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Mohammadi, Somayeh and PourKarimi, Latif and Zschäbitz, Manuel and Aretz, Tristan and De Mecquenem, Ninon and Leser, Ulf and Reinert, Knut (2024) Optimizing Job/Task Granularity for Metagenomic Workflows in Heterogeneous Cluster Infrastructures. In: EDBT/ICDT 2024 Joint Conference: 8th International workshop on Data Analytics solutions for Real-LIfe APplications (DARLI-AP).

Schubotz, Moritz and Ferrer, Eloi and Stegmüller, Johannes and Mietchen, Daniel and Teschke, Olaf and Pusch, Larissa and Conrad, T. O. F. (2023) Bravo MaRDI: A Wikibase Knowledge Graph on Mathematics. In: Proceedings of the 4th Wikidata Workshop 2022 co-located with the 22st International Semantic Web Conference (ISWC2023), Athens, Greece, November 2023. (In Press)

Matera, S. and Merdon, C. and Runge, D. (2023) Reduced Basis Approach for Convection-Diffusion Equations with Non-linear Boundary Reaction Conditions. In: International Conference on Finite Volumes for Complex Applications, 30 October - 3 November 2023, Strasbourg, France.

Royset, Johannes and Ruthotto, Lars and Schillings, Claudia and Surowiec, Thomas M. (2023) Workshop Report 21w5167 Optimization under Uncertainty: Learning and Decision Making in 2021. In: held virtually hosted by the, Feb 8 - 12, 2023, Banff International Research Station for Mathematical Innovation and Discovery (BIRS).

Knaust, Marius and Seiler, Enrico and Reinert, Knut and Steinke, Thomas (2022) Co-Design for Energy Efficient and Fast Genomic Search: Interleaved Bloom Filter on FPGA. In: The 2022 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays (FPGA '22), 27 February - 1 March 2022, virtual.

Kim, J.J. and Kim, J. and Reinert, K. (2020) Vaquita-LR: A new bioinformatics tool for identifying structural variants using long and short reads. In: Abstracts from the 53rd European Society of Human Genetics (ESHG) Conference: Interactive e-Posters. In: 53rd European Society of Human Genetics (ESHG) Conference, June 6–9, 2020, virtual.

Harikrishnan, A. P. and Ansorge, C. and Klein, R. and Vercauteren, N. (2020) The curious nature of hairpin vortices. Gallery of Fluid Motion. In: 73th Annual Meeting of the APS Division of Fluid Dynamics, November 22, 2020 — November 24, 2020, Chicago, IL Virtual.

Haghdoost, M.R. and Thethy, B.S. and Nadolski, M. and Klein, R. and Honnery, D. and Hennington- Mitchell, D. and Seo, B. and Oberleithner, K. and Paschereit, O. (2020) Evaluation of Shock Dividers using Numerical and Experimental Methods. In: AIAA SciTech.

Schuster, Ingmar and Mollenhauer, Mattes and Klus, Stefan and Muandet, K. (2020) Kernel Conditional Density Operators. In: 23rd International Conference on Artificial Intelligence and Statistics (AISTATS), August 26 - 28, 2020, Online.

Schäpel, J.S. and King, R. and Yücel, F. and Völzke, F. and Paschereit, O. C. and Klein, R. (2018) Fuel injection control for a valve array in a Shockless Explosion Combustor. In: ASME Turbo Expo 2018: Turbomachinery Technical Conference and Exposition, June 11–15, 2018, Oslo, Norway.

Gerber, S. and Münch, M. and Plagge, M. and Kermas, P. and Klein, R. (2017) Konvergenzverhalten von fvDOM-Strahlungsmodellen. In: 5. Magdeburger Brand- und Explosionsschutztage, 23.-24.3.17.

Rähse, T.S. and Paschereit, C. O. and Stathopoulos, P. and Berndt, P. and Klein, R. (2017) Gas dynamic simulation of shockless explosion combustion for gas turbine power cycles. In: ASME Turbo-Expo 2017.

Djordjevic, N. and Hanraths, N. and Gray, J. and Berndt, P. and Moeck, J. (2017) Numerical Study on the Reduction of NOx Emissions From Pulse Detonation Combustion. In: ASME GT2017.

Berndt, P. and Klein, R. and Paschereit, O. C. (2016) A Kinetics Model For The Shockless Explosion Combustion. In: Turbo Expo Turbomachinery Technical Conference & Exposition, June 13 – 17, 2016 , COEX Convention Center, SEOUL SOUTH KOREA.

Gray, J. and Vinkeloe, J. and Berndt, P. and Moeck, J. and Paschereit, O. C. and Klein, R. and Stathopoulos, P. (2016) Thermodynamic Evaluation of Pulse Detonation Combustion for Gas Turbine Power Cycles. In: Turbo Expo Turbomachinery Technical Conference & Exposition, June 13 – 17, 2016, COEX Convention Center, SEOUL SOUTH KOREA.

Dolaptchiev, S. and Klein, R. (2016) A multi-scale model for the planetary and synoptic motions in the atmosphere. In: Annual Meeting of the European Geophysical Union, 2016, Frankfurt. (Unpublished)

Plöntzke, J. and Berg, M. and Stötzel, C. and Röblitz, S. (2015) A systems biology approach to bovine fertility and metabolism: Introduction of a glucose insulin model. In: BIOMAT - Proceedings of the 15th International Symposium on Mathematical and Computational Biology, 07.11.2015 - 11.11.2015, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India - USA.

Plagge, M. and Münch, M. (2015) Bug oder Feature? Über numerische Lichtschutzfaktoren im fvDOM-Strahlungsmodell. In: 3. vfdb-Workshop Brandschutzforschung, 26./27. März 2015, Otto-von-Guericke Universität Magdeburg, Hochschule Magdeburg. (Unpublished)

Stötzel, C. and Ehrig, R. and Boer, H.M.T. and Plöntzke, J. and Röblitz, S. (2015) Exploration of different wave patterns in a model of the bovine estrous cycle by Fourier analysis. In: BIOMAT - Proceedings of the 14th International Symposium on Mathematical and Computational Biology, 02.11.2014 - 08.11.2014, Bedlewo - Poland.

Wolff, S. and Schäpel, J.S. and Berndt, P. and King, R. (2015) State estimation for homogeneous 1-D Euler Equation by Unscented Kalman Filtering. In: ASME 2015 Dynamic Systems and Control Conference 2., 28.-30. Oktober 2015, Columbus, Ohio. (Submitted)

Münch, M. (2015) Vertrauenswürdige Brandsimulationen - Können kleinskalige Brandexperimente helfen? In: 29. Fachtagung Brandschutz bei Sonderbauten, 15.-16. September 2015, Institut für Baustoffe, Massivbau und Brandschutz (iBMB), Braunschweig.

Münch, M. (2015) Zwischen Glaskugel und Wissenschaft. Wann sind Brandsimulationen vertrauenswürdig? In: 4. Magdeburger Brand- und Explosionsschutztage, 26./27. März 2015, Otto-von-Guericke Universität Magdeburg, Hochschule Magdeburg. (Unpublished)

Ehrig, R. and Dierkes, T. and Schäfer, S. and Röblitz, S. and Tronci, E. and Mancini, T. and Salvo, I. and Alimguzhin, V. and Mari, F. and Melatti, I. and Massini, A. and Krüger, T. H. C. and Egli, M. and Ille, F. and Leeners, B. (2015) An integrative approach for model driven computation of treatments in reproductive medicine. In: BIOMAT - Proceedings of the 15th International Symposium on Mathematical and Computational Biology, 07.11.2015 - 11.11.2015, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India - USA.

Bienert, A. and Richter, K. and Stelling, N. and Maas, H.-G (2014) 3D-Vegetationsmodell aus Laserscannerdaten für forstmeteorologische Anwendungen am Beispiel des TurbEFA-Projektes. In: 8. Biomet Tagung "Mensch-Pflanze-Atmosphäre im 21. Jahrhundert", 2.-3.12.14, Dresden.

Gantner, Robert N. and Schillings, Claudia and Schwab, Christoph (2014) Multilevel Monte Carlo for Bayesian Inverse Problems. In: Swiss Numerics Day 2014, April 2014, Universität Zürich.

Koltai, Péter and Junge, Oliver (2014) Quantized nonlinear feedback design by a split dynamic programming approach. In: 21st International Symposium on Mathematical Theory of Networks and Systems (MTNS 2014), Groningen (The Netherlands).

Queck, R. and Bernhofer, C. and Goldberg, V. and Harmansa, S. and Bienert, A. and Maas, H.-G and Schlegel, F. and Stiller, J. and Eipper, T. and Hildebrand, V. (2014) TurbEFA: Ein interdisziplinärer Ansatz zur Untersuchung der turbulenten Strömung an einer Waldlichtung. In: 8. Biomet Tagung "Mensch-Pflanze-Atmosphäre im 21. Jahrhundert", 2.-3.12.14, Dresden.

Klein, R. and Benacchio, T. and O'Neill, W.P. (2014) Using the sound-proof limit for balanced data initialization. In: ECMWF Seminar on Numerical Methods for Atmosphere and Ocean Modelling, 2-5 September 2013, Reading, UK.

Münch, M. and Gerber, S. and Oevermann, M. (2013) Analyse von verschiedenen Verbrennungsmodellen im Hinblick auf Brandsimulationen in praktischen Geoemtrien. In: 3. Magdeburger Brand- und Explosionsschutztag, 21./22. März 2013, Otto-von-Guericke Universität Magdeburg.

Münch, M. (2013) CFD-basierte Ingenieurmethoden im Brandschutz - Möglichkeiten und Grenzen. In: 2. Darmstädter Ingenieurkongress Bau und Umwelt, 12. und 13. März 2013, TU Darmstadt.

de la Garza, L. and Krüger, J. and Schärfe, Ch. and Röttig, M. and Aiche, S. and Reinert, K. and Kohlbacher, O. (2013) From the Desktop to the Grid: conversion of KNIME Workflows to gUSE. In: IWSG (International Workshop on Science Gateways), 3-5 June 2013, Zurich, Switzerland.

Siragusa, E. and Weese, D. and Reinert, K. (2013) Scalable string similarity search/join with approximate seeds and multiple backtracking. In: Proceedings of the Joint EDBT/ICDT 2013 Workshops, Genoa, Italy.

Bobusch, B. and Berndt, P. and Paschereit, O. C. and Klein, R. (2013) Shockless explosion combustion - An innovative way of efficient constant volume combustion in gas turbines. In: 24th ICDERS Conference Proceedings, , 2013, Taipei, Taiwan.

Schwab, Christoph and Schillings, Claudia (2013) Sparse Quadrature Approach to Bayesian Inverse Problems. In: SIAM Conference on Computational Science and Engineering.

Mukhopadhyay, A. and Carneiro, J. and Jasor, G. and Polifke, W. (2012) A Comparative Assessment of Presumed Function Method of Moments and Quadrature Method of Moments for Simulation of Polydisperse Flows. In: Theoretical and Applied Mechanics, August 19--24, Beijing, China.

Münch, M. (2012) On the application of CFD in fire safety - Between theory and practice or the user’s role. In: Computational methods in modern railway design, September 10-14, Vienna, Austria.

Wandel, M. and Thormann, L and Münch, M. (2011) Anwendung von Simulationsrechnungen in der Brandschutzaufklärung. In: vfdb Jahresfachtagung 2011, 30. Mai bis 1. Juni 2011, Berlin.

Jasor, G. and Wacker, U. and Beheng, K.D. and Polifke, W. (2011) Application of Quadrature Method of Moments for Sedimentation and Coagulation of Raindrops. In: International Metstroem Conference, Juni 2011, Berlin.

Audusse, E. and Klein, R. and Nguyen, D.D. and Vater, S. (2011) Preservation of the discrete geostrophic equilibrium in shallow water flows. In: Finite Volumes for Complex Applications VI - Problems& Perspectives, 6.6.-10.6. 2011, Prague, Czech Republic.

Vater, S. and Klein, R. and Knio, O.M. (2011) Scale-selective time integration for Long-Wave Linear Acoustics. In: Finite Volumes for Complex Applications VI - Problems & Perspectives, 6.6.-10.6. 2011, Prague, Czech Republic.

Alexandrov, K. and Harlander, U. and Egbers, C. (2010) Definition und Vergleich von Zuständen eines rotierenden Zylinderspalts unter Betrachtung skalenseparierter Strömungsstrukturen. In: 18. Fachtagung Lasermethoden in der Strömungsmesstechnik , 7-9. September 2010, Cottbus.

Hertel, C. and Fröhlich, J. (2010) Error reduction in LES via adaptive moving grids. In: Quality and Reliability of Large-Eddy Simulations II QLES2009, 9-11 September 2009, Pisa (Italy). (Submitted)

Bastigkeit, I. and Fischer , R. and Leitl, B. and Schatzmann, M. (2010) Fundamental quality requirements for the generation of LES-specific validation data sets from systematic wind tunnel model experiments. In: Fifth International Symposium on Computational Wind Engineering (CWE2010), May 23-27, 2010, Chapel Hill, North Carolina, USA. (Unpublished)

Fischer , R. and Bastigkeit, I. and Leitl, B. and Schatzmann, M. (2010) Generation of spatio-temporally high resolved datasets for the validation of LES-models simulating flow and dispersion phenomena within the lower atmospheric boundary layer. In: Fifth International Symposium on Computational Wind Engineering (CWE2010), May 23-27, 2010, Chapel Hill, North Carolina, USA. (Unpublished)

Hertel, C. and Fröhlich, J. (2010) Large-Eddy Simulation with adaptive refinement for the flow over periodic hills. In: DLES8, 07.-09.07.2010, Eindhoven, Niederlande. (In Press)

Djurdjevac, N. and Sarich, M. and Schütte, Ch. (2010) On Markov State Models for Metastable Processes. In: ICM 2010.

Klein, R. (2010) On the regime of validity of sound-proof model equations for atmospheric flows. In: ECMWF, Non-hydrostatic Modelling Workshop, November 2010, Reading UK.

Hertwig, D. and Leitl, B. and Schatzmann, M. (2010) Organized turbulent structures –- The link between experimental data and LES modeling. In: Fifth International Symposium on Computational Wind Engineering, May 23-27, 2010, Chapel Hill, North Carolina, USA. (Unpublished)

Alber, I. and Ransiek, A. (2010) Tagungsbericht XVII ISA World Congress of Sociology „Sociology on the move“. In: World Congress of Sociology „Sociology on the move", 11-17 July 2010, Göteborg, Schweden.

von Larcher, T. and Harlander, U. and Egbers, C. (2010) Untersuchungen von Welleninteraktionen in einer thermisch getriebenen, rotierenden Zylinderspaltströmung mittels LDA und Thermographie. In: 18. GALA-Fachtagung Lasermethoden in der Strömungsmesstechnik, 7.-9. September 2010, Cottbus.

Mueller, A. and Behrens, J. and Giraldo, F.X. and Wirth, V. (2010) An adaptive discontinuous Galerkin method for modeling cumulus clouds. In: Fifth European Conference on Computational Fluid Dynamics, ECCOMAS CFD 2010, 14-17 June 2010, Lisbon, Portugal. (Submitted)

Wirth, V. (2010) The dynamics of orographic banner clouds. In: The 90th American Meteorological Society Annual Meeting, 19. Januar 2010, Atlanta, GA, USA. (Unpublished)

Münch, M. (2009) Verification and Validation of CFD-Models applied to fire detection. In: 14th International Conference on Automatic Fire Detection, 8.-10. September 2009, Duisburg, Germany.

von Larcher, T. and Klein, R. (2009) Multiple Scales in Fluid Dynamics and Meteorology - The DFG Priority Programme 1276 MetStröm. In: Newton Institute Scoping Meeting on Multi-scale Modelling of the Atmosphere and Ocean , 25-26 March 2009, University of Reading, UK.

Bordas, R. and Hanke, K. and Bencs, P. and Thévenin, D. (2009) 2D-PIV Measurements in a Two-Phase Wind Tunnel Normal to the Main Flow. In: XXIII. microCAD International Scientific Conference, Miskolc, Hungary.

Mellado, J.- P. and Schmidt, H. and Stevens, B. and Peters, N. (2009) Analysis of the cloud top mixing layer using DNS. In: The Sixth International Symposium on Turbulence and Shear Flow, 22-24th June 2009, Seoul National University, Korea. (Submitted)

Hartmann, C. (2009) Balancing of dissipative Hamiltonian systems. In: Proceedings of MATHMOD 2009; I. Troch, F. Breitenecker (eds.); ARGESIM Report no. 35.

Queck, R. and Bienert, A. and Harmansa, S. (2009) Calculating advective fluxes in tall canopies – Towards better wind speed distribution using 3D vegetation scans in high resolution. In: Atmospheric Transport and Chemistry in Forest Ecosystems, Oct 5 - 8, 2009., Castle of Thurnau.

Münch, M. (2009) Ist eine Gebietszerlegung in mehrere Gitter bei FDS-Simulationen zulässig? In: 2. FDS-Usergroup Treffen, 4.-5. Dezember 2008, hhpberlin, Rotherstr. 19, 10245 Berlin.

Bordas, R. and Thévenin, D. (2009) Modeling cumulus clouds in a two-phase wind tunnel. In: EGU General Assembly 2009, Vienna, Austria.

Queck, R. and Bienert, A. and Harmansa, S. (2009) Modeling wind fields in tall canopies - towards better momentum distribution using 3D vegetation scans in high resolution. In: 2nd International Conference “Wind Effects on Trees”. , 13-16 October 2009, Albert-Ludwigs-University of Freiburg, Germany. (Unpublished)

Jiménez, C. and Schmidt, H. (2009) Numerical simulation of the response of planar flames to acoustic waves. In: Tercera Reunión de la Sección Española del Instituto de Combustión , 21.-22.Mai 2009, Valladolid, Spain. (Unpublished)

Harlander, U. and von Larcher, T. and Wang, Y. and Egbers, C. (2009) PIV- and LDV-measurements of baroclinic wave interactions in a thermally driven rotating annulus. In: EULAG workshop, October 7, 2008, Bad Tölz.

Münch, M. (2009) Richtig schnell rechnen. In: 3. FDS-Usergroup Treffen, 29.-30. Oktober 2009, hhpberlin, Rotherstr. 19, 10245 Berlin. (Unpublished)

Schaedle, A. and Ruprecht, D. and Schmidt, F. (2009) Transparent Boundary Conditions Based on the Pole Condition. In: The 9th International Conference on Mathematical and Numerical Aspects of Waves Propagation, 15th-19th June 2009, Pau, France.

Jiménez, C. and Schmidt, H. (2009) Unsteady response of premixed flames to acoustic pressure pulses under variation of the complexity of the reaction mechanism. In: Fourth European Combustion Meeting (ECM2009), 14 - 17 April 2009, Vienna, Austria. (Unpublished)

Münch, M. (2009) Verifikation und Validierung bei der Softwareentwicklung. In: 1. FDS-Usergroup Treffen, 7. März 2008, hhpberlin, Rotherstr. 19, 10245 Berlin.

Ullrich, Alexander and Forst, Christian V. (2009) k-PathA: k-shortest Path Algorithm. In: High Performance Computational Systems Biology (HiBi 2009), September 2009, Trento, Italy.

Weese, D. and Schulz, M. H. (2008) Efficient String Mining under Constraints via the Deferred Frequency Index. In: Proceedings of the 8th Industrial Conference on Data Mining (ICDM'08).

Kühnlein, C. (2008) Adaptive meshes for meteorological applications. In: Atmospheric Boundary Layers: Concepts, Observations, and Numerical Simulations, Les Houches, Frankreich. (Unpublished)

Münch, M. and Klein, R. (2008) Critical numerical aspects for field model applications. In: EUSAS conference on "Fire Safety Engineering and Smoke Control in Buildings", January 22-23, 2007, Vienna, Austria.

Moeck, J. and Oevermann, M. and Paschereit, O. C. and Klein, R. and Schmidt, H. (2008) Experimental and Numerical investigation of thermoacoustical instabilities in a flat flame burner. In: 32nd International Symposium on Combustion, August 3-8, 2008, Montreal, Canada. (Submitted)

Schulz, M. H. and Weese, D. and Rausch, T. and Döring, A. and Reinert, K. and Vingron, M. (2008) Fast and Adaptive Variable Order Markov Chain Construction. In: Proceedings of the 8th International Workshop in Algorithms in Bioinformatics (WABI'08).

Münch, M. (2008) Modellierung der Rauchausbreitung bei Gebäudebränden. In: Meterologisches Kolloquium, 10. Juli 2008, Berlin, FU-Berlin, Institut für Meterologie. (Unpublished)

Kühnlein, C. and Dörnbrack, A. (2008) Scalar advection with adaptive moving meshes. In: 1st International Workshop of EULAG Users, 7. Oktober 2008, Bad Tölz.

Schmidt, H. and Mellado, J.- P. and Peters, N. and Stevens, B. (2008) Towards a modular superparameterization for Stratocumulus clouds considering unsteady entrainment. In: 4th PAN-GCSS Meeting on "Advances in Modeling and Observing Clouds and Convection", 2-6 June 2008, Toulouse, France.

Münch, M. and Gebauer, J. and Klein, R. (2008) Verification and Validation of CFD Models for Smoke Spreading Predictions. In: 9th Int. IAFSS Symposium , 21 - 26. Sept. 2008, Karlsruhe.

Harlander, U. and von Larcher, T. and Wang, Y. and Egbers, C. (2008) The heated rotating annulus: PIV- and LDV-measurements of multiple-scale interactions in quasi-turbulent flows. In: 14th International Symposium on Application of Laser Techniques to Fluid Mechanics, Lisbon, Portugal.

May, P. and Klau, G. W. and Bauer, M. and Steinke, T. (2007) Accelerated microRNA Precursor Detection Using the Smith-Waterman Algorithm on FPGAs. In: Proc. of GCCB 2006.

Fasulo, D. and Emde, A.-K. and Wang, L.-Y. and Edwards, N. J. (2007) Alignment of Mass Spectrometry Data by Clique Finding and Optimization. In: Systems Biology and Computational Proteomics.

von Kleist, M. and Kloft, Ch. and Huisinga, W. (2007) Combining Systems Biology with Physiologically Based Pharmacokinetics to Support the Understanding of Drug Effects. In: Proceedings of the 2nd Foundations of Systems Biology in Engineering Conference, FOSBE 2007, 09.-12.09.2007, Stuttgart, Germany.

Held, M. and Meerbach, E. and Hinderlich, S. and Reutter, W. and Schütte, Ch. (2007) Conformational Studies of UDP-GlcNAc in Environments of Increasing Complexity. In: From Computational Biophysics to Systems Biology.

Schulz-Trieglaff, O. and Hussong, R. and Gröpl, C. and 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).

Futterer, B. and von Larcher, T. and Egbers, C. (2007) GeoFlow: The ISS experiment and 3D numerical simulation on thermal convection in spherical shell. In: Biennial Symposium and General Assembly, 4-7 September, 2007, European Low Gravity Research Association (ELGRA), Florence Italy.

González, L. and Rozgonyi, T. and Ambrosek, D. and Pérez-Hernández, G. and Maroulis, G. and Simos, T. E. (2007) Laser Control of Wavepacket Photodissociation and Photoisomerization Dynamics in Isolated Molecules. In: ICCMSE 2007, 25–30 September 2007 , Corfu (Greece).

Dolaptchiev, S. and Klein, R. (2007) Model Equations For Atmospheric Motions on Planetary Scales. In: European Geosciences Union, Vienna.

Schmidt, H. and Veynante, D. and Klein, R. (2007) A Modular Two Scale Capturing/Tracking Scheme for Turbulent Premixed Flames. In: 21th Intl. Colloquium on the Dynamics of Explosions and Reactive Systems, 2007, Poitiers.

Schaedle, A. and Ruprecht, D. and Schmidt, F. (2007) Transparent boundary conditions - the pole condition approach. In: The 8th International Conference on Mathematical and Numerical Aspects of Waves, 23rd - 27th July 2007, Reading UK.

Klein, R. (2007) A Unified Approach to Meteorological Modelling based on Multiple Scales Asymptotics. In: European Geosciences Union, Vienna.

Moeck, J. and Schmidt, H. and Oevermann, M. and Paschereit, O. C. and Klein, R. (2007) An asymptotically motivated hyrodynamic-acoustic two-way coupling for modeling thermoacoustic instabilities in a Rijke tube. In: Fourteenth Intl. Congress on Sound and Vibration (ICSV14), , 9-12 July 2007, Cairns, Australia, (2007).

Reinert, K. and Bauer, M. and Döring, A. and Halpern, A. L. (2007) A general paradigm for fast and adaptive clustering of biological sequences. In: German Conference on Bioinformatics (GCB 2007).

Ruprecht, D. and Majda, A. J. and Klein, R. (2007) A multiscale model for the interaction of bulk microscale hot towers with convective scale motions. In: European Geosciences Union, General Assembly 2007, 15 – 20 April 2007, Vienna.

Telgmann, R. and von Kleist, M. and Huisinga, W. (2006) Software Supported Modelling in Pharmacokinetics. In: Computational Life Sciences II.

Weiße, A. Y. and Horenko, I. and Huisinga, W. (2006) Adaptive Approach for Modelling Variability in Pharmacokinetics. In: Computational Life Sciences II.

Walter, J. and Schütte, Ch. (2006) Conditional Averaging for Diffusive Fast-Slow Systems: A Sketch for Derivation. In: Analysis, Modeling and Simulation of Multiscale Problems.

Schmidt, H. and Klein, R. (2006) Extension of a front capturing/tracking scheme for premixed flames to a novel type of two scale turbulence modeling. In: Proc. SIAM Conference on Numerical Combustion, April 23 - 26, 2006, Granada, Spain.

Schmidt, H. and Oevermann, M. and Münch, M. and Klein, R. (2006) Flame Front Capturing/Tracking Methods for Zero Mach Number Combustion. In: 31th Int. Symp. on Combustion, Aug 6-11, 2006, The Combustion Institute, Heidelberg.

Dellnitz, M. and Molo, M. and Metzner, Ph. and Preis, R. and Schütte, Ch. (2006) Graph Algorithms for Dynamical Systems. In: Analysis, Modeling and Simulation of Multiscale Problems.

Lange, E. and Gröpl, C. and Reinert, K. and Hildebrandt, A. (2006) High Accuracy Peak-Picking of Proteomics Data using Wavelet Techniques. In: Proceedings of the 11th Pacific Symposium on Biocomputing (PSB-06).

Münch, M. (2006) Kritische Numerische Aspekte bei der Anwendung von Feldmodellen. In: 55. Jahresfachtagung der Vereinigung zur Förderung des Deutschen Brandschutzes e.V., 21. - 25. Mai 2006, Salzburg.

Meerbach, E. and Dittmer, E. and Horenko, I. and Schütte, Ch. (2006) Multiscale Modelling in Molecular Dynamics: Biomolecular Conformations as Metastable States. In: Computer Simulations in Condensed Matter: Systems: From Materials to Chemical Biology. Volume I.

Cohen, D. and Jahnke, T. and Lorenz, K. and Lubich, Ch. (2006) Numerical Integrators for Highly Oscillatory Hamiltonian Systems: A Review. In: Analysis, Modeling and Simulation of Multiscale Problems.

Münch, M. and Schmidt, H. and Oevermann, M. and Klein, R. (2006) Numerical Investigation of the Baroclinic Torque in the Context of Smoke Spread. In: 31th Int. Symp. on Combustion, Aug. 6-11, 2006, The Combustion Institute, Heidelberg.

Reinert, K. and Kohlbacher, O. and Gröpl, C. and Lange, E. and Schulz-Trieglaff, O. and Sturm, M. and Pfeifer, N. (2006) OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics. In: Computational Proteomics.

Horenko, I. and Schmidt-Ehrenberg, J. and Schütte, Ch. (2006) Set-Oriented Dimension Reduction: Localizing Principal Component Analysis via Hidden Markov Models. In: Computational Life Sciences II.

Vater, S. and Klein, R. (2006) Stability of a Projection Method for the Zero Froude Number Shallow Water Equations. In: Eleventh International Conference on Hyperbolic Problems Theory, Numerics, Applications, July 17-21, 2006, École Normale Supérieure de Lyon, France.

Kohlbacher, O. and Reinert, K. and Gröpl, C. and Lange, E. and Pfeiffer, N. and Schulz-Trieglaff, O. and Sturm, M. (2006) TOPP - The OpenMS Proteomics Pipeline. In: Proceedings of the 5th European Conference on Computational Biology (ECCB 2006).

Schmidt, H. and Münch, M. and Klein, R. and Oevermann, M. (2006) A Zero Mach Number Projection Method Coupled To External Acoustics. In: 77th Annual Meeting of the Gesellschaft für Angewandte Mathematik und Mechanik e.V., March 27-31, 2006, TU-Berlin.

Gröpl, C. (2005) An Algorithm for Feature Finding in LC/MS Raw Data. In: Computational Proteomics.

Gröpl, C. and Lange, E. and Reinert, K. and Sturm, M. and Huber, Ch. and Mayr, B. M. and Klein, C. L. (2005) Algorithms for the automated absolute quantification of diagnostic markers in complex proteomics samples. In: Proceedings of the 1st International Symposium on Computational Life Science (CompLife05).

Bauer, M. and Klau, G. W. and Reinert, K. (2005) Fast and Accurate Structural RNA Alignment by Progressive Lagrangian Relaxation. In: Proceedings of the 1st International Symposium on Computational Life Science (CompLife-05).

Lange, E. and Gröpl, C. and Reinert, K. and Hildebrandt, A. (2005) High-accuracy peak picking of proteomics data. In: Computational Proteomics.

Klein, R. and Schmidt, H. and Carqué, G. and Münch, M. and Oevermann, M. (2005) Mehrskalen-asymptotische Verfahren zur Kontrolle thermoakustischer Prozesse in Brennkammern. In: SFB 557, Teilprojekt B8, 17. März 2005, Berlin. (Unpublished)

Huisinga, W. and Schmidt, Bernd (2005) Metastability and Dominant Eigenvalues of Transfer Operators. In: New Algorithms for Macromolecular Simulation.

Bauer, M. and Klau, G. W. and Reinert, K. (2005) Multiple Structural RNA Alignment with Lagrangian Relaxation. In: Proceedings of the 5th Workshop on Algorithms Bioinformatics (WABI-05).

Mikusky, E. and Owinoh, A.Z. and Klein, R. (2005) On the influence of diabatic effects on the motion of 3D-mesoscale vortices within a baroclinic shear flow. In: Third MIT Conference on Computational Fluid and Solid Mechanics, June 14-17, 2005.

Reinert, K. and Kohlbacher, O. and Gröpl, C. and Lange, E. and Schulz-Trieglaff, O. and Sturm, M. and Pfeifer, N. (2005) OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics. In: Computational Proteomics.

Bodirsky, M. and Gröpl, C. and Kang, M. (2005) Sampling Unlabeled Biconnected Planar Graphs. In: Proceedings of the 16th Annual International Symposium on Algorithms and Computation (ISAAC05).

Schulz-Trieglaff, O. (2005) Software Platforms for Computational Proteomics. In: Computational Proteomics.

Schütte, Ch. and Forster, R. and Meerbach, E. and Fischer, A. (2005) Uncoupling-Coupling Techniques for Metastable Dynamical Systems. In: Domain Decomposition Methods in Science and Engineering.

Bodirsky, M. and Gröpl, C. and Johannsen, D. and Kang, M. (2005) A direct decomposition of 3-connected planar graphs. In: Proceedings of the 17th Annual International Conference on Formal Power Series and Algebraic Combinatorics (FPSAC05).

Münch, M. (2004) Brandsimulationsprogramme, Eine Einführung. In: Seminar Vorbeugender Brandschutz, 28. Okt. 2004, Berliner Feuerwehr. (Unpublished)

Münch, M. and Lorenz, S. (2004) MathInside! Wie Mathematik helfen kann. In: Innovationen im Bauwesen, 6. Sept. 2004, Berlin, InnovationsZentrum Bau Berlin e.V.. (Unpublished)

Deuflhard, P. and Schütte, Ch. (2004) Molecular Conformation Dynamics and Computational Drug Design. In: Applied Mathematics Entering the 21st Century.

Klau, G. W. and Rahmann, S. and Schliep, A. and Reinert, K. (2004) Optimal Robust Non-Unique Probe Selection Using Integer Linear Programming. In: Proceedings of the Twelfth International Conference on Intelligent Systems for Molecular Biology (ISMB-04).

Bauer, M. and Klau, G. W. (2004) Structural Alignment of Two RNA Sequences with Lagrangian Relaxation. In: Proceedings of the 15th International Symposium, ISAAC 2004, Hong Kong.

Schütte, Ch. and Huisinga, W. (2003) Biomolecular Conformations can be Identified as Metastable Sets of Molecular Dynamics. In: Special Volume: Computational Chemistry.

Bodirsky, M. and Gröpl, C. and Kang, M. (2003) Decomposing, Counting, and Generating Unlabeled Cubic Planar Graphs. In: European Conference on Combinatorics, Graph Theory, and Applications EUROCOMB'03 Prague.

Bodirsky, M. and Gröpl, C. and Kang, M. (2003) Generating labeled planar graphs uniformly at random. In: Proceedings of ICALP 2003.

Schütte, Ch. and Huisinga, W. and Meyn, S. (2003) Metastability of Diffusion Processes. In: Nonlinear Stochastic Dynamics.

Ochs, S. and Hinkelmann, R. and Neunhäuserer, L. and Süß, M. and Helmig, R. and Gebauer, S. and Kornhuber, R. (2002) Adaptive methods for the equidimensional modelling of flow and transport processes in fractured aquifers. In: 5th International Conference on Hydroscience and Engineering, ICHE2002, Advances in Hydro-Science and -Engineering., Sept. 17-21, 2002, Warschau.

Fischer, A. and Schütte, Ch. and Deuflhard, P. and Cordes, F. (2002) Hierarchical Uncoupling-Coupling of Metastable Conformations. In: Computational Methods for Macromolecules: Challenges and Applications.

Althaus, E. and Caprara, A. and Lenhof, H.-P. and Reinert, K. (2002) Multiple Sequence alignment with arbitrary gap costs: Computing an optimal solution using polyhedral combinatorics. In: Proceedings of the 1st European Conference on Computational Biology (ECCB 2002).

Halpern, A. L. and Huson, D. H. and Reinert, K. (2002) Segment Match refinment and applications. In: Proceedings of the 2nd Workshop on Algorithms Bioinformatics (WABI-02).

Huson, D. H. and Halpern, A. L. and Lai, Z. and Myers, E. W. and Reinert, K. and Sutton, G. G. (2001) Comparing Assemblies using Fragments and Mate-pairs. In: Proceedings of the 1st Workshop on Algorithms Bioinformatics (WABI-01).

Huson, D. H. and Reinert, K. and Kravitz, S. A. and Remington, K. A. and Delcher, A. L. and Dew, I. M. and Flanigan, M. J. and Halpern, A. L. and Lai, Z. and Mobarry, C. M. and Sutton, G. G. and Myers, E. W. (2001) Design of a compartmentalized Shotgun Assembler for the Human Genome. In: Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology (ISMB-01).

Klein, R. and Botta, N. and Owinoh, A.Z. (2001) Distinguished limits, multiple scales asymptotics, and numerics for atmospheric flows. In: 13th Conference on Atmospheric and Oceanic Fluid Dynamics, July 2001, American Meteorological Society, Breckenridge, Colorado.

Huson, D. H. and Reinert, K. and Myers, E. W. (2001) The Greedy Path-Merging Algorithm for Sequence Assembly. In: Proceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB-01).

Gröpl, C. and Hougardy, S. and Nierhoff, T. and Prömel, H.-J. (2001) Lower bounds for approximation algorithms for the Steiner tree problem. In: Proceedings of the 27th International Workshop on Graph-Theoretic Concepts in Computer Science (2001).

Schütte, Ch. and Huisinga, W. and Deuflhard, P. (2001) Transfer Operator Approach to Conformational Dynamics in Biomolecular Systems. In: Ergodic Theory, Analysis, and Efficient Simulation of Dynamical Systems.

Turner, R. J. and Chaturvedi, K. and Edwards, N. J. and Halpern, A. L. and Huson, D. H. and Kohlbacher, O. and Miller, J. R. and Reinert, K. and Remington, K. A. and Schwartz, R. and Walenz, B. and Yooseph, S. and Istrail, S. (2001) Visualization Challenges for a New Cyberpharmaceutical Computing. In: IEEE 2001 Symposium on Parallel and Large-Data Visualization and Graphics.

von Klinski, S. and Derz, C. and Weese, D. and Tolxdorff, T. (2000) Model-based image processing using snakes and mutual information. In: Society of Photo-Optical Instrumentation Engineers (SPIE).

Botta, N. and Klein, R. and Almgren, A. (2000) Asymptotic Analysis of a Dry Atmosphere. In: Proc. 3rd Europ. Conf. on Num. Math., Jyväskylä, Finland.

Schütte, Ch. and Huisinga, W. (2000) Biomolecular Conformations as Metastable Sets of Markov Chains. In: Proceedings of the 38th Annual Allerton Conference on Communication, Control, and Computing, Monticello, Illinoins/USA.

Schütte, Ch. and Huisinga, W. (2000) On Conformational Dynamics induced by Langevin Processes. In: Equadiff 99.

Schütte, Ch. and Cordes, F. (2000) On Dynamical Transitions between Conformational Ensembles. In: Molecular Dynamics on Parallel Computers.

Galliat, T. and Huisinga, W. and Deuflhard, P. (2000) Self-Organizing Maps Combined with Eigenmode Analysis for Automated Cluster Identification. In: Neural Computation.

Schütte, Ch. and Bornemann, F. A. (1999) Approximation Properties and Limits of the Quantum-Classical Molecular Dynamics Model. In: Computational Molecular Dynamics: Challenges, Methods, Ideas.

Deuflhard, P. and Dellnitz, M. and Junge, O. and Schütte, Ch. (1999) Computation of Essential Molecular Dynamics by Subdivision Techniques. In: Computational Molecular Dynamics: Challenges, Methods, Ideas.

Klein, R. and Breitung, W. and Coe, I. and Grönig, H. and He, L. and Olivier, H. and Rehm, W. and Studer, E. and Vendel, J. (1999) Models and Criteria for Prediction of Deflagration-to-Detonation Transition(DDT) in Hydrogen-Air-Steam Systems under Severe Accident Conditions. In: Fission Safety (FISA 99), European Commission, 1999.

Schütte, Ch. and Nettesheim, P. (1999) Nonadiabatic Effects in Quantum-Classical Molecular Dynamics. In: Scientific Computing in Chemical Engineering II.

Nettesheim, P. and Schütte, Ch. (1999) Numerical Integrators for Quantum-Classical Molecular Dynamics. In: Computational Molecular Dynamics: Challenges, Methods, Ideas.

Schneider, T. and Klein, R. (1999) Overcoming Mass Losses in Level-Set-Based Interface Tracking Schemes. In: 2nd International Conference on Finite Volume for Complexe Application, 1999.

Nettesheim, P. and Reich, S. (1999) Symplectic Multiple-Time-Stepping Integrators for Quantum-Classical Molecular Dynamics. In: Computational Molecular Dynamics: Challenges, Methods, Ideas.

Klein, R. and Breitung, W. and Coe, I. and Grönig, H. and He, L. and Olivier, H. and Rehm, W. and Studer, E. and Vendel, J. (1998) Models and Criteria for Prediction of Deflagration-to-Detonation Transition(DDT) in Hydrogen-Air-Steam Systems under Severe Accident Conditions. In: Fission Safety (FISA 98), European Commission, 1998.

Gröpl, C. and Prömel, H.-J. and Srivastav, A. (1998) Size and Structure of Random Ordered Binary Decision Diagrams (Extended Abstract). In: STACS 98.

Lenhof, H.-P. and Reinert, K. and Vingron, M. (1998) A polyhedral approach to RNA sequence structure alignment. In: Proceedings of the Second Annual International Conference on Computational Molecular Biology (RECOMB-98).

Worlikar, A.S. and Knio, O.M. and Klein, R. (1997) Numerical simulation of acoustically-generated temperature gradients in short thermoacoustics stacks: A validation study. In: 32nd National Heat Transfer Conference, Heat Transfer--Baltimore, 214, August 10-12, 1997, Baltimore.

Reinert, K. and Lenhof, H.-P. and Mutzel, P. and Kececioglu, J. D. (1997) A branch-and-Cut algorithm for multiple sequence alignment. In: Proceedings of the First Annual International Conference on Computational Molecular Biology (RECOMB-97).

Bradford, P. G. and Reinert, K. (1996) Lower Bounds for Row Minima Searching. In: Proceedings of the 23rd International Colloquium on Automata, Languages, and Programming 1996 (ICALP-96), LNCS 1099.

Smiljanovski, V. and Klein, R. (1994) Flame Front Tracking via in-Cell Reconstruction. In: Proceedings of 5th International Conference on Hyperbolic Systems, June 1994, SUNY Stony Brook.

Munz, C.-D. and Klein, R. (1994) The Multiple Pressure Variable Approach for the Numerical Approximation of Weakly Compressible Fluid Flow. In: Proc. Intl. Conf. on Numerical Methods for Fluid Flows, Prag, June 1994.

Klein, R. and Lange, K. and Willems, W. and Munz, C.-D. (1994) Semi-Implicit High Resolution Schemes for Low Mach Number Flows. In: Proceedings of 5th International Conference on Hyperbolic Systems, June 1994, SUNY Stony Brook.