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Alexander Donath, PhD.

has moved to:

Centre for Molecular Biodiversity Research (zmb)
Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)
Adenauerallee 160
53113 Bonn, Germany

phone: +49 228 9122-344
fax: +49 228 9122-295
web: http://www.zfmk.de

This page is obsolete.

I now work at the zmb, ZFMK in Bonn, Germany. Here is my new page.



Work.

since 05/2011
Computational Genomics - Head of Section, Coordinator HPC, zmb, ZFMK, Bonn, Germany.

09/2006 - 12/2006
Student apprentice at the TBI, University of Vienna, Austria.

10/2005 - 09/2006
Student assistant (SHK) at the Professur für Bioinformatik, Universität Leipzig, Germany.

05/2005 - 12/2005
Student assistant (SHK) at the Institut für Informatik, Universität Leipzig, Germany.


Studies.

11/2007 - 05/2011
PhD studies at the Professur für Bioinformatik, Universität Leipzig, Germany.

04/2007 - 10/2007
Diploma student at the Professur für Bioinformatik, Universität Leipzig, Germany.
[Supplementary material] [diploma talk webcam shots]

09/2002 - 10/2007
Diploma studies in Computer Science (specialization in Bioinformatics), Universität Leipzig, Germany.


Publications. (outdated)

Deletion analysis of the 3' long terminal repeat sequence of plant retrotransposon
Tto1 identifies 125 base pairs as sufficient for first strand transfer. [link]
A Tramontano, A Donath, SH Bernhart, K Reiche, Gudrun Böhmdorfer, PF Stadler, A Bachmair.
Virology, 412, 1:75-82, 2011.

Evolution of 7SK RNA and its Protein Partners in Metazoa. [link]
M Marz*, A Donath*, N Verstraete, VT Nguyen, PF Stadler, O Bensaude.
Mol. Biol. Evol., 26, 12:2821-30, 2009. *co-first authorship

The Expansion of the Metazoan MicroRNA Repertoire. [link]
J Hertel, M Lindemeyer, K Missal, C Fried, A Tanzer, C Flamm, IL Hofacker, PF Stadler.
and The Students of Bioinformatics Computer Labs 2004 and 2005.
BMC Genomics, 7(25), 2006.


For working papers, search here for 'donath'.

Book Chapters. (outdated)

Noncoding RNA. [link]
A Donath, S Findeiß, J Hertel, M Marz, W Otto, C Schulz, PF Stadler, S Wirth.
In Evolutionary Genomics and Systems Biology.
G Caetano-Anollés (ed.). Wiley-Blackwell, Hoboken. pp 251-293, 2010.
ISBN: 978-0-470-19514-7


Talks. (outdated)

2011 - Hannover, Germany
Title: MITOS: Automatic Annotation of Metazoan Mitochondrial Genomes.

2010 - Vysoka Lipa, Czech Republic
Title: Detection of Rate Variation by Maximum Likelihood Optimization.

2010 - Bled, Slovenia
Title: Don't believe the RefSeq! or: How to annotate a genome.

2008 - Ljubljana, Slovenia
Title: TIR domain-containing Proteins.

2007 - Bled, Slovenia
Title: Attenuated Parasites in Regulatory Networks.

2006 - Leipzig, Germany
Title: Tto1 Retrotransposon - Interaction sites (and encapsidation signals).

2006 - Leipzig, Germany
Title: The Mutated Subsequence Problem.


Posters. (outdated)

2009 - Halle/Saale, Germany
German Conference on Bioinformatics 2009
Title: Improved Automatic Annotation of Metazoan Mitochondrial Genomes.

2008 - Barcelona, Spain
ICREA conference on the Origin and Early Evolution of Metazoans.
Title: Phylogeny from RNA Secondary Structure.


Software.

gappy v1.0
gappy extracts splids (split-inducing indels) from a given alignment and creates a binary absence/presence matrix. gappy is implemented in the C++. The tool reads multiple sequence alignments in FASTA format. The user can select a minimum and maximum indel length for determining splids. By default, the output is a FASTA file, containing the binary coded splid absence/presence information, and some summary statistics. Output is also available in PHYLIP and NEXUS format. Download.

GA.c
A simple genetic algorithm which uses an external evaluation function can be found here.
Makes use of the Mersenne Twister.
randr.pl v0.5b
A small (and crude) perl script for creating sets of random user specific rna/dna/protein sequences.
[man page]
~ By the time you've read this, you've already read it! ~