Inferring biological networks by sparse identification of nonlinear dynamics
Inferring the structure and dynamics of network models is critical to understanding the
functionality and control of complex systems, such as metabolic and regulatory biological …
functionality and control of complex systems, such as metabolic and regulatory biological …
Gene regulatory network inference: an introductory survey
VA Huynh-Thu, G Sanguinetti - Gene regulatory networks: Methods and …, 2019 - Springer
Gene regulatory networks are powerful abstractions of biological systems. Since the advent
of high-throughput measurement technologies in biology in the late 1990s, reconstructing …
of high-throughput measurement technologies in biology in the late 1990s, reconstructing …
Warm nights disrupt transcriptome rhythms in field-grown rice panicles
JS Desai, LMF Lawas, AM Valente… - Proceedings of the …, 2021 - National Acad Sciences
In rice, a small increase in nighttime temperature reduces grain yield and quality. How warm
nighttime temperatures (WNT) produce these detrimental effects is not well understood …
nighttime temperatures (WNT) produce these detrimental effects is not well understood …
RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique
X Jiang, X Zhang - BMC bioinformatics, 2022 - Springer
Background Current gene regulatory network (GRN) inference methods are notorious for a
great number of indirect interactions hidden in the predictions. Filtering out the indirect …
great number of indirect interactions hidden in the predictions. Filtering out the indirect …
Layers of regulation of cell-cycle gene expression in the budding yeast Saccharomyces cerevisiae
In the budding yeast Saccharomyces cerevisiae, transcription factors (TFs) regulate the
periodic expression of many genes during the cell cycle, including gene products required …
periodic expression of many genes during the cell cycle, including gene products required …
A general model-based causal inference method overcomes the curse of synchrony and indirect effect
To identify causation, model-free inference methods, such as Granger Causality, have been
widely used due to their flexibility. However, they have difficulty distinguishing synchrony …
widely used due to their flexibility. However, they have difficulty distinguishing synchrony …
Reconciling conflicting models for global control of cell-cycle transcription
Models for the control of global cell-cycle transcription have advanced from a CDK-APC/C
oscillator, a transcription factor (TF) network, to coupled CDK-APC/C and TF networks …
oscillator, a transcription factor (TF) network, to coupled CDK-APC/C and TF networks …
[HTML][HTML] Characterization of multiscale logic operations in the neural circuits
Background: Ever since the seminal work by McCulloch and Pitts, the theory of neural
computation and its philosophical foundation known as 'computationalism'have been central …
computation and its philosophical foundation known as 'computationalism'have been central …
Inferring causality in biological oscillators
Motivation Fundamental to biological study is identifying regulatory interactions. The recent
surge in time-series data collection in biology provides a unique opportunity to infer …
surge in time-series data collection in biology provides a unique opportunity to infer …
Inferring gene regulatory networks using transcriptional profiles as dynamical attractors
Genetic regulatory networks (GRNs) regulate the flow of genetic information from the
genome to expressed messenger RNAs (mRNAs) and thus are critical to controlling the …
genome to expressed messenger RNAs (mRNAs) and thus are critical to controlling the …