| A deep learning approach to antibiotic discovery JM Stokes, K Yang, K Swanson, W Jin, A Cubillos-Ruiz, NM Donghia, ... Cell 180 (4), 688-702. e13, 2020 | 1667 | 2020 |
| Probiotic strains detect and suppress cholera in mice N Mao, A Cubillos-Ruiz, DE Cameron, JJ Collins Science Translational Medicine 10 (445), eaao2586, 2018 | 206 | 2018 |
| Engineering living therapeutics with synthetic biology A Cubillos-Ruiz, T Guo, A Sokolovska, PF Miller, JJ Collins, TK Lu, ... Nature Reviews Drug Discovery 20 (12), 941-960, 2021 | 160 | 2021 |
| Evolutionary radiation of lanthipeptides in marine cyanobacteria A Cubillos-Ruiz, JW Berta-Thompson, JW Becker, WA Van Der Donk, ... Proceedings of the National Academy of Sciences 114 (27), E5424-E5433, 2017 | 69 | 2017 |
| Imaging secondary metabolism of Streptomyces sp. Mg1 during cellular lysis and colony degradation of competing Bacillus subtilis SR Barger, BC Hoefler, A Cubillos-Ruiz, WK Russell, DH Russell, ... Antonie Van Leeuwenhoek 102, 435-445, 2012 | 66 | 2012 |
| Analysis of the genetic variation in Mycobacterium tuberculosis strains by multiple genome alignments A Cubillos-Ruiz, J Morales, MM Zambrano BMC research notes 1 (1), 110, 2008 | 58 | 2008 |
| An engineered live biotherapeutic for the prevention of antibiotic-induced dysbiosis A Cubillos-Ruiz, MA Alcantar, NM Donghia, P Cárdenas, J Avila-Pacheco, ... Nature biomedical engineering 6 (7), 910-921, 2022 | 45 | 2022 |
| IS-seq: a novel high throughput survey of in vivo IS 6110 transposition in multiple Mycobacterium tuberculosis genomes A Reyes, A Sandoval, A Cubillos-Ruiz, KE Varley, I Hernández-Neuta, ... BMC genomics 13 (1), 1-15, 2012 | 36 | 2012 |
| Nitrate reductase assay for the rapid detection of pyrazinamide resistance in Mycobacterium tuberculosis using nicotinamide A Martin, A Cubillos-Ruiz, A Von Groll, P Del Portillo, F Portaels, ... Journal of antimicrobial chemotherapy 61 (1), 123-127, 2008 | 32 | 2008 |
| Genomic signatures of the haarlem lineage of Mycobacterium tuberculosis: implications of strain genetic variation in drug and vaccine development A Cubillos-Ruiz, A Sandoval, V Ritacco, B López, J Robledo, N Correa, ... Journal of clinical microbiology 48 (10), 3614-3623, 2010 | 31 | 2010 |
| Nitrogen cost minimization is promoted by structural changes in the transcriptome of N-deprived Prochlorococcus cells RW Read, PM Berube, SJ Biller, I Neveux, A Cubillos-Ruiz, SW Chisholm, ... The ISME journal 11 (10), 2267-2278, 2017 | 25 | 2017 |
| Toward a genetic system in the marine cyanobacterium Prochlorococcus R Laurenceau, C Bliem, MS Osburne, JW Becker, SJ Biller, ... Access microbiology 2 (4), 2020 | 21 | 2020 |
| Discovery of a structural class of antibiotics with explainable deep learning F Wong, EJ Zheng, JA Valeri, NM Donghia, MN Anahtar, S Omori, A Li, ... Nature, 1-9, 2023 | 19 | 2023 |
| Probiotic strains detect and suppress cholera in mice. Sci Transl Med 10: eaao2586 N Mao, A Cubillos-Ruiz, DE Cameron, JJ Collins | 14 | 2018 |
| Beyond metagenomics: integration of complementary approaches for the study of microbial communities A Cubillos-Ruiz, H Junca, S Baena, I Venegas, MM Zambrano Metagenomics: theory, methods and applications. Caister Academic Press …, 2010 | 8 | 2010 |
| Engineered bacteria recycle tumor metabolic waste to boost immunotherapy JR Cubillos-Ruiz, A Cubillos-Ruiz Cell Host & Microbe 29 (12), 1725-1727, 2021 | 5 | 2021 |
| Ecology and evolution of lanthipeptides in marine picocyanobacteria AF Cubillos-Ruiz, JW Thompson, JW Becker, SW Chisholm, Y Shi, ... Massachusetts Institute of Technology, 2015 | 3 | 2015 |
| Genomic Variability of Mycobacterium tuberculosis MM Zambrano, G Hernández-Neuta, I Hernández-Neuta, A Sandoval, ... Understanding Tuberculosis-Deciphering the Secret Life of the Bacilli, 2012 | 2 | 2012 |
| Viral video: Live imaging of virus-host encounters K Son, JS Guasto, A Cubillos-Ruiz, SW Chisholm, MB Sullivan, R Stocker APS Division of Fluid Dynamics Meeting Abstracts, L5. 009, 2014 | 1 | 2014 |
| Visualizing viral transport and host infection K Son, J Guasto, A Cubillos-Ruiz, M Sullivan, R Stocker, MIT Team APS Division of Fluid Dynamics Meeting Abstracts, R26. 002, 2013 | 1 | 2013 |
James J CollinsMIT; Wyss Institute, Harvard; Broad Institute of MIT & HarvardVerified email at mit.edu
