About Me

Scientist at Arcadia Science 

Pronouns: She/Her




I am a microbiologist and I study the viruses that infect bacteria (bacteriophages). 

During my PhD in the Bondy-Denomy lab at UCSF, I studied how bacteriophages use anti-CRISPR proteins to survive being attacked by the bacterial CRISPR-Cas immune system. As a Miller Research Fellow in Jill Banfield's lab, I used genome-resolved metagenomics to discover phages that use alternative genetic codes in human and animal microbiomes. 

As a Scientist at Arcadia Science, I combine experimental and metagenomic techniques to explore the amazing diversity of bacteriophages on our planet. 


PhD in Biomedical Sciences                                                                                                         2014-2020
Advisor: Joe Bondy-Denomy
University of California, San Francisco

BSc in Microbiology                                                                                                                      2010-2014
Advisor: Jon Boyle
University of Pittsburgh



Peters S, Borges AL, Giannone RJ, Morowitz M, Banfield JF, Hettich R. Validation that human microbiome phages use alternative genetic coding with TAG stop read as Q. bioRxiv. (2022). doi: https://doi.org/10.1101/2022.01.06.475225 


Rubin BE, Diamond S, Cress BF, Crits-Christoph A, Lou YC, Borges AL, Shivram H, He C, Xu M, Zhou Z, Smith SJ, Rovinksy R, Smock DCJ, Tang K, Owend TK, Krishnappa N, Sachdeva R, Barrangou R, Deutschbauer AM, Banfield JF, Doudna JA.  Species- and site-specific genome editing in complex bacterial communities. Nat. Microbiol. (2021).

Chen LX, Jaffe AL, Borges AL, Penav PI, Nelson TC, Warren LA, Banfield JF. Phage-encoded ribosomal protein S21 expression is linked to late stage phage replication. bioRxiv. (2021). doi: https://doi.org/10.1101/2021.10.11.463225

Borges AL, Lou YC, Sachdeva R, Al-Shayeb B, Jaffe AL, Santini JM, Banfield JF. Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes. bioRxiv. (2021). doi: https://doi.org/10.1101/2021.08.26.457843

Crisci MA, Chen LX, Devoto AE, Borges AL , Bordin N, Sachedeva R, Tett A, Sharrar AM, Segata N, Debenedetti F, Burt R, Wood RM, Rowden LJ, Corsini PM, van Winden S, Holmes MA, Lei S, Banfield JF, Santini JM. Closely related Lak megaphages replicate in the microbiomes of diverse animals. iScience : 102875 (2021).

Borges AL. How to train your bacteriophage. [Commentary] PNAS 118 (28) (2021).

Borges AL. The Art of Being Single. [Commentary] The CRISPR Journal 4(1):16-17 (2021).

Leon LM, Park AE, Borges AL, Zhang JY, Bondy-Denomy J. Mobile element warfare via CRISPR and anti-CRISPR in Pseudomonas aeruginosa. Nucleic Acids Res. (2021). doi:10.1093/nar/gkab006


Gussow AB, Park AE, Borges AL, Shmakov SA, Makanrova KS, Wolf YI, Bondy-Denomy J, Koonin EV. Novel anti-CRISPR protein families predicted with a machine-learning approach. Nat. Comms. 11(1): 3784. (2020).

Govindarajan S, Borges AL, Bondy-Denomy J. Distinct subcellular localization of a Type I CRISPR complex and the Cas3 nuclease in bacteria. bioRxiv (2020). doi: https://doi.org/10.1101/2020.09.29.318501

Borges AL, Castro B, Govindarajan S, Solvik T, Escalante V, Bondy-Denomy J. Bacterial alginate regulators and phage homologs repress CRISPR-Cas immunity. Nat. Microbiol. 5(5): 679-687.(2020).


Crowley VM, Catching A, Taylor HN, Borges AL, Metcalf J, Bondy-Denomy J, Jackson R.A. A Type IV-A CRISPR-Cas system in Pseudomonas aeruginosa mediates RNA-guided plasmid interference in vivo. The CRISPR Journal 2(6):434-440. (2019).

Stanley SY, Borges AL, Chen K, Swaney DL, Krogan NJ, Bondy-Denomy J, Davidson AR. Anti-CRISPR-Associated Proteins Are Crucial Repressors of Anti-CRISPR Transcription. Cell 178(6):1452-1464 (2019).

Roux S, Krupovic M, Daly RA, Borges AL, Nayfach S, Schulz F, Sharrar A, Matheus Carnevali PB, Cheng JF, Ivanova NN, Bondy-Denomy J, Wrighton KC, Woyke T, Visel A, Kyrpides NC, Eloe-Fadrosh EA. Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes. Nat Microbiol. 4(11):1894-1906 (2019).


Marino ND*, Zhang JY*, Borges AL*, Sousa AA, Leon LM, Rauch BJ, Walton RT, Berry JD, Joung JK, Kleinstiver BP, Bondy-Denomy J. Discovery of widespread Type I and Type V CRISPR-Cas inhibitors. Science 362(6411):240-242 (2018).

* These authors contributed equally to this work

Borges AL, Zhang JY, Rollins MF, Osuna BA, Wiedenheft B, Bondy-Denomy J.Bacteriophage Cooperation Suppresses CRISPR-Cas3 and Cas9 Immunity. Cell 174(4):917-925 (2018).

2017 and prior 

Borges AL, Davidson AR, Bondy-Denomy J. The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs. Annu. Rev. Virol. 4(1):37-59 (2017).

Walzer KA, Wier GM, Dam RA, Srinivasan AR, Borges AL, English ED, Herrmann DC, Schares G, Dubey JP and Boyle JP. Hammondia hammondi harbors functional orthologs of the host-modulating effectors GRA15 and ROP16 but is distinguished from Toxoplasma gondii by a unique transcriptional profile. Eukaryot. Cell 13(12):1507-18 (2014).

Adomako-Ankomah Y, Wier GM, Borges AL, Wand HE and Boyle JP. Differential locus expansion distinguishes Toxoplasmatinae species and closely related strains of Toxoplasma gondii. MBio 5(1):e01003-13 (2014).

Awards & Honors

Nat L. Sternberg Thesis Prize, 2020
UC-Berkeley Miller Fellowship, 2020
UCSF Chancellor's Award for LGBTQIA Leadership, 2019
Harold M. Weintraub Graduate Award, 2019
UCSF Dean's Award for Excellence in Mentoring, 2019
UCSF Hooper Foundation Microbiology and Immunology Fellowship, 2018
NSF Honorable Mention - Graduate Research Fellowship Program, 2016
Barry M. Goldwater Scholarship, 2013
Samuel D. Colella Research Award, 2013
University of Pittsburgh Mentor/Mentee Summer Research Fellowship Program, 2012
University of Pittsburgh Honors College Full Tuition Scholarship, 2010
National Merit Scholarship, 2010