Theses Page

OUTDATED! Go to: https://kvv.imp.fu-berlin.de/x/8RK4cp

Available topics

• If you are interested in doing your thesis in algorithmic bioinformatics as a student of Computer Science or Bioinformatics you can also send us an email to discuss more topics than the ones below.

Bachelor

Topic	Type	Student	Academic Advisor	Project	Remark
Improving the Location Algorithm in FM Indices - Implementation of FMtrees	BSc		Christopher Pockrandt	SeqAn		edit
A data structure for efficient coordinate system translation between a reference and a donor genome with SVs, SNPs and small indels	BSc	N.N.	Rene Rahn	SeqAn		edit
Efficient exact motif discovery	BSc	Gergana Stanilova	Knut Reinert	SeqAn		edit
Improvement of graph based realignment in SeqAn	BSc	N.N.	Knut Reinert	SeqAn		edit
Region Filter	BSc	Dorian Joswig	Hannes Hauswedell, Knut Reinert	SeqAn		edit
SeqAn in Browser	BSc	Max Pohl	Hannes Hauswedell, Knut Reinert	SeqAn		edit
Evaluation of the impact of protein alphabet reductions in a protein local aligner	Bsc	Kristin Knorr	Hannes Hauswedell, Knut Reinert	SeqAn		edit
Tree-based map alignment for LC-MS maps	BSc	Maria Tromifova	Chris Bielow, Knut Reinert	OpenMS		edit
Evaluation of strategies for k-mer counting in bins	BSc		Enrico Seiler	SeqAn		edit

Master

Topic	Type	Student	Academic Advisor	Project	Remark
Implementation and evaluation of efficient suffix array construction algorithms in C++	BSc or MSc	N.N.	Christopher Pockrandt	SeqAn		edit
Simulation of Genomes and Genome Evolution	MSc	N.N.	Knut Reinert	SeqAn		edit
Devising a method to generate flexible Filters	MSc	N.N.	Knut Reinert	SeqAn		edit
Syntenic assembly of guinea pig (wild one vs domestic)	MSc	N.N.	Camila Mazzoni, Knut Reinert	SeqAn	collaboration with external group	edit
Partitioning and clustering sequence blocks in the DREAM index	MSc	N.N.	Knut Reinert	SeqAn		edit
Analysis of protein-DNA interactions from ChIP-seq data	MSc	N.N.	Dr. Marcel Grunert, Knut Reinert		collaboration with ECRC	edit

Research Project

Topic	Type	Student	Academic Advisor	Project	Remark
						edit

Ongoing Theses

This page and its subpages should be used by students to

• write about the topic and the progress of their theses
• make an appointment with their advisor or any other SeqAn/OpenMS developer
• write down the results of the advisor meetings

Bachelor

Topic	Type	Student	Academic Advisor	Project	Remark
NGS Data Cleaning	BSc	Anne-Marie Tumescheit	Manuel Holtgrewe, Knut Reinert	SeqAn	Could also become a MSc thesis.	edit
Design and implementation of a SNP efficient Journaled String	BSc	Matthias Loose	Reneé Rahn	SeqAn		edit
Implementing 01*0 seed search strategy using the bidirectional FM index in SeqAn	BSc	Jan Gütig	Christopher Pockrandt, Knut Reinert	SeqAn		edit

Master

Topic	Type	Student	Academic Advisor	Project	Remark
Developing new local RNA aligner based on LARA	MSc	Benjamin Strauch	Dr. Gunnar Klau, Knut Reinert	SeqAn	collaboration with CWI in Amsterdam	edit

Research Project

Topic	Type	Student	Academic Advisor	Project	Remark
Implementierung ein Genom-Proteom mappers	FPr	Mathias Kuhring	Renard, Knut Reinert		extern	edit

Completed Theses

Bachelor

Topic	Type	Student	Academic Advisor	Project	Remark
Annotation of the wild guinea pig	BSc	Tino Schüllermann	Camila Mazzoni, Knut Reinert	SeqAn	collaboration with external group	edit
BLAST Implementation in SeqAn	BSc	Florian Siemer	Jochen Singer, Knut Reinert	SeqAn		edit
Fast BWT construction in small space	BSc	Lars Zerbe	Jochen Singer, Knut Reinert	SeqAn		edit
Flexbar	BSc	Sebastian Roskosch	Jochen Singer	SeqAn		edit
Implementation and Evaluation of a Myrimatch Adapter	BSc	Dimitri Schachmann	Chris Bielow, Knut Reinert	OpenMS		edit
Comparative Genomics with MEGAN and RazerS	BSc	Hannes Hauswedell	David Weese, Knut Reinert	SeqAn		edit
Complemented palindromes	BSc	Felix Heeger	David Weese, Knut Reinert	SeqAn		edit
Overlap Module for NGS Pipeline	BSc	Sabrina Krakau	Marcel Schulz, David Weese	SeqAn		edit
Suche nach Read-Profilen in ChIP-Seq Datensätzen	BSc	Tibor Pacalat	Gogol-Döring, Knut Reinert			edit
Approximate String Matching (Hamming Distance)	BSc	Holger Schmeisky	Manuel Holtgrewe, Knut Reinert	SeqAn		edit
Implementing a Motif finder based on STELLAR and SeqAn::TCoffee	BSc	Vishalini Vimalakanthan	Knut Reinert, Birte Kehr	SeqAn		edit
Comparing graphs for genome alignment	BSc	Moritz Kiekeben	Kathrin Trappe	SeqAn		edit
Plagiatsvisualisierung in iOS	BSc	Jörn Ehmann	Knut Reinert	SeqAn		edit
Journaling raw sequences	Bsc	Svenja Mehringer	René Rahn, Knut Reinert	SeqAn		edit
Implementing a Peptide Indexer in SeqAn and OpenMS	BSc	N.N.	Christopher Pockrandt, Knut Reinert	SeqAn, OpenMS		edit
Evaluation of index based seeding strategies	BSc	Thimo Wellner	Christopher Pockrandt	SeqAn		edit

Master

Topic	Type	Student	Academic Advisor	Project	Remark
Parallel suffix array construction	Dipl	David Iwanowitsch	David Weese	SeqAn		edit
Read mapping pipelines in KNIME	MSc	Kyanoush Yahosseini	David Weese, Knut Reinert	SeqAn		edit
Capture Compound MS analysis	MSc	Katharina Stenin	Stephan Aiche, Knut Reinert	OpenMS	Collaboration with Caprotec	edit
Implementation of a BlastX alternative	MSc	Hannes Hauswedel	Jochen Singer, Knut Reinert	SeqAn		edit
Develop a read mapper for bisulfite treated reads	MSc	Sabrina Krakau	David Weese, Knut Reinert	SeqAn		edit
GPGPU with SeqAn	MSc	Lars Lagner	David Weese, Knut Reinert	SeqAn		edit
Parallelism in SeqAn	MSc	Konrad Rudolph	Manuel Holtgrewe, Knut Reinert	SeqAn		edit
Incremental Substring Indices	MSc	Paul Pyl	David Weese, Knut Reinert	SeqAn		edit
Parallelization of RazerS	MSc	Martin Riese	David Weese, Knut Reinert	SeqAn		edit
Implementation of SCFGs in SeqAn	MSc	Jonas Heise	Manuel Holtgrewe, Knut Reinert	SeqAn		edit
Analysis of sequence variation in human genomes	MSc	Kerstin Neubert	Anne-Katrin Emde, Knut Reinert	SeqAn		edit
Multi read assignment	MSc	Leon Kuchenbecker	Knut Reinert	SeqAn		edit
Genomes per Mail	MSc	René Märker	David Weese, Knut Reinert	SeqAn		edit
FM Index	MSc	Jochen Singer	David Weese, Knut Reinert	SeqAn		edit
Multi-Split-Mapping of NGS reads	MSc	Kathrin Trappe	Anne-Katrin Emde, Knut Reinert	SeqAn		edit
Implementation of gapped seed suffix arrays and LAST	MSc	Sascha Meiers	David Weese, Knut Reinert, Birte Kehr	SeqAn		edit
Extending SeqAn::TCoffee for deep alignments	MSc	Oleg Yasnev	Rahn, Knut Reinert	SeqAn		edit
SIMD Extension of DP algorithms	MSc	Stefan Budach	René Rahn, Knut Reinert	SeqAn		edit
Bidirectional BWT and applications	MSc	Christopher Pockrandt	Hauswedell, Knut Reinert	SeqAn		edit

Research Project

Topic	Type	Student	Academic Advisor	Project	Remark
RNA Secondary Structure Filter	FPr	Peter Hansen	David Weese, Knut Reinert	SeqAn	edit

Assistance

We offer a weekly support for SeqAn related theses. Please make an appointment below:

Date	Time	Place	Academic Advisor	Attendee(s)
					edit

Please check this page for last-minute updates of time or place of your appointment.