Andreas Hildebrandt, Prof. Dr.

Head of Scientific Computing and Bioinformatics

Scientific Computing and Bioinformatics
Institute of Computer Science
Johannes Gutenberg University
Staudingerweg 9
55128 Mainz, Germany

Office: 03-433
Phone: +49 (0) 6131 39 23334
Fax: +49 (0) 6131 39 23534



Seifert, T, Lund, A, Kneissl, B, Mueller, SC, Tautermann, CS, and Hildebrandt, A (2014).
SKINK: a web server for string kernel based kink prediction in α-helices

Cabezas-Wallscheid, N, Eichwald, V, de Graaf, J, Löwer, M, Lehr, H, Kreft, A, Eshkind, L, Hildebrandt, A, Abassi, Y, Heck, R, Dehof, AK, Ohngemach, S, Sprengel, R, Wörtge, S, Schmitt, S, Lotz, J, Meyer, C, Kindler, T, Zhang, D, Kaina, B, Castle, JC, Trumpp, A, Sahin, U, and Bockamp, E (2013).
Instruction of haematopoietic lineage choices, evolution of transcriptional landscapes and cancer stem cell hierarchies derived from an AML1-ETO mouse model
EMBO Molecular Medicine, 5(12):1804–1820.

Dehof, AK, Loew, S, Lenhof, H, and Hildebrandt, A (2013).
NightShift: NMR Shift Inference by General Hybrid Model Training – a Framework for NMR Chemical Shift Prediction.
BMC Bioinformatics, 14(1):98.

Hildebrandt, AK, Althaus, E, Lenhof, H, Hung, C, Tholey, A, and Hildebrandt, A (2013).
Efficient Interpretation of Tandem Mass Tags in Top-Down Proteomics
In: German Conference on Bioinformatics 2013, ed. by Tim Beißbarth and Martin Kollmar and Andreas Leha and Burkhard Morgenstern and Anne-Kathrin Schultz and Stephan Waack and Edgar Wingender, vol. 34, pp. 56–67, Dagstuhl, Germany, Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik. OpenAccess Series in Informatics (OASIcs) (ISBN: 978-3-939897-59-0).

Hildebrandt, AK, Dietzen, M, Lengauer, T, Lenhof, H, Althaus, E, and Hildebrandt, A (2013).
Efficient computation of root mean square deviations under rigid transformations
Journal of Computational Chemistry:n/a–n/a.

Maixner, F, Overath, T, Linke, D, Janko, M, Guerriero, G, van den Berg, BHJ, Stade, B, Leidinger, P, Backes, C, Jaremek, M, Kneissl, B, Meder, B, Franke, A, Egarter-Vigl, E, Meese, E, Schwarz, A, Tholey, A, Zink, A, and Keller, A (2013).
Paleoproteomic study of the Iceman’s brain tissue.
Cellular and Molecular Life Sciences CMLS .

Marquardt, JU, Fischer, K, Baus, K, Kashyap, A, Ma, S, Krupp, M, Linke, M, Teufel, A, Zechner, U, Strand, D, Thorgeirsson, SS, Galle, PR, and Strand, S (2013).
SIRT6 dependent genetic and epigenetic alterations are associated with poor clinical outcome in HCC patients

Nickels, S, Stockel, D, Mueller, S, Lenhof, H, Hildebrandt, A, and Dehof, A (2013).
PresentaBALL – A powerful package for presentations and lessons in structural biology
In: Biological Data Visualization (BioVis), 2013 IEEE Symposium on, pp. 33-40.

Becker, D, Sfakianakis, I, Krupp, M, Staib, F, Gerhold-Ay, A, Victor, A, Binder, H, Blettner, M, Maass, T, Thorgeirsson, S, Galle, PR, and Teufel, A (2012).
Genetic signatures shared in embryonic liver development and liver cancer define prognostically relevant subgroups in HCC
Molecular cancer, 11(1):55.

Benz, F, Hildebrandt, A, and Hack, S (2012).
A Dynamic Program Analysis to find Floating-Point Accuracy Problems
In: PLDI ’12: Proceedings of the 2012 ACM SIGPLAN Conference on Programming Language Design and Implementation.

Dietzen, M, Zotenko, E, Hildebrandt, A, and Lengauer, T (2012).
On the applicability of elastic network normal modes in small-molecule docking.
J Chem Inf Model, 52(3):844-56.

Krupp, M, Itzel, T, Maass, T, Hildebrandt, A, Galle, PR, and Teufel, A (2012).
CellLineNavigator: a workbench for cancer cell line analysis
Nucleic acids research.

Krupp, M, Marquardt, JU, Sahin, U, Galle, PR, Castle, J, and Teufel, A (2012).
RNA-Seq Atlas – A reference database for gene expression profiling in normal tissue by next generation sequencing

Nickels, S, Sminia, H, Mueller, S, Kools, B, Dehof, AK, Lenhof, H, and Hildebrandt, A (2012).
ProteinScanAR – An augmented reality web application for high school education in biomolecular life sciences
In: Proceedings of the 6th International Symposium on Information Visualization in Biomedical Informatics (IVBI) 2012.

Slawski, M, Hussong, R, Tholey, A, Jakoby, T, Gregorius, B, Hildebrandt, A, and Hein, M (2012).
Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching.
BMC Bioinformatics, 13:291.

Teufel, A, Becker, D, Weber, SN, Dooley, S, Breitkopf-Heinlein, K, Maass, T, Hochrath, K, Krupp, M, Marquardt, JU, Kolb, M, Korn, B, Niehrs, C, Zimmermann, T, Godoy, P, Galle, PR, and Lammert, F (2012).
Identification of RARRES1 as a core regulator in liver fibrosis
Journal of Molecular Medicine (Berlin, Germany).

Bardhan, JP and Hildebrandt, A (2011).
A Fast Solver for Nonlocal Electrostatic Theory in Biomolecular Science and Engineering
In: Design Automation Conference (DAC), 2011 48th ACM/EDAC/IEEE.

Dehof, AK, Rurainski, A, Bui, QB, Böcker, S, Lenhof, H, and Hildebrandt, A (2011).
Automated bond order assignment as an optimization problem
Bioinformatics, 27(5):619-625.

Kneissl, B, Müller, SC, Tautermann, CS, and Hildebrandt, A (2011).
String Kernels and High-Quality Data Set for Improved Prediction of Kinked Helices in α-Helical Membrane Proteins
Journal of Chemical Information and Modeling, 51(11):3017-3025.

Krupp, M, Maass, T, Marquardt, JU, Staib, F, Tobias, B, König, R, Biesterfeld, S, Galle, PR, Tresch, A, and Teufel, A (2011).
The functional cancer map: a systems-level synopsis of genetic deregulation in cancer.
BMC Med Genomics, 4:53.

Rey, JW, Schreiner, O, Barreiros, AP, Heise, M, Krupp, M, Schuchmann, M, Otto, G, Galle, PR, and Teufel, A (2011).
Acute renal failure and liver dysfunction after subcutaneous injection of 3-sn-phosphatidylcholine(Lipostabil®)-case report.
Z Gastroenterol, 49:340-343.

Buchkremer, S, Hendel, J, Krupp, M, Weinmann, A, Schlamp, K, Maass, T, Staib, F, Galle, PR, and Teufel, A (2010).
Library of molecular associations: curating the complex molecular basis of liver diseases.
BMC Genomics, 11(1):189.

Gregorius, B, Schaumloffel, D, Hildebrandt, A, and Tholey, A (2010).
Characterization of metal-labelled peptides by matrix-assisted laser desorption/ionization mass spectrometry and tandem mass spectrometry.
Rapid Commun Mass Spectrom, 24(22):3279-89.

Hildebrandt, A, Dehof, A, Rurainski, A, Bertsch, A, Schumann, M, Toussaint, NC, Moll, A, Stockel, D, Nickels, S, Müller, SC, Lenhof, HP, and Kohlbacher, O (2010).
BALL – Biochemical Algorithms Library 1.3.
BMC Bioinformatics, 11(1):531.

Kugamoorthy, G, Nakasone, A, Hildebrandt, A, and Prendinger, H (2010).
A novel three-dimensional collaborative online platform for bio-molecular modeling.
Proc 10th Int’l Symp on Smart Graphics (SG’10), Banff, Canada (Springer LNCS, Berlin Heidelberg 2010.6).

Maass, T, Sfakianakis, I, Staib, F, Krupp, M, Galle, PR, and Teufel, A (2010).
Microarray-based gene expression analysis of hepatocellular carcinoma.
Curr Genomics, 11:261-268.

Marsalek, L, Georgiev, I, Dehof, AK, Lenhof, H, Slusallek, P, and Hildebrandt, A (2010).
Real-Time Ray Tracing of Complex Molecular Scenes
In: Proceedings of the IVbm 10 – Information Visualization in Biomedical Informatics.

Phillips, M, Georgiev, I, Dehof, AK, Nickels, S, Marsalek, L, Lenhof, H, Hildebrandt, A, and Slusallek, P (2010).
Measuring Properties of Molecular Surfaces Using Ray Casting
Proceedings of 9th International Workshop on High Performance Computational Biology.

Singh, KK, Erkelenz, S, Rattay, S, Dehof, AK, Hildebrandt, A, Schulze-Osthoff, K, Schaal, H, and Schwerk, C (2010).
Human SAP18 mediates assembly of a splicing regulatory multiprotein complex via its ubiquitin-like fold.

Weggler, S, Rutka, V, and Hildebrandt, A (2010).
A new numerical method for nonlocal electrostatics in biomolecular simulations
Journal of Computational Physics, 229(11):4059-4074.

Dehof, AK, Rurainski, A, Lenhof, H, and Hildebrandt, A (2009).
Automated Bond Order Assignment as an Optimization Problem
Proceedings of the German Conference On Bioinformatics 2009:201–210.

Hussong, R and Hildebrandt, A (2009).
Signal Processing in Proteomics
In: Proteome bioinformatics: Informatics for mass spectrometry based protein science, ed. by Simon Hubbard, Andrew Jones. Humana Press, chap. 11, pp. 145-161. Methods of Molecular Biology.

Hussong, R, Gregorius, B, Tholey, A, and Hildebrandt, A (2009).
Highly accelerated feature detection in proteomics data sets using modern graphics processing units
Bioinformatics, 25:1937–1943.

Kneissl, B, Leonhardt, B, Hildebrandt, A, and Tautermann, CS (2009).
Revisiting Automated G-Protein Coupled Receptor Modeling: The Benefit of Additional Template Structures for a Neurokinin-1 Receptor Model
Journal of Medicinal Chemistry, 52(10):3166-3173.

Leinenbach, A, Hartmer, R, Lubeck, M, Kneissl, B, Elnakady, YA, Baessmann, C, Müller, R, and Huber, CG (2009).
Proteome Analysis of Sorangium cellulosum Employing 2D-HPLC-MS/MS and Improved Database Searching Strategies for CID and ETD Fragment Spectra
Journal of Proteome Research, 8(9):4350-4361.

Rurainski, A, Hildebrandt, A, and Lenhof, H (2009).
A consensus line search algorithm for molecular potential energy functions.
J Comput Chem, 30(9):1499-509.

Wang, C, Maass, T, Krupp, M, Thieringer, F, Strand, S, Wörns, MA, Barreiros, AP, Galle, PR, and Teufel, A (2009).
A systems biology perspective on cholangiocellular carcinoma development: focus on MAPK-signaling and the extracellular environment.
J Hepatology, 50:1122-1131.

Schlamp, K, Weinmann, A, Krupp, M, Maass, T, Galle, PR, and Teufel, A (2008).
BlotBase: a northern blot database.
Gene, 427:47-50.

Schulz-Trieglaff, O, Hussong, R, Gröpl, C, Leinenbach, A, Hildebrandt, A, Huber, C, and Reinert, K (2008).
Computational Quantification of Peptides from LC-MS Data
Journal of Computational Biology, 15(7):685–704.

Sturm, M, Bertsch, A, Gröpl, C, Hildebrandt, A, Hussong, R, Lange, E, Pfeifer, N, Schulz-Trieglaff, O, Zerck, A, Reinert, K, and Kohlbacher, O (2008).
OpenMS – An open-source software framework for mass spectrometry
BMC Bioinformatics 2008, 9(163).

Zhang, F, Skoda, MW, Jacobs, RM, Zorn, S, Martin, RA, Martin, CM, Clark, GF, Weggler, S, Hildebrandt, A, Kohlbacher, O, and Schreiber, F (2008).
Reentrant Condensation of Proteins in Solution Induced by Multivalent Counterions
Physical Review Letters, 101(14):148101.

Backes, C, Keller, A, Küntzer, J, Kneissl, B, Comtesse, N, Elnakady, YA, Müller, R, Meese, E, and Lenhof, H (2007).
GeneTrail—advanced gene set enrichment analysis
Nucleic Acids Research, 35(2):W186-W192.

Hildebrandt, A, Blossey, R, Rjasanow, S, Kohlbacher, O, and Lenhof, H (2007).
Electrostatic potentials of proteins in water: a structured continuum approach.
Bioinformatics, 23(2):e99-103.

Hussong, R and Hildebrandt, A (2007).
The Isotope Wavelet: A Signal Theoretic Framework for Analyzing Mass Spectrometry Data
No source specified

Hussong, R, Tholey, A, and Hildebrandt, A (2007).
Efficient Analysis of Mass Spectrometry Data Using the Isotope Wavelet
In: COMPLIFE 2007: The Third International Symposium on Computational Life Science, pp. 139–49, American Institute of Physics (AIP) Proceedings Volume 940.

Küntzer, J, Kneissl, B, Kohlbacher, O, and Lenhof, H (2007).
Abstract analysis of pathways using the BN++ software framework
BMC Systems Biology, 1(2):24.

Schulz-Trieglaff, O, Hussong, R, Gröpl, C, Hildebrandt, A, and Reinert, K (2007).
A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry Data
In: Proceedings of the Eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB 2007), Lecture Notes in Bioinformatics (LNBI) 4453, pp. 473–87, Springer. Lecture Notes in Bioinformatics.

Teufel, A, Weinmann, A, Krupp, M, Budinger, M, and Galle, PR (2007).
Genome-wide analysis of factors regulating gene expression in liver.
Gene, 389:114-121.

Hildebrandt, A, Kohlbacher, O, and Lenhof, H (2006).
Modelling Protein-Protein and Protein-DNA Interactions
In: Bioinformatics – From Genomes to Drugs, ed. by Thomas Lengauer. Wiley-VCH, chap. 17, pp. 601-651.

Keller, A, Ludwig, N, Comtesse, N, Hildebrandt, A, Meese, E, and Lenhof, H (2006).
A minimally invasive multiple marker approach allows highly efficient detection of meningioma tumors.
BMC Bioinformatics, 7:539.

Krupp, M, Weinmann, A, Galle, PR, and Teufel, A (2006).
Actin binding LIM protein 3 (abLIM3).
Int J Mol Med, 17:129-133.

Küntzer, J, Blum, T, Gerasch, A, Backes, C, Hildebrandt, A, Kaufmann, M, Kohlbacher, O, and Lenhof, H (2006).
BN++ – A Biological Information System
In: Proceedings of the 3rd International Workshop Integrative Bioinformatics, Rothamsted Research.

Lange, E, Gröpl, C, Reinert, K, Kohlbacher, O, and Hildebrandt, A (2006).
High-Accuracy Peak Picking of Proteomics Data using Wavelet Techniques
In: Proceedings of the Pacific Symposium on Biocomputing (PSB 2006).

Moll, A, Hildebrandt, A, Lenhof, H, and Kohlbacher, O (2006).
BALLView: An object-oriented molecular visualization and modeling framework
J. Comput.-Aided Mol. Des., 19(11):791.

Moll, A, Hildebrandt, A, Lenhof, H, and Kohlbacher, O (2006).
BALLView: A tool for research and education in molecular modeling
Bioinformatics, 22(3):365–366.

Teufel, A, Krupp, M, Weinmann, A, and Galle, PR (2006).
Current bioinformatics tools in genomic biomedical research (Review).
Int J Mol Med, 17:967-973.

Toll, H, Berger, P, Hofmann, A, Hildebrandt, A, Oberacher, H, Lenhof, HP, and Huber, CG (2006).
Glycosylation patterns of human chorionic gonadotropin revealed by liquid chromatography-mass spectrometry and bioinformatics.
Electrophoresis, 27(13):2734-2746.

Comtesse, N, Zippel, A, Walle, S, Monz, D, Backes, C, Fischer, U, Mayer, J, Ludwig, N, Hildebrandt, A, Keller, A, Steudel, W, Lenhof, H, and Meese, E (2005).
Complex humoral immune response against a benign tumor: frequent antibody response against specific antigens as diagnostic targets.
Proc Natl Acad Sci U S A, 102(27):9601-6.

Moll, A, Hildebrandt, A, Kerzmann, A, Lenhof, H, and Kohlbacher, O (2005).
BALLView – An Open Source Tool for Molecular Modeling and Visualization
In: Tagungsband zum doIT Software-Forschungstag 2005, ed. by D. Spath, K. Haasis, D. Klumpp, pp. 203–214, Stuttgart, MFG Stiftung. Aktuelle Trends in der Softwareforschung.

von Mering, C, Jensen, LJ, Snel, B, Hooper, SD, Krupp, M, Foglierini, M, Jouffre, N, Huynen, M, and Bork, P (2005).
STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
Nucleic Acids Res, 33:D433-437.

Hildebrandt, A, Blossey, R, Rjasanow, S, Kohlbacher, O, and Lenhof, H (2004).
Novel formulation of nonlocal electrostatics
Phys. Rev. Lett., 93:108104.

Hildebrandt, A, Kohlbacher, O, Blossey, R, and Lenhof, H (2003).
Using nonlocal electrostatics for solvation free energy computations: ions and small molecules

Kohlbacher, O, Burchardt, A, Hildebrandt, A, Moll, A, Bayer, P, and Lenhof, H (2001).
A NMR-spectra-based scoring function for protein docking
In: RECOMB 2001, Proceedings of the Fifth Annual International Conference on Computational Molecular Biology, ed. by David Sankoff and Thomas Lengauer, pp. 169-177, ACM press.

Kohlbacher, O, Burchardt, A, Moll, A, Hildebrandt, A, Bayer, P, and Lenhof, H (2001).
Structure prediction of protein complexes by a NMR-based protein docking algorithm
J. Biomol. NMR, 20:15-21.