Publications

Althaus, E, Hoffmann, S, Kupilas, J, and Thaden, E (2012).
A Column Generation Approach to Scheduling of Real-Time Networks
In: Proceedings of the World Congress on Engineering and Computer Science (WCECS), vol. 1, pp. 224–229, IAENG, San Francisco, USA, IAENG (ISBN: 978-988-19251-6-9).

Grunzke, R, Birkenheuer, G, Blunk, D, Breuers, S, Brinkmann, A, Gesing, S, Herres-Pawlis, S, Kohlbacher, O, Krüger, J, Kruse, M, Müller-Pfefferkorn, R, Schäfer, P, Schuller, B, Steinke, T, and Zink, A (2012).
A Data Driven Science Gateway for Computational Workflows
In: Proceedings of the UNICORE Summit 2012, Dresden, Germany.

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.

Liu, Y, Schmidt, B, and Maskell, DL (2012).
A fast CUDA compatible short read aligner to large genomes
In: GPU Technology Conference 2012 (GTC 2012), Poster.

Liu, Y, Schmidt, B, and Maskell, DL (2012).
A fast CUDA compatible short read aligner to large genomes
In: GPU Technology Conference 2012 (GTC 2012).

Gesing, S, Herres-Pawlis, S, Birkenheuer, G, Brinkmann, A, Grunzke, R, Kacsuk, P, Kohlbacher, O, Kozlovszky, M, Krüger, J, Müller-Pfefferkorn, R, Schäfer, P, and Steinke, T (2012).
A Science Gateway Getting Ready for Serving the International Molecular Simulation Community
Proceedings of Science - EGICF12-EMITC2.

Gesing, S, Grunzke, R, Krüger, J, Birkenheuer, G, Wewior, M, Schäfer, P, Schuller, B, Schuster, J, Herres-Pawlis, S, Breuers, S, Balaskó, �, Kozlovszky, M, Fabri, AS, Packschies, L, Kacsuk, P, Blunk, D, Steinke, T, Brinkmann, A, Fels, G, Müller-Pfefferkorn, R, Jäkel, R, and 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.

Seeland, M, Karwath, A, and Kramer, S (2012).
A Structural Cluster Kernel for Learning on Graphs
In: Proceedings of the 18th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, pp. 516-524.

Meister, D, Kaiser, J, Brinkmann, A, Kuhn, M, Kunkel, J, and Cortes, T (2012).
A Study on Data Deduplication in HPC Storage Systems
In: Proceedings of Supercomputing 2012, New York, NY, USA, ACM. SC '12.

Grzonka, S, Karwath, A, Dijoux, F, and Burgard, W (2012).
Activity-Based Estimation of Human Trajectories
IEEE Transactions on Robotics, 28(1):234–245.

Dangelmaier, W, Fischer, M, Huber, D, Laroque, C, and Süß, T (2008).
Aggregated 3D-Visualization of a Distributed Simulation Experiment of a Queuing System
In: Winter Simulation Conference (WSC´ 08), ed. by Mason, S. J. and Hill, R. and Moench, L. and Rose, O., pp. 2012 - 2020, IEEE, Omnipress.

Schlitt, S, Gorelik, TE, Stewart, AA, Schömer, E, Raasch, T, and Kolb, U (2012).
Application of clustering techniques to electron-diffraction data: determination of unit-cell parameters
Acta Crystallographica Section A, 68(5):536–546.

Süß, T, Koch, C, Jähn, C, Fischer, M, and Meyer auf der Heide, F (2012).
Asynchronous Occlusion Culling on Heterogeneous PC Clusters for Distributed 3D Scenes
In: Advances in Visual Computing, vol. 7431, pp. 502-512, Springer Berlin Heidelberg. Lecture Notes in Computer Science. (ISBN: 978-3-642-33178-7).

Groß, D, Heil, U, Schulze, R, Schömer, E, and Schwanecke, U (2012).
Auto calibration of a cone-beam-CT
Medical Physics, 39(10):5959-5970.

Berenbrink, P, Brinkmann, A, Friedetzky, T, and Nagel, L (2012).
Balls into bins with related random choices
J. Parallel Distrib. Comput., 72(2):246-253.

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.

Althaus, E and Dumitriu, D (2012).
Certifying Feasibility and Objective Value of Linear Programs
Operations Research Letters.

Gütlein, M, Karwath, A, and Kramer, S (2012).
CheS-Mapper – Chemical Space Mapping and Visualization in 3D
Journal of Cheminformatics, 4(7).

Pesch, R, Böck, M, and Zimmer, R (2012).
ConReg: Analysis and Visualization of Conserved Regulatory Networks in Eukaryotes
In: Proceedings of the German Conference on Bioinformatics (GCB) 2012, Open Access Series in Informatics of the Schloss Dagstuhl (accepted).

Niehörster, O, Brinkmann, A, Keller, A, Kleineweber, C, Krüger, J, and Simon, J (2012).
Cost-Aware and SLO-Fulfilling Software as a Service
Journal of Grid Computing, 10(3):553-577.

Liu, Y, Schmidt, B, and Maskell, DL (2012).
CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform
Bioinformatics, 28(14):1830-1837.

Kaiser, J, Meister, D, Brinkmann, A, and Effert, S (2012).
Design of an exact data deduplication cluster
In: Mass Storage Systems and Technologies (MSST), 2012 IEEE 28th Symposium on, pp. 1–12, IEEE.

Limbach, S, Schömer, E, and Wernli, H (2012).
Detection, tracking and event localization of jet stream features in 4-D atmospheric data
Geoscientific Model Development, 5(2):457–470.

Shao, J, Yang, Q, Wohlschlaeger, A, and Sorg, C (2012).
Discovering Aberrant Patterns of Human Connectome in Alzheimer’s Disease via Subgraph Mining
In: IEEE International Conference on Data Mining, Workshop on Biological Data Mining and its Applications in Healthcare (BioDM), in press.

Li, R and Kramer, S (2012).
Efficient Redundancy Reduced Subgroup Discovery via Quadratic Programming
In: The 15th International Conference on Discovery Science, pp. 125–138, Lyon, France, Springer-Verlag. Lecture Notes in Artificial Intelligence (LNAI).

Kaiser, J, Meister, D, Hartung, T, and Brinkmann, A (2012).
ESB: Ext2 Split Block Device
In: Proceedings of the 18th IEEE International Conference on Parallel and Distributed Systems (ICPADS), Singapore.

Liu, Y and Schmidt, B (2012).
Evaluation of GPU-based seed generation for computational genomics using Burrows-Wheeler transform
In: 11th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2012), pp. 684-690, IEEE.

Liu, Y and Schmidt, B (2012).
Evaluation of GPU-based seed generation for computational genomics using Burrows-Wheeler transform
In: 11th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2012), IEEE.

Wirawan, A, Kwoh, CK, Chew, PTK, Aquino, MCD, Loon, SC, See, J, Zheng, C, and Lin, W (2012).
Feature Selection for Computer-Aided Angle Closure Glaucoma Mechanism Detection
Journal of Medical Imaging and Health Informatics , 2(4):438-444.

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.

von Dziegielewski, A, Hemmer, M, and Schömer, E (2012).
High Quality Surface Mesh Generation for Swept Volumes
In: Proc. IEEE International Conference on Robotics and Automation (ICRA'12), St. Paul.

von Dziegielewski, A, Hemmer, M, and Schömer, E (2011).
High Quality Surface Mesh Generation for Swept Volumes
In: EuroCG Workshop on Computational Geometry.

Böck, M, Ogishima, S, Tanaka, H, Kramer, S, and Kaderali, L (2012).
Hub-Centered Gene Network Reconstruction using Automatic Relevance Determination
PLoS ONE, 7(5):e35077.

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).

Schmidt, J, Hapfelmeier, A, Schmidt, W, and Wollina, U (2012).
Improving Wound Score Classification with Limited Remission Spectra
International Wound Journal, Wiley-Blackwell, 9(2):189-98.

Hapfelmeier, A, Schmidt, J, and Kramer, S (2013).
Incremental Linear Model Trees on Massive Datasets: Keep it Simple, Keep it Fast
In: Proceedings of the 28th Symposium On Applied Computing, accepted.

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.

Schmidt, B, Aribowo, H, and Dang, H (2012).
Iterative Sparse Matrix-Vector Multiplication for Accelerating the Block Wiedemann Algorithm over GF(2) on Multi-GPU Systems
Concurrency and Computation: Practice and Experience.

Nguyen, TD, Schmidt, B, Zheng, Z, and Kwoh, CK (2012).
Large-Scale Clustering of Short Reads for Metagenomics on GPUs
In: Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, ed. by Mourad Elloumi and Albert Y. Zomaya. Wiley-Blackwell, chap. to appear, pp. .

Nguyen, TD, Schmidt, B, Zheng, Z, and Kwoh, CK (2012).
Large-Scale Clustering of Short Reads for Metagenomics on GPUs
In: Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, ed. by Mourad Elloumi and Albert Y. Zomaya. Wiley-Blackwell, chap. to appear, pp. .

Liu, Y and Schmidt, B (2012).
Long read alignment based on maximal exact match seeds
Bioinformatics, 28(18):i318-i324.

Seeland, M, Pfahringer, B, and Kramer, S (2012).
Maximum Common Subgraph Based Locally Weighted Regression
In: Proceedings of the 27th Symposium On Applied Computing, pp. 484-491.

Plant, C, Thai, SM, Shao, J, Theis, F, Meyer-Baese, A, and Boehm, C (2012).
Measuring Non-Gaussianity by Phi-transformed and Fuzzy Histograms
Advances in Artificial Neural Systems:in press.

Heil, U, Gross, D, Schulze, R, Schwanecke, U, and Schömer, E (2011).
Metal artifact reduction in x-ray computed tomography: Inpainting versus missing value
In: Nuclear Science Symposium and Medical Imaging Conference (NSS/MIC), 2011 IEEE, pp. 2675 - 2677 (ISBN: 978-1-4673-0118-3).

Seeland, M, Kramer, S, and Pfahringer, B (2013).
Model Selection Based Product Kernel Learning for Regression on Graphs
In: Proceedings of the 28th Symposium On Applied Computing, to appear.

Kovacs, J, Araujo, F, Boychenko, S, Keller, M, and Brinkmann, A (2012).
Monitoring UNICORE jobs executed on Desktop Grid resources
In: Proceedings of the 36th International Convention on Information and Communication Technology, Electronics and Microelectronics (MIPRO), Opatija/Abaazia, Crotia.

Yang, Q, Shao, J, Scholz, M, Boehm, C, and Plant, C (2012).
Multi-label classification model for Sustainable Flood Retention Basins
Environmental Modelling & Software, 32:27–36.

Wicker, J, Pfahringer, B, and Kramer, S (2012).
Multi-Label Classification using Boolean Matrix Decomposition
In: Proceedings of the 27th Symposium On Applied Computing, pp. 498-505, ACM.

Berenbrink, P, Czumaj, A, Englert, M, Friedetzky, T, and Nagel, L (2012).
Multiple-Choice Balanced Allocation in (Almost) Parallel.
In: APPROX-RANDOM, ed. by Gupta, Anupam and Jansen, Klaus and Rolim, José D. P. and Servedio, Rocco A., vol. 7408, pp. 411-422, Springer. Lecture Notes in Computer Science (ISBN: 978-3-642-32511-3).

Liu, Y, Schroeder, J, and Schmidt, B (2013).
Musket: a multistage k-mer spectrum based error corrector for Illumina sequence data
Bioinformatics, 29(3):308-315.

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.

Popov, I, Brinkmann, A, and Friedetzky, T (2012).
On the Influence of PRNGs on Data Distribution
In: Proceedings of the 20th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP), pp. 536-543, Munich, Germany (ISBN: 978-1-4673-0226-5).

Congiu, G, Grawinkel, M, Narasimhamurthy, S, and Brinkmann, A (2012).
One Phase Commit: A Low Overhead Atomic Commitment Protocol for Scalable Metadata Services
In: Proceedings of the 4th Workshop on Interfaces and Architectures for Scientific Data Storage (IASDS), Beijing, China.

Geilke, M, Frank, E, and Kramer, S (2012).
Online Estimation of Discrete Densities using Classifier Chains
Miscellaneous publication, ECML-PKDD 2012 workshop Instant Interactive Data Mining.

Schmidt, J and Kramer, S (2012).
Online Induction of Probabilistic Real Time Automata
In: Proceedings of the 2012 IEEE International Conference on Data Mining (ICDM 2012).

Endler, S and Perl, J (2012).
Optimizing practice and competition in marathon running by means of the meta-model PerPot
In: Pre-Olympic Congress on Sports Science and Computer Science in Sport, ed. by Yong Jiang and Arnold Baca, pp. 127-131.

Perl, J and Endler, S (2012).
PerPot Individual Anaerobe Threshold Marathon Scheduling
International Journal of Computer Science in Sport, 11(2).

Geilke, M and Zilles, S (2012).
Polynomial-Time Algorithms for Learning Typed Pattern Languages
In: Proceedings of the 6th International Conference on Language and Automata Theory and Applications, pp. 277-288.

Danso-Amoako, E, Scholz, M, Kalimeris, N, Yang, Q, and Shao, J (2012).
Predicting dam failure risk for sustainable flood retention basins: A generic case study for the wider Greater Manchester area
Computers, Environment and Urban Systems, 36(5):423-433 .

Ganzert, S, Kramer, S, and Guttmann, J (2012).
Predicting the lung compliance of mechanically ventilated patients via statistical modeling
Physiological Measurement, 33:345-359.

Shao, J, Myers, N, Yang, Q, Feng, J, Plant, C, Böhm, C, Förstl, H, Kurz, A, Zimmer, C, Meng, C, Riedl, V, Wohlschläger, A, and Sorg, C (2012).
Prediction of Alzheimer's disease using individual structural connectivity networks.
Neurobiol Aging.

Yang, Q, Shao, J, and Scholz, M (2012).
Prediction of Sustainable Flood Retention Basin Characteristics using a Self-Organizing Map
Environmental Engineering and Management Journal.

Beisel, T, Wiersema, T, Plessl, C, and Brinkmann, A (2012).
Programming and Scheduling Model for Supporting Heterogeneous Accelerators in Linux
In: Proceedings of the 3rd Workshop on Computer Architecture and Operating System Co-design (CAOS), Paris, France.

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.

von Dziegielewski, A, Erbes, R, and Schömer, E (2010).
Real Time Offset Surfaces
In: EuroCG Workshop on Computational Geometry.

Lim, KG, Kwoh, CK, Hsu, LY, and Wirawan, A (2012).
Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance
Briefings in Bioinformatics.

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.

Schmidt, J, Ansorge, S, and Kramer, S (2012).
Scalable Induction of Probabilistic Real-Time Automata Using Maximum Frequent Pattern Based Clustering
In: Proceedings of the twelfth SIAM International Conference on Data Mining, pp. to appear, SIAM / Omnipress.

Perl, J, Memmert, D, Baca, A, Endler, S, Grunz, A, Rebel, M, and Schmidt, A (2012).
Sensors, Monitoring and Model-Based Data Analysis in Sports, Exercise and Rehabilitation
In: Healthcare Sensor Networks. Challenges Towards Practical Implementation, ed. by Lai, Begg and Palaniswami, pp. 375-405, CRC Press.

Shao, J (2012).
Synchronization on Data Mining
LAP LAMBERT Academic Publishing.

Shao, J, He, X, Bohm, C, Yang, Q, and Plant, C (2012).
Synchronization-Inspired Partitioning and Hierarchical Clustering
IEEE Transactions on Knowledge and Data Engineering, 99(PrePrints).

Dang, H and Schmidt, B (2012).
The Sliced COO format for Sparse Matrix-Vector Multiplication on CUDA-enabled GPUs
In: International Conference on Computational Science.

Grawinkel, M, Süß, T, Best, G, Popov, I, and Brinkmann, A (2012).
Towards Dynamic Scripted pNFS Layouts
In: Proceedings of the 7th Parallel Data Storage Workshop (PDSW), Salt Lake City, Utah, USA.

Duchrow, T, Schröer, M, Griesbach, B, Kasperski, S, Maas genannt Bermpohl, G, Kramer, S, and Kirchner, F (2012).
Towards Electric Mobility Data Mining
In: IEEE International Electric Vehicle Conference (IEVC) 2012, pp. 1-6, IEEE.

Hapfelmeier, A, Mertes, C, Schmidt, J, and Kramer, S (2012).
Towards Real-Time Machine Learning
In: ECML-PKDD 2012 Workshop: Instant Interactive Data Mining.

Birkenheuer, G, Brinkmann, A, Kaiser, J, Keller, A, Keller, M, Kleineweber, C, Konersmann, C, Niehörster, O, Schäfer, T, Simon, J, and Wilhelm, M (2012).
Virtualized HPC: a contradiction in terms?
Softw. Pract. Exper., 42(4):485–500.

Herres-Pawlis, S, Birkenheuer, G, Brinkmann, A, Gesing, S, Grunzke, R, Jäkel, R, Kohlbacher, O, Krüger, J, and dos Santos Vieira, I (2012).
Workflow-enhanced conformational analysis of guanidine zinc complexes via a science gateway
Studies in Health Technology and Informatics, 175:142-151.