David M. Gilbert

The paper introduces RepTile, a framework to infer single-cell replication states from imaging data, revealing locus-specific dependencies of replication initiation on subnuclear position.

This study shows that microhomology-mediated end joining (MMEJ) repairs single-ended DSBs at replication forks, working with BIR and being regulated by ATR and Pol{theta}.

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

The paper identifies and characterizes Autosomal Inactivation/Stability Centers (I/SCs) as loci with allele-specific epigenetic regulation of replication timing and gene expression, showing dosage sensitivity and implications for human diseases.

The paper identifies subERCEs as master transcription factor binding sites that drive early replication timing and transcription in mESCs, functioning as both enhancers and structural chromatin organizers.

This study identifies RIF1's role in restoring H3K9me3 post-replication by facilitating SUV39H1, HP1, and PP1 recruitment and restraining Aurora kinase activity.

The paper examines genome organization in human cells relative to nuclear locales, finding that gene expression and replication timing correlate with different nuclear structures and that LADs and iLADs compete for lamina attachment.

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

The paper identifies centromeric transposable elements and epigenetic features in the eastern hoolock gibbon that contribute to karyotypic variation and chromosomal instability.

The paper manipulates transcription to show it can advance replication timing but is not required for the switch to early replication.

The paper investigates how strand-asymmetric processes like replication and transcription influence DNA damage, repair, and mutagenesis, revealing mechanisms that shape cancer genome evolution.

The paper investigates DNA break dynamics at recurrent DNA break clusters (RDCs) in mouse neural progenitor cells, revealing how replication-transcription collisions influence DSB formation and orientation.

This study shows RIF1 regulates early replication timing and origin activity in B cells by interacting with MCM proteins, influencing gene replication without major effects on gene expression or genome organization.

This study shows that Brd2 depletion does not alter genome replication timing or A/B compartmentalization in mouse embryonic stem cells.

The paper investigates Ki67's role in chromatin organization by analyzing its genomic interactions and dynamics during the cell cycle in human cells.

This study shows that cohesin-mediated loops in G1 phase determine the genomic location of replication origins in S phase by anchoring replication initiation zones.

The paper identifies hundreds of epigenetically controlled long noncoding RNA genes essential for chromosome replication and stability, validating their role in chromosomal integrity.

This paper introduces TIP-seq, a high-throughput single-cell method for mapping DNA binding sites, achieving higher coverage and signal-to-noise than existing methods.

This study uses Optical Replication Mapping to map human DNA replication initiation sites and finds that replication initiation is stochastic and not confined to specific origins.

This study identifies RIF1 as a molecular hub that co-regulates nuclear organisation and replication timing through its interaction with PP1, revealing distinct functional requirements for these processes.

This study shows that replication timing (RT) is essential for maintaining the global epigenetic state and genome compartmentalization in human cells, with RIF1 playing a central role in this process.

This paper describes a directed protein evolution method to enhance the catalytic efficiency of CRISPR-Cas9 variants, showing up to 4-fold improvement in AceCas9 and 2-fold increase in HDR-based gene insertion for SpyCas9.

The paper introduces SPIN, a method to identify genome-wide nuclear spatial localization patterns by integrating nuclear compartment mapping and chromatin interaction data.

The paper develops a custom ENCODE annotation for cancer genomics, highlighting TF-RBP interactions and network rewiring during oncogenesis, and validates findings using experimental assays.

The paper defines the temporal choreography of DNA replication in mammalian cells using High Resolution Repli-Seq, revealing conserved replication timing patterns and cell-type-specific correlations with chromatin features.

The paper investigates how gene activation affects nuclear lamina interactions and shows that transcription can locally rewire these interactions without broadly altering chromosomal regions.

The paper constructs replication timing networks from human cell types and identifies master regulators and novel trans interactions between transcription factors and RT changes.

The paper identifies a fragility signature linked to replication stress and transcription in chromosomal instability by analyzing replication timing and gene expression.

The paper identifies cis-regulatory elements (ERCEs) that control domain-wide replication timing, chromatin compartmentalization, and transcription in mouse embryonic stem cells.

The paper defines RT states as cell type-specific replication timing profiles using a Hidden Markov Model and finds they provide new functional insights into the human genome.