RNA velocity—current challenges and future perspectives
RNA velocity has enabled the recovery of directed dynamic information from single‐cell
transcriptomics by connecting measurements to the underlying kinetics of gene expression …
transcriptomics by connecting measurements to the underlying kinetics of gene expression …
Principles of maximum entropy and maximum caliber in statistical physics
The variational principles called maximum entropy (MaxEnt) and maximum caliber
(MaxCal)<? format?> are reviewed. MaxEnt originated in the statistical physics of Boltzmann …
(MaxCal)<? format?> are reviewed. MaxEnt originated in the statistical physics of Boltzmann …
Generalizing RNA velocity to transient cell states through dynamical modeling
RNA velocity has opened up new ways of studying cellular differentiation in single-cell RNA-
sequencing data. It describes the rate of gene expression change for an individual gene at a …
sequencing data. It describes the rate of gene expression change for an individual gene at a …
RNA velocity unraveled
We perform a thorough analysis of RNA velocity methods, with a view towards
understanding the suitability of the various assumptions underlying popular …
understanding the suitability of the various assumptions underlying popular …
Ribozyme-based insulator parts buffer synthetic circuits from genetic context
Synthetic genetic programs are built from circuits that integrate sensors and implement
temporal control of gene expression,,,. Transcriptional circuits are layered by using …
temporal control of gene expression,,,. Transcriptional circuits are layered by using …
Identifiability analysis for stochastic differential equation models in systems biology
Mathematical models are routinely calibrated to experimental data, with goals ranging from
building predictive models to quantifying parameters that cannot be measured. Whether or …
building predictive models to quantifying parameters that cannot be measured. Whether or …
Systematic identification of signal-activated stochastic gene regulation
Although much has been done to elucidate the biochemistry of signal transduction and gene
regulatory pathways, it remains difficult to understand or predict quantitative responses. We …
regulatory pathways, it remains difficult to understand or predict quantitative responses. We …
Size-dependent increase in RNA polymerase II initiation rates mediates gene expression scaling with cell size
Cell size varies during the cell cycle and in response to external stimuli. This requires the
tight coordination, or" scaling," of mRNA and protein quantities with the cell volume in order …
tight coordination, or" scaling," of mRNA and protein quantities with the cell volume in order …
Studying stochastic systems biology of the cell with single-cell genomics data
Recent experimental developments in genome-wide RNA quantification hold considerable
promise for systems biology. However, rigorously probing the biology of living cells requires …
promise for systems biology. However, rigorously probing the biology of living cells requires …
Moment-based inference predicts bimodality in transient gene expression
Recent computational studies indicate that the molecular noise of a cellular process may be
a rich source of information about process dynamics and parameters. However, accessing …
a rich source of information about process dynamics and parameters. However, accessing …