Systems biology for crop improvement
In recent years, generation of large‐scale data from genome, transcriptome, proteome,
metabolome, epigenome, and others, has become routine in several plant species. Most of …
metabolome, epigenome, and others, has become routine in several plant species. Most of …
A comprehensive overview and critical evaluation of gene regulatory network inference technologies
Gene regulatory network (GRN) is the important mechanism of maintaining life process,
controlling biochemical reaction and regulating compound level, which plays an important …
controlling biochemical reaction and regulating compound level, which plays an important …
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 …
Review and assessment of Boolean approaches for inference of gene regulatory networks
Boolean descriptions of gene regulatory networks can provide an insight into interactions
between genes. Boolean networks hold predictive power, are easy to understand, and can …
between genes. Boolean networks hold predictive power, are easy to understand, and can …
[HTML][HTML] Network-based approaches for modeling disease regulation and progression
Molecular interaction networks lay the foundation for studying how biological functions are
controlled by the complex interplay of genes and proteins. Investigating perturbed processes …
controlled by the complex interplay of genes and proteins. Investigating perturbed processes …
[HTML][HTML] Graph representation learning for single-cell biology
Single cell RNA sequencing measures gene expression at an unprecedented resolution
and scale and allows the analysis of cellular phenotypes which was not possible before. In …
and scale and allows the analysis of cellular phenotypes which was not possible before. In …
Network-based analysis of fluid flows: Progress and outlook
The network of interactions among fluid elements and coherent structures gives rise to the
incredibly rich dynamics of vortical flows. These interactions can be described with the use …
incredibly rich dynamics of vortical flows. These interactions can be described with the use …
From biological data to oscillator models using SINDy
Periodic changes in the concentration or activity of different molecules regulate vital cellular
processes such as cell division and circadian rhythms. Developing mathematical models is …
processes such as cell division and circadian rhythms. Developing mathematical models is …
Systems biology approaches to understanding the human immune system
Systems biology is an approach to interrogate complex biological systems through large-
scale quantification of numerous biomolecules. The immune system involves> 1,500 …
scale quantification of numerous biomolecules. The immune system involves> 1,500 …
From time-series transcriptomics to gene regulatory networks: A review on inference methods
M Marku, V Pancaldi - PLOS Computational Biology, 2023 - journals.plos.org
Inference of gene regulatory networks has been an active area of research for around 20
years, leading to the development of sophisticated inference algorithms based on a variety …
years, leading to the development of sophisticated inference algorithms based on a variety …