Maria Nattestad

This study compares Element Avidity sequencing to Illumina sequencing, finding higher accuracy in mapping and variant calling, especially at lower coverages and in challenging genomic regions.

DeepPolisher improves genome assembly accuracy by reducing errors using a transformer model and phasing method, achieving over 70% indel error reduction.

This paper introduces a local haplotype approximation method to improve variant calling accuracy across long-read sequencing platforms without increasing computational overhead.

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

The paper evaluates variant calling in difficult genomic regions using short- and long-read sequencing, showing improved performance with new methods and multi-technology approaches.

The paper introduces a haplotype-aware variant calling pipeline for nanopore and PacBio HiFi data, achieving high accuracy in variant detection and de novo assembly polishing.

DeepConsensus improves PacBio HiFi read accuracy and assembly quality using a gap-aware transformer model.

DeepTrio improves variant calling in family trios using deep learning, achieving higher accuracy than DeepVariant, especially at lower coverages.

The paper provides a dataset of 9 gold-standard samples sequenced on multiple platforms and protocols to benchmark sequencing and analysis methods.

BigTop provides a 3D VR visualization of GWAS data, enhancing interaction and exploration beyond traditional 2D Manhattan plots.

The paper uses long-read sequencing to analyze structural variations in the SK-BR-3 breast cancer cell line, revealing complex rearrangements and novel gene fusions.

The paper introduces open-source tools for detecting structural variations using long-read sequencing, achieving high sensitivity and precision in complex regions and identifying novel variants in human genomes.

GenomeScope estimates genome size, heterozygosity, and repeat content from short reads to aid in genome analysis parameter selection.

SplitThreader analyzes genomic rearrangements and copy number changes in cancer genomes to identify gene fusions and variant categories.

The paper introduces Ribbon, a visualization tool for complex genome alignments and structural variation, addressing limitations of one-dimensional genome browsers.

This paper introduces FALCON and FALCON-Unzip algorithms to assemble diploid genomes from SMRT sequencing data, demonstrating improved contiguity and phasing compared to short-read methods.