All theses labeled with 
are not yet assigned to a
student. Please contact the tutors if you are interested.
All theses that are not listed under a year are ongoing, others are finished
projects.
| Developping a Web based Benchmark database for read mapping |
| Project: SeqAn | Tutor(s) : Reinert | ||
| The goal is to develop a carefully desigend benchmark dataset of real and artificial data sets for "approximate" read mapping. Also all current read mappers should be compared using the benchmark. (This position is vacant. Please contact the tutors if you are interested.) | |||
| Processing huge LC-MS/MS data sets on-the-fly |
| Project: OpenMS | Tutor(s) : Gröpl | ||
| Processing huge data sets generated by state-of-the art LC-MS/MS technology requires efficient usage of external memory and parallelization.. (This position is vacant. Please contact the tutors if you are interested.) | |||
| GUI supported parameter optimization |
| Project: OpenMS | Tutor(s) : Gröpl, Bielow | ||
| In dieser Arbeit sollen eine GUI (graphical user interface) und Methoden zur Parameter-Optimierung implementiert werden, um Wissenschaftlern den Einsatz von OpenMS im Wet-Lab erleichtern. (This position is vacant. Please contact the tutors if you are interested.) | |||
| Implementation of MSA with quasi affine gap costs in SEQAN |
| Project: SEQAN | Tutor(s) : Reinert | ||
| In this thesis a generalization of the DP based programming with "quasi"-affine gap costs should be implmented in SEQAN. (This position is vacant. Please contact the tutors if you are interested.) | |||
| Implementation of DCA using MSA |
| Project: SEQAN | Tutor(s) : Reinert | ||
| In this thesis the OMA algorithm (Stoye et al) should be implemented in SEQAN. (This position is vacant. Please contact the tutors if you are interested.) | |||
| Aligning Alignments |
| Project: SEQAN | Tutor(s) : Reinert | ||
| In this thesis the algorithm of Kececioglu et al. for aligning alignments should be implemented in SEQAN and evaluated. (This position is vacant. Please contact the tutors if you are interested.) | |||
| Realigning sequence reads |
| Project: SEQAN | Tutor(s) : Reinert/Weese | ||
| Gegeben ist eine Menge von sequenzierten Reads mit zugehörigen paarweisen lokalen Alignments zu einem Referenzgenom. In dieser Arbeit soll die Idee des ReAligner-Algorithmus von Anson und Myers verwendet werden, um die paarweisen Alignments zu multiplen Alignments zwischen Reads und Genom zu erweitern und Konsensus-Strukturen zu berechnen. (This position is vacant. Please contact the tutors if you are interested.) | |||
| Alignment Refinement |
| Date: 2008/2009 | Project: SEQAN | Tutor(s) : Reinert/Rausch | |
| Progressive alignment is the predominant heurisitic to solve the multiple sequence alignment problem. As a greedy technique it has, however, several limitations. Two methods have been proposed to alleviate these shortcomings of the algorithm, (1) consistency and (2) alignment refinement. The purpose of this thesis is to implement, evaluate and compare different methods and strategies of alignment refinement. (This position is vacant. Please contact the tutors if you are interested.) | |||
| Alignment and retention time correction of LC-MS/MS measurements based on peptide identifications |
| Project: OpenMS | Tutor(s) : Gröpl | ||
| Develop an OpenMS/TOPP tool addressing the following tasks: (1) correction of instabilities of the retention time (2) multiple alignment of the LC-MS/MS signals caused by peptides (3) compute and maintain a consensus over many experiments. | |||
| Local Alignment Extension |
| Date: 11/2007 | Project: SeqAn | Tutor(s) : Döring/Weese/Reinert | |
| In dieser Arbeit sollen verschiedene Extension-Strategien für die Suche lokaler Alignments evaluiert und für die Softwarebibliothek SeqAn implementiert werden. | |||
| Repeat Resolution |
| Date: 02/2008 | Project: SeqAn | Tutor(s) : Reinert/Rausch/Döring | |
| Thema dieser Arbeit ist die Entwicklung und Implementierung von Algorithmen zur Auflösung von Repeats. | |||
| Entwicklung einer Peptid-Spektrenbibliothek und Vergleich verschiedener massenspektrometrischer Quantifikationsstrategien |
| Date: 01.06.2006 | Project: OpenMS | Tutor(s) : Reinert/Weckwerth | |
| Neben der Weiterentwicklung einer Peptidspektrendatenbank, sollen Quantifizierungsalgorithmen evaluiert werden. | |||
| Incremental Substring Indices |
| Project: SeqAn | Tutor(s) : Reinert/Weese | ||
| Es sollen Methoden entwickelt werden, mit denen inkrementelle Änderungen eines Textes (bspw. das Einfügen oder Entfernen von kurzen Sequenzen) auch auf bereits erzeugte zugehörige Substring-Indizes (bspw. Enhanced Suffix Array, Lazy Suffix Tree) angewendet werden können, ohne sie komplett neu aufzubauen. | |||
| A tool for peptide mass fingerprinting enhanced by calibration |
| Date: 01.01.2008 - 30.06.2008 | Project: OpenMS | Tutor(s) : C Gröpl, J Gobom | |
| Peptide mass finger printing (PMF) is a method for identifying peptides in LC/MS data. Mass calibration is used as a preprocessing to improve the accuracy. | |||
| Algorithmic improvements and automated parameter learning for feature finding in LC-MS and CE-MS data |
| Date: Starting November 2007 | Project: OpenMS | Tutor(s) : Gröpl | |
| Extracting the signals of peptides and other chemical compounds from LC-MS or CE-MS measurements is an important step in proteomics and metabolomics data processing pipelines. This process is called feature finding. | |||
Theses from 2008
| RNA chimer detection pipeline |
| Date: 01.08.2006 | Project: RNA Analysis | Tutor(s) : Reinert/Döring | |
| The goal is to evaluate different chimerdetection packages using data from the Venter Institute and a self written Chimerism Simulator. | |||
Theses from 2007
| RNA Scanner |
| Date: 12.10.2006 | Project: Algorithms | Tutor(s) : Reinert/Bauer | |
| Ziel der Masterarbeit ist die Entwicklung eines schnellen RNA-Scanners, der -bei gegebener Beschreibung einer ncRNA-Familie (z.B. ein Form eines multiplen Alignments mit Konsensusstruktur)- nach homologen Strukturen in genomischen Sequenzen sucht. | |||
| Machine Learning for the Quality Assessment of LC/MS data |
| Date: 26.08.2006 | Project: OpenMS | Tutor(s) : Ole Schulz-Trieglaff / Knut Reinert | |
| An understanding of the physics of a mass spectrometer is key for the development of effective algorithms. However, many physical characterics of the instrument are not fully understood. The aim of this Master or Diploma thesis is twofold. The first step is to develop a simple model of a mass spectrometer and to explore its value for the generation of artificial LC/MS data. In a second step, the student should evaluate different machine learning techniques for the classification of the generated data, but also of real data sets generated from our collaborators. | |||
| Classification of peptide pattern derived from CE-MS data |
| Date: 2006 | Project: Proteomics / Machine learning | Tutor(s) : Reinert/Schulz-Trieglaff |
| Fast Peptide Mass Index |
| Date: 13.11.2006 | Project: OpenMS | Tutor(s) : Gröpl | |
| Implementation of a fast peptide mass index in OpenMS. | |||
| Progressives Genomalignment |
| Date: 2007 | Project: Seqan | Tutor(s) : Reinert/Döring | |
| In dieser Arbeit soll ein Verfahren zum Alignment mehrerer Genome entwickelt werden, das angelehnt an die Idee des Software Tools T-Coffee funktioniert. Zentraler Bestandteil ist dabei die Programmierung eines Match-Refinement-Algorithmus. Die Implementierung erfolgt in der Softwarebibliothek SeqAn. | |||
| Algorithmen zur Motifsuche |
| Date: 2006 | Project: Seqan | Tutor(s) : Reinert/Döring | |
| Ziel dieser Arbeit ist es, verschiedene gängige Verfahren zur Suche gemeinsamer Motive in einer Liste gegebener Sequenzen innerhalb der Softwarebibliothek SeqAn zu implementieren und miteinander zu vergleichen. | |||
Theses from 2006
| Globale Rekalibrierung von LCMS Daten mittels geometrischem Hashing |
| Date: 04.08.2006 | Project: OpenMS | Tutor(s) : Gröpl/Lange | |
| Implementierung und Erprobung von Algorithmen zum Alignieren von LCMS Daten entlang der Retentionszeit. | |||
| Entwurf und Implementierung eines generischen Substring-Index |
| Date: 02.05.2006 | Project: Seqan | Tutor(s) : Reinert/Döring | |
| Entwicklung und Implementierung eines generischen abstrakten Datentyps "Substring-Index" unter Verwendung von suffix arrays für die Softwarebibliothek Seqan. | |||
| Chaining von Alignment-Fragmenten |
| Date: 2006 | Project: Seqan | Tutor(s) : Reinert/Döring | |
| Entwicklung eines generischen Range-Trees für die Softwarebibliothek Seqan. Anwendung dieses Range-Trees auf das Problem des Chaining von Alignment-Fragmenten zu einem globalen Sequenzalignment. | |||
| Multidimensionales Peak-Fitting in LC/MS Daten |
| Date: 01.01.2006 | Project: OpenMS | Tutor(s) : Reinert/Lange | |
| Der bestehende Peak Picking Algorithmus soll um wichtige Funktionalitäten, wie beispielsweise die Trennung überlappender Peaks, erweitert werden. | |||
| Multiple Contact Map Overlap Alignment |
| Date: 01.02.2006 | Project: Algorithms | Tutor(s) : Reinert/Bauer | |
| Ein bereits existierender Algorithmus zum Berechnen des maximalen 'contact map overlaps' zweier Proteine soll auf multiple Proteinstrukturen erweitert werden. | |||
Theses from 2005
| Verteiltes Rechnen in der Bioinformatik |
| Date: 18.05.2004 | Tutor(s) : Reinert/Döring | ||
| Verteilte Implementierung verschiedener bioinformatischer Algorithmen und Auswertung der automatischen Lastverteilung von Open-Mosix. | |||
Theses from 2004
| Implementation of efficient q-gram filters and extension algorithms |
| Project: Seqan | Tutor(s) : Reinert/Döring | ||
| Goal of the thesis is to 1) implement a simple index structure together with (gapped) q-gram filters, and 2) implement an efficient extension phase. The implmentation should replace BLAST in a mRNA<->EST search pipeline at the MDC in Berlin. | |||