Dr. Fabian Birzele

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Forschung

Alternatives Spleißing (mehr)
Proteinstrukturvergleich und -alignment (mehr)
Proteinstrukturvorhersage (mehr)

Lehre

WS 2008/09	Betreuung und Organisation des genomorientierten Praktikums
	Vorlesung "Java Game Development" im Rahmen des Programmierpraktikums
	Betreuung des Hauptseminars Aktuelle Probleme der Bioinformatik
SS 2008	Betreuung der Vorlesung Algorithmische Bioinformatik III
	Betreuung des Hauptseminars Aktuelle Probleme der Bioinformatik
WS 2007/08	Betreuung und Organisation des genomorientierten Praktikums

Publikationen

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

Vorträge

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)

Lebenslauf

Ausbildung
Januar 2009	Promotion, LFE Bioinformatik, LMU München
Juni 2005 - Februar 2009	Wissenschaftlicher Mitarbeiter, LFE Bioinformatik, LMU München
2000-2005	Studium der Bioinformatik an der LMU München und der TU München, Abschluss: Diplom
1990-1999	Abitur, Gabrieli-Gymnasium Eichstätt
Arbeitserfahrung und Praktika
Seit März 2009	PostDoc bei Boehringer Ingelheim Pharma, Biberach (Next Generation Sequencing und Genomics)
Seit März 2008	Freier Softwareentwickler und IT-Berater bei der K-Tronik GmbH München und für die dresskit GmbH, München
2001-2004	Studentischer Mitarbeiter und Tutor für verschiedene Vorlesungen, Praktika und in Forschungsprojekte an der GSF, Neuherberg (Prof. H.W. Mewes), Lehrstuhl für Datenbanksysteme, LMU München (Prof. H.P. Kriegel) and the LFE Bioinformatik, LMU München (Prof. R. Zimmer),
Juli-September 2003	Praktikum bei Dr. Paul Bates, Cancer Research UK, London
2001-2002	GPC Biotech, Matrinsried, München
1999-2000	Zivildienst (Caritas Altenheim St. Elisabeth, Eichstätt)

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