Dr. Fabian Birzele

E-Mail:

Research

Alternative Splicing (more)
Protein structure comparison (more)
Protein structure prediction (more)

Teaching

WS 2008/09	Tutor for and organization of the genome-oriented lab course
	Lecture "Java Game Development" for the programming lab course
	Tutor for the seminar Current Problems in Bioinformatics II
SS 2008	Tutor for the lecture Algorithmic Bioinformatics III
	Tutor for the seminar Current Problems in Bioinformatics II
WS 2007/08	Tutor for and organization of the genome-oriented lab course

Publications

Submitted

Papers

Fabian Birzele, E. Hoffmann, Gergely Csaba, Ralf Zimmer. Alternative Splicing of Protein Repeats. BMC Structural Biology, Submitted.

BibTex

Fabian Birzele, Ralf Zimmer. Alternative Splicing and Proteome Complexity in Mass Spectrometry. PLoS Computational Biology, Submitted.

BibTex

Gergely Csaba, Fabian Birzele, Ralf Zimmer. On the Similarity of Protein Structures. submitted, Submitted.

BibTex

R. Küffner, Fabian Birzele, Ralf Zimmer. PASS: Reliable detection of alternative splicing with microarrays. BMC Bioinformatics, Submitted.

BibTex

2009

Papers

Gergely Csaba, Fabian Birzele, Ralf Zimmer. Systematic Comparison of SCOP and CATH: A new Gold Standard for Protein Structure Analysis. BMC Structural Biology, vol 9, no. 23, 2009.

BibTex

Fabian Birzele, Gergely Csaba, Florian Erhard, Caroline C. Friedel, R. Küffner, Tobias Petri, Lukas Windhager, Ralf Zimmer. Algorithmische Systembiologie mit Petrinetzen – Von qualitativen zu quantitativen Systemmodellen. Informatik-Spektrum, vol 32, no. 4, pp. 310-319, 2009.

DOI
Journal version

BibTex

Theses

Fabian Birzele. Alternative Splicing and Protein Structure Evolution. PhD Thesis, LMU München, January 2009.

E-Dissertation

BibTex

2008

Papers

Fabian Birzele, Gergely Csaba, Ralf Zimmer. Alternative splicing and protein structure evolution. Nucleic Acids Res., vol 36, pp. 550–558, Feb 2008.

BibTex

Fabian Birzele, Jan Gewehr, Ralf Zimmer. AutoPSI: a database for automatic structural classification of protein sequences and structures. Nucleic Acids Res., vol 36, pp. 398–401, Jan 2008.

BibTex

Fabian Birzele, R. Küffner, Franziska Meier, Florian Oefinger, Christian Potthast, Ralf Zimmer. ProSAS: a database for analyzing alternative splicing in the context of protein structures. Nucleic Acids Res., vol 36, pp. D63–68, Jan 2008.

BibTex

Gergely Csaba, Fabian Birzele, Ralf Zimmer. Protein structure alignment considering phenotypic plasticity. Bioinformatics, vol 24, pp. 98–104, Aug 2008.

BibTex

2007

Papers

Fabian Birzele, Jan Gewehr, Gergely Csaba, Ralf Zimmer. Vorolign - Fast Structural Alignment using Voronoi Contacts. Bioinformatics, vol 23, no. 2, pp. e205-e211, 2007.

BibTex

2006

Papers

Fabian Birzele, Stefan Kramer. A new representation for protein secondary structure prediction based on frequent patterns. Bioinformatics, vol 22, pp. 2628–2634, Nov 2006.

BibTex

2005

Papers

Fabian Birzele, Jan Gewehr, Ralf Zimmer. QUASAR–scoring and ranking of sequence-structure alignments. Bioinformatics, vol 21, no. 24, pp. 4425–4426, Dec 2005.

BibTex

A. Facius, C. Englbrecht, Fabian Birzele, A. Groscurth, S. Benjamin, S. Wanka, HW Mewes. PRIME: a graphical interface for integrating genomic/proteomic databases. Proteomics, vol 5, no. 1, pp. 76-80, 2005.

BibTex

Refereed talks

2008	Fabian Birzele, Gergely Csaba and Ralf Zimmer, Alternative Splicing and Protein Structure Evolution, Highlights Paper Track, Refereed Talk, ISMB 2008, Toronto
	Fabian Birzele, Gergely Csaba and Ralf Zimmer, Alternative Splicing and Protein Structure Evolution, Highlights Paper Track, Refereed Talk, GCB 2008, Dresden

Software

ProSAS Database	Database for analyzing alternative splicing events in several mamalian genomes with respect to protein structure (implemented in Java using the Zkoss framework).
AutoPSI Database	Database combining AutoSCOP and Vorolign predictions for protein sequences and structures (implemented in Java using the Zkoss framework).
Vorolign	Fast and flexible structural alignment using Voronoi contacts (Server Version)
Apriori on Patterns	Tool to search for frequent regular expressions in a database of protein sequences (written in PERL)
Quasar	A flexible system for scoring and ranking sequence-structure alignments (written in Java)
Download SpliCQ	Software to predict (differential) alternative splicing events in next generation sequencing data (written in Java)

Curriculum Vitae

Education
January 2009	PhD, Bioinformatics Group, University of Munich (LMU Munich)
June 2005 - February 2009	PhD-Student, Bioinformatics Group, University of Munich (LMU Munich)
2000-2005	Bioinformatics course, University of Munich (LMU Munich) and Technical University of Munich (TU Munich), Diploma degree (M.sc equiv.)
1990-1999	Abitur, Gabrieli-Gymnasium Eichstätt
Working experience and internships
Since March 2009	PostDoc at Boehringer Ingelheim Pharma, Biberach (Next Generation Sequencing and Genomics)
Since March 2008	Free software developer and IT consultant for K-tronik GmbH, Munich and dresskit GmbH, Munich
2001-2004	Student assistant and tutor for different lectures, lab courses and research projects at the GSF, Neuherberg (Prof. H.W. Mewes), chair for database systems, LMU Munich (Prof. H.P. Kriegel) and the chair for bioinformatics, LMU Munich (Prof. R. Zimmer).
July-September 2003	Visiting Researcher at Biomolecular Modelling Lab (Dr. Paul Bates), Cancer Research UK, London
2001-2002	GPC Biotech, Matrinsried, München
1999-2000	Civilian Service at an old people's home (Caritas Altenheim St. Elisabeth, Eichstätt)

Search

Links and Functions

Language Selection

User Menu

Breadcrumb Navigation

Main Navigation

Content

Service Menu

Footer