Zobrazeno 1 - 10
of 10
pro vyhledávání: '"Cameron R. Lamoureux"'
Publikováno v:
mSystems, Vol 8, Iss 5 (2023)
ABSTRACT The transcriptional regulatory network (TRN) of the phytopathogen Pseudomonas syringae pv. tomato DC3000 regulates its response to environmental stimuli, including interactions with hosts and neighboring bacteria. Despite the importance of t
Externí odkaz:
https://doaj.org/article/03434c73c09b45f4ba4bb8c89908a950
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
Publikováno v:
BMC Bioinformatics, Vol 22, Iss 1, Pp 1-13 (2021)
Abstract Background Independent component analysis is an unsupervised machine learning algorithm that separates a set of mixed signals into a set of statistically independent source signals. Applied to high-quality gene expression datasets, independe
Externí odkaz:
https://doaj.org/article/ec2650cc4bbf4a1e875e230588096569
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
https://doi.org/10.1101/2023.05.10.540184
Autor:
Cameron R. Lamoureux, Reo Yoo, Saugat Poudel, Al-bulushi T, Bernhard O. Palsson, Yuan Yuan, Anand V. Sastry, Siddharth Chauhan, Kevin Rychel
Publikováno v:
Yoo, R, Rychel, K, Poudel, S, Al-Bulushi, T, Yuan, Y, Chauhan, S, Lamoureux, C, Palsson, B O & Sastry, A 2022, ' Machine Learning of All Mycobacterium tuberculosis H37Rv RNAseq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection ', mSphere, vol. 7, no. 2 . https://doi.org/10.1128/msphere.00033-22
Mycobacterium tuberculosis is one of the most consequential human bacterial pathogens, posing a serious challenge to 21st century medicine. A key feature of its pathogenicity is its ability to adapt its transcriptional response to environmental stres
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::92e58de14988c802b984a691645a3dcf
https://orbit.dtu.dk/en/publications/733eebfb-0578-492a-a4b5-79aadd59466a
https://orbit.dtu.dk/en/publications/733eebfb-0578-492a-a4b5-79aadd59466a
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
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
Autor:
Reo Yoo, Al Bulushi T, Zachary B. Haiman, Bernhard O. Palsson, Anand V. Sastry, Siddharth Chauhan, Saugat Poudel, Cameron R. Lamoureux, Yara Seif, Kevin Rychel
We are firmly in the era of biological big data. Millions of omics datasets are publicly accessible and can be employed to support scientific research or build a holistic view of an organism. Here, we introduce a workflow that converts all public gen
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::2893d352275b349083d34729e19ba39b
https://doi.org/10.1101/2021.07.01.450581
https://doi.org/10.1101/2021.07.01.450581
Autor:
Cameron R. Lamoureux, Katherine T. Decker, Anand V. Sastry, Kevin Rychel, Ye Gao, John Luke McConn, Daniel C. Zielinski, Bernhard O. Palsson
SummaryTranscriptomic data is accumulating rapidly; thus, development of scalable methods for extracting knowledge from this data is critical. We assembled a top-down transcriptional regulatory network forEscherichia colifrom a 1035-sample, single-pr
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::c3414416fab64e5a6fdf53459f3ddb90
https://doi.org/10.1101/2021.04.08.439047
https://doi.org/10.1101/2021.04.08.439047
Autor:
Bernhard O. Palsson, Anand V. Sastry, Byung-Kwan Cho, Cameron R. Lamoureux, Zachary A. King, Patrick V. Phaneuf, Donghui Choe, Kumari Sonal Choudhary, Ye Gao, Troy E. Sandberg
Publikováno v:
Nucleic Acids Research
Lamoureux, C R, Choudhary, K S, King, Z A, Sandberg, T E, Gao, Y, Sastry, A V, Phaneuf, P V, Choe, D, Cho, B-K & Palsson, B O 2020, ' The Bitome: digitized genomic features reveal fundamental genome organization ', Nucleic Acids Research, vol. 48, no. 18, gkaa774, pp. 10157-10163 . https://doi.org/10.1093/nar/gkaa774
Lamoureux, C R, Choudhary, K S, King, Z A, Sandberg, T E, Gao, Y, Sastry, A V, Phaneuf, P V, Choe, D, Cho, B-K & Palsson, B O 2020, ' The Bitome: digitized genomic features reveal fundamental genome organization ', Nucleic Acids Research, vol. 48, no. 18, gkaa774, pp. 10157-10163 . https://doi.org/10.1093/nar/gkaa774
A genome contains the information underlying an organism's form and function. Yet, we lack formal framework to represent and study this information. Here, we introduce the Bitome, a matrix composed of binary digits (bits) representing the genomic pos
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