Leveraging independent component analysis to unravel transcriptional regulatory networks: A critical review and future directions
Y Zhang, J Zhao, X Sun, Y Zheng, T Chen… - Biotechnology Advances, 2024 - Elsevier
Transcriptional regulatory networks (TRNs) play a crucial role in exploring microbial life
activities and complex regulatory mechanisms. The comprehensive reconstruction of TRNs …
activities and complex regulatory mechanisms. The comprehensive reconstruction of TRNs …
The Potential of Meta-Proteomics and Artificial Intelligence to Establish the Next Generation of Probiotics for Personalized Healthcare
The symbiosis of probiotic bacteria with humans has rendered various health benefits while
providing nutrition and a suitable environment for their survival. However, the probiotics …
providing nutrition and a suitable environment for their survival. However, the probiotics …
iModulonMiner and PyModulon: software for unsupervised mining of gene expression compendia
Public gene expression databases are a rapidly expanding resource of organism responses
to diverse perturbations, presenting both an opportunity and a challenge for bioinformatics …
to diverse perturbations, presenting both an opportunity and a challenge for bioinformatics …
iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets
EA Catoiu, J Krishnan, G Li, XA Lou… - Nucleic Acids …, 2025 - academic.oup.com
Abstract iModulons—sets of co-expressed genes identified through independent component
analysis (ICA) of high-quality transcriptomic datasets—provide an unbiased, modular view of …
analysis (ICA) of high-quality transcriptomic datasets—provide an unbiased, modular view of …
Meta-analysis Driven Strain Design for Mitigating Oxidative Stresses Important in Biomanufacturing
As the availability of data sets increases, meta-analysis leveraging aggregated and
interoperable data types is proving valuable. This study leveraged a meta-analysis workflow …
interoperable data types is proving valuable. This study leveraged a meta-analysis workflow …
Inferred regulons are consistent with regulator binding sequences in E. coli
S Qiu, X Wan, Y Liang, CR Lamoureux… - PLOS Computational …, 2024 - journals.plos.org
The transcriptional regulatory network (TRN) of E. coli consists of thousands of interactions
between regulators and DNA sequences. Regulons are typically determined either from …
between regulators and DNA sequences. Regulons are typically determined either from …