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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OUTDATED!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  
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  
Efficient exact motif discovery BSc Gergana Stanilova Knut Reinert SeqAn  
Improvement of graph based realignment in SeqAn BSc N.N. Knut Reinert SeqAn  
Region Filter BSc Dorian Joswig Hannes Hauswedell, Knut Reinert SeqAn  
SeqAn in Browser BSc Max Pohl Hannes Hauswedell, Knut Reinert SeqAn  
Evaluation of the impact of protein alphabet reductions in a protein local aligner Bsc Kristin Knorr Hannes Hauswedell, Knut Reinert SeqAn  
Tree-based map alignment for LC-MS maps BSc Maria Tromifova Chris Bielow, Knut Reinert OpenMS  
Evaluation of strategies for k-mer counting in bins BSc   Enrico Seiler SeqAn  

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  
Simulation of Genomes and Genome Evolution MSc N.N. Knut Reinert SeqAn  
Devising a method to generate flexible Filters MSc N.N. Knut Reinert SeqAn  
Syntenic assembly of guinea pig (wild one vs domestic) MSc N.N. Camila Mazzoni, Knut Reinert SeqAn collaboration with external group
Partitioning and clustering sequence blocks in the DREAM index MSc N.N. Knut Reinert SeqAn  
Analysis of protein-DNA interactions from ChIP-seq data MSc N.N. Dr. Marcel Grunert, Knut Reinert   collaboration with ECRC

Research Project

Topic Type Student Academic Advisor Project Remark
           

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.
Design and implementation of a SNP efficient Journaled String BSc Matthias Loose Reneé Rahn SeqAn  
Implementing 01*0 seed search strategy using the bidirectional FM index in SeqAn BSc Jan Gütig Christopher Pockrandt, Knut Reinert SeqAn  

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

Research Project

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

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

Master

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

Research Project

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

Assistance

We offer a weekly support for SeqAn related theses. Please make an appointment below:
Date Time Place Academic Advisor Attendee(s)
         

Please check this page for last-minute updates of time or place of your appointment.
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Topic revision: r108 - 23 Sep 2019, KasseckeUserTopic - This page was cached on 01 Feb 2025 - 15:56.

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