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Niehus, Sebastian (2022) Multi-Sample Approaches and Applications for Structural Variant Detection. PhD thesis, Freie Universität Berlin.

Krannich, Thomas (2022) Contributions to the detection of non-reference sequences in population-scale NGS data. PhD thesis, Freie Universität Berlin.

Giesselmann, Pay (2021) Genome Analysis Methods using Long Read Nanopore Sequencing. PhD thesis, Freie Universität Berlin.

Hauswedell, Hannes Peer (2021) SeqAn3 – Sequence Analysis and Modern C++. PhD thesis, Freie Universität Berlin.

Rodrigues de Melo Costa, Verônica (2021) Genome-wide Determination Of Splicing Efficiency And Dynamics From RNA-Seq Data. PhD thesis, Freie Universität Berlin.

Jäger, Marten (2020) Annotation und Interpretation von Varianten und Polymorphismen im humanen Genom. PhD thesis, Freie Universität Berlin.

Krakau, Sabrina (2020) Statistical models to capture protein-RNA interaction footprints from truncation-based CLIP-seq data. PhD thesis, Freie Universität Berlin.

Löber, Ulrike (2019) Development of Bioinformatic Tools for Retroviral Analysis from High Throughput Sequence Data. PhD thesis, Freie Universität Berlin.

Dadi, Temesgen Hailemariam (2019) Whole Genome Shotgun Sequencing Based Taxonomic Profiling Methods for Comparative Study of Microbial Communities. PhD thesis, Freie Universität Berlin.

Pockrandt, Christopher Maximilian (2019) Approximate String Matching - Improving Data Structures and Algorithms. PhD thesis, Freie Universität Berlin.

Kaiser, A. (2019) Data-driven approaches to study the dynamical stability of the stably stratified boundary layer. Masters thesis, TU Berlin.

Kaiser, A. (2019) Stably Stratified Atmospheric Boundary Layers: Event Detection and Classification for Turbulent Time Series. Other thesis, Freie Universität Berlin.

Piro, Vitor C (2018) Reference and taxonomy based methods for classification and abundance estimation of organisms in metagenomic samples. PhD thesis, Freie Universität Berlin.

Trappe, Kathrin (2018) Computational Methods for Integrative Structural Variant Analysis Across Species Boundaries. PhD thesis, Freie Universität Berlin.

Kuchenbecker, Sven-Leon (2018) Analysis of Antigen Receptor Repertoires Captured by High Throughput Sequencing. PhD thesis, Freie Universität Berlin.

Papke, A. (2017) Atmospheric vortex stability under vertical shear. PhD thesis, FU Berlin, FB Mathematik & Informatik.

Waidmann, M. (2017) Towards a Strictly Conservative Hybrid Level-Set Volume-of-Fluid Finite Volume Method for Zero Mach Number Two-Phase Flow. PhD thesis, Freie Universität Berlin.

Okonechnikov, Konstantin (2016) High-throughput RNA sequencing: a step forward in transcriptome analysis. PhD thesis, Freie Universität Berlin.

Rams, Mona (2016) A new approach for biomarker detection using fusion networks. Masters thesis, Freie Universität Berlin.

You, Xintian Arthur (2015) Tailored Analysis in Studying Transcriptome Landscape. PhD thesis, Freie Universität Berlin.

Weber, Britta (2015) Reconstruction of Microtubule Centerlines from Electron Tomograms. PhD thesis, Freie Universität Berlin.

Holtgrewe, Manuel (2015) Engineering Algorithms for Personal Genome Pipelines. PhD thesis, Freie Universität Berlin.

Siragusa, Enrico (2015) Approximate string matching for high-throughput sequencing. PhD thesis, Freie Universität Berlin.

Andreotti, Sandro (2015) Linear Programming and Integer Linear Programming in Bioinformatics. PhD thesis, Freie Universität Berlin.

Hu, Jialu (2015) Algorithms to Identify Functional Orthologs And Functional Modules from High- Throughput Data. PhD thesis, Freie Universität Berlin.

Ozdoba, Christopher (2015) Ensemble Machine Learning Techniques for Analyzing Large Biological Datasets Using the SAP In-Memory Database HANA. Masters thesis, Freie Universität Berlin.

Fröhner, Christoph (2015) Reversible integrators for particle based reaction-diffusion simulations. Masters thesis, FU Berlin.

Benacchio, T. (2014) A blended semi-implicit numerical model for weakly compressible atmospheric dynamics. PhD thesis, Freie Universität Berlin.

Kehr, Birte (2014) Contributions to computing and modeling multiple whole-genome alignments. PhD thesis, Freie Universität Berlin.

Bauer, Chris (2014) Exploiting Proteomics Data. PhD thesis, Freie Universität Berlin.

Zerck, Alexandra (2014) Optimal precursor ion selection for LC-MS/MS based proteomics. PhD thesis, Freie Universität Berlin.

Emde, Anne-Katrin (2013) Next-generation sequencing algorithms - from read mapping to variant detection. PhD thesis, Freie Universität Berlin.

Love, Michael I. (2013) Statistical analysis of high-throughput sequencing count data. PhD thesis, Freie Universität Berlin.

Aiche, S. (2013) Inferring Proteolytic Processes from Mass Spectrometry Time Series Data. PhD thesis, Freie Universität Berlin.

Weese, D. (2013) Indices and Applications in High-Throughput Sequencing. PhD thesis, Freie Universität Berlin.

Schaller, Christoph (2013) STORMicroscopy: A Mathematical Analysis. Masters thesis, FU Berlin.

Bielow, Chris (2012) Quantification and simulation of liquid chromatography-mass spectrometry data. PhD thesis, Freie Universität Berlin.

Bielow, C. (2012) Quantification and Simulation of Liquid Chromatography-Mass Spectrometry Data. PhD thesis, Freie Universität Berlin.

Prinz, J.-H. (2012) Advanced estimation methods for Markov models of dynamical systems. PhD thesis, FU Berlin.

Nüske, F. (2012) A variational approach for conformation dynamics. Masters thesis, FU Berlin.

Vitalini, Francesca (2011) Effect of a point mutation on the conformational ensemble of an intrisecally disordered peptide: a molecular dynamics study on Amyloid-β. Masters thesis, Università degli Studi Roma Tre, Thesis developed at UC Berkeley.

Ullrich, Alexander (2011) Computational Studies on the Evolution of Metabolism. PhD thesis, Universität Leipzig.

Vercauteren, N. (2011) Water Vapor and Heat Exchanges over Lakes. PhD thesis, École polytechnique fédérale de Lausanne EPFL.

Seibert, Johannes (2010) Investigation of the reaction-diffusion processes of rod cell disc membrane photoactivation with single-particle resolution. Masters thesis, FU Berlin.

Rausch, Tobias (2010) Dissecting multiple sequence alignment methods. PhD thesis, Freie Universität Berlin.

Ruprecht, D. (2010) Analysis of a Multi-Scale Asymptotic Model for Internal Gravity Waves in a Moist Atmosphere. PhD thesis, Freie Universität Berlin.

Kavalar, Martin (2010) Conformational Dynamics of a Peptide Ligand in Solvent and in Complex with a MHC-I Protein. Masters thesis, FU Berlin.

Gogol-Döring, Andreas (2009) SeqAn. PhD thesis, Freie Universität Berlin.

Schulz-Trieglaff, Ole (2009) Computational methods for Quantitative Peptide Mass Spectrometry. PhD thesis, Freie Universität Berlin.

Weiße, Andrea Y. (2009) Global Sensitivity Analysis of Ordinary Differential Equations. PhD thesis, FU Berlin.

Azhand, Arash (2009) Diffusion Processes with Hidden States from Single Molecule Experiments. Masters thesis, FU Berlin and TU Berlin.

Lüdge, Torsten (2009) A theoretical model of conformational transitions in biomolecules based on single-molecule Förster resonance electron transfer measurements. Masters thesis, FU Berlin and TU Berlin.

Carqué, G. (2009) Derivation and Validation of an Asymptotic Column Model for Deep Convective Precipitating Clouds. PhD thesis, Freie Universität Berlin.

Keller, B. (2009) Algorithms for the Analysis of Biomolecular Simulations: Ensemble Averages, Marginal Distributions, Clustering and Markov Models. PhD thesis, ETH Zürich.

Dittmer, E. (2009) Hidden Markov Models with Time-Continuous Output Behavior. PhD thesis, FU Berlin.

Meerbach, E. (2009) Off- and Online Detection of Dynamical Phases in Time Series. PhD thesis, Free University of Berlin.

Conrad, T. O. F. (2008) New statistical algorithms for the analysis of mass spectrometry time-of- flight mass data with applications in clinical diagnostics. PhD thesis, Freie Universität Berlin.

Lange, Eva (2008) Analysis of mass spectrometric data - peak picking and map alignment. PhD thesis, Freie Universität Berlin.

Bais, Abha Singh (2008) Annotated Alignments. PhD thesis, Freie Universität Berlin.

Bauer, Markus Johann (2008) A combinatorial approach to RNA sequence-structure alignments. PhD thesis, Freie Universität Berlin.

Thöns, Ch. (2008) Parallelizing Multigrid Solvers for Contact Problems on IBM’s Cell Processor. Masters thesis, Freie Universität Berlin.

Dolaptchiev, S. (2008) Asymptotic models for planetary scale atmospheric motions. PhD thesis, Freie Universität Berlin.

Fischbach, M. (2008) Methods for modeling metastable conformational dynamics from trajectory data. Masters thesis, FU Berlin.

Sakalli, I. (2008) Parallelization Strategies for a Brownian Dynamics Algorithm. Other thesis, FU Berlin.

Metzner, Ph. (2007) Transition Path Theory for Markov Processes. PhD thesis, Free University of Berlin.

Rungsarityotin, Wasinee (2007) Algorithm to identify protein complexes from high-throughput data. PhD thesis, Freie Universität Berlin.

Wolski, Witold Eryk (2007) Analysis of sets and collections of Peptide Mass Fingerprint data. PhD thesis, Freie Universität Berlin.

Hartmann, C. (2007) Model Reduction in Classical Molecular Dynamics. PhD thesis, Freie Universität Berlin.

Held, M. (2007) Conformational Studies of UDP-N-Acetyl-Glucosamine in Environments of Increasing Complexity. Masters thesis, FU Berlin.

Tomm, S. (2007) Fehlererfassung für die Large Eddy Simulation auf gestreckten Gittern. Masters thesis, Universität Karlsruhe.

Mikusky, E. (2007) On the structure of concentrated atmospheric vortices in a gradient wind regime and its motion on synoptic scales. PhD thesis, Universität Hamburg.

Bernhard, S. (2006) Transient integral boundary layer method to simulate entrance flow conditions in one-dimensional arterial blood flow. PhD thesis, Georg-August-Universität Göttingen.

Rausch, T. (2006) Discovering causes of multifactorial diseases. Masters thesis, Hasso-Plattner-Institut für Softwaresystemtechnik GmbH, Universität Potsdam.

Weese, D. (2006) Entwurf und Implementierung eines generischen Substring-Index. Other thesis, Humboldt-University.

Walter, J. (2006) Averaging for Diffusive Fast-Slow Systems with Metastability in the Fast Variable. PhD thesis, Free University of Berlin.

Vercauteren, N. (2006) Numerical investigation of solutions of Langevin equations. Masters thesis, Freie Universität Berlin, EPFL.

Noé, F. (2006) Transition Networks: Computational Methods for the Comprehensive Analysis of Complex Rearrangements in Proteins. PhD thesis, University of Heidelberg.

Lorenz, S. (2006) The model-data-overlap: A new approach to parameter estimation, model validation, selection and discrimination. PhD thesis, Free University of Berlin.

Rack, A. (2005) Prediction of Post-translational Modifications of Proteins from 2-DE/MS Data. Masters thesis, Freie Universität Berlin.

Conrad, T. O. F. (2004) Metabolic Pathways. Other thesis, Monash University Melbourne.

Conrad, T. O. F. (2003) Berechnung von freien Energie Flächen am Beispiel des Alanin-Dipeptides. Other thesis, Freie Universität Berlin.

Fischer, A. (2003) An Uncoupling-Coupling Method for Markov Chain Monte Carlo Simulations with an Application to Biomolecules. PhD thesis, Free University of Berlin.

Noé, F. (2002) The Evolution of Cell Colonies in Volvocacean Algae: Investigation by theoretical analysis and computer simulation. Masters thesis, Cork Institute of Technology, Ireland.

Schäfer-Bung, B. (2001) Theoretische Untersuchung des Renner–Teller Effekts in asymmetrischen vieratomigen Molekülen. PhD thesis, Universität Bonn.

Huisinga, W. (2001) Metastability of Markovian Systems A transfer operator based approach in application to molecular dynamics. PhD thesis, Free University of Berlin.

Gröpl, C. (1999) Binary Decision Diagrams for Random Boolean Functions. PhD thesis, Humboldt-Universität zu Berlin.

Schütte, Ch. (1999) Partial Wigner transforms and the quantum-classical Liouville equation. Other thesis, UNSPECIFIED.

Schmidt, B. (1998) Making and Breaking of Chemical Bonds: Dynamics of elementary reactions from gas phase to condensed phase. Other thesis, Free University Berlin.

Gröpl, C. (1996) Über Approximationsalgorithmen zur Färbung k-färbbarer Graphen, die vektorchromatische Zahl und andere Varianten der vartheta-Funktion. Masters thesis, Rheinische Friedrich-Wilhelms-Universität Bonn.

Münch, M. (1996) Einsatz von CFD bei der Modellierung natürlicher Brände - Ein Vergleich zwischen Simulationsrechnung und Experiment. Masters thesis, Technische Universität Braunschweig.

Klein, R. (1994) Zur Dynamik schlanker Wirbel. PhD thesis, RWTH Aachen.

Schmidt, B. (1992) Struktur und Spektren von Molekülclustern. PhD thesis, Universität Göttingen.

Schmidt, B. (1988) Messungen differentieller, elastischer Wirkungsquerschnitte an den Systemen He-Kr, He-Xe. Masters thesis, Universität Göttingen.

Klein, R. (1988) Stoßinduzierte Zündung und der Übergang zur Detonation in engen Spalten. PhD thesis, RWTH Aachen.

Klein, R. (1985) Kumulative Effekte aufgrund schwacher Druckwellen bei der Kompression eines reagierenden Gasgemisches. PhD thesis, RWTH Aachen.