iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia.

Autor: Anand V Sastry, Yuan Yuan, Saugat Poudel, Kevin Rychel, Reo Yoo, Cameron R Lamoureux, Gaoyuan Li, Joshua T Burrows, Siddharth Chauhan, Zachary B Haiman, Tahani Al Bulushi, Yara Seif, Bernhard O Palsson, Daniel C Zielinski

Publikováno v: PLoS Computational Biology, Vol 20, Iss 10, p e1012546 (2024)

Public gene expression databases are a rapidly expanding resource of organism responses to diverse perturbations, presenting both an opportunity and a challenge for bioinformatics workflows to extract actionable knowledge of transcription regulatory

Externí odkaz: https://doaj.org/article/012b0c0d41224b3b907edb195e4abdcc

Inferred regulons are consistent with regulator binding sequences in E. coli.

Autor: Sizhe Qiu, Xinlong Wan, Yueshan Liang, Cameron R Lamoureux, Amir Akbari, Bernhard O Palsson, Daniel C Zielinski

Publikováno v: PLoS Computational Biology, Vol 20, Iss 1, p e1011824 (2024)

The transcriptional regulatory network (TRN) of E. coli consists of thousands of interactions between regulators and DNA sequences. Regulons are typically determined either from resource-intensive experimental measurement of functional binding sites,

Externí odkaz: https://doaj.org/article/4b004a6fbf5042ac9478a0f1892886dc

Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins

Autor: Yujiro Hirose, Saugat Poudel, Anand V. Sastry, Kevin Rychel, Cameron R. Lamoureux, Richard Szubin, Daniel C. Zielinski, Hyun Gyu Lim, Nitasha D. Menon, Helena Bergsten, Satoshi Uchiyama, Tomoki Hanada, Shigetada Kawabata, Bernhard O. Palsson, Victor Nizet

Publikováno v: mSystems, Vol 8, Iss 3 (2023)

ABSTRACT Streptococcus pyogenes can cause a wide variety of acute infections throughout the body of its human host. An underlying transcriptional regulatory network (TRN) is responsible for altering the physiological state of the bacterium to adapt t

Externí odkaz: https://doaj.org/article/3b43ea8193f84eecb3e9e294107d3b83

Machine learning uncovers thePseudomonas syringaetranscriptome in microbial communities and during infection

Autor: Heera Bajpe, Kevin Rychel, Cameron R. Lamoureux, Anand V. Sastry, Bernhard O. Palsson

The transcriptional regulatory network (TRN) of the phytopathogenPseudomonas syringaepv.tomatoDC3000 regulates its response to environmental stimuli, including interactions with hosts and neighboring bacteria. Despite the importance of transcriptiona

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::72b5a9b14a71507a870db73d851eb870
https://doi.org/10.1101/2023.05.10.540184

Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal Thermoacidophile Sulfolobus acidocaldarius

Autor: Reo Yoo, Saugat Poudel, Tahani Al Bulushi, Bernhard O. Palsson, Kevin Rychel, Siddharth Chauhan, Yuan Yuan, Anand V. Sastry, Cameron R. Lamoureux

Publikováno v: Frontiers in Microbiology, Vol 12 (2021)
Chauhan, S M, Poudel, S, Rychel, K, Lamoureux, C, Yoo, R, Al Bulushi, T, Yuan, Y, Palsson, B O & Sastry, A V 2021, ' Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal Thermoacidophile Sulfolobus acidocaldarius ', Frontiers in Microbiology, vol. 12, 753521 . https://doi.org/10.3389/fmicb.2021.753521

Dynamic cellular responses to environmental constraints are coordinated by the transcriptional regulatory network (TRN), which modulates gene expression. This network controls most fundamental cellular responses, including metabolism, motility, and s

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::07e9a39bf7c1bab4506708b1298322d1
https://www.frontiersin.org/articles/10.3389/fmicb.2021.753521/full