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.