Bacillus sp. as a microbial cell factory: Advancements and future prospects

J Qian, Y Wang, Z Hu, T Shi, Y Wang, C Ye… - Biotechnology …, 2023 - Elsevier
Bacillus sp. is one of the most distinctive gram-positive bacteria, able to grow efficiently
using cheap carbon sources and secrete a variety of useful substances, which are widely …

Production of proteins and commodity chemicals using engineered Bacillus subtilis platform strain

Q Zhang, Y Wu, M Gong, H Zhang, Y Liu… - Essays in …, 2021 - portlandpress.com
Currently, increasing demand of biochemicals produced from renewable resources has
motivated researchers to seek microbial production strategies instead of traditional chemical …

The silkworm (Bombyx mori) gut microbiota is involved in metabolic detoxification by glucosylation of plant toxins

S Yuan, Y Sun, W Chang, J Zhang, J Sang… - Communications …, 2023 - nature.com
Herbivores have evolved the ability to detoxify feed components through different
mechanisms. The oligophagous silkworm feeds on Cudrania tricuspidata leaves (CTLs) …

iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning

K Rychel, K Decker, AV Sastry, PV Phaneuf… - Nucleic acids …, 2021 - academic.oup.com
Independent component analysis (ICA) of bacterial transcriptomes has emerged as a
powerful tool for obtaining co-regulated, independently-modulated gene sets (iModulons) …

Pulcherriminic acid modulates iron availability and protects against oxidative stress during microbial interactions

V Charron-Lamoureux, L Haroune… - Nature …, 2023 - nature.com
Siderophores are soluble or membrane-embedded molecules that bind the oxidized form of
iron, Fe (III), and play roles in iron acquisition by microorganisms. Fe (III)-bound …

Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network

HG Lim, K Rychel, AV Sastry, GJ Bentley, J Mueller… - Metabolic …, 2022 - Elsevier
Bacterial gene expression is orchestrated by numerous transcription factors (TFs).
Elucidating how gene expression is regulated is fundamental to understanding bacterial …

High-resolution temporal profiling of E. coli transcriptional response

A Miano, K Rychel, A Lezia, A Sastry, B Palsson… - Nature …, 2023 - nature.com
Understanding how cells dynamically adapt to their environment is a primary focus of
biology research. Temporal information about cellular behavior is often limited by both small …

Adaptive laboratory evolution and independent component analysis disentangle complex vancomycin adaptation trajectories

A Fait, Y Seif, K Mikkelsen, S Poudel… - Proceedings of the …, 2022 - National Acad Sciences
Human infections with methicillin-resistant Staphylococcus aureus (MRSA) are commonly
treated with vancomycin, and strains with decreased susceptibility, designated as …

Optimal dimensionality selection for independent component analysis of transcriptomic data

JL McConn, CR Lamoureux, S Poudel, BO Palsson… - BMC …, 2021 - Springer
Background Independent component analysis is an unsupervised machine learning
algorithm that separates a set of mixed signals into a set of statistically independent source …

Independent component analysis recovers consistent regulatory signals from disparate datasets

AV Sastry, A Hu, D Heckmann, S Poudel… - PLoS computational …, 2021 - journals.plos.org
The availability of bacterial transcriptomes has dramatically increased in recent years. This
data deluge could result in detailed inference of underlying regulatory networks, but the …