I enjoy combining my IT and science skills to deliver high performance and scalable scientific algorithms, applications, and web sites for large user communities.
More than 15 years of experience in software development for bioinformatics and clinical diagnostics.
- Technical and scientific lead at the San Diego team.
- Development of scaleable bioinformatics algorithms and applications.
- Data integration of 60+ biological databases.
- Development of new algorithms for the comparison of protein sequences and 3D structures.
- Annotation of genetic variation data, mapping on protein sequence, function, interaction, and 3D structural data.
- Web-based visualization of scientific data.
- Using Google Analytics data to guide the planning of new features.
Engineering Lead / Principal Engineer June 2017-nowInvitae
Invitae is the Nr. 1 contributor of interpreted variants at Clinvar. I am Engineering Lead for the Interpretation Platform that allows the company to scale up our clinical reporting workflows to thousands of samples per day.
Protein Data Bank
Senior Scientist (February 2008 - May 2017)http://www.rcsb.org
With over 300,000 unique users per month from over 160 countries around the world, the RCSB PDB is one of the worldwide leading Biological Databases. The RCSB PDB's primary citation is in the top 100 of Nature's most-cited research of all time.
Wellcome Trust Sanger Institute
Research Associate (2004 - 2008)
Development of Distributed Annotation System for data integration of genomic and protein data. Mapping of SNP data onto 3D structure. Participation in large scale genome and protein annotation projects in national and international collaborations.http://www.sanger.ac.uk
University of Salzburg
Research Assistant 1999-2003
Teaching various lectures and practical courses in bioinformatics and introduction to protein structure to undergraduate and graduate students.http://www.came.sbg.ac.at
- 2021 -
- VRS - Global Aliance for Genomic Health
I am part of the leadership team for the Variation Representation spec. We are developing a specification (plus implementation) for the description of genomic variation.
- 2011 - 2017
Journal PLoS Computational
Biology Editor Software Section
Building up a new section for the journal with the goal of publishing open source software of exceptional importance that has been shown to provide new biological insights.Some of the articles that are published in this section are amongst the most widely read for the journal.
- 2009 - 2017
BioJava - Project
BioJava is a widely used library for processing of biological data. It is used in teaching for the demonstration of solutions to common bioinformatics problems. It provides analytical and statistical routines, contains parsers for common file formats, and allows the manipulation of biological sequences and structures.
Under my leadership we authored 2 publications that currently have more than 170 citations. We also migrated the project to GitHub where it is flourishing with an active developer base.
- Referee for journals: Bioinformatics, Briefings in Bioinformatics, Nucleic Acid Research, PLoS comp. biol, PLoS ONE, Protein Science
Ph.D. degree in group of Manfred Sippl
Center of Applied Molecular EngineeringTitle: WILMA - a platform for the automated annotation of protein sequences [more]
Diploma Thesis in group of Manfred Sippl.
Center of Applied Molecular EngineeringTitle: Deriving substitution matrices for amino acids and secondary structure [more]
- studies in biology / genetics with special focus on bioinformatics