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

Discovery of antibiotics that selectively kill metabolically dormant bacteria

Authors: Zheng, Erica J., Valeri, Jacqueline A., Andrews, Ian W., Krishnan, Aarti, Bandyopadhyay, Parijat, Anahtar, Melis N., Herneisen, Alice, Schulte, Fabian, Linnehan, Brooke, Wong, Felix, Stokes, Jonathan M., Renner, Lars D., Lourido, Sebastian, Collins, James J.

Source: In Cell Chemical Biology 18 April 2024 31(4):712-728

LADL: light-activated dynamic looping for endogenous gene expression control

Authors: Kim, Ji, Rege, Mayuri, Valeri, Jacqueline, Dunagin, Margaret, Metzger, Aryeh, Titus, Katelyn, Gilgenast, Thomas, Gong, Wanfeng, Beagan, Jonathan, Raj, Arjun, Phillips-Cremins, Jennifer

Source: Nature methods. 16(7):633-639

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100182780685.0x000001&indx=1&recIds=ETOCvdc_100182780685.0x000001

Discovery of a structural class of antibiotics with explainable deep learning.

Authors: Wong, Felix, Zheng, Erica J., Valeri, Jacqueline A., Donghia, Nina M., Anahtar, Melis N., Omori, Satotaka, Li, Alicia, Cubillos-Ruiz, Andres, Krishnan, Aarti, Jin, Wengong, Manson, Abigail L., Friedrichs, Jens, Helbig, Ralf, Hajian, Behnoush, Fiejtek, Dawid K., Wagner, Florence F., Soutter, Holly H., Earl, Ashlee M., Stokes, Jonathan M., Renner, Lars D.

Source: Nature; Feb2024, Vol. 626 Issue 7997, p177-185, 9p

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

BioAutoMATED: An end-to-end automated machine learning tool for explanation and design of biological sequences

Authors: Valeri, Jacqueline A., Soenksen, Luis R., Collins, Katherine M., Ramesh, Pradeep, Cai, George, Powers, Rani, Angenent-Mari, Nicolaas M., Camacho, Diogo M., Wong, Felix, Lu, Timothy K., Collins, James J.

Source: In Cell Systems 21 June 2023 14(6):525-542

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

Combination Antibiotic-Focused Machine Learning Models for Integration into Experimental Workflows

Authors: Ambatipudi, Mythri

Contributors: Collins, James J, Valeri, Jacqueline

Source: Ambatipudi, Mythri. 2022. Combination Antibiotic-Focused Machine Learning Models for Integration into Experimental Workflows. Bachelor's thesis, Harvard College.

Subject Terms: antibiotic resistance, antibiotics, artificial intelligence, combination, computational, machine learning, Bioengineering, Bioinformatics

File Description: application/pdf; application/pdf

Access URL: https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37372715