For updated list of publications see google scholar page:

# denotes co-first author

^ denotes co-second author

* denotes co-senior author

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


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. bioRxiv. 2016


#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


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