Burkhard Morgenstern

This paper explores using insertions and deletions as phylogenetic signal in alignment-free sequence comparison, showing that indels alone can produce phylogenetic trees comparable to existing alignment-free methods.

S-conLSH maps noisy long reads to reference genomes without alignment, achieving high sensitivity and speed.

This paper introduces App-SpaM, an alignment-free method for phylogenetic placement of short reads, achieving comparable accuracy to alignment-based methods but with significantly faster performance.

This study identifies media-dependent secretome responses in Verticillium longisporum, revealing specific exoproteome patterns in plant-related environments and identifying Nlp2 and Nlp3 as key effectors for plant infection.

Smash++ identifies genomic rearrangements without sequence alignment, using data compression, and validates results against existing methods and FISH analysis.

This paper reviews alignment-free sequence comparison methods, focusing on SpaM approaches that use spaced word matches to estimate phylogenetic distances.

Read-SpaM estimates phylogenetic distances from low-coverage bacterial sequencing reads without assembly or alignment.

The paper develops a method to estimate phylogenetic distances using k-mer matches and introduces Slope-SpaM, showing high accuracy for up to 0.5 substitutions per site.

This paper benchmarks alignment-free sequence comparison methods across five research applications and provides a web resource for evaluating and comparing these methods.

Prot-SpaM estimates evolutionary distances between proteomes using alignment-free methods, outperforming other approaches on simulated and real data.