A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks

Autor: Max A English, Miguel A Alcantar, James J Collins

Publikováno v: Molecular Systems Biology, Vol 19, Iss 6, Pp 1-22 (2023)

Abstract In bacteria, natural transposon mobilization can drive adaptive genomic rearrangements. Here, we build on this capability and develop an inducible, self‐propagating transposon platform for continuous genome‐wide mutagenesis and the dynam

Externí odkaz: https://doaj.org/article/32cd5e4f5b854b8a8c7b26deef4c5bc5

Sequence-to-function deep learning frameworks for engineered riboregulators

Autor: Jacqueline A. Valeri, Katherine M. Collins, Pradeep Ramesh, Miguel A. Alcantar, Bianca A. Lepe, Timothy K. Lu, Diogo M. Camacho

Publikováno v: Nature Communications, Vol 11, Iss 1, Pp 1-14 (2020)

The design of synthetic biology circuits remains challenging due to poorly understood design rules. Here the authors introduce STORM and NuSpeak, two deep-learning architectures to characterize and optimize toehold switches.

Externí odkaz: https://doaj.org/article/d92e1c3c09eb4750aa706310533722cf

Modulating the evolutionary trajectory of tolerance using antibiotics with different metabolic dependencies

Autor: Erica J. Zheng, Ian W. Andrews, Alexandra T. Grote, Abigail L. Manson, Miguel A. Alcantar, Ashlee M. Earl, James J. Collins

Publikováno v: Nature Communications. 13

Antibiotic tolerance, or the ability of bacteria to survive antibiotic treatment in the absence of genetic resistance, has been linked to chronic and recurrent infections. Tolerant cells are often characterized by a low metabolic state, against which

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::92b92c7fe9e6b60701e527be6969c094
https://doi.org/10.1038/s41467-022-30272-0

A CRISPR-based assay for the detection of opportunistic infections post-transplantation and for the monitoring of transplant rejection

Autor: Michael M, Kaminski, Miguel A, Alcantar, Isadora T, Lape, Robert, Greensmith, Allison C, Huske, Jacqueline A, Valeri, Francisco M, Marty, Verena, Klämbt, Jamil, Azzi, Enver, Akalin, Leonardo V, Riella, James J, Collins

Publikováno v: Nature biomedical engineering. 4(6)

In organ transplantation, infection and rejection are major causes of graft loss. They are linked by the net state of immunosuppression. To diagnose and treat these conditions earlier, and to improve long-term patient outcomes, refined strategies for

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::b9788887dd186593d859377bd5fb4d55
https://pubmed.ncbi.nlm.nih.gov/32284553

A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action

Autor: Douglas McCloskey, Allison J. Lopatkin, Lars Schrübbers, Sarah N Wright, Graham C. Walker, Sangeeta Satish, Bernhard O. Palsson, Amir Nili, Miguel A. Alcantar, Meagan Hamblin, Jason H. Yang, James J. Collins

Publikováno v: PMC
Cell
Yang, J H, Wright, S N, Hamblin, M, McCloskey, D, Alcantar, M A, Schrübbers, L, Lopatkin, A J, Satish, S, Nili, A, Palsson, B O, Walker, G C & Collins, J J 2019, ' A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action ', Cell, vol. 177, no. 6, pp. 1649-1661.e9 . https://doi.org/10.1016/j.cell.2019.04.016

© 2019 Elsevier Inc. Current machine learning techniques enable robust association of biological signals with measured phenotypes, but these approaches are incapable of identifying causal relationships. Here, we develop an integrated “white-box”

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a17b6e733d1b694dcad766ea0231ee40
https://hdl.handle.net/1721.1/135182