D.A.J. Rand
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View article: Dynamic Landscape Analysis of Cell Fate Decisions: Predictive Models of Neural Development From Single-Cell Data
Dynamic Landscape Analysis of Cell Fate Decisions: Predictive Models of Neural Development From Single-Cell Data Open
SUMMARY Building a mechanistic understanding of cell fate decisions remains a fundamental goal of developmental biology, with implications for stem cell therapies, regenerative medicine and understanding disease mechanisms. Single-cell tra…
View article: Bistable boundary conditions implying codimension 2 bifurcations
Bistable boundary conditions implying codimension 2 bifurcations Open
We consider generic families X θ of smooth dynamical systems depending on parameters where P is a 2-dimensional simply connected domain and assume that each X θ only has a finite number of restpoints and periodic orbits. We prove that…
View article: TimeTeller: A tool to probe the circadian clock as a multigene dynamical system
TimeTeller: A tool to probe the circadian clock as a multigene dynamical system Open
Recent studies have established that the circadian clock influences onset, progression and therapeutic outcomes in a number of diseases including cancer and heart diseases. Therefore, there is a need for tools to measure the functional sta…
View article: Bayesian Inference for Stochastic Oscillatory Systems Using the Phase-Corrected Linear Noise Approximation
Bayesian Inference for Stochastic Oscillatory Systems Using the Phase-Corrected Linear Noise Approximation Open
Funding: BS acknowledges funding from BBSRC grant BB/K003097/1 and the Edinburgh Mathematical Society.
View article: Bistable boundary conditions implying codimension 2 bifurcations
Bistable boundary conditions implying codimension 2 bifurcations Open
We consider generic families $X_\param$ of smooth dynamical systems depending on parameters $\param\in P$ where $P$ is a 2-dimensional simply connected domain and assume that each $X_\param$ only has a finite number of restpoints and perio…
View article: What Makes News Sharable on Social Media?
What Makes News Sharable on Social Media? Open
With the rise of social media, everyone has the potential to be both a consumer and producer of online content. Although one might assume that people share news because they believe it to be true, worldwide concerns about the spread of mis…
View article: TimeTeller: a tool to probe the circadian clock as a multigene dynamical system
TimeTeller: a tool to probe the circadian clock as a multigene dynamical system Open
A bstract Recent studies have established that the circadian clock influences onset, progression and therapeutic outcomes in a number of diseases including cancer and heart diseases. Therefore, there is a need for tools to measure the func…
View article: Quantifying attention via dwell time and engagement in a social media browsing environment
Quantifying attention via dwell time and engagement in a social media browsing environment Open
Modern computational systems have an unprecedented ability to detect, leverage and influence human attention. Prior work identified user engagement and dwell time as two key metrics of attention in digital environments, but these metrics h…
View article: Sir Erik Christopher Zeeman. 4 February 1925—13 February 2016
Sir Erik Christopher Zeeman. 4 February 1925—13 February 2016 Open
Sir Erik Christopher Zeeman, formerly Foundation Professor of Mathematics at the University of Warwick, Principal of Hertford College, Oxford, and Vice-President of the Royal Society, was for over 40 years a leading figure in British mathe…
View article: How many others have shared this? Experimentally investigating the effects of social cues on engagement, misinformation, and unpredictability on social media
How many others have shared this? Experimentally investigating the effects of social cues on engagement, misinformation, and unpredictability on social media Open
Unlike traditional media, social media typically provides quantified metrics of how many users have engaged with each piece of content. Some have argued that the presence of these cues promotes the spread of misinformation. Here we investi…
View article: Dynamical landscapes of cell fate decisions
Dynamical landscapes of cell fate decisions Open
The generation of cellular diversity during development involves differentiating cells transitioning between discrete cell states. In the 1940s, the developmental biologist Conrad Waddington introduced a landscape metaphor to describe this…
View article: Bayesian inference for stochastic oscillatory systems using the phase-corrected Linear Noise Approximation
Bayesian inference for stochastic oscillatory systems using the phase-corrected Linear Noise Approximation Open
Likelihood-based inference in stochastic non-linear dynamical systems, such as those found in chemical reaction networks and biological clock systems, is inherently complex and has largely been limited to small and unrealistically simple s…
View article: Do explanations increase the effectiveness of AI-crowd generated fake news warnings?
Do explanations increase the effectiveness of AI-crowd generated fake news warnings? Open
Social media platforms are increasingly deploying complex interventions to help users detect false news. Labeling false news using techniques that combine crowd-sourcing with artificial intelligence (AI) offers a promising way to inform us…
View article: Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions
Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions Open
Fate decisions in developing tissues involve cells transitioning between discrete cell states, each defined by distinct gene expression profiles. The Waddington landscape, in which the development of a cell is viewed as a ball rolling thro…
View article: Geometry of gene regulatory dynamics
Geometry of gene regulatory dynamics Open
Significance Genetic screens have enumerated the genes that control the process of self-organization that converts a featureless fertilized egg into an embryo. Even the elementary steps may involve 10 genes, so models that attempt to repre…
View article: The Emergence of “Us and Them” in 80 Lines of Code: Modeling Group Genesis in Homogeneous Populations
The Emergence of “Us and Them” in 80 Lines of Code: Modeling Group Genesis in Homogeneous Populations Open
Psychological explanations of group genesis often require population heterogeneity in identity or other characteristics, whether deep (e.g., religion) or superficial (e.g., eye color). We use game-theoretical agent-based models to explore …
View article: Quantifying cell transitions in C. elegans with data-fitted landscape models
Quantifying cell transitions in C. elegans with data-fitted landscape models Open
Increasing interest has emerged in new mathematical approaches that simplify the study of complex differentiation processes by formalizing Waddington’s landscape metaphor. However, a rational method to build these landscape models remains …
View article: Hyperinflammation evokes different antiviral TMPRSS2 and ADAM17 expression responses in human gut xenograft versus host mouse gut although overall genomic responses are similar
Hyperinflammation evokes different antiviral TMPRSS2 and ADAM17 expression responses in human gut xenograft versus host mouse gut although overall genomic responses are similar Open
The global spread of the newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the pandemic outbreak of coronavirus disease 2019 (COVID-19), an inflammatory disease that is primarily affecting the respirator…
View article: A quantitative landscape of cell fate transitions identifies principles of cellular decision-making
A quantitative landscape of cell fate transitions identifies principles of cellular decision-making Open
Fate decisions in developing tissues involve cells transitioning between a set of discrete cell states, each defined by a distinct gene expression profile. Geometric models, often referred to as Waddington landscapes, in which developmenta…
View article: Quantifying cell transitions in<i>C. elegans</i>with data-fitted landscape models
Quantifying cell transitions in<i>C. elegans</i>with data-fitted landscape models Open
Increasing interest has emerged in new mathematical approaches that simplify the study of complex differentiation processes by formalizing Waddington’s landscape metaphor. However, a rational method to build these landscape models remains …
View article: Transcription Factor Pit-1 Affects Transcriptional Timing in the Dual-Promoter Human Prolactin Gene
Transcription Factor Pit-1 Affects Transcriptional Timing in the Dual-Promoter Human Prolactin Gene Open
Gene transcription occurs in short bursts interspersed with silent periods, and these kinetics can be altered by promoter structure. The effect of alternate promoter architecture on transcription bursting is not known. We studied the human…
View article: Reasoning about Climate Change
Reasoning about Climate Change Open
Why is disbelief in anthropogenic climate change widespread despite broad scientific consensus to the contrary? A widely-held explanation involves politically motivated (“system 2”) reasoning: Rather than helping uncover truth, people use …
View article: Multiplexing information flow through dynamic signalling systems
Multiplexing information flow through dynamic signalling systems Open
We consider how a signalling system can act as an information hub by multiplexing information arising from multiple signals. We formally define multiplexing, mathematically characterise which systems can multiplex and how well they can do …
View article: Agent-Based Modeling: A Guide for Social Psychologists
Agent-Based Modeling: A Guide for Social Psychologists Open
Agent-based modeling is a longstanding but underused method that allows researchers to simulate artificial worlds for hypothesis testing and theory building. Agent-based models (ABMs) offer unprecedented control and statistical power by al…
View article: Guidelines for Genome-Scale Analysis of Biological Rhythms
Guidelines for Genome-Scale Analysis of Biological Rhythms Open
Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the d…
View article: Multiplexing information flow through dynamic signalling systems
Multiplexing information flow through dynamic signalling systems Open
We consider how a signalling system can act as an information hub by multiplexing information arising from multiple signals. We formally define multiplexing, mathematically characterise which systems can multiplex and how well they can do …
View article: Disentangling juxtacrine from paracrine signalling in dynamic tissue
Disentangling juxtacrine from paracrine signalling in dynamic tissue Open
Prolactin is a major hormone product of the pituitary gland, the central endocrine regulator. Despite its physiological importance, the cell-level mechanisms of prolactin production are not well understood. Having significantly improved th…
View article: TimeTeller: a New Tool for Precision Circadian Medicine and Cancer Prognosis
TimeTeller: a New Tool for Precision Circadian Medicine and Cancer Prognosis Open
Recent studies have established that the circadian clock influences onset, progression and therapeutic outcomes in a number of diseases including cancer and heart disease. Therefore, there is a need for tools to measure the functional stat…
View article: Parameter sensitivity analysis for biochemical reaction networks
Parameter sensitivity analysis for biochemical reaction networks Open
Biochemical reaction networks describe the chemical interactions occurring between molecular populations inside the living cell. These networks can be very noisy and complex and they often involve many variables and even more parameters. P…
View article: Understanding the functions of carbon in the negative active-mass of the lead–acid battery: A review of progress
Understanding the functions of carbon in the negative active-mass of the lead–acid battery: A review of progress Open
The addition of supplementary carbon to lead–acid batteries that are intended for use in emerging automotive duties can provide improvement in two aspects of performance. (i) In both hybrid electric and battery electric vehicles that are d…