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation. Electrophoresis 30: 3736-3747
 
Böcker S, Briesemeister S, Klau GW (2009) On Optimal Comparability Editing with Applications to Molecular Diagnostics. BMC Bioinformatics 10: S61
 
Althaus E, Klau GW, Kohlbacher O, Lenhof H-P, Reinert K. (2009) Integer Linear Programming in Computational Biology. Efficient Algorithms. Springer, Vol. 5760, pp. 199-218.
 
Ahrends R, Lichtner B, Bertsch A, Kohlbacher O, Trusch M, Schlüter H (2009) Application of displacement chromatography for the proteome analysis of a human plasma protein fraction. J Chromatogr A 1217: 3321-3329
 
Zhang F, Skoda MWA, Jacobs RMJ, Zorn S, Martin RA, Martin CM, Clark GF, Weggler S, Hildebrandt A, Kohlbacher O, Schreiber F (2008) Reentrant Condensation of Proteins ins Solution Induced by Multivalent Counterions. Phys Rev Lett 101: 148101
 
Toussaint NC, Dönnes P, Kohlbacher O (2008) A Mathematical Framework for the Selection of an Optimal Set of Peptides for Epitope-based Vaccines. PLoS Comput Biol 4: e1000246
 
Timm W, Scherbart A, Böcker S, Kohlbacher O, Nattkemper TW (2008) Peak Intensity Prediction in MALDI-TOF Mass Spectrometry: A Machine Learning Study to Support Quantitative Proteomics. BMC Bioinformatics 9: 443
 
Sturm M, Bertsch A, Gröpl C, Hildebrandt A, Hussong R, Lange E, Pfeifer N, Schulz-Trieglaff O, Zerck A, Reinert K, Kohlbacher O (2008) OpenMS - An open-source software framework for mass spectrometry. BMC Bioinformatics 9: 163
 
Seebeck B, Reulecke I, Kämper A, Rarey M (2008) Modeling of metal interaction geometries for protein-ligand docking. Proteins: Struct, Funct, Bioinf 71: 1237-1254
 
Schulz-Trieglaff O, Pfeifer N, Gröpl C, Kohlbacher O, Reinert K (2008) LC-MSsim - a simulation software for Liquid ChromatographyMass Spectrometry data. BMC Bioinformatics 9: 423
 
Schultheiss SJ, Busch W, Lohmann JU, Kohlbacher O, Rätsch G. (2008) KIRMES: Kernel-based Identification of Regulatory Modules in Euchromatic Sequences. Proc. German Conference Bioinformatikcs (GCB 2008). GI, pp. 158-167.
 
Reinert K, Huber C, Marcus K, Linial M, Kohlbacher O. (2008) 08101 Executive Summary and Abstracts Collection - Computational Proteomics. Computational Proteomics. Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany, Dagstuhl, Germany.
 
Reinert K, Conrad T, Kohlbacher O (2008) Bioinformatics Support for Mass Spectrometric Quality Control. In Proteomics Sample Preparation, pp 423-447. Weinheim
 
Raub S, Steffen A, Kämper A, Marian CM (2008) AIScore - Chemically diverse empirical scoring function employing quantum chemical binding energies of hydrogen-bonded complexes. J Chem Inf Model 48: 1492–-1510
 
Pfeifer N, Kohlbacher O. (2008) Multiple Instance Learning Allows MHC Class II Epitope Predictions across Alleles. Proceedings of the 8th Workshop on Algorithms in Bioinformatics (WABI 2008), Lecture Note in Bioinformatics vol. 5251. Springer, pp. 210-221.
 
Peifer C, Urich R, Schattel V, Abdaleh M, Röttig M, Kohlbacher O, Laufer S (2008) Implications for selectivity of 3,4-diarylquinolinones as p38aMAP kinase inhibitors. Bioorg Med Chem Lett 18: 1431-1435
 
Kerzmann A, Fuhrmann J, Kohlbacher O, Neumann D (2008) BALLDock/SLICK: A new Method for Protein-Carbohydrate Docking. J Chem Inf Model 48: 1616-1625
 
Keller AC, Backes C, Al-Awadhi M, Gerasch A, Küntzer J, Kohlbacher O, Kaufmann M, Lenhof H-P (2008) GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments. BMC Bioinformatics 9: 552
 
Feldhahn M, Thiel P, Schuler M, Hillen N, Stevanovic S, Rammensee H-G, Kohlbacher O (2008) EpiToolKit - A web server for computational immunomics. Nucleic Acids Res 36: W519-522
 
Borgatti S, Kobourov S, Kohlbacher O, Mutzel P. (2008) 08191 Abstracts Collection - Graph Drawing with Applications to Bioinformatics and Social Sciences. Graph Drawing with Applications to Bioinformatics and Social Sciences. Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany, Dagstuhl, Germany.
 
Borgatti S, Kobourov S, Kohlbacher O, Mutzel P. (2008) 08191 Executive Summary - Graph Drawing with Applications to Bioinformatics and Social Sciences. Graph Drawing with Applications to Bioinformatics and Social Sciences. Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany, Dagstuhl, Germany.
 
Blum T, Kohlbacher O (2008) Using atom mapping rules for an improved detection of relevant routes in weighted metabolic networks. J Comput Biol 15: 565-576
 
Blum T, Kohlbacher O (2008) MetaRoute - fast search for relevant metabolic routes for interactive network navigation and visualization. Bioinformatics 24: 2108-2109
 
Böcker S, Briesemeister S, Klau GW. (2008) Exact Algorithms for Cluster Editing: Evaluation and Experiments. Proc. of Workshop on Experimental Algorithms (WEA 2008). Springer, Vol. 5038, pp. 289-302.
 
Böcker S, Briesemeister S, Bui QB, Truss A. (2008) Going Weighted: Parameterized Algorithms for Cluster Editing. Proc. of Conference on Combinatorial Optimization and Applications (COCOA 2008). Springer, Vol. 5165, pp. 1-12.
 
Böcker S, Briesemeister S, Bui QB, Truss A. (2008) A fixed-parameter approach for Weighted Cluster Editing. Proc. of Asia-Pacific Bioinformatics Conference (APBC 2008). Imperial College Press, Vol. 5, pp. 211-220.
 
Albrecht M, Estrella-Balderrama A, Geyer M, Gutwenger C, Klein K, Kohlbacher O, Schulz M. (2008) 08191 Working Group Summary - Visually Comparing a Set of Graphs. Graph Drawing with Applications to Bioinformatics and Social Sciences. Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany, Dagstuhl, Germany.
 
Sturm M, Quinten S, Huber CG, Kohlbacher O (2007) A statistical learning approach to the modeling of chromatographic retention of oligonucleotides incorporating sequence and secondary structure data. Nucl Acids Res 35: 4195-4202
 
Steffen A, Thiele C, Tietze S, Strassnig C, Kämper A, Lengauer T, Wenz G, Apostolakis J (2007) Improved cyclodextrin-based receptors for camptothecin by inverse virtual screening. Chem Eur J 13: 6801-6809
 
Steffen A, Karasz M, Thiele C, Lengauer T, Kämper A, Wenz G, Apostolakis J (2007) Combined similarity and QSPR virtual screening for guest molecules of beta-cyclodextrin. New J Chem 31: 1941-1949
 
Shatkay H, Höglund A, Brady S, Blum T, Dönnes P, Kohlbacher O (2007) SherLoc : High-Accuracy Prediction of Protein Subcellular Localization by Integrating Text and Protein Sequence Data. Bioinformatics 23: 1410-1417
 
Pfeifer N, Leinenbach A, Huber CG, Kohlbacher O (2007) Statistical learning of peptide retention behavior in chromatographic separations: A new kernel-based approach for computational proteomics. BMC Bioinformatics 8: 468
 
Mitschke J, Fuss J, Blum T, Höglund A, Reski R, Kohlbacher O, Rensing S. (2007) Prediction of dual protein targeting to plant organelles. Proceedings of the German Conference on Bioinformatics (GCB 2007).
 
Küntzer J, Backes C, Blum T, Gerasch A, Kaufmann M, Kohlbacher O, Lenhof H-P (2007) BNDB - The Biochemical Network Database. BMC Bioinformatics 8: 367
 
Kohlbacher O, Reinert K, Gröpl C, Lange E, Pfeifer N, Schulz-Trieglaff O, Sturm M (2007) TOPP - The OpenMS Proteomics Pipeline. Bioinformatics 23: e191-e197
 
Hildebrandt A, Rjasanow S, Blossey R, Kohlbacher O, Lenhof H-P (2007) Electrostatic potentials of proteins in water: a structured continuum approach. Bioinformatics 23: e99-e100
 
Hildebrandt A, Kohlbacher O, Lenhof H-P (2007) Modeling Protein–Protein and Protein–DNA Docking. In Bioinformatics - From Genomes to Drugs, pp 601-650.
 
Blum T, Kohlbacher O. (2007) Finding relevant biotransformation routes in weighted metabolic networks using atom mapping rules. Proceedings of the German Conference on Bioinformatics (GCB 2007).
 
Sturm M, Quinten S, Huber CG, Kohlbacher O. (2006) A machine learning approach for prediction of DNA and peptide retention times. Proceedings of the Dagstuhl Seminar on Computational Proteomics 2005. Internationales Begegnungs- und Forschungszentrum (IBFI), Schloss Dagstuhl, Germany.
 
Reinert K, Kohlbacher O, Gröpl C, Lange E, Schulz-Trieglaff O, Sturm M, Pfeifer N. (2006) OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics. Computational Proteomics. Internationales Begegnungs- und Forschungszentrum fuer Informatik (IBFI), Schloss Dagstuhl, Germany.
 
Peifer C, Krasowski A, Hämmerle N, Kohlbacher O, Dannhardt G, Totzke F, Schächtele C, Laufer S (2006) Profile and Molecular Modeling of 3-(Indole-3-yl)-4-(3,4,5-trimethoxyphenyl)-1 H-pyrrole-2,5-dione (1) as a Highly Selective VEGF-R2/3 Inhibitor. J Med Chem 49: 7549-7553
 
Neumann D, Kohlbacher O, Merkwirth C, Lengauer T (2006) A fully computational model for predicting percutaneous drug absorption. J Chem Inf Model 46: 424-429
 
Moll A, Hildebrandt A, Lenhof H-P, Kohlbacher O (2006) BALLView: A tool for research and education in molecular modeling. Bioinformatics 22: 365-366
 
Moll A, Hildebrandt A, Lenhof H-P, Kohlbacher O (2006) BALLView: An object-oriented molecular visualization and modeling framework. J Comput-Aided Mol Des 19: 791
 
Mayr B, Kohlbacher O, Reinert K, Sturm M, Gröpl C, Lange E, Klein C, Huber CG (2006) Absolute Myoglobin Quantitation in Serum by Combining Two-Dimensional Liquid Chromatography-Electrospray Ionization Mass Spectrometry and Novel Data Analysis Algorithms. J Proteome Res 5: 414-421
 
Lange E, Gröpl C, Reinert K, Kohlbacher O, Hildebrandt A. (2006) High-Accuracy Peak Picking of Proteomics Data using Wavelet Techniques. Proceedings of the Pacific Symposium on Biocomputing (PSB 2006).
 
Küntzer J, Blum T, Gerasch A, Backes C, Hildebrandt A, Kaufmann M, Kohlbacher O, Lenhof H-P. (2006) BN++ - A Biological Information System. Proceedings of the 3rd International Workshop Integrative Bioinformatics. Rothamsted Research.
 
Kohlbacher O, Quinten S, Sturm M, Mayr B, Huber C (2006) Structure-Activity Relationships in Chromatography: Retention Prediction of Oligonucleotides with Support Vector Regression. Angew Chemie Int Ed 45: 7009-7012
 
Kerzmann A, Neumann D, Kohlbacher O (2006) SLICK - Scoring and Energy Functions for Protein-Carbohydrate Interactions. J Chem Inf Model 46: 1635-1642
 
Huson DH, Kohlbacher O, Lupas A, Nieselt K, Zell A (2006) German Conference on Bioinformatics, Vol. P-83,  Bonner Köllen Verlag: Gesellschaft für Informatik e.V.
 
Höglund A, Dönnes P, Blum T, Adolph H-W, Kohlbacher O (2006) MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs, and amino acid composition. Bioinformatics 22: 1158-1165
 
Höglund A, Blum T, Brady S, Dönnes P, Miguel JS, Rocheford M, Kohlbacher O, Shatkay H. (2006) Significantly improved prediction of subcellular localization by integrating text and protein sequence data. Proceedings of the Pacific Symposium on Biocomputing (PSB 2006). PSB.
 
Dönnes P, Kohlbacher O (2006) SVMHC: a server for prediction of MHC-binding peptides. Nucleic Acids Res 34: W194-W197
 
Baldes C, König P, Neumann D, Lenhof H-P, Kohlbacher O, Lehr C-M (2006) Development of a fluorescence-based assay for screening of modulators of human Organic Anion Transporter 1B3 (OATP1B3). Eur J Pharm Biopharm 62: 39-43
 
Supper J, Dönnes P, Kohlbacher O (2005) Analysis of MHC-Peptide Binding Using Amino Acid Property-Based Decision Rules. Springer Lecture Notes in Computer Science (LNCS) 3686: 446-453
 
Schuler MM, Dönnes P, Nastke M-D, Kohlbacher O, Rammensee H-G, Stevanovic S (2005) SNEP: SNP-derived Epitope Prediction program for minor H antigens. Immunogenetics 57: 816-820
 
Schuler M, Dönnes P, Nastke M, Kohlbacher O, Rammensee H-G, Stevanovic S. (2005) SNEP: SNP-derived Epitope Prediction program for minor H antigens. Joint Annual Meeting of the German and Scandinavian Societies of Immunology, 21-24 September 2005, Kiel, Germany. Immunobiology 210(6-8), pp. 361-622.
 
Rausch C, Weber T, Kohlbacher O, Wohlleben W, Huson D (2005) Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using Transductive Support Vector Machines (TSVM). Nucl Acids Res 33: 5799-5808
 
Moll A, Hildebrandt A, Kerzmann A, Lenhof H-P, Kohlbacher O. (2005) BALLView - An Open Source Tool for Molecular Modeling and Visualization. Tagungsband zum doIT Software-Forschungstag 2005. MFG Stiftung, Stuttgart, pp. 203-214.
 
Klein CL, Kohlbacher O, Huber C, Reinert K (2005) Reference methods and materials in standardisation and quality assurance. FEBS J 272
 
Höglund A, Dönnes P, Blum T, Adolph H-W, Kohlbacher O. (2005) Using N-terminal targeting sequences, amino acid composition, and sequence motifs for predicting protein subcellular localization. Proceedings of the German Conference on Bioinformatics (GCB 2005). GI, pp. 45-59.
 
Höglund A, Dönnes P, Adolph H, Kohlbacher O (2005) From prediction of subcellular localization to functional classification: Discrimination of DNA-packing and other nuclear proteins. Online Journal of Bioinformatics 6: 51-64
 
Gröpl C, Lange E, Reinert K, Kohlbacher O, Sturm M, Huber C, Mayr B, Klein C. (2005) Algorithms for the automated absolute quantification of diagnostic markers in complex proteomics samples. Proceedings of the 1st Symposium on Computational Life Sciences (CLS 2005). Springer LNBI 3695, pp. 151-161.
 
Dönnes P, Kohlbacher O (2005) Integrated modelling of the major events in the MHC class I antigen processing pathway. Protein Sci 14: 2132-2140
 
Berthold M, Glen R, Diederichs K, Kohlbacher O, Fischer I (2005) Computational Life Sciences, Vol. 3695: Springer Lecture notes in Bioinformatics.
 
Neumann D, Lehr C-M, Lenhof H-P, Kohlbacher O (2004) Computational modeling of the sugar–lectin interaction. Advanced Drug Delivery Reviews 56: 437-457
 
Kohlbacher O, Reinert K (2004) Differenzielle Proteomanalyse - Experimentelle Methoden, Algorithmische Herausforderungen. IT - Information Technology 46: 31-38
 
Kerzmann A, Neumann D, Kohlbacher O (2004) High-Accuracy Prediction of Protein-Carbohydrate Interactions. Trends in Glycoscience and Glycotechnology 16: S26
 
Istrail S, Florea L, Halldorsson BV, Kohlbacher O, Schwartz RS, Yap VB, Yewdell JW, Hoffman SL (2004) Comparative Immuno-Peptidomics of Humans and their Pathogens. Proc Natl Acad Sci USA 101: 13268
 
Höglund A, Kohlbacher O (2004) From sequence to structure and back again: approaches for predicting protein-DNA binding. Proteome Science 2: 3
 
Hildebrandt A, Blossey R, Rjasanow S, Kohlbacher O, Lenhof H-P (2004) Novel formulation of nonlocal electrostatics. Phys Rev Lett 93: 108104
 
Dönnes P, Höglund A, Sturm M, Comtesse N, Backes C, Meese E, Kohlbacher O, Lenhof H-P (2004) Integrative analysis of cancer-related data using CAP. FASEB Journal 18: 1465-1467
 
Dönnes P, Höglund A (2004) Predicting Protein Subcellular Localization: Past, Present, and Future. Genomics Proteomics Bioinformatics 2: 209-215
 
Sandelin A, Höglund A, Lenhard B, Wasserman W (2003) Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes. Funct Integr Genomics 3: 125-134
 
Hildebrandt A, Kohlbacher O, Blossey R, Lenhof H-P. (2003) Using nonlocal electrostatics for solvation free energy computations: ions and small molecules.
 
Florea L, Halldórsson B, Kohlbacher O, Schwartz R, Hoffman S, Istrail S. (2003) Epitope Prediction Algorithms for Peptide based Vaccine Design. Proceedings of the 2nd IEEE Computer Society Conference on Bioinformatics. IEEE Computer Society, pp. 17-26.
 
Sirava M, Schäfer T, Eiglsperger M, Kaufmann M, Kohlbacher O, Bornberg-Bauer E, Lenhof H-P (2002) BioMiner - modeling, analysing, and visualizing biochemical pathways and networks. Bioinformatics 19: S219-230
 
Neumann D, Kohlbacher O, Lenhof H-P, Lehr C-M (2002) Protein-sugar interactions: Calculated versus experimental binding energies. Eur J Biochem 269: 1518-1524
 
Neumann D, Kerzmann A, Kohlbacher O. (2002) Modelling the sugar-lectin interaction by computer simulated docking. Abstracts of the 20th Interlec Meeting. University of Copenhagen, Copenhagen, Denmark, p. 116.
 
Dönnes P, Elofsson A (2002) Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics 3
 
Althaus E, Kohlbacher O, Lenhof HP, Müller P (2002) A Combinatorial Approach to Protein Docking with Flexible Side-Chains. J Comput Biol 9: 597-612
 
Turner RJ, Chaturvedi K, Edwards NJ, Fasulo D, Halpern AL, Huson DH, Remington KA, Schwartz R, Walenz B, Yooseph S, Istrail S. (2001) Visualization Challenges for a New Cyberpharmaceutical Computing Paradigm. Proceedings of the IEEE Symposium on Parallel and Large-Data Visualization and Graphics (PVG2001), San Diego, USA,, pp. 7-18.
 
Kohlbacher O, Burchardt A, Moll A, Hildebrandt A, Bayer P, Lenhof H-P (2001) Structure prediction of protein complexes by a NMR-based protein docking algorithm. J Biomol NMR 20: 15-21
 
Kohlbacher O, Burchardt A, Hildebrandt A, Moll A, Bayer P, Lenhof H-P. (2001) A NMR-spectra-based scoring function for protein docking. RECOMB 2001, Proceedings of the Fifth Annual International Conference on Computational Molecular Biology. ACM press, pp. 169-177.
 
Kohlbacher O. (2001) BALL - A Framework for Rapid Application Development in Molecular Modeling. Beiträge zum Heinz-Billing-Preis 2000. Gesellschaft für wissenschaftliche Datenverarbeitung mbH, Göttingen, pp. 13-28.
 
Neumann D, Kohlbacher O, Haltner E, Lenhof H-P, Lehr C-M. (2000) Modeling the Sugar Lectin Interaction by Computational Chemistry Relevant to Drug Design. Proc. 3rd World Meeting on Pharmaceutics, Biopharmaceutics and Pharmaceutical Technology, p. 233.
 
Kohlbacher O, Lenhof H-P (2000) BALL - Rapid Software Prototyping in Computational Molecular Biology. Bioinformatics 16: 815-824
 
Boghossian NP, Kohlbacher O, Lenhof HP (2000) Rapid software prototyping in molecular modeling using the biochemical algorithms library (BALL). J Exp Algorithmics 5: 16
 
Althaus E, Kohlbacher O, Lenhof H-P, Müller P. (2000) A branch and cut algorithm for the optimal solution of the side-chain placement problem. Max-Planck-Institute für Informatik, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany.
 
Althaus E, Kohlbacher O, Lenhof H-P, Müller P. (2000) A Combinatorial Approach to Protein Docking with Flexible Side-Chains. RECOMB 2000 - Proceedings of the Fourth Annual International Conference on Computational Molecular Biology. ACM press, pp. 15-24.
 
Kohlbacher O, Lenhof H-P. (1999) Rapid Software Prototyping in Computational Molecular Biology. Proceedings of the German Conference on Bioinformatics (GCB'99).
 
Boghossian NP, Kohlbacher O, Lenhof H-P. (1999) BALL: Biochemical Algorithms Library. Algorithm Engineering, 3rd International Workshop, WAE'99, Proceedings. Springer, pp. 330-344.
 
Boghossian NP, Kohlbacher O, Lenhof H-P. (1999) BALL: Biochemical Algorithms Library. Max-Planck-Institut für Informatik, Saarbrücken, Germany.
 
Neumann D, Haltner E, Lehr C-M, Kohlbacher O, Lenhof H-P. (1998) Investigating the Sugar-Lectin Interaction by Computational Chemistry: Tunneling the Epithelial Barrier. Abstracts of the 18th Interlec Meeting, p. 549.