Alexander J. Nederbragt

The paper evaluates two graph-based read mappers against a hybrid baseline approach, showing the baseline improves mapping accuracy to graph-based references.

NucBreak detects structural errors in genome assemblies using paired-end Illumina reads, showing high sensitivity and precision compared to existing tools.

The paper presents a high-quality chromosome-level genome assembly of the nine-spined stickleback, revealing evolutionary insights and chromosomal rearrangements compared to the three-spined stickleback.

The paper introduces a method for calling ChIP-Seq peaks on graph-based reference genomes and demonstrates its ability to detect more motif-enriched peaks than MACS2.

NucMerge improves genome assembly accuracy by integrating alternative assemblies and paired-end Illumina reads, outperforming existing tools in error correction and rearrangement detection.

The paper analyzes the grayling genome to study regulatory divergence of Ss4R duplicates after whole genome duplication, finding purifying selection and adaptive divergence in brain-related and immune functions.

The paper sequenced and assembled the haddock genome, revealing high tandem repeat density and expanded immune gene families common to codfishes.

The paper improves the Atlantic cod genome assembly using long-read sequencing and multiple assembly programs, revealing a high density of tandem repeats and heterozygous variation.

The paper presents draft genomes of two clinical Bacillus cereus isolates, showing high similarity to reference strains, highlighting their opportunistic pathogenic potential.