Amnon Koren

Minute amounts of helicase-deficient truncated RECQL4 are sufficient for DNA replication.

This study identifies KLHDC3 as a rescue factor for RECQL4 mutations, showing that low levels of a truncated RECQL4 protein can support DNA replication without requiring its ATPase or helicase domains.

DNA replication in early mammalian embryos is patterned, predisposing lamina-associated regions to fragility

The paper shows that DNA replication patterns in early mammalian embryos are established early, with late replicating regions near the nuclear lamina showing fragility and predisposing long genes to genetic changes.

Incomplete Reprogramming of DNA Replication Timing in Induced Pluripotent Stem Cells

The paper examines DNA replication timing in iPSCs, finding that some exhibit delayed replication at heterochromatic regions, which persists through differentiation and may affect their quality.

Multifactorial heterogeneity of the human mutation landscape related to DNA replication dynamics

The paper investigates mutation landscape heterogeneity across individuals and cell types, identifying replication timing biases and mutation load as key factors.

Telomere-to-telomere human DNA replication timing profiles

This study reports telomere-to-telomere replication timing profiles in human using the T2T-CHM13 genome assembly, showing replication timing in centromeres and heterochromatin.

High-throughput analysis of single human cells reveals the complex nature of DNA replication timing control

The paper uses single-cell whole-genome sequencing to analyze DNA replication timing in human cells, revealing variability in replication initiation sites and subtypes.

Integrated Genome and Transcriptome Analyses Reveal the Mechanism of Genome Instability in Ataxia with Oculomotor Apraxia 2

The paper identifies how SETX mutations cause genome instability in AOA2 by increasing transcription stress and impairing repair mechanisms.

Delayed DNA replication in haploid human embryonic stem cells

The paper profiles DNA replication timing in haploid and diploid human ESCs, identifying delayed replication in autosomal regions and linking it to X chromosome dosage and polyploid cell underreplication.

The Genetic Architecture of DNA Replication Timing in Human Pluripotent Stem Cells

This study identifies genetic regulators of DNA replication timing in human pluripotent stem cells, revealing a histone code and combinatorial regulatory mechanisms.

Sequencing Micronuclei Reveals the Landscape of Chromosomal Instability

The paper develops MN-seq to sequence DNA in micronuclei, revealing factors contributing to chromosomal instability and introducing scMN-seq for single-cell analysis.

Cancer mutational processes vary in their association with replication timing and chromatin accessibility

The paper analyzes mutational signatures in tumors to determine their association with replication timing and chromatin accessibility, finding signature-specific associations and clinical relevance of SBS16 in liver cancer.

Replication timing analysis in polyploid cells reveals Rif1 uses multiple mechanisms to promote underreplication in Drosophila.

The paper shows Rif1 promotes underreplication in Drosophila polyploid cells through both upstream and downstream roles relative to SUUR in controlling replication timing.

Comprehensive analysis of DNA replication timing in genetic diseases and gene knockouts identifies MCM10 as a novel regulator of the replication program

Robust foreground detection in somatic copy number data

dryclean improves somatic copy number alteration detection in cancer genomes by reducing read depth waviness through signal processing.

Tumor mutational landscape is a record of the pre-malignant state

The paper predicts cancer cell-of-origin from DNA sequences by matching mutational landscapes to chromatin modification patterns in normal tissues.

Germline DNA replication timing shapes mammalian genome composition

The paper measures DNA replication timing in mouse germline cells and shows it strongly correlates with mutation rates, recombination hotspots, and genomic features compared to somatic tissues.