Jan O. Korbel

The paper shows that escaping replicative crisis and achieving immortality precedes complex genome evolution in cancer cells.

The paper presents a population-scale Y chromosome reference panel with 142 assemblies, revealing structural and epigenetic variation across 180,000 years of evolution.

MechanoMaST integrates mechanical and transcriptomic data from tissue samples to enable spatial correlation with high accuracy, revealing a stiffness-related gene signature in colorectal cancer.

The paper assembles and characterizes 2,110 human centromeres, revealing novel haplotypes, mobile element insertions, and mutation rate variation across chromosomes.

The paper develops a hierarchical classification framework combining epigenetic and genetic data with machine learning to improve diagnosis and risk stratification in hematologic malignancies.

HOROSCOPE uses k-mer signatures to infer centromere architecture and length from short-read data, revealing continental structure and cancer-related rearrangements.

The paper identifies genomic and transcriptomic features of telomere maintenance mechanisms in complex karyotype sarcomas, linking ALT status to therapeutic vulnerabilities.

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 shows that autophagy selectively degrades micronuclei with nuclear envelope defects, preventing chromosomal instability by eliminating missegregated chromosomal material.

This paper reviews current smart microscopy implementations and proposes a framework for interoperability to improve collaboration and standardization in the field.

The paper introduces MAGIC, a platform combining imaging and genomics to study de novo chromosome rearrangements, finding that dicentric chromosomes initiate CA events and TP53 deficiency increases CA rates.

This study uses single-cell whole genome amplification to link somatic mutations to cell identity and ancestry in a live donor.

This paper introduces salad, a sparse denoising model for efficient protein backbone generation, and demonstrates its effectiveness for various protein design tasks.

The paper introduces the JEDI marker as a universal biodiversity measure, demonstrating its applicability across ecological scales and providing an automated bioinformatic workflow for standardized analysis.

This study integrates spatial and multi-omic data from bladder cancer patients to show L1 retrotransposition drives genomic instability, ecDNA formation, and a viral mimicry response.

The paper uses long-read sequencing to characterize structural variants in 1,019 samples from the 1000 Genomes Project, identifying 167,291 sequence-resolved SVs and highlighting their genomic and functional implications.

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

This paper introduces DLVPM, a deep learning method for integrating multi-modal cancer data, showing improved performance in mapping associations between genetic, epigenetic, and histological features.

The paper identifies CFHR5 variants that reduce AMD risk by lowering FHR-5 levels and altering complement pathway activity.

This study identifies treatment-resistant stem-like T-ALL cells that expand during relapse using single-cell RNA sequencing of pediatric T-ALL patient samples.

AlphaDesign uses AlphaFold to design novel protein structures, including monomers, dimers, and higher-order complexes, showing structural integrity and conformational switching capabilities.

This study shows that p53 deficiency causes hypertranscription and nucleotide insufficiency, leading to replication stress and genomic instability, including chromothripsis.

The paper develops a Hi-C analysis pipeline to catalog TADs and loops in human genomes and quantifies the impact of SVs on chromatin structure and gene expression.

The paper introduces NAHRwhals, a method to detect serial structural variations in long-read genomes, identifies 37 sSV loci in humans, and shows their relevance to disease.

This study identifies cell type-specific molecular consequences of mosaic structural variants in hematopoietic stem and progenitor cells across aging.

SVarp discovers haplotype-resolved structural variants using a pangenome reference and long reads, achieving high recall in simulated and real data.

MosaiCatcher v2 provides a standardized workflow for single-cell structural variation detection using Strand-seq, enhancing reproducibility and portability in human genetics research.

The paper investigates DUP-TRP/INV-DUP genomic rearrangements in neurodevelopmental disorders, identifying four SV haplotypes and refining template switching points using multiple sequencing technologies.

The paper presents long-read assemblies of 43 diverse human Y chromosomes, revealing extensive structural complexity and variation across 180,000 years of evolution.

The paper introduces MuAt, a deep learning model that learns representations of somatic mutations to predict tumour types and subtypes with high accuracy.