List of all publications

This folder holds the following references to publications, sorted by year and author.

There are 57 references in this bibliography folder.

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.

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
Bioinformatics.

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.
RNA.

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.