Gunnar W. Klau

Barcode Crosstalk in ONT Multiplex Sequencing: Quantification and Mitigation Strategies

The paper quantifies barcode crosstalk in ONT multiplex sequencing and evaluates mitigation strategies across three protocols, finding that protocol C eliminates crosstalk completely.

POTTR: Identifying Recurrent Trajectories in Evolutionary and Developmental Processes using Posets

POTTR identifies recurrent mutation trajectories in cancer and development using posets, resolving uncertainty in phylogenies and discovering significant new patterns.

Sequence-to-graph alignment based copy number calling using a network flow formulation

This paper introduces Floco, a network flow-based method for copy number calling on genome graphs, improving accuracy by up to 43% compared to read depth estimation.

Anticlustering for Sample Allocation To Minimize Batch Effects

The paper introduces anticlustering to balance batches and minimize batch effects in high-throughput sequencing, showing improved balance compared to existing methods.

Small molecule machine learning: All models are wrong, some may not even be useful

The paper evaluates coverage bias in small molecule datasets and proposes methods to assess and improve dataset representativeness for machine learning models.

MetaGut: Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing

MetaGut uses long-read shotgun metagenomics to analyze gut microbiome composition and antibiotic resistance genes in patients undergoing alloHSCT, revealing significant inter-individual and temporal variability.

Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data

This paper presents a method for haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data, achieving high-quality chromosome-level assemblies with haplotype-specific resolution.

HOGVAX: Exploiting Peptide Overlaps to Maximize Population Coverage in Vaccine Design with Application to SARS-CoV-2

HOGVAX selects peptides to maximize population coverage in vaccine design by exploiting sequence overlaps, achieving high coverage and robust immunity against SARS-CoV-2 variants.

CATHI: An interactive platform for comparative genomics and homolog identification

CATHI provides an intuitive platform for comparative genomics and homolog identification, integrating tools like BLAST and MAFFT to streamline analysis for biologists without programming expertise.

Haplotype Threading: Accurate Polyploid Phasing from Long Reads

This paper introduces a novel two-stage method for polyploid haplotype phasing using long reads, achieving lower error rates than existing methods in challenging regions.

The Homo-Edit Distance Problem

The paper introduces the homo-edit distance problem and presents a polynomial-time dynamic programming solution for computing it.

WhatsHap: fast and accurate read-based phasing

Re-aligning reads to both alleles gives WhatsHap the lowest PacBio switch error rates (full coverage: 0.24% real, 0.02% simulated) and better indel phasing than hapCUT and phASER.

Computational Pan-Genomics: Status, Promises and Challenges

This paper reviews computational pan-genomics, discussing its status, potential, and challenges across multiple biological disciplines.