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DNA replication fork speed underlies cell fate changes and promotes reprogramming
It is shown that totipotent cells of the early mouse embryo have slow DNA replication fork speed and that 2CLCs recapitulate this feature, suggesting that fork speed underlies the transition to a totipotency-like state.
Measuring and Modeling Single-Cell Heterogeneity and Fate Decision in Mouse Embryos.
A review of recent studies that characterize cellular heterogeneity at different levels during mouse development, from the two-cell stage up to gastrulation, and mathematical modeling approaches that help researchers interpret these findings.
Independent channels for miRNA biosynthesis ensure efficient static and dynamic control in the regulation of the early stages of myogenesis.
Characterisation of the transcriptional dynamics underpinning the function, fate, and migration of the mouse Anterior Visceral Endoderm
A previously unknown requirement of Ephrin- and Semaphorin-signalling for AVE migration is identified and point to a tight coupling of transcriptional state and position in the AVE and reveal molecular heterogeneities underpinning its migratory behaviour and function.
Statistics of optimal information flow in ensembles of regulatory motifs.
This work uses methods of statistical field theory to calculate the statistics of the maximal mutual information achievable by tuning the input variable only in an ensemble of regulatory motifs, such that a single controller regulates N targets.
Prediction of gene expression time series and structural analysis of gene regulatory networks using recurrent neural networks
- Michele Monti, Jonathan Fiorentino, E. Milanetti, Giorgio Gosti, G. Tartaglia
- 13 September 2021
This work aims to demonstrate the power of data-driven, evidence-based, and scalable approaches to improve the quality and efficiency of the currently developed approaches to genome regulation.
The role of cell geometry and cell-cell communication in gradient sensing
This work generalizes the existing mathematical models to investigate how short- and long-range cellular communication can increase gradient sensing in two-dimensional models of epithelial tissues and identifies the optimal setting that corresponds to different types of communication.
Letter to the editor. NAA and JFK: Can revisionism take us home?
- Jonathan Fiorentino
- 28 March 2008
Occasionally during the course of the human learning experience we are faced with an anomaly. An aberration of sorts, which try as we might, defies appropriate classification. The recent paper by…
STREAMLINE: Structural and Topological Performance Analysis of Algorithms for the Inference of Gene Regulatory Networks from Single-Cell Transcriptomic Data
A three-step benchmarking pipeline called STREAMLINE is devised that quantifies the ability of algorithms to capture topological properties of networks and identify hubs and provides guidance on which algorithm should be used depending on the global network property of interest.
Multi-omics analysis reveals a crucial role for Retinoic Acid in promoting epigenetic and transcriptional competence of an in vitro model of human Pharyngeal Endoderm
This work provides a novel in vitro protocol for the derivation of bona fide PE cells from hPSCs and reveals the epigenetic dynamics that occur during human PE differentiation, providing a solid resource and foundation for research focused on the development of PE derivatives and modeling of their developmental defects in genetic syndromes.