Marcel Martin

In utero barcoding of mouse mesoderm reveals the clonal architecture of organ mesenchyme

The paper uses in utero barcoding and single-cell transcriptomics to map clonal relationships in mouse mesoderm-derived tissues, revealing lineage relationships in liver and heart mesenchyme.

Multi-context seeds enable fast and high-accuracy read mapping

The paper introduces multi-context seeds to improve read mapping accuracy while maintaining speed and memory efficiency.

AEMB: a computationally efficient abundance estimation method for metagenomic binning

AEMB improves metagenomic binning efficiency by reducing computational demands while maintaining binning accuracy.

Designing efficient randstrobes for sequence similarity analyses

This paper introduces new randstrobe construction methods, identifies biases in previous approaches, and improves accuracy in short-read mapping.

Clonally heritable gene expression imparts a layer of diversity within cell types

The paper identifies heritable transcriptional diversity within cell types by studying clonal human lymphocytes and mouse brain cells, showing clone-specific chromatin accessibility leads to distinct gene expression.

minute: A MINUTE-ChIP data analysis workflow

minute is a computational workflow for processing multiplexed ChIP-seq data to generate normalized, scaled bigWig files for quantitative comparative analysis.

Cell types and clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics

This study uses single-cell and spatial transcriptomics to reveal clonal relationships and cell types in the mouse brain, showing fate-restricted progenitor cells and microglia origins.

Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants

Sarek provides a portable and reproducible workflow for analyzing germline and somatic variants from whole-genome sequencing data.

De novo assembly of two Swedish genomes reveals missing segments from the human GRCh38 reference and improves variant calling of population-scale sequencing data

The paper performs de novo assembly of two Swedish genomes, identifies novel sequences absent from GRCh38, and shows improved variant calling with these sequences.

Bioconda: A sustainable and comprehensive software distribution for the life sciences

Bioconda provides a sustainable, comprehensive distribution of bioinformatics software using Conda for reproducible analysis across platforms.

SweGen: A whole-genome map of genetic variability in a cross-section of the Swedish population

SweGen provides a high-quality whole-genome map of genetic variation in the Swedish population, useful for clinical genetics and association studies.

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.

Read-Based Phasing of Related Individuals

This paper combines read-based phasing and genetic haplotyping to improve haplotype inference in related individuals, achieving higher accuracy and more phased variants than either method alone.