A high-throughput synthetic biology approach for studying combinatorial chromatin-based transcriptional regulation

Authors: Alcantar, Miguel A., English, Max A., Valeri, Jacqueline A., Collins, James J.

Source: In Molecular Cell 20 June 2024 84(12):2382-2396

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

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

Source: Molecular systems biology. 19(6)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100185027534.0x000001&indx=1&recIds=ETOCvdc_100185027534.0x000001

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

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

Source: In Cell 30 May 2019 177(6):1649-1661

Blood volume measurement using cardiovascular magnetic resonance and ferumoxytol: preclinical validation

Authors: Ramasawmy, Rajiv, Rogers, Toby, Alcantar, Miguel, McGuirt, Delaney, Khan, Jaffar, Kellman, Peter, Xue, Hui, Faranesh, Anthony, Campbell-Washburn, Adrienne, Lederman, Robert, Herzka, Daniel

Source: Journal of cardiovascular magnetic resonance. 20(1):1-10

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100181169223.0x000001&indx=1&recIds=ETOCvdc_100181169223.0x000001

Sequence-to-function deep learning frameworks for engineered riboregulators

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

Source: Nature communications. 11(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100174499843.0x000001&indx=1&recIds=ETOCvdc_100174499843.0x000001

Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials.

Authors: Yurkovich, James T.^1,2, Alcantar, Miguel A.¹, Haiman, Zachary B.¹, Palsson, Bernhard O.^1,2,3 palsson@ucsd.edu

Source: PLoS Computational Biology. 8/7/2018, Vol. 14 Issue 8, p1-16. 16p. 4 Graphs.

Subject Terms: *ALLOSTERIC regulation, *POLYNOMIALS, *ALLOSTERIC enzymes, *LIGANDS (Biochemistry), *BIOCHEMISTRY

An engineered live biotherapeutic for the prevention of antibiotic-induced dysbiosis.

Authors: Cubillos-Ruiz, Andrés, Alcantar, Miguel A., Donghia, Nina M., Cárdenas, Pablo, Avila-Pacheco, Julian, Collins, James J.

Source: Nature Biomedical Engineering; Jul2022, Vol. 6 Issue 7, p910-921, 12p

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

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

Source: Nature Communications; 5/9/2022, Vol. 13 Issue 1, p1-11, 11p

Subject Terms: ANTIBIOTICS, BACTERIAL metabolism, ESCHERICHIA coli, DISEASE relapse, TREATMENT effectiveness

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

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

Source: Nature Biomedical Engineering; Jun2020, Vol. 4 Issue 6, p601-609, 9p