David M. Gilbert
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View article: P05.05.A INTEGRATED MULTI-OMICS AND MULTI-SPECTRAL PROFILING OF PLASMA EXTRACELLULAR VESICLES REVEALS HIGHLY ACCURATE LIQUID BIOPSY BIOMARKERS FOR GLIOMA DIAGNOSIS.
P05.05.A INTEGRATED MULTI-OMICS AND MULTI-SPECTRAL PROFILING OF PLASMA EXTRACELLULAR VESICLES REVEALS HIGHLY ACCURATE LIQUID BIOPSY BIOMARKERS FOR GLIOMA DIAGNOSIS. Open
BACKGROUND Liquid biopsy approaches are revolutionising the management of patients with extracranial solid tumours. However, the techniques investigated have not been effective in neuro-oncology. There is therefore an urgent need to develo…
View article: Autosomal Allelic Inactivation: Variable Replication and Dosage Sensitivity
Autosomal Allelic Inactivation: Variable Replication and Dosage Sensitivity Open
Autosomal monoallelic gene expression and asynchronous replication between alleles are well-established features of imprinted genes and genes regulated by allelic exclusion. Inactivation/Stability Centers (I/SCs) are recently described aut…
View article: Interferon-dependent R-loop induction by Zika virus contributes to growth attenuation
Interferon-dependent R-loop induction by Zika virus contributes to growth attenuation Open
Zika virus (ZIKV) infection in human neural progenitors triggers DNA damage and activates DNA damage response, leading to cell cycle arrest that can retard brain development. Here, we link the ZIKV-induced S phase arrest to replication for…
View article: Author response: Major nuclear locales define nuclear genome organization and function beyond A and B compartments
Author response: Major nuclear locales define nuclear genome organization and function beyond A and B compartments Open
View article: Complete sequencing of ape genomes
Complete sequencing of ape genomes Open
View article: Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function
Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function Open
Models of nuclear genome organization often propose a binary division into active versus inactive compartments yet typically overlook nuclear bodies. Here we integrated analysis of sequencing and image-based data to compare genome organiza…
View article: Author response: Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function
Author response: Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function Open
View article: Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon
Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon Open
View article: Author response: Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function
Author response: Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function Open
View article: Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function
Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function Open
Models of nuclear genome organization often propose a binary division into active versus inactive compartments yet typically overlook nuclear bodies. Here we integrated analysis of sequencing and image-based data to compare genome organiza…
View article: Transcription can be sufficient, but is not necessary, to advance replication timing
Transcription can be sufficient, but is not necessary, to advance replication timing Open
DNA replication timing (RT) is correlated with transcription during cell fate changes but there are many exceptions and our understanding of this relationship suffers from a paucity of reductionist approaches. Here, we manipulated length a…
View article: Evaluating the Impact of Orientation on Study Approaches Among First-Year Medical Students: A Quantitative Study in a Rural US Medical School using the Modified ASSIST Questionnaire
Evaluating the Impact of Orientation on Study Approaches Among First-Year Medical Students: A Quantitative Study in a Rural US Medical School using the Modified ASSIST Questionnaire Open
View article: An integrated view of the structure and function of the human 4D nucleome
An integrated view of the structure and function of the human 4D nucleome Open
The dynamic three-dimensional (3D) organization of the human genome (the “4D Nucleome”) is closely linked to genome function. Here, we integrate a wide variety of genomic data generated by the 4D Nucleome Project to provide a detailed view…
View article: Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon
Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon Open
Summary Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here we characterize assemb…
View article: Complete sequencing of ape genomes
Complete sequencing of ape genomes Open
We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled …
View article: Author response: Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function
Author response: Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function Open
Models of nuclear genome organization often propose a binary division into active versus inactive compartments, yet they overlook nuclear bodies. Here we integrated analysis of sequencing and image-based data to compare genome organization…
View article: Major nuclear locales define nuclear genome organization and function beyond A and B compartments
Major nuclear locales define nuclear genome organization and function beyond A and B compartments Open
Models of nuclear genome organization often propose a binary division into active versus inactive compartments yet typically overlook nuclear bodies. Here, we integrated analysis of sequencing and image-based data to compare genome organiz…
View article: Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function
Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function Open
Models of nuclear genome organization often propose a binary division into active versus inactive compartments, yet they overlook nuclear bodies. Here we integrated analysis of sequencing and image-based data to compare genome organization…
View article: Strand-resolved mutagenicity of DNA damage and repair
Strand-resolved mutagenicity of DNA damage and repair Open
DNA base damage is a major source of oncogenic mutations 1 . Such damage can produce strand-phased mutation patterns and multiallelic variation through the process of lesion segregation 2 . Here we exploited these properties to reveal how …
View article: Linear interaction between replication and transcription shapes DNA break dynamics at recurrent DNA break Clusters
Linear interaction between replication and transcription shapes DNA break dynamics at recurrent DNA break Clusters Open
View article: Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function
Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function Open
Models of nuclear genome organization often propose a binary division into active versus inactive compartments yet typically overlook nuclear bodies. Here we integrated analysis of sequencing and image-based data to compare genome organiza…
View article: Emergence of replication timing during early mammalian development
Emergence of replication timing during early mammalian development Open
View article: RIF1 regulates early replication timing in murine B cells
RIF1 regulates early replication timing in murine B cells Open
View article: Brd2 is dispensable for genome compartmentalization and replication timing
Brd2 is dispensable for genome compartmentalization and replication timing Open
Replication Timing (RT) refers to the temporal order in which the genome is replicated during S phase. Early replicating regions correlate with the transcriptionally active, accessible euchromatin (A) compartment, while late replicating re…
View article: Nucleolus and centromere TSA-Seq reveals variable localization of heterochromatin in different cell types
Nucleolus and centromere TSA-Seq reveals variable localization of heterochromatin in different cell types Open
Genome differential positioning within interphase nuclei remains poorly explored. We extended and validated TSA-seq to map genomic regions near nucleoli and pericentric heterochromatin in four human cell lines. Our study confirmed that sma…
View article: Master transcription factor binding sites constitute the core of early replication control elements
Master transcription factor binding sites constitute the core of early replication control elements Open
Eukaryotic genomes replicate in a defined temporal order called the replication timing (RT) program. RT is developmentally regulated with potential to drive cell fate transitions, but mechanisms controlling RT remain elusive. We previously…
View article: Linear Interaction Between Replication and Transcription Shapes DNA Break Dynamics at Recurrent DNA Break Clusters
Linear Interaction Between Replication and Transcription Shapes DNA Break Dynamics at Recurrent DNA Break Clusters Open
Recurrent DNA break clusters (RDCs) are replication-transcription collision hotspots; many are unique to neural progenitor cells. Through high-resolution replication sequencing and a capture-ligation assay in mouse neural progenitor cells …
View article: Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project
Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project Open
View article: Transposase expression, element abundance, element size, and DNA repair determine the mobility and heritability of PIF/Pong/Harbinger transposable elements
Transposase expression, element abundance, element size, and DNA repair determine the mobility and heritability of PIF/Pong/Harbinger transposable elements Open
Introduction: Class II DNA transposable elements account for significant portions of eukaryotic genomes and contribute to genome evolution through their mobilization. To escape inactivating mutations and persist in the host genome over evo…
View article: Recherche de vérité et construction du récit d’après le premier livre de Thucydide
Recherche de vérité et construction du récit d’après le premier livre de Thucydide Open
Considéré avec Hérodote comme l’un des « pères de l’histoire », Thucydide est l’un des auteurs grecs les plus étudiés, à tel point que les innombrables travaux qui portent sur la Guerre du Péloponnèse , œuvre difficile, fascinante et probl…