Sebastian Deorowicz

This study identifies age-associated k-mer signals in canine buccal and cell-free DNA using alignment-free k-mer analysis and ridge regression models.

MKMC enables reference-free transcriptomic analysis using k-mer representations, detecting isoform-specific events and matching alignment-based methods in differential expression and age prediction.

This paper organizes a community challenge to develop automated virus taxonomy classification tools and evaluates their performance on a combined dataset of expert-curated and metagenomic sequences.

FAMSA2 provides high-accuracy multiple sequence alignments for large-scale protein datasets with significantly improved speed.

FLASH predicts phenotype from sequence using deep learning, achieving high accuracy on unseen variants and identifying new virulence predictors across microbes.

MDCompress introduces a new trajectory compression format and software that reduces file size and improves compression/decompression speed for molecular dynamics simulations.

The paper introduces SPLASH, a reference-free algorithm for detecting sequence variation from RNA-seq data, and applies it to discover novel regulatory mechanisms in plant transcriptomes.

The paper presents an nf-core framework for comparing multiple sequence aligners, aiming to streamline deployment and evaluation of MSA tools in HPC environments.

Vclust clusters viral genomes efficiently and accurately using Lempel-Ziv parsing for average nucleotide identity, outperforming existing tools.

sc-SPLASH enables reference-free discovery in scRNA-seq and spatial transcriptomics, uncovering novel transcriptomic features like V(D)J recombination and secreted repeat proteins.

Graphite uses a colored De Bruijn graph to paint genomes, reducing matches and revealing new biological insights in microbial genomics.

ProteStAr compresses protein structure files efficiently, offering better compression ratios than existing tools while maintaining reconstruction accuracy.

The paper introduces SPLASH and compactors to efficiently discover microbial genetic elements and perform strain typing without reference genomes.

SPLASH2 is an efficient, scalable algorithm for discovering regulated sequence variation in RNA-seq data, revealing new biology in single-cell and bulk datasets without parameter tuning.

The paper introduces Cuttlefish 2, a tool that significantly speeds up and reduces memory usage for constructing compacted de Bruijn graphs from large genomic datasets.

AGC provides a compact representation of assembled genomes, reducing storage space by 2-3 orders of magnitude while enabling efficient extraction of contig parts.

CoLoRd compresses third-generation sequencing data by an order of magnitude without affecting downstream analysis accuracy.

PHIST predicts prokaryotic hosts of viruses from their genomic sequences, improving accuracy and speed over existing methods.

Whisper 2 improves indel variant calling quality while maintaining fast runtime compared to existing short-read-mapping tools.

VCFShark compresses VCF files more efficiently than standard methods, reducing their size by up to an order of magnitude.

FQSqueezer improves FASTQ file compression by using k-mer-based methods, achieving better compression ratios than existing tools.

GTShark compresses large genotype datasets and single samples to achieve previously unattainable file sizes.

Whisper improves sequencing data mapping by sorting reads and using suffix arrays, achieving faster performance with comparable accuracy to Bowtie2 and BWA-MEM.

The paper introduces MSAC, a compression algorithm for multiple sequence alignment files, achieving up to six times better compression than gzip.

Kmer-db estimates evolutionary distances between pathogens using k-mers, achieving 44x faster performance than Mash on a modern workstation.

FaStore compresses FASTQ files with lossy modes, achieving better compression ratios than existing methods while maintaining variant calling accuracy.

GTC is a compressed data structure for genetic variation data that improves compression ratio and query speed compared to existing solutions.