20 citations · 23 across the 5 of their papers we have counts for
5 papers
Portability of Scientific Workflows in NGS Data Analysis: A Case Study
Christopher Schiefer, Marc Bux, Joergen Brandt +4
The analysis of next-generation sequencing (NGS) data requires complex computational workflows consisting of dozens of autonomously developed yet interdependent processing steps. W…
Optimum Search Schemes for Approximate String Matching Using Bidirectional FM-Index
Kiavash Kianfar, Christopher Pockrandt, Bahman Torkamandi +2
Finding approximate occurrences of a pattern in a text using a full-text index is a central problem in bioinformatics and has been extensively researched. Bidirectional indices hav…
EPR-dictionaries: A practical and fast data structure for constant time searches in unidirectional and bidirectional FM-indices
Christopher Pockrandt, Marcel Ehrhardt, Knut Reinert
We introduce a new, practical method for conducting an exact search in a uni- and bidirectional FM index in time per step while using bits o…
Hidden breakpoints in genome alignments
Birte Kehr, Knut Reinert, Aaron E. Darling
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, ch…
Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem
Sandro Andreotti, Gunnar W. Klau, Knut Reinert
Peptide sequencing from mass spectrometry data is a key step in proteome research. Especially de novo sequencing, the identification of a peptide from its spectrum alone, is still…