For updated list of publications see google scholar page:

# denotes co-first author

^ denotes co-second author

* denotes co-senior author

Kim, J., Kratz, A., Chen, S., Sheng, J., Kim, H.K., Zhang, L., Singh, B.K., Chavez, A. High-throughput tagging of endogenous loci for rapid characterization of protein function. Science Advances. 2024; 10(18):eadg8771 PMC11062585. Video summary of manuscript.

#Lampe, G.D., #King, R.T., Halpin-Healy, T.S., Klompe, S.E., Hogan, M.I., Vo, P.L.H., Tang, S., Chavez, A., Sternberg, S.H. Targeted DNA integration in human cells without double-strand breaks using CRISPR RNA-guided transposases. Nature Biotechnology. 2024; 42:87-98. PMCID: PMC10620015

#Duan, Y., #Zhou, H., #Liu, X., #Iketani, S., #Lin, M., Zhang, X., Bian, Q., Wang, H., Sun, H., Hong, S.J., Culbertson, B., Mohri, H., Luck, M.I., Zhu, Y., Liu, X., Lu, Y., Yang, X., Yang, K., Sabo, Y., Chavez, A., Goff, S.P., Rao, Z., *Ho, D.H., *Yang, H. Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Nature. 2023; Early access publication. https://doi.org/10.1038/s41586-023-06609-0

Lao, Y-H., Ji, R., Zhou, J.K., Snow, K.J., Kwon, N., Saville, E., He, S., Chauhan, S., Chun-Wei, C., Malika, D.S., Zhang, H., Quek, C.H., Cai, S., Li, M., Gaitan, Y., Bechtel, L., Wu, S-Y., Lutz, C.M., Tomer, R., Murray, S.A., Chavez, A., *Konofagou, E.E., *Leong, K.W. Focused ultrasound-mediated brain genome editing. PNAS. 2023; 120(34) e2302910120.

Resnick, S.J., Qamar, S., Sheng, J., Huang, L.H., Nixon-Abell, Melore, S., Chung, C.W., Li, X., Wang, J., Zhang, N., Shneider, N.A., St. George-Hyslop, P., Chavez, A. A multiplex platform to identify mechanisms and modulators of proteotoxicity in neurodegeneration. bioRxiv. 2022.

#Iketani, S., #Mohri, H., #Culbertson, B., #Hong, S.J., Duan, Y., Luck, M.I., Annavajhala, M.K., Guo, Y., Sheng, Z., Uhlemann, A-C., Sabo, Y., Yang, H., *Chavez, A., *Ho. D.D. Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir. Nature. 2022

#Iketani, S., #Hong, S.J., #Sheng, J., Culbertson, B., Fallah, F., Bahari, F., Aditham, A., Kratz, A.F., Cortes, M.L., Tian, R., Goff, S.P., Motazeri, H., Sabo, Y., Ho, D.D., Chavez, A. Functional map of SARS-CoV-2 3CL protease reveals tolerant and immutable sites. Cell Host and Microbe. 2022; 30:1–9

#Liu, L., #Iketani, S., #Guo, Y., #Casner, R.G., #Reddem, E.R., #Nair, M.S., #Yu, J., #J.F.-W., Chen, Wang, M., Cerruti, G., Li, Z., Morano, N.C., Castagna, C.D., Corredor, L., Chu, H., Yuan, S., Poon, V. K.-M., Chan C. C.-S., Chen, Z., Luo, Y., Cunningham, M., Chavez, A., Yin, M. T., Perlin, D.S., Tsuji, M., Yuen K.-Y., Kwong, P.D., Sheng, Z., *Huang, Y., *Shapiro, L., *Ho, D.D. An antibody class with a common CDRH3 motif broadly neutralizes sarbecoviruses. Science Translational Medicine. 2022; 14:646.

Liu, H., Iketani, S., Zask, A., Khanizeman, N., Bednarova, E., Forouhar, F., Fowler, B., Hong, S.J., Mohri, H., Nair, M.S., Huang, Y., Tay, N.E.S., Lee, S., Karan, C., Resnick, S.J., Quinn, C., Li, W., Shion, H., Jurschenko, C., Lauber, T.M., Stokes, M.E., *Rovis, T., *Chavez, A., *Ho, D.D., *Stockwell, B.R. Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19. Nature Communications. 2022; 13:1891

Sheng, J., Hod, E.A., Vlad, G., Chavez, A. Quantifying protein abundance on single cells using split‑pool sequencing on DNA‑barcoded antibodies for diagnostic applications. Scientific Reports. 2022; 12:884

Dang, N., Lance-Byrne, A., Tung, A., Guo, X., Cicchi, R.J., Buchthal, J., *Chavez, A., *Yeo, N.C. Generation and application of a versatile CRISPR toolkit for mammalian cell engineering. Synthetic Biology. 2021; 6(1), 1-12

Iketani, S., Forouhar, F., Liu, H., Hong, S.J., Lin, F-Y., Nair, M.S., Zask, A., Huang, Y., Xing, L., *Stockwell, B.R., *Chavez, A., *Ho, D.D. Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors. Nature Communications. 2021; 12:2016

Resnick, S.J., Iketani, S., Hong, S.J., Zask, A., Liu, H., Kim, S., Melore, S., Nair, M.S., Huang, Y., Tay, N.E.S., Rovis, R., Yang, H.W., *Stockwell, B.R., *Ho, D.D., *Chavez, A. A simplified cell-based assay to identify coronavirus 3CL protease inhibitors. Journal of Virology. 2021; JVI.02374-20 (online ahead of print)

Moghadam, F., LeGraw, R., Velazquez, J.J., Yeo, N.C., Xu, C., Park, J., Chavez, A., Ebrahimkhani, M.R., Kiani, S. Nature Cell Biology. 2020; 22:1143-1154

Nobel, C., Min, J., Olejarz, J., Buchthal, J., Chavez, A., Smidler, A.L., DeBenedictis, E.A., Church, G.M., Nowak, M.A., and Esvelt, K.M. Daisy-chain gene drives for the alteration of local populations. PNAS. 2019; doi: 10.1073/pnas.1716358116

Xiong, K., Marquart, K.F., Karottki, K.J.C., Li, S., Shamie, I., Lee, J.S., Gerling, S., Yeo, N-C., Chavez, A., Lee, G.M., Lewis, N.E., Kildegaard, H.F. Reduced Apoptosis in Chinese Hamster Ovary Cells via Optimized CRISPR Interference. Biotechnology and Bioengineering. 2019; doi: 10.1002/bit.26969

Labun, K., Guo, X., Chavez, A., Church, G., Gagnon, J.A., Valen, E. Accurate analysis of genuine CRISPR editing events with ampliCan. Genome Research. 2019; doi: 10.1101/gr.244293.118

Wensing, L., Sharma, J., Uthayakumar, D., Proteau, Y., Chavez, A., Shapiro, R.S. A CRISPR Interference Platform for Efficient Genetic Repression in Candida albicans. mSphere. 2019; 4: e00002-19

Halder, V., Porter, C.B.M., Chavez, A., Shapiro, R.S., Design, execution, and analysis of CRISPR-Cas9-based deletions and genetic interaction networks in the fungal pathogen Candida albicans. Nature Protocols. 2019; 14:955-975

#Nageshwaran, S., #Chavez, A., Yeo, N-C., Guo, X., Lance-Byrne, A., Tung, A., Collins, J.J., Church, G.M. CRISPR Guide RNA Cloning for Mammalian Systems. JoVE. 2018; 2:140

#Yeo, N-C., *#Chavez, A., Lance-Byrne, A., Chan, Y., Menn, D., Milanova, D., Kuo, C-C., Guo, X., Sharma, S., Tung, A., Cecchi, R.J., Tuttle, M., Pradhan, S., Lim, E.T., Davidsohn, N., Ebrahimkhani, M.R., Collins, J.J., Lewis, N.E., *Kiani, S., *Church, G.M., An enhanced CRISPR repressor for targeted mammalian gene regulation. Nature Methods. 2018; doi: 10.1038/s41592-018-0048-5.

Clarke, R., Heler, R., MacDougall, M.S., Yeo, N-C., Chavez, A., Regan, M., Hanakahi, L., Church, G.M., Marraffini, L.A., Merrill, B.J. Enhanced Bacterial Immunity and Mammalian Genome Editing via RNA-Polymerase-Mediated Dislodging of Cas9 from Double-Strand DNA Breaks. Molecular Cell. 2018; 71:42-55.

#Guo, X., *#Chavez, A., #Tung, A., Chan, Y., Kaas, C., Yin, Y., Cecchi, R., Garnier, S.L., Kelsic, E.D., Schubert, M., DiCarlo, J.E., Collins, J.J., *Church, G.M., High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR–Cas9 in yeast. Nature Biotechnology. 2018; doi:10.1038/nbt.4147.

Chan, Y., Chan, Y.K., Goodman, D.B., Guo, X., Chavez, A., Lim, E.T., Church, G.M., Enabling multiplexed testing of pooled donor cells through whole-genome sequencing. Genome medicine 10 (1), 31.

Bester, A.C., ^Lee, J.D., ^Chavez, A., Lee, Y-R., Nachmani, D., Vora, S., Victor, J., Sauvageau, M., Monteleone, E., Rinn, J.L., Provero, P., Church, G.M., Clohessy, J.G., Pandolfi, P.P. An Integrated Genome Wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance. Cell. 2018; 173 (3), 649-664. e20

*#Chavez, A., #Pruitt, B.W., Tuttle, M., Shapiro, R.S., Cecchi, R.J., Winston, J., Turczyk, B.M., Tung, M., Collins, J.J., and Church, G.M*. Precise Cas9 targeting enables genomic mutation prevention. PNAS. 2018; doi: 10.1073/pnas.1718148115.

Shapiro, R.S., Chavez, A., Collins, J.J. CRISPR technologies: a toolkit for making genetically intractable microbes tractable. Nature Reviews Microbiology. 2018; doi:10.1038/s41579-018-0002-7

#Shapiro, R.S., #Chavez, A., Porter, C.B.M., Hamblin, M., Kaas, C.S., DiCarlo, J.E., Zeng, G., Xu, X., Revtovich, A.V., Kirienko, N.V., Wang, Y., *Church, G.M., and *Collins, J.J. A CRISPR Cas9-based gene drive platform for genetic interaction analysis in Candida albicans. Nature Microbiology. 2017; doi: 10.1038/s41564-017-0043-0.

Chari, R., Yeo, N.C., Chavez, A., Church, G.M. sgRNA Scorer 2.0: A Species-Independent Model To Predict CRISPR/Cas9 Activity. ACS Synthetic Biology. 2017; 6:902-90: NIHMS: 857197

Rock, J.M., Hopkins, F.F., Chavez, A., Diallo, M., Gerrick, E.R., Prichard, J.R., Church, G.M., Rubin, E.J., Sassetti, C.M., Schnappinger, D., and Fortune, S.M. Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform. Nature Microbiology. 2016; 2:16274: PMCID: PMC5302332

#Chavez, A., #Tuttle, M., Pruitt, B.W., Ewen-Campen, B., Chari, R., Ter-Ovanesyan, D., Haque, S.J., Cecchi, R.J., Kowal, E.J., Buchthal, J., Housden, B.E., Perrimon, N., Collins, J.J., and Church, G. Comparison of Cas9 activators in multiple species. Nature Methods. 2016; 13:563-567: PMCID: PMC4927356

#Kiani, S., #Chavez, A., Tuttle, M., Hall, R.N., Chari, R., Ter-Ovanesyan, D., Qian, J., Pruitt, B.W., Beal, J., Vora, S., Buchthal, J., Kowal, E.J., Ebrahimkhani, M.R., Collins, J.J., Weiss, R., Church., G. Cas9 gRNA engineering for genome editing, activation and repression. Nature Methods. 2015; 12:1051-1054: PMCID: PMC4666719

#DiCarlo, J.E., #Chavez, A., Dietz, S.L., Esvelt, K.M., Church, G.M. Safeguarding CRISPR-Cas9 gene drives in yeast. Nature Biotechnology. 2015; 33:1250-1255: PMCID: PMC4675690

#Chavez, A., #Scheiman, J., #Vora, S., Pruitt, B.W., Tuttle, M., P R Iyer, E., Lin, S., Kiani, S., Guzman, C. D., Wiegand, D.J., Ter-Ovanesyan, D., Braff, J.L., Davidsohn, N., Housden, B.E., Perrimon, N., Weiss, R., Aach, J., Collins, J.J., and Church, G.M. Highly efficient Cas9-mediated transcriptional programming. Nature Methods. 2015; 12:326-328: PMCID: PMC4393883

Jaiswal, S., Fontanillas, P., Flannick, J., Manning, A., Grauman, P. V., Mar, B. G., Lindsley, R. C., Mermel, C. H., Burtt, N., Chavez, A., Higgins, J. M., Moltchanov, V., Kuo, F. C., Kluk, M. J., Henderson, B., Kinnunen, L., Koistinen, H. A., Ladenvall, C., Getz, G., Correa, A., Banahan, B. F., Gabriel, S., Kathiresan, S., Stringham, H. M., McCarthy, M. I., Boehnke, M., Tuomilehto, J., Haiman, C., Groop, L., Atzmon, G., Wilson, J. G., Neuberg, D., Altshuler, D., and Ebert, B. L. Age-related clonal hematopoiesis associated with adverse outcomes. N. Engl. J. Med. 2014; 371:2488–2498: PMCID: PMC4306669

#Glineburg M.R., #Chavez A., Agrawal V., Brill S.J., Johnson F.B. Resolution by unassisted Top3 points to template switch recombination intermediates during DNA replication. J Biol Chem. 2013; 288:33193-33204: PMCID: PMC3829166

Platt, J. M., Ryvkin, P., Wanat, J. J., Donahue, G., Ricketts, M. D., Barrett, S. P., Waters, H. J., Song, S., Chavez, A., Abdallah, K. O., Master, S. R., Wang, L. S., and Johnson, F. B. Rap1 relocalization contributes to the chromatin-mediated gene expression profile and pace of cell senescence. Genes & Development. 2013; 27:1406-1420: PMCID: PMC3701195

Chi, A.W-S., Chavez, A., Xu, L., Weber, B.N., Shestova, O., Schaffer, A., Wertheim, G., Pear, W.S., Izon, D., Bhandoola, A. Identification of Flt3+CD150– myeloid progenitors in adult mouse bone marrow that harbor T lymphoid developmental potential. Blood. 2011; 118:2723-2732: PMCID: PMC3172791

Weber, B.N., Chi, A.W., Chavez, A., Yashiro-Ohtani, Y., Yang, Q., Shestova, O., Bhandoola, A. A critical role for TCF-1 in T-lineage specification and differentiation. Nature. 2011; 476:63-68: PMCID: PMC3156435

Chavez, A., Agrawal, V., Johnson, F.B. Homologous recombination-dependent rescue of Smc5/6 deficiency. J Biol Chem. 2011; 286:5119-5125: PMCID: PMC3037623

Chavez, A., George, V., Agrawal, V., Johnson, F.B. Sumoylation and the structural maintenance of chromosomes (Smc) 5/6 complex slow senescence through recombination intermediate resolution. J Biol Chem. 2010; 285:11922-11930: PMCID: PMC2852929

Kozak, M.L., Chavez, A., Dang, W., Berger, S.L., Ashok, A., Guo, X., Johnson, F.B. Inactivation of the Sas2 histone acetyltransferase delays senescence driven by telomere dysfunction. EMBO J. 2009; 29:158-70: PMCID: PMC2808364

Lee, J.Y., Mogen, J.L., Chavez, A., Johnson F.B. Sgs1 RecQ helicase inhibits survival of Saccharomyces cerevisiae cells lacking telomerase and homologous recombination. J Biol Chem. 2008; 283:29847-29858: PMCID: PMC2573055

Turaga, R.V., Massip, L., Chavez, A., Johnson F.B., Lebel M. Werner and Bloom Syndrome proteins prevent DNA breaks upon chromatin structure alteration. Aging Cell. 2007; 6:471-81

Nollen, E.A., Garcia, S.M., van Haaften, G., Kim, S., Chavez, A., Morimoto, R.I., Plasterk, R.H. Genome-wide RNA interference screen identifies previously undescribed regulators of polyglutamine aggregation. Proc. Natl. Acad. Sci. U. S. A. 2004; 101:6403-6408: PMCID: PMC404057

Patents:

Church, G.M., Vora, S., Chavez, A., Chen, J., Pruitt, B. 2017. Methods of Modulating Expression of Target Nucleic Acid Sequences in a Cell. U.S. Patent Application 62/470,538, filed March 13, 2017.

Guo, X., Kaas, C., and Chavez, A. 2016. Methods of genetically altering yeast to produce yeast variants. U.S. Patent Application 62/396,395, filed September 19, 2016.

Kaas, C., and Chavez, A. 2016. Methods for screening using barcoded libraries. U.S. Patent Application 62/358,878, filed July 6, 2016.

Guo, X., Chavez, A., Schubert, M., and Kelsic E. 2016. Library-scale engineering of metabolic pathways. U.S. Patent Application 62/348,438, filed June 10, 2016.

Esvelt, K.M., Min, J., Noble, C.M., Buchthal, J., Chavez, A. 2016. Methods to design and use gene drives. U.S. Patent Application 62/333,580, filed May 9, 2016.

Chavez, A. 2016. Mutant cas proteins. U.S. Patent Application 62/310,018, filed March 18, 2016.

Chavez, A., and Pruitt, B.W., 2015. Cas discrimination using tuned guide RNA. U.S. Patent Application 62/266,851, filed December 14, 2015.

Hu, J., and Chavez, A., 2015. Methods of making guide RNA. U.S. Patent Application 62/220,524, filed September 19, 2015.

Chavez, A., and Tuttle, M., 2015. Cas9 genome editing and transcriptional regulation. U.S. Patent Application 62/200,303, filed August 3, 2015.

Chavez, A., Poelwijk F., and Church G.M., 2013. Mutant Cas9 proteins. U.S. Patent 9,074,199, granted July 7, 2015

Publications