Experience
From 2020
Lead Bioinformatician at Quantro Therapeutics
- Planning and setup of the cloud-based production-grade computational environment for concurrent processing of >100k targeted SLAM-seq libraries.
- Leading the computational development of the innovative time-resolved high-throughput transcriptomics QUANTROseq drug discovery platform.
- Machine-learning driven identification of highly-selective transcriptional fingerprints of disease causing transcription factors in our reference compound datasets.
- Building and leading QUANTRO's computational team.
- Planning and overseeing QUANTRO's IT and computational infrastructure and processes.
2014-2020
Senior Bioinformatician at the IMP Research Institute for Molecular Pathology
- Lead bioinformatics method and algorithm development for the SLAM-seq sequencing technology.
- Development a cloud-computing virus screening pipeline on Amazon Web Services (AWS) that scales to big data, analysing the entire 11,000 patient samples (100 TB raw data) of The Cancer Genome Atlas .
- Design of the genome-wide Vienna sgRNA libraries for pooled CRISPR screens.
- Co-development of the VBC score for selection of sgRNAs that effectively produce loss-of-function alleles.
- Technology development on the Oxford Nanopore Sequencing platform to detect translocations at single-base pair resolution genome-wide.
- Member of the Vienna Covid-19 Detection Initiative (VCDI) performing comparative genomics of > 5M sequenced SARS-CoV-2 genomes worldwide to identify conserved domains for sensitive primer design to detect COVID-19 infections, de-novo assembly and quantification of viral RNAs for primer target selection for sensitive SARS-CoV-2 detection.
- Project supervision and mentoring of Bioinformatics Master students:
- CRISPRepo: database and front-end development for integrating, visualizing and querying CRISPR screening data and metadata.
- Characterization of replication origins: Method development for and integration of DNA replication origin mapping (SNS-seq), replication timing sequencing (RepliSeq), genome-wide chromatin contact mapping (HiC) and ChIP-Seq data.
2017-2019
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 .
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 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.
- 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
2020-2023
PhD in Molecular Biosciences, Arndt von Haeseler Group, University Vienna
2009-2012
Master’s Degree in Bioinformatics, Medical University Vienna
2009
Erasmus Semester at the Stockholm Bioinformatics Center, Stockholm, Sweden
2006-2009
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