Experience
From 2017
Contractor for Lexogen GmbH

  • Lead development of the SLAMdunk product backend.
  • Optimizing and porting established variant-callers for nucleotide-conversion detection.
  • Containerization of so ware packages using Docker.
  • Deployment of Docker containers on the Bluebee private cloud platform .
  • License assessment and resource benchmarking .

From 2014
Bioinformatician at the IMP Research Institute for Molecular Pathology

  • Data mining public datasets in the cloud .
  • Lead bioinformatics method and algorithm development for the SLAM-seq sequencing technology.
  • Design of genome-wide shRNA and sgRNA libraries for pooled RNAi /CRISPR screens in human and mouse and screen analysis.
  • Project lead on database and front-end development for integrating, visualizing and querying screening and NGS data and metadata utilizing the on-campus sequencing facility API
  • Establishment of Oxford Nanopore Sequencing (ONT) protocols in the lab (first lab at IMP).

2012-2014
Bioinformatician at Sophia Genetics SA

  • Lead development, maintenance and optimization of a targeted gene sequencing and exome-sequencing pipeline building system forming the bioinformatics backend of the Sophia DDM ® SaaS platform .
  • Tailoring pipelines for diagnostic gene panel kits on various sequencing platforms (Roche 454 / ionTorrentPGM / Illumina MiSeq) for major hospitals and labs in Switzerland and across Europe .
  • Conducting genetic test kit validation studies with key diagnostic kit developer sat European level .
  • Product presentations for prospective and established customers and on conferences .

2012
Bioinformatician at the Max F. Perutz Laboratories

  • De-novo genome assembly of Clunio marinus:
    • Contig assembly, filtering and completeness assessment
    • Setup of the de-novo gene annotation pipeline and genome browser (MAKER,GMOD)
  • Scaffold N50 of 1.9Mb, 98 % completeness.
  • Better assembly quality than honeybee, Tribolium or the monarch butterly.
  • Served as basis to unravel the genomic basis of circadian and circalunar timing adaptations.
  • Served as basis to unravel the genomic basis of circadian and circalunar timing adaptations.
  • Hosted at ClunioBase and published in Nature.

2010-2012
Project student at the Center for Integrative Bioinformatics Vienna

  • Massive parallelization of sequence alignments on the CPU and cluster
    https://github.com/t-neumann/versalignLib
  • Software development of an evaluation framework for reference-mapping software.
  • De-novo transcriptome assembly of RNA-seq data for Idiosepius pygmaeus.

2009
Research intern at the SBC Stockholm Bioinformatics Center

  • Network analysis of the gene interaction database FunCoup to in-silico identify and evaluate novel neurodegenerative disease candidate genes.
Education
2009
Master’s Degree in Bioinformatics, Medical University Vienna

2007
Erasmus Semester at the Stockholm Bioinformatics Center, Stockholm, Sweden

2007-2009
Bachelor’s Degree in Bioinformatics, University for Applied Sciences Hagenberg
Computers skills
• Programming
C/C++, Java
• Scripting
Python, R/Bioconductor, Bash, Perl

• Versioning
Git, SVN
• Containers
Docker, Singularity

• Platforms
Linux, Mac OS X, AWS, Windows
• Building
CMake, Maven

• Frameworks
EJB / CDI, Hibernate / JPA, JSF + PrimeFaces
• Parallelization
SSE/AVX, OpenCL, OpenMP, MPI
Languages
• German
Native
• English
Full professional proficiency
• Spanish
Elementary proficiency
Interests
Sports
Beachvolleyball, Cycling, Bouldering, Slacklining, Badminton

Music
Piano, Guitar, Drums

Other
Reading news, languages, travelling