Publications

Postdoc

Conserved jumbo phage factors required for protein import into a phage nucleus. Kokontis C, Klein TA, Silas S, Bondy-Denomy J. Pre-print (Not yet peer-reviewed). 2024. doi: 10.1101/2024.03.27.586873

Activation of programmed cell death and counter-defense functions of phage accessory genes. Silas S, Carion H, Makarova KS, Laderman E, Godinez DS, Johnson M, Fossati A, Swaney D, Bocek M, Koonin EV, Bondy-Denomy J. Pre-print (Not yet peer-reviewed). 2023. doi: 10.1101/2023.04.06.535777

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.

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. Peer-reviewed and previously pre-printed. 2023. PMID: 36750095. doi: 10.1016/j.cell.2022.12.041

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