Publications

Postdoc

Bacteriophages inhibit and evade cGAS-like immune function in bacteria. Huiting E, Cao X, Ren J, Athukoralage JS, Luo Z, Silas S, An N, Carion H, Zhou Y, Fraser JS, Feng Y, Bondy-Denomy J. Cell. 2025 Sep 4;188(18):5118. doi: 10.1016/j.cell.2025.08.009. Epub 2025 Aug 22. Erratum for: Cell. 2023 Feb 16;186(4):864-876.e21. doi: 10.1016/j.cell.2022.12.041. PMID: 40848727; PMCID: PMC12483331.

Anti-restriction functions of injected phage proteins revealed by peeling back layers of bacterial immunity. Silas S, Carion H, Makarova KS, Sanchez Godinez D, Haniyur S, Volino L, Yee WX, Fossati A, Swaney D, Bocek M, Koonin EV, Bondy-Denomy J. Nat Commun. 2025 Aug 22;16(1):7828. doi: 10.1038/s41467-025-63056-3. PMID: 40846711; PMCID: PMC12373910.

Activation of bacterial programmed cell death by phage inhibitors of host immunity. Silas S, Carion H, Makarova KS, Laderman ES, Todeschini T, Kumar P, Johnson M, Bocek M, Nobrega FL, Koonin EV, Bondy-Denomy J. Mol Cell. 2025 May 1;85(9):1838-1851.e10. doi: 10.1016/j.molcel.2025.04.010. PMID: 40315827; PMCID: PMC12088041.

H1 Connect Recommendation of [Silas S et al., BioRxiv 2023 (:)]. Marraffini L and Aviram N. In H1 Connect, 08 Jun 2023. Recommendation: Exceptional, F1000 Research. Marraffini L.A., Aviram N.

Multi-interface licensing of protein import into a phage nucleus. Kokontis C, Klein TA, Silas S, Bondy-Denomy J. Nature. 2025 Mar;639(8054):456-462. doi: 10.1038/s41586-024-08547-x. Epub 2025 Feb 5. PMID: 39910297; PMCID: PMC12165441.

Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome. Wolf YI*, Silas S*, Wang Y, Wu S, Bocek M, Kazlauskas D, Krupovic M, Fire AZ, Dolja VV, Koonin EV. Peer reviewed (not previously pre-printed). 2020. PMID: 32690954. doi: 10.1038/s41564-020-0755-4

Rapid deployment of SARS-CoV-2 testing: The CLIAHUB. Crawford E., et al. PLoS Pathog. 2020. Oct 28;16(10):e1008966. 

Industry

A novel high-throughput molecular counting method with single base-pair resolution enables accurate single-gene NIPT. Tsao DS, Silas S, Landry BP, Itzep NP, Nguyen AB, Greenberg S, Kanne CK, Sheehan VA, Sharma R, Shukla R, Arora PN, Atay O. Peer-reviewed and previously pre-printed. 2019. PMID: 31591409. doi: 10.1038/s41598-019-50378-8

Quality Control Templates for ensuring validity of sequencing- based assays. Tsao D., Silas S., Atay O. Patent US11629381B2, 05 Jan 2018. 

PhD

A Reverse Transcriptase-Cas1 fusion protein contains a Cas6 domain required for both CRISPR RNA Biogenesis and RNA Spacer Acquisition. Mohr G, Silas S, Stamos JL, Makarova KS, Markham LM, Yao J, Lucas-Elío P, Sanchez-Amat A, Fire AZ, Koonin EV, Lambowitz AM. Peer reviewed (not previously pre-printed). 2018. PMID: 30344094. doi: 10.1016/j.molcel.2018.09.013

Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems. Silas S, Lucas-Elio P, Jackson SA, Aroca-Crevillén A, Hansen LL, Fineran PC, Fire AZ, Sánchez-Amat A. Peer reviewed (not previously pre-printed). 2017. PMID: 28826484. doi: 10.7554/eLife.27601

On the origin of RNA-acquiring CRISPR systems and their mysteriously diverse spacers. Silas S, Makarova KS, Shmakov S, Páez-Espino D, Mohr G, Liu Y, Davison M, Roux S, Krishnamurthy SR, Fu BXH, Hansen LL, Wang D, Sullivan MB, Millard A, Clokie MR, Bhaya D, Lambowitz AM, Kyrpides NC, Koonin EV, Fire AZ. Peer reviewed (not previously pre-printed). 2017. PMID: 28698278. doi: 10.1128/mBio.00897-17

Direct CRISPR spacer acquisition from RNA by a natural reverse-transcriptase-Cas1 fusion protein. Silas S, Mohr G, Sidote DJ, Markham LM, Sanchez-Amat A, Bhaya D, Lambowitz AM, Fire AZ. Peer reviewed (not previously pre-printed). 2016. PMID: 26917774. doi: 10.1126/science.aad4234

CRISPR goes retro. Sontheimer E.J., Marraffini L.A. Perspective, Science 351(6276)

CRISPR memories of RNA. Waldron D. Highlight, Nature Reviews Genetics 17(4)

Pre-PhD

Human IgE responses to different splice variants of Schistosoma mansoni tropomyosin: associations with immunity. Silas S, Fitzsimmons CM, Jones FM, Pinot de Moira A, Wawrzyniak J, Tukahebwa EM, Dunne DW. Peer reviewed (not previously pre-printed). 2014. PMID: 24657550. doi: 10.1016/j.ijpara.2014.02.004

Wild-type D. melanogaster as an alternative model system for investigating the pathogenicity of C. albicans. Glittenberg MT, Silas S, MacCallum DM, Gow NA, Ligoxygakis P. Peer reviewed (not previously pre-printed). 2011. PMID: 21540241. doi: 10.1242/dmm.006619