Publications

Optimizing polymerase chain reaction (PCR) using machine learning (2021) Nicholas J. Cordaro, Andrew J. Kavran, Michael Smallegan, Megan Palacio, Nickolaus Lammer, Tyler S. Brant, Vanessa DuMont, Naiara Doherty Garcia, Suzannah Miller, Tara Jourabchi, Sara L. Sawyer, Aaron Clauset. BioRxiv. link.

RNase L limits host and viral protein synthesis via inhibition of mRNA export (2021) James M. Burke, Alison R. Gilchrist, Sara L. Sawyer, Roy Parker. Science Advances. link.

Just 2% of SARS-CoV-2-positive individuals carry 90% of the virus circulating in communities (2021) Qing Yang, Tassa K. Saldi, Erika Lasda, Carolyn J. Decker, Camille L. Paige, Denise Muhlrad, Patrick K. Gonzales, Morgan R. Fink, Kimngan L. Tat, Cole R. Hager, Jack C. Davis, Christopher D. Ozeroff, Nicholas R. Meyerson, Stephen K. Clark, Will T. Fattor, Alison R. Gilchrist, Arturo Barbachano-Guerrero, Emma R. Worden-Sapper, Sharon S. Wu, Gloria R. Brisson, Matthew B. McQueen, Robin D. Dowell, Leslie Leinwand, Roy Parker, Sara L. Sawyer. PNAS. link.

Saliva TwoStep for rapid detection of asymptomatic SARS-CoV-2 carriers (2021) Qing Yang, Nicholas R Meyerson, Stephen K Clark, Camille L Paige, Will T Fattor, Alison R Gilchrist, Arturo Barbachano-Guerrero, Benjamin G Healy, Emma R Worden-Sapper, Sharon S Wu, Denise Muhlrad, Carolyn J Decker, Tassa K Saldi, Erika Lasda, Patrick K Gonzales, Morgan R Fink, Kimngan L Tat, Cole R Hager, Jack C Davis, Christopher D Ozeroff, Gloria R Brisson, Matthew B McQueen, Leslie Leinwand, Roy Parker, Sara L Sawyer. eLIFE, link.

Positive Natural Selection in Genes of the Type I Interferon Response in Primates (2021) Elena Judd*, Alison Gilchrist*, Nicholas Meyerson, Sara L. Sawyer. BMC Ecology and Evolution, link.

Nuku, a family of primate retrocopies derived from KU70 (2021) Paul A Rowley, Aisha Ellahi, Kyudong Han, Jagdish Suresh Patel, James T Van Leuven, Sara L Sawyer  G3: Genes, Genomes, Genetics link.

Two-stage maximum likelihood classifier for identifying host protein targets of the dengue protease (2020) Jacob T Stanley, Alison R Gilchrist, Alex C Stabell, Mary A Allen, Sara L Sawyer, Robin D Dowell. Pacific Symposium on Biocomputing. vol 25, pages 487-498

dsRNA-Seq: Identification of viral infection by purifying and sequencing dsRNA (2019) Carolyn J Decker, Halley R Steiner, Laura L Hoon-Hanks, James H Morrison, Kelsey C Haist, Alex C Stabell, Eric M Poeschla, Thomas E Morrison, Mark D Stenglein, Sara L Sawyer, Roy Parker. Viruses v11, p 943

Selective Use of Primate CD4 Receptors by HIV-1. (2019)  Warren CJ, Meyerson NR, Dirasantha O, Feldman ER, Wilkerson GK, Sara L Sawyer. PLoS Biology, 17(6): e3000304.

A glycan shield on chimpanzee CD4 protects against infection by primate lentiviruses (HIV/SIV). (2019) Warren CJ, Meyerson NR, Stabell AC, Fattor WT, Wilkerson GK, Sara L Sawyer. Proc. Natl. Acad. Sci. USA, 

A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species. (2019) Hawkins JA, Kaczmarek ME, Müller MA, Drosten C, Press WH, Sara L Sawyer. Proc. Natl. Acad. Sci. USA,

How host genetics dictates successful viral zoonosis. (2019) Cody J. Warren and Sara L Sawyer. PLoS Biology 17(4): e3000217.

This is a comprehensive review of how the process of viral zoonosis works.

TRIM5 restricts flavivirus replication by targeting the viral protease for proteasomal degradation. (2019) Chiramel AI, Meyerson NR, McNally KL, Broeckel RM, Montoya VR, Méndez-Solís O, Robertson SJ, Sturdevant GL, Lubick KJ, Nair V, Youseff BH, Ireland RM, Bosio KM, Kim K, Luban J, Hirsch VM, Bouamr F, Taylor RT, Sara L Sawyer, Best SM. Cell Reports, 27, 3269–3283.

dsRNA-Seq: Identification of Viral Infection by Purifying and Sequencing dsRNA. (2019) Decker CJ, Steiner HR, Hoon-Hanks LR, Morrison JH, Haist KC, Stabell AC, Poeschla EM, Morrison TE, Stenglein MD, Sara L Sawyer, Parker R. Viruses, 11, 943; doi:10.3390/v11100943.

Species-specific deamidation of cGAS facilitates herpes simplex virus lytic replication. (2018) Zhang J, Zhao J, Li J, Xu S, He S, Zeng Y, Xie L, Xie N, Liu T, Lee K, Seo GJ,Chen L, Stabell AC, Sara L Sawyer, Jung J, Huang C, Feng P. Cell Host and Microbe. 24, 234–248

Control of Yeast Retrotransposons Mediated Through Nucleoporin Evolution. (2018) Rowley PA, Patterson K, Sandmeyer SB, Sara L Sawyer. PLoS Genetics, e1007325

Dengue viruses cleave STING in humans but not in non-human primates, their presumed natural reservoir. (2018) Stabell AC, Meyerson NR, Gullberg RC, Gilchrist AR, Webb KJ, Old WM, Perera R, Sara L Sawyer. eLIFE, e31919.

Species-specific vulnerability of RanBP2 shaped the evolution of SIV as it transmitted in African apes. (2018) Meyerson NR, Stabell AC, Vieira D, Diaz-Griffero F, Sara L Sawyer. PLoS Pathogens, 14(3):e1006906.

TRIM25 is a restriction factor that specifically targets influenza virus ribonucleoproteins to block the onset of RNA chain elongation. (2017) Meyerson NR, Zhou L, Guo YR, Zhou C, Tao YJ, Krug RM, Sara L Sawyer. Cell Host and Microbe, 22(5):627-638.e7

Owl monkey CCR5 reveals synergism between CD4 and CCR5 in HIV-1 entry. (2017) Nahabedian J, Sharma A, Kaczmarek ME, Wilkerson GK, Sara L Sawyer, Overbaugh J. Virology, 512:180-186.

Non-human Primate Schlafen11 Inhibits Production of Both Host and Viral Proteins. (2016) Stabell AC, Hawkins J, Li M, Gao X, David M, Press WH, Sara L Sawyer PLoS Pathogens 12(12): e1006066.

An Intrinsically Disordered Region of the DNA Repair Protein Nbs1 Is a Species-Specific Barrier to Herpes Simplex Virus 1 in Primates. (2016) Lou DI, Kim ET, Meyerson NR, Pancholi NJ, Mohni KN, Enard D, Petrov DA, Weller SK, Weitzman MD, Sara L Sawyer. Cell Host & Microbe, 20(2), 178–188.

Claus O. Wilke and Sara L Sawyer (2016). At the mercy of viruses. eLIFE, 5, e16758.

Rowley PA, Ho B, Bushong S, Johnson A, Sara L Sawyer (2016) XRN1 Is a Species-Specific Virus Restriction Factor in Yeasts. PLoS Pathogens 12(10): e1005890.

Ng M, Ndungo E, Kaczmarek ME, Herbert AS, Binger T, Kuehne AI, Jangra RK, Hawkins JA, Gifford RJ, Biswas R, Demogines A, James RM, Yu M, Brummelkamp TR, Drosten C, Wang L-F, Kuhn JH, Muller MA, Dye JM, Sara L Sawyer, Chandran K. (2015). Filovirus receptor NPC1 contributes to species-specific patterns of ebolavirus susceptibility in bats. eLIFE, 4, e11785.

Hussmann JA, Patchett S, Johnson A, Sara L Sawyer, Press WH (2015). Understanding Biases in Ribosome Profiling Experiments Reveals Signatures of Translation Dynamics in Yeast. PLoS Genetics, 11(12), e1005732.

Kerr SA, Jackson EL, Lungu OI, Meyer AG, Demogines A, Ellington AD, Georgiou G, Wilke CO,  Sara L Sawyer (2015). Computational and Functional Analysis of the Virus-Receptor Interface Reveals Host Range Trade-Offs in New World Arenaviruses. Journal of Virology, 89(22), 11643–11653.

McBee RM, Rozmiarek SA, Meyerson NR, Rowley PA, Sara L Sawyer (2015). The effect of species representation on the detection of positive selection in primate gene data sets. Molecular Biology and Evolution, 32(4), 1091–1096.

Meyerson NR, Sharma A, Wilkerson GK, Overbaugh J, Sara L Sawyer (2015). Identification of Owl Monkey CD4 Receptors Broadly Compatible with Early-Stage HIV-1 Isolates. Journal of Virology, 89(16), 8611–8622.

Hussmann JA, Lou DI, Sara L Sawyer, Press WH (2014). Reply to Schmitt et al.: Data-filtering schemes for avoiding double-counting in circle sequencing. Proc Natl Acad Sci USA, 111(16), E1561.

Peng L, Adler M, Demogines A, Borrell A, Liu H, Tao L, Tepp WH, Zhang SC, Johnson EA, Sara L Sawyer, Dong M (2014). Widespread Sequence Variations in VAMP1 across Vertebrates Suggest a Potential Selective Pressure from Botulinum Neurotoxins. PLoS Pathogens, 10(7), e1004177.

Lou DI, McBee RM, Le UQ, Stone AC, Wilkerson GK, Demogines AM, Sara L Sawyer (2014). Rapid evolution of BRCA1 and BRCA2 in humans and other primates. BMC Evolutionary Biology, 14, 155.

Meyerson NR, Rowley PA, Swan CH, Le DT, Wilkerson GK, Sara L Sawyer (2014). Positive selection of primate genes that promote HIV-1 replication. Virology, 454-455, 291–298.

White TE, Brandariz-Nuñez A, Valle-Casuso JC, Knowlton C, Kim B, Sara L Sawyer, Diaz-Griffero F (2014). Effects of human SAMHD1 polymorphisms on HIV-1 susceptibility. Virology, 460-461(C), 34–44.

Demogines A, Abraham J, Choe H, Farzan M, Sara L Sawyer (2013). Dual host-virus arms races shape an essential housekeeping protein. PLoS Biology, 11(5), e1001571.

Lou DI, Hussmann JA, McBee RM, Acevedo A, Andino R, Press WH,  Sara L Sawyer (2013). High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing. Proc Natl Acad Sci USA, 110(49), 19872–19877.

Abrams AJ, Cannatella DC, Hillis DM, Sara L Sawyer (2013). Recent host-shifts in ranaviruses: signatures of positive selection in the viral genome. J General Virology, 94(Pt 9), 2082–2093.

Malfavon-Borja R, Sara L Sawyer, Wu LI, Emerman M, Malik HS (2013). An evolutionary screen highlights canonical and noncanonical candidate antiviral genes within the primate TRIM gene family. Genome Biology and Evolution, 5(11), 2141–2154.

Voit RA, McMahon MA, Sara L Sawyer, Porteus MH (2013). Generation of an HIV Resistant T-Cell Line by Targeted “Stacking” of Restriction Factors. Molecular Therapy, 21(4), 786–795.

Kaelber JT, Demogines A, Harbison CE, Allison AB, Goodman LB, Ortega AN, Sara L Sawyer, Parrish CR (2012). Evolutionary reconstructions of the transferrin receptor of Caniforms supports canine parvovirus being a re-emerged and not a novel pathogen in dogs. PLoS Pathogens, 8(5), e1002666.

Demogines A, Farzan M, Sara L Sawyer (2012). Evidence for ACE2-Utilizing Coronaviruses (CoVs) Related to Severe Acute Respiratory Syndrome CoV in Bats. Journal of Virology, 86(11), 6350–6353.

Demogines A, Truong KA, Sara L Sawyer (2012). Species-specific features of DARC, the primate receptor for Plasmodium vivax and Plasmodium knowlesi. Molecular Biology and Evolution, 29(2), 445–449.

Sara L Sawyer and Nels C. Elde (2012). A cross-species view on viruses. Current Opinion in Virology, 2(5), 561–568.

Lee K, Mulky A, Yuen W, Martin TD, Meyerson NR, Choi L, Yu H, Sara L Sawyer, KewalRamani VN (2012). HIV-1 Capsid-Targeting Domain of Cleavage and Polyadenylation Specificity Factor 6. Journal of Virology, 86(7), 3851–3860.

Han K, Lou DI, Sara L Sawyer (2011). Identification of a genomic reservoir for new TRIM genes in primate genomes. PLoS Genetics, 7(12), e1002388.

Meyerson NR, Sara L Sawyer (2011). Two-stepping through time: mammals and viruses. Trends in Microbiology, 19(6), 286–294.

Demogines A, East AM, Lee J-H, Grossman SR, Sabeti PC, Paull TT, Sara L Sawyer (2010). Ancient and recent adaptive evolution of primate non-homologous end joining genes. PLoS Genetics, 6(10), e1001169.

Johnson WE and Sara L Sawyer (2009). Molecular evolution of the antiretroviral TRIM5 gene. Immunogenetics, 61(3), 163–176.

Tareen SU, Sara L Sawyer, Malik HS, Emerman M. (2009). An expanded clade of rodent Trim5 genes. Virology, 385(2), 473–483.

Sawyer SL, Emerman M, Malik HS. (2007) Discordant evolution of the adjacent antiretroviral genes TRIM22 and TRIM5 in mammals. PLoS Pathogens, 3(12): e197.

Sawyer SL and Malik HS. (2006) Positive selection of yeast nonhomologous end-joining genes and a retrotransposon conflict hypothesis. Proc Natl Acad Sci USA, 103(47): 17614-9.

Sawyer SL, Wu LI, Akey JM, Emerman M, Malik HS. (2006) High Frequency Persistence of an Impaired Allele of the Retroviral Defense Gene TRIM5 in Humans. Current Biology, 16(1): 95-100.

Sawyer SL, Wu LI, Emerman M, Malik HS. (2005) Positive selection of primate TRIM5 identifies a critical species-specific retroviral restriction domain. Proc Natl Acad Sci USA, 102(8): 2832-7.

Sawyer SL, Emerman M, Malik HS. (2004) Ancient adaptive evolution of the primate antiviral DNA editing enzyme, APOBEC3G. PLoS Biology, 2(9): e275.

Sawyer SL, Cheng IH, Chai W, Tye BK. (2004) Mcm10 and Cdc45 Cooperate in Origin Activation in Saccharomyces cerevisiae. Journal of Molecular Biology, 340: 195-202.

Tye BK and Sawyer S. (2000) The hexameric eukaryotic MCM helicase: building symmetry from nonidenticle parts. Journal of Biological Chemistry, 275(45): 34833-6.

Homesley L, Lei M, Kawasaki Y, Sawyer S, Christensen T, Tye BK. (2000) Mcm10 and the MCM2-7 complex interact to initiate DNA synthesis and to release replication factors from origins. Genes and Development, 14(8): 913-926.