| Discovery of widespread type I and type V CRISPR-Cas inhibitors ND Marino, JY Zhang, AL Borges, AA Sousa, LM Leon, BJ Rauch, ... Science 362 (6411), 240-242, 2018 | 236 | 2018 |
| Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes S Roux, M Krupovic, RA Daly, AL Borges, S Nayfach, F Schulz, A Sharrar, ... Nature microbiology 4 (11), 1895-1906, 2019 | 234 | 2019 |
| The discovery, mechanisms, and evolutionary impact of anti-CRISPRs AL Borges, AR Davidson, J Bondy-Denomy Annual review of virology 4, 37-59, 2017 | 212 | 2017 |
| Bacteriophage cooperation suppresses CRISPR-Cas3 and Cas9 immunity AL Borges, JY Zhang, MCF Rollins, BA Osuna, B Wiedenheft, ... Cell 174 (4), 917-925. e10, 2018 | 159 | 2018 |
| Species-and site-specific genome editing in complex bacterial communities BE Rubin, S Diamond, BF Cress, A Crits-Christoph, YC Lou, AL Borges, ... Nature microbiology 7 (1), 34-47, 2022 | 156 | 2022 |
| Anti-CRISPR-associated proteins are crucial repressors of anti-CRISPR transcription SY Stanley, AL Borges, KH Chen, DL Swaney, NJ Krogan, ... Cell 178 (6), 1452-1464. e13, 2019 | 139 | 2019 |
| Machine-learning approach expands the repertoire of anti-CRISPR protein families AB Gussow, AE Park, AL Borges, SA Shmakov, KS Makarova, YI Wolf, ... Nature communications 11 (1), 3784, 2020 | 78 | 2020 |
| Mobile element warfare via CRISPR and anti-CRISPR in Pseudomonas aeruginosa LM Leon, AE Park, AL Borges, JY Zhang, J Bondy-Denomy Nucleic acids research 49 (4), 2114-2125, 2021 | 61 | 2021 |
| A Type IV-A CRISPR-Cas System in Pseudomonas aeruginosa Mediates RNA-Guided Plasmid Interference In Vivo VM Crowley, A Catching, HN Taylor, AL Borges, J Metcalf, ... The CRISPR Journal 2 (6), 434-440, 2019 | 57 | 2019 |
| Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes AL Borges, YC Lou, R Sachdeva, B Al-Shayeb, PI Penev, AL Jaffe, S Lei, ... Nature microbiology 7 (6), 918-927, 2022 | 35* | 2022 |
| Bacterial alginate regulators and phage homologs repress CRISPR–Cas immunity AL Borges, B Castro, S Govindarajan, T Solvik, V Escalante, ... Nature microbiology 5 (5), 679-687, 2020 | 35 | 2020 |
| Differential Locus Expansion Distinguishes Toxoplasmatinae Species and Closely Related Strains of Toxoplasma gondii Y Adomako-Ankomah, GM Wier, AL Borges, HE Wand, JP Boyle MBio 5 (1), 10.1128/mbio. 01003-13, 2014 | 34 | 2014 |
| Closely related Lak megaphages replicate in the microbiomes of diverse animals MA Crisci, LX Chen, AE Devoto, AL Borges, N Bordin, R Sachdeva, A Tett, ... Iscience 24 (8), 2021 | 23* | 2021 |
| Experimental validation that human microbiome phages use alternative genetic coding SL Peters, AL Borges, RJ Giannone, MJ Morowitz, JF Banfield, RL Hettich Nature communications 13 (1), 5710, 2022 | 20 | 2022 |
| Hammondia hammondi harbors functional orthologs of the host-modulating effectors GRA15 and ROP16 but is distinguished from Toxoplasma gondii by a unique transcriptional profile KA Walzer, GM Wier, RA Dam, AR Srinivasan, AL Borges, ED English, ... Eukaryotic cell 13 (12), 1507-1518, 2014 | 18 | 2014 |
| Phage-encoded ribosomal protein S21 expression is linked to late-stage phage replication LX Chen, AL Jaffe, AL Borges, PI Penev, TC Nelson, LA Warren, ... ISME communications 2 (1), 31, 2022 | 10 | 2022 |
| Distinct subcellular localization of a type i CRISPR complex and the Cas3 nuclease in bacteria S Govindarajan, A Borges, S Karambelkar, J Bondy-Denomy Journal of Bacteriology 204 (5), e00105-22, 2022 | 8 | 2022 |
| How to train your bacteriophage AL Borges Proceedings of the National Academy of Sciences 118 (28), e2109434118, 2021 | 5 | 2021 |
| Infant gut DNA bacteriophage strain persistence during the first 3 years of life YC Lou, LX Chen, AL Borges, J West-Roberts, BA Firek, MJ Morowitz, ... Cell Host & Microbe 32 (1), 35-47. e6, 2024 | 4 | 2024 |
| Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2’-fucosyllactose utilization can be facilitated by coexisting species YC Lou, BE Rubin, MC Schoelmerich, KS DiMarco, AL Borges, ... Nature Communications 14 (1), 7417, 2023 | 3 | 2023 |
Joseph Bondy-DenomyAssociate Professor, UCSFVerified email at ucsf.edu
