Benjamin Audit
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View article: Thermodynamics of nucleosome breathing and positioning
Thermodynamics of nucleosome breathing and positioning Open
Nucleosomes are fundamental units of chromatin in which a length of genomic DNA is wrapped around a histone octamer spool in a left-handed superhelix. Large-scale nucleosome maps show a wide distribution of DNA wrapping lengths, which in s…
View article: Identifying a Piecewise Affine Signal From Its Nonlinear Observation—Application to DNA Replication Analysis
Identifying a Piecewise Affine Signal From Its Nonlinear Observation—Application to DNA Replication Analysis Open
International audience
View article: A comparative analysis of gene expression profiling by statistical and machine learning approaches
A comparative analysis of gene expression profiling by statistical and machine learning approaches Open
Motivation Many machine learning (ML) models developed to classify phenotype from gene expression data provide interpretations for their decisions, with the aim of understanding biological processes. For many models, including neural netwo…
View article: Nanotiming: telomere-to-telomere DNA replication timing profiling by nanopore sequencing
Nanotiming: telomere-to-telomere DNA replication timing profiling by nanopore sequencing Open
Current temporal studies of DNA replication are either low-resolution or require complex cell synchronisation and/or sorting procedures. Here we introduce Nanotiming, a nanopore sequencing-based method producing high-resolution, telomere-t…
View article: Identifying a piecewise affine signal from its nonlinear observation -- application to DNA replication analysis
Identifying a piecewise affine signal from its nonlinear observation -- application to DNA replication analysis Open
DNA replication stands as one of the fundamental biological processes crucial for cellular functioning. Recent experimental developments enable the study of replication dynamics at the single-molecule level for complete genomes, facilitati…
View article: A Comparative Analysis of Gene Expression Profiling by Statistical and Machine Learning Approaches
A Comparative Analysis of Gene Expression Profiling by Statistical and Machine Learning Approaches Open
Many machine learning models have been proposed to classify phenotypes from gene expression data. In addition to their good performance, these models can potentially provide some understanding of phenotypes by extracting explanations for t…
View article: Decoding Nucleosome-Depleted Regions: Insights from Epigenetic Marks, Nucleosome Size, and Thermodynamic Modelling
Decoding Nucleosome-Depleted Regions: Insights from Epigenetic Marks, Nucleosome Size, and Thermodynamic Modelling Open
Elucidating the global and local rules that govern genome-wide nucleosome organisation and chromatin architecture remains a critical challenge. Thermodynamic modelling based on DNA elastic properties predicts the presence of sequence-encod…
View article: Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths
Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths Open
In human and other metazoans, the determinants of replication origin location and strength are still elusive. Origins are licensed in G1 phase and fired in S phase of the cell cycle, respectively. It is debated which of these two temporall…
View article: Studying Limits of Explainability by Integrated Gradients for Gene Expression Models
Studying Limits of Explainability by Integrated Gradients for Gene Expression Models Open
Understanding the molecular processes that drive cellular life is a fundamental question in biological research. Ambitious programs have gathered a number of molecular datasets on large populations. To decipher the complex cellular interac…
View article: Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths
Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths Open
In human and other metazoans, the determinants of replication origin location and strength are still elusive. Origins are licensed in G1 phase and fired in S phase of the cell cycle, respectively. It is debated which of these two temporall…
View article: Organization of DNA Replication Origin Firing in Xenopus Egg Extracts: The Role of Intra-S Checkpoint
Organization of DNA Replication Origin Firing in Xenopus Egg Extracts: The Role of Intra-S Checkpoint Open
During cell division, the duplication of the genome starts at multiple positions called replication origins. Origin firing requires the interaction of rate-limiting factors with potential origins during the S(ynthesis)-phase of the cell cy…
View article: Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution
Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution Open
The nucleosome is a major modulator of DNA accessibility to other cellular factors. Nucleosome positioning has a critical importance in regulating cell processes such as transcription, replication, recombination or DNA repair. The DNA sequ…
View article: Organization of DNA Replication Origin Firing in Xenopus Egg Extracts : The Role of Intra-S Checkpoint
Organization of DNA Replication Origin Firing in Xenopus Egg Extracts : The Role of Intra-S Checkpoint Open
Background: During cell division, the duplication of the genome starts at multiple positions called replication origins. Origin firing requires the interaction of rate-limiting factors with potential origins during the S(ynthesis)-phase of…
View article: Coupling Between Sequence-Mediated Nucleosome Organization and Genome Evolution
Coupling Between Sequence-Mediated Nucleosome Organization and Genome Evolution Open
The nucleosome is a major modulator of DNA accessibility to other cellular factors. Nucleosome positioning has a critical importance in regulating cell processes such as transcription, replication, recombination or DNA repair. The DNA sequ…
View article: Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zones
Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zones Open
Eukaryotic DNA replication initiates during S phase from origins that have been licensed in the preceding G1 phase. Here, we compare ChIP-seq profiles of the licensing factors Orc2, Orc3, Mcm3, and Mcm7 with gene expression, replication ti…
View article: Author response: Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zones
Author response: Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zones Open
Article Figures and data Abstract Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Eukaryotic DNA replication initiates durin…
View article: Human ORC/MCM density is low in active genes and correlates with replication time but does not solely define replication initiation zones
Human ORC/MCM density is low in active genes and correlates with replication time but does not solely define replication initiation zones Open
Eukaryotic DNA replication initiates during S phase from origins that have been licensed in the preceding G1 phase. Here, we compare ChIP-seq profiles of the licensing factors Orc2, Orc3, Mcm3, and Mcm7 with gene expression, replication ti…
View article: Organization of DNA replication origin firing in<i>Xenopus</i>egg extracts : the role of intra-S checkpoint
Organization of DNA replication origin firing in<i>Xenopus</i>egg extracts : the role of intra-S checkpoint Open
During cell division, the duplication of the genome starts at multiple positions called replication origins. Origin firing requires the interaction of rate-limiting factors with potential origins during the S(ynthesis)-phase of the cell cy…
View article: Spatial and temporal regularization to estimate COVID-19 Reproduction Number <i>R</i>(<i>t</i>): Promoting piecewise smoothness via convex optimization
Spatial and temporal regularization to estimate COVID-19 Reproduction Number <i>R</i>(<i>t</i>): Promoting piecewise smoothness via convex optimization Open
Among the different indicators that quantify the spread of an epidemic, such as the on-going COVID-19, stands first the reproduction number which measures how many people can be contaminated by an infected person. In order to permit the mo…
View article: FORK-seq: replication landscape of the<i>Saccharomyces cerevisiae</i>genome by nanopore sequencing
FORK-seq: replication landscape of the<i>Saccharomyces cerevisiae</i>genome by nanopore sequencing Open
Genome replication mapping methods profile cell populations, masking cell-to-cell heterogeneity. Here, we describe FORK-seq, a nanopore sequencing method to map replication of single DNA molecules at 200 nucleotide resolution. By quantifyi…
View article: Active transcription regulates ORC/MCM distribution whereas replication timing correlates with ORC density in human cells
Active transcription regulates ORC/MCM distribution whereas replication timing correlates with ORC density in human cells Open
Eukaryotic replication initiates during S phase from origins that have been licensed in the preceding G1 phase. Here, we compare ChIP-seq profiles of the licensing factors Orc2, Orc3, Mcm3, and Mcm7 with replication initiation events obtai…
View article: Mapping DNA replication with nanopore sequencing
Mapping DNA replication with nanopore sequencing Open
We have harnessed nanopore sequencing to study DNA replication genome-wide at the single-molecule level. Using in vitro prepared DNA substrates, we characterized the effect of bromodeoxyuridine (BrdU) substitution for thymidine on the MinI…
View article: Developmental and cancer-associated plasticity of DNA replication preferentially targets GC-poor, lowly expressed and late-replicating regions
Developmental and cancer-associated plasticity of DNA replication preferentially targets GC-poor, lowly expressed and late-replicating regions Open
The spatiotemporal program of metazoan DNA replication is regulated during development and altered in cancers. We have generated novel OK-seq, Repli-seq and RNA-seq data to compare the DNA replication and gene expression programs of twelve…
View article: The eukaryotic bell-shaped temporal rate of DNA replication origin firing emanates from a balance between origin activation and passivation
The eukaryotic bell-shaped temporal rate of DNA replication origin firing emanates from a balance between origin activation and passivation Open
The time-dependent rate of origin firing per length of unreplicated DNA presents a universal bell shape in eukaryotes that has been interpreted as the result of a complex time-evolving interaction between origins and limiting firing …