A sight on single-cell transcriptomics in plants through the prism of cell-based computational modeling approaches: benefits and challenges for data analysis

A Bobrovskikh, A Doroshkov, S Mazzoleni… - Frontiers in …, 2021 - frontiersin.org
Single-cell technology is a relatively new and promising way to obtain high-resolution
transcriptomic data mostly used for animals during the last decade. However, several …

Numerical algorithm for morphogen synthesis region identification with indirect image-type measurement data

A Penenko, U Zubairova, Z Mukatova… - … of Bioinformatics and …, 2019 - World Scientific
Diffusion–reaction models are used to describe development processes in the framework of
morphogen theory. The images of the concentration fields for the subset of the interacting …

Nucleation of stem cell domains in a bistable activator–inhibitor model of the shoot apical meristem

D Battogtokh, JJ Tyson - Chaos: An Interdisciplinary Journal of …, 2022 - pubs.aip.org
Shoot apical meristems (SAMs) give rise to all above-ground tissues of a plant. Expansion of
meristematic tissue is derived from the growth and division of stem cells that reside in a …

Cell-based models in plant developmental biology: insights into hybrid approaches

B Hay Mele, F Giannino, CE Vincenot… - Frontiers in …, 2015 - frontiersin.org
Computer models are nowadays part of the biologist's toolbox for studying biological
dynamics and processes. Tissue development and functioning results from extremely …

Inverse modeling of diffusion-reaction processes with image-type measurement data

A Penenko, Z Mukatova - 2018 11th International …, 2018 - ieeexplore.ieee.org
The inverse source problem for 1D diffusion-reaction model is considered. The
measurement data is given as the images of the concentration fields dynamics for the subset …

Применение технологии CUDA для моделирования процессов реакции-диффузии на двумерном клеточном ансамбле

АВ Пененко, ТС Троеглазова, УС Зубаирова… - Математическая …, 2014 - mathnet.ru
В рамках теории морфогенов рост, формообразование и дифференцировка ткани,
состоящей из клеток, могут быть описаны математическими моделями типа реакции …

Models of regulation of stem cell niche structure in shoot apical meristem

US Zubairova, SV Nikolaev - Russian Journal of Genetics: Applied …, 2014 - Springer
The experimental data obtained to date has provided grounds for certain concepts of stem
cell niche regulation in shoot apical meristem (SAM). Mathematical modeling is used to …

Adjoint Ensemble Methods for the Inverse Modeling of Biological Processes

A Penenko, U Zubairova, A Bobrovskikh… - 2020 Cognitive …, 2020 - ieeexplore.ieee.org
The general inverse modeling framework based on the ensembles of the adjoint equation
solutions is considered in the context of biomedical applications with the advection-diffusion …

Usage of Parallel Algorithms Based on CUDA Technology for Realisation of Reaction-Diffusion Models of Two-Dimensional Cellular Ensemble

AV Penenko, TS Troeglazova, US Zubairova… - Matematicheskaya …, 2014 - mathnet.ru
AV Penenko, TS Troeglazova, US Zubairova, D. Zh. Bayshibaev, SN Nikolaev, “Usage of
Parallel Algorithms Based on CUDA Technology for Realisation of Reaction-Diffusion …