Dr Sascha Steinbiss | Senior Software Developer

This person is a member of Sanger Institute Alumni.

Steinbiss, Sascha

Sascha's current work within the Parasite Genomics team is focused on the development of new efficient software tools for automatic parasite genome annotation and curation.

After having worked as a software developer in the web based training industry for several years, I studied computer science and bioinformatics at the University of Hamburg, Germany.

In Prof. Stefan Kurtz's genome informatics group, I designed, implemented and extended software for de novo identification and annotation of LTR retrotransposons using index-based sequence analysis techniques. This resulted in an improved version of LTRharvest as well as the additional orthogonal tools LTRdigest and LTRsift which aim to provide a workflow for de novo identification and annotation of LTR retroelements. As a basis for these tools, I also worked on various methods and tools for efficient sequence storage and annotation handling, with a particular focus on software engineering to maximise efficiency and reusability of the implemented code in a free toolkit called GenomeTools.

I joined the parasite genomics group in December 2013 to work on automatic parasite genome annotation, particularly of trypanosomatids. For this task I use state of the art technologies for sequence analysis, workflow processing, and web development to deliver useful software tools to the parasitology community.

Publications

  • Companion: a web server for annotation and analysis of parasite genomes.

    Steinbiss S, Silva-Franco F, Brunk B, Foth B, Hertz-Fowler C et al.

    Nucleic acids research 2016;44;W1;W29-34

  • GenomeTools: a comprehensive software library for efficient processing of structured genome annotations.

    Gremme G, Steinbiss S and Kurtz S

    IEEE/ACM transactions on computational biology and bioinformatics 2013;10;3;645-56

  • Fine-grained annotation and classification of de novo predicted LTR retrotransposons.

    Steinbiss S, Willhoeft U, Gremme G and Kurtz S

    Nucleic acids research 2009;37;21;7002-13

  • AnnotationSketch: a genome annotation drawing library.

    Steinbiss S, Gremme G, Schärfer C, Mader M and Kurtz S

    Bioinformatics (Oxford, England) 2009;25;4;533-4

  • The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion.

    Bennett HM, Mok HP, Gkrania-Klotsas E, Tsai IJ, Stanley EJ et al.

    Genome biology 2014;15;11;510

  • Genome organization and DNA accessibility control antigenic variation in trypanosomes.

    Müller LSM, Cosentino RO, Förstner KU, Guizetti J, Wedel C et al.

    Nature 2018

  • Companion: a web server for annotation and analysis of parasite genomes.

    Steinbiss S, Silva-Franco F, Brunk B, Foth B, Hertz-Fowler C et al.

    Nucleic acids research 2016;44;W1;W29-34

  • The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion.

    Bennett HM, Mok HP, Gkrania-Klotsas E, Tsai IJ, Stanley EJ et al.

    Genome biology 2014;15;11;510

  • GenomeTools: a comprehensive software library for efficient processing of structured genome annotations.

    Gremme G, Steinbiss S and Kurtz S

    IEEE/ACM transactions on computational biology and bioinformatics 2013;10;3;645-56

  • Fine-grained annotation and classification of de novo predicted LTR retrotransposons.

    Steinbiss S, Willhoeft U, Gremme G and Kurtz S

    Nucleic acids research 2009;37;21;7002-13

  • AnnotationSketch: a genome annotation drawing library.

    Steinbiss S, Gremme G, Schärfer C, Mader M and Kurtz S

    Bioinformatics (Oxford, England) 2009;25;4;533-4

Steinbiss, Sascha
Sascha's Timeline
2014

Dr. rer. nat. in Computer Science, University of Hamburg, Germany

2013

Joined the Sanger Institute

2008

Diplom in Bioinformatics, University of Hamburg, Germany