Selected Publications

Bioconda: sustainable and comprehensive software distribution for the life sciences

Preprint PDF Code Project

ddRAGE: A data set generator to evaluate ddRADseq analysis software

PDF Code Project

TaxMapper: An Analysis Tool, Reference Database and Workflow for Metatranscriptome Analysis of Eukaryotic Microorganisms

PDF Code

Simulation of Double Digest Restriction Site Associated DNA Sequencing Data

PDF Code Project

Recent Publications

Bioconda: sustainable and comprehensive software distribution for the life sciences

Preprint PDF Code Project

ddRAGE: A data set generator to evaluate ddRADseq analysis software

PDF Code Project

TaxMapper: An Analysis Tool, Reference Database and Workflow for Metatranscriptome Analysis of Eukaryotic Microorganisms

PDF Code

Simulation of Double Digest Restriction Site Associated DNA Sequencing Data

PDF Code Project

Simulating ddRADseq Reads with RAGE

PDF Code Project

Estimation of genetic diversity with RAD sequencing and mutation-tolerant hashing

Clustering of ddRAD-Seq reads with randomized hash functions for biodiversity analysis

Recent & Upcoming Talks

Workshop: Genome Assembly
2017-10-25 13:00
Genome Assembly
2016-06-17 13:00
Searching for Genes in Bacterial Genomes
2016-02-18 13:00

Recent Posts

Since the 1.32 update of Rust, memory profiling with heaptrack became incredibly easy.

CONTINUE READING

Our group attended GCB2017 in Tübingen.

CONTINUE READING

Example of how to manage the python environment in gitlab CI with conda.

CONTINUE READING

Since I did not find a good tutorial for this, here I collected the steps needed to set up Gitlab CI for a small Python project.

CONTINUE READING

Software

RAGE

A simulation tool for ddRADseq data for the validation of analysis tools and pipelines.

Dinopy

Python and Cython library for genomic sequence IO.

Teaching

Most courses were held in German and have German titles. Hover over the links for a translation.

Courses at TU Dortmund

Winter semester 2014/ 2015

Course Language
Practical courses and classes for EINI (Einführung in die Informatik für Logistiker, Wirtschaftsingenieure und Wirtschaftsmathematiker) German
Project group 583 Algorithmen zur Entdeckung krebsauslösender Genvarianten German

Summer semester 2014

Practical courses for DAP II (Datenstrukturen, Algorithmen und Programmierung II) German
Project group 583 Algorithmen zur Entdeckung krebsauslösender Genvarianten German

Winter semester 2013/ 2014

Practical courses and classes for EINI (Einführung in die Informatik für Logistiker, Wirtschaftsingenieure und Wirtschaftsmathematiker) German

Other courses

2015

Tutorial “Scientific Illustration and Presentation with Inkscape”, Inhouse Seminar of the Chair of Genome Informatics at the Faculty of Medicine at Duisburg-Essen University. German

2014

Guest seminar (in cooperation with Corinna Ernst) “LaTeX: GrundTeXniken”, Internal Doctoral Kolloquium of the Institute for Advanced Study in the Humanities (KWI), Essen. German

2012

“Python on Android Smartphones”, Inhouse Seminar of the group for Bioinformatics for High-Throughput Technologies at Computer Science Chair XI - Algorithm Engineering, TU Dortmund. German
Tutorial “OpenCV with Python”, Inhouse Seminar of the group for Bioinformatics for High-Throughput Technologies at Computer Science Chair XI - Algorithm Engineering, TU Dortmund. German

(Co-) Supervised Theses

Bachelor Theses

  • D. Rieks, 2018 – Eigenschaften von Min-Hashing auf q-Grammen
  • U. Jentsch, 2015 – Konzeption, Implementierung und Kombination von Algorithmen auf Sequenzen in Haskell
  • S. Bartsch, 2014 – Entwickelung eines Verfahrens zur effizienten Analyse von RAD-Daten

Master Theses

  • T. Hartmann, 2017 – Separating genetic variants from sequencing errors based on technical features
  • F. Mölder, 2014 – Bias-Korrekturverfahren für Genexpressionsdaten aus RNA-seq

Contact