Noise in biomolecular systems: Modeling, analysis, and control implications

C Briat, M Khammash - Annual Review of Control, Robotics, and …, 2023 - annualreviews.org
While noise is generally associated with uncertainties and often has a negative connotation
in engineering, living organisms have evolved to adapt to (and even exploit) such …

Advanced methods for gene network identification and noise decomposition from single-cell data

Z Fang, A Gupta, S Kumar, M Khammash - Nature Communications, 2024 - nature.com
Central to analyzing noisy gene expression systems is solving the Chemical Master
Equation (CME), which characterizes the probability evolution of the reacting species' copy …

[HTML][HTML] Stochastic filtering for multiscale stochastic reaction networks based on hybrid approximations

Z Fang, A Gupta, M Khammash - Journal of Computational Physics, 2022 - Elsevier
In the past few decades, the development of fluorescent technologies and microscopic
techniques has greatly improved scientists' ability to observe real-time single-cell activities …

Filtered finite state projection method for the analysis and estimation of stochastic biochemical reaction networks

E D'Ambrosio, Z Fang, A Gupta, S Kumar… - bioRxiv, 2022 - biorxiv.org
Time-lapse microscopy has become increasingly prevalent in biological experimentation, as
it provides single-cell trajectories that unveil valuable insights into underlying networks and …

Effective filtering approach for joint parameter-state estimation in SDEs via Rao-blackwellization and modularization

Z Fang, A Gupta, M Khammash - arXiv preprint arXiv:2311.00836, 2023 - arxiv.org
Stochastic filtering is a vibrant area of research in both control theory and statistics, with
broad applications in many scientific fields. Despite its extensive historical development …

A scalable approach for solving chemical master equations based on modularization and filtering

Z Fang, A Gupta, M Khammash - bioRxiv, 2022 - biorxiv.org
Solving the chemical master equation (CME) that characterizes the probability evolution of
stochastically reacting processes is greatly important for analyzing intracellular reaction …

Stochastic filtering of reaction networks partially observed in time snapshots

M Rathinam, M Yu - Journal of Computational Physics, 2024 - Elsevier
Stochastic reaction network models arise in intracellular chemical reactions, epidemiological
models and other population process models, and are a class of continuous time Markov …

[PDF][PDF] A Bibliography of Publications in SIAM Journal on Numerical Analysis: 2010–2019

NHF Beebe - 2024 - ctan.math.utah.edu
A Bibliography of Publications in SIAM Journal on Numerical Analysis: 2010–2019 Page 1
A Bibliography of Publications in SIAM Journal on Numerical Analysis: 2010–2019 Nelson …