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In this paper, a mixed-effect modeling scheme is proposed to construct a predictor for different features of cancer tumor. For this purpose, a set of features is extracted from two groups of patients with the same type of cancer but with…
We introduce a multivariate hidden Markov model to jointly cluster time-series observations with different support, i.e. circular and linear. Relying on the general projected normal distribution, our approach allows for bimodal and/or…
This paper is concerned with conditions for the existence of oscillations in gene regulatory networks with negative cyclic feedback, where time delays in transcription, translation and translocation process are explicitly considered. The…
Confirmation bias, the tendency to interpret information in a way that aligns with one's preconceptions, can profoundly impact scientific research, leading to conclusions that reflect the researcher's hypotheses even when the observational…
Time delay estimation plays a critical role in control, stabilization and state estimation of many practical system with time delay. In this paper, we propose a method to estimate delay for discrete time linear multiple-input…
Considerable interest has recently been focused on studying multiple phenotypes simultaneously in both epidemiological and genomic studies, either to capture the multidimensionality of complex disorders or to understand shared etiology of…
Temporal data such as time series can be viewed as discretized measurements of the underlying function. To build a generative model for such data we have to model the stochastic process that governs it. We propose a solution by defining the…
We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are…
In real-world systems, phase transitions often materialize abruptly, making it difficult to design appropriate controls that help uncover underlying processes. Some agent-based computational models display transformations similar to phase…
Time--delayed feedback is exploited for controlling noise--induced motion in coherence resonance oscillators. Namely, under the proper choice of time delay, one can either increase or decrease the regularity of motion. It is shown that in…
We study the noise characteristics of stochastic oscillations in protein number dynamics of simple genetic oscillatory systems. Using the three-component negative feedback transcription regulatory system called the repressilator as a…
A class of multivariate mixed survival models for continuous and discrete time with a complex covariance structure is introduced in a context of quantitative genetic applications. The methods introduced can be used in many applications in…
This paper considers fixed effects estimation and inference in linear and nonlinear panel data models with random coefficients and endogenous regressors. The quantities of interest -- means, variances, and other moments of the random…
Stochastic kinetic models of genetic expression are able to describe protein fluctuations. A comparative study of the canonical and a feedback model is given here by using stochastic simulation methods. The feedback model is skeleton model…
Circadian rhythms are archetypical examples of nonlinear oscillations. While these oscillations are usually attributed to circuits of biochemical interactions among clock genes and proteins, recent experimental studies reveal that they are…
Gene expression is a stochastic process in which cells produce biomolecules essential to the function of life. Modern experimental methods allow for the measurement of biomolecules at single-cell and single-molecule resolution over time.…
Models of physical systems are used to explain and predict experimental results and observations. When students encounter discrepancies between the actual and expected behavior of a system, they revise their models to include the newly…
We consider varying-coefficient models for mixed synchronous and asynchronous longitudinal covariates, where asynchronicity refers to the misalignment of longitudinal measurement times within an individual. We propose three different…
We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of…
The paper introduces a novel methodology for the identification of coefficients of switched autoregressive linear models. We consider the case when the system's outputs are contaminated by possibly large values of measurement noise. It is…