Maximilian Haeussler

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

The paper constructs a high-resolution human pangenome structural variant resource, identifies disease-associated SVs, and demonstrates its utility in filtering variants from probands and associating SVs with traits in a large cohort.

The paper identifies YBX1 as a key transcription factor in shaping human prefrontal cortex molecular identity through CRISPR activation screens and organoid experiments.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

The paper integrates single-cell and spatial multiomic data to show widespread reactivation of developmental programs in diseased human hearts, with insights into transcriptional factors and localized fetal reactivation.

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

The paper demonstrates a framework using BRC-Analytics and agentic AI to standardize RNA-seq analysis of fungal pathogens, achieving reproducible results across studies with differing annotations.

KegAlign improves pairwise genome alignment speed using GPU acceleration and diagonal partitioning, achieving 150x faster alignment than lastZ for human/mouse genomes.

The paper presents a single-nucleus RNA sequencing atlas of Aedes aegypti mosquitoes, identifying novel cell types and sexual dimorphism in gene expression across tissues.

The paper introduces BRC-Analytics, a browser-based platform for pathogen genomics, demonstrating its use in analyzing measles virus evolutionary dynamics and revealing asymmetric frame evolution under selective pressures.

This study uses single-cell analysis of dup15q syndrome to identify developmental and postnatal molecular changes in autism, revealing cell-type specific dysregulation and shared vulnerabilities with idiopathic ASD.

The paper maps MAVE data to human reference sequences to improve variant functional assay utility for genomics applications.

The paper integrates seven single-cell transcriptomic datasets to generate 225 meta-modules, identifying key gene networks involved in human cortical cell subtype specification and validating their roles in neurodevelopment.

PanSci, a single-cell transcriptome atlas of over 20 million cells throughout the mouse lifespan, unveils the temporal architecture of aging-associated cellular population dynamics, organ-specific immune cell shifts, and the lymphocytes role in organismal aging.

This study maps cell types and their spatial distribution in multiple sclerosis lesions to understand disease progression and identify potential therapeutic targets.

The paper investigates epigenomic and 3D chromatin conformation changes in human frontal cortex and hippocampus development using sn-m3C-seq, finding distinct chromatin conformations in neurons and glial cells and linking risk variants to regulatory regions.

The paper introduces a genome browser track for visualizing dynamic DNA sequence features at single nucleotide resolution using machine learning-derived scores.

The UCSC Cell Browser allows visualization of gene expression and metadata in single-cell datasets through a web interface and Python package.

The paper identifies molecular subtypes of human interneuron progenitors and immature interneurons using single-cell RNA sequencing and compares them to mouse data, revealing species-specific gene programs.

The paper reports a SARS-CoV-2 lineage with mutations from known variants of concern that is rejected by sequence repositories due to a deletion, suggesting underestimation of its frequency.

The paper introduces an interactive scRNA-Seq analysis environment based on Galaxy, integrating ~70 functions for scalable and accessible single-cell data analysis.

Single-cell RNA sequencing of 289,000 first-trimester human brain cells identifies nine telencephalic progenitor subpopulations, a transient mesenchymal-like population, human-enriched C1orf61+ and ID4+ progenitors, and low early organoid fidelity.

The paper models TBX5 haploinsufficiency in iPSC-derived cardiomyocytes to identify gene regulatory network imbalances linked to congenital heart disease.

The paper describes a SARS-CoV-2 genome browser that integrates molecular data from multiple sources for visualization and analysis.

AMELIE 2 improves Mendelian disorder diagnosis by matching patient phenotypes and genotypes to primary literature, achieving high accuracy and efficiency.

The UCSC Repeat Browser provides a tool for visualizing and analyzing repeat elements in the genome, enabling the study of evolutionary conflicts across species.

The paper maps chromatin accessibility in developing human brain and organoids using scATAC-seq, revealing cell type-specific regulatory elements and their role in neurodevelopment.

AVADA automatically curates a database of pathogenic variants from full-text literature, outperforming existing methods and providing more variants than ClinVar.

The paper profiles CRISPR/Cas9-induced mutational outcomes and develops a predictive model based on sequence context to guide DSB repair outcomes.