Alejandro Chavez, MD

Pathology - Anatomic & Clinical
Profile Headshot


Academic Appointments

  • Assistant Professor of Pathology & Cell Biology

Hospital Affiliations

  • NewYork-Presbyterian / Columbia University Irving Medical Center


  • Spanish


  • Male

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Credentials & Experience

Education & Training

  • BA, 2004 Genetics and Molecular Biology, Northwestern University
  • MD, PhD, 2011 Cell and Molecular Biology, University of Pennsylvania - School of Medicine
  • Residency: 2014 Massachuetts General Hospital
  • Fellowship: 2017 Massachusettes General Hospital


Our research group strives to push the boundaries of genetic engineering by developing new methods with which to modify and regulate eukaryotic genomes. We apply these tools ourselves or through collaboration to gain fundamental biological insights with a particular focus towards understanding neurodegenerative diseases and cancer.

Our work employs a variety of techniques ranging from oligo chip synthesis and library-based screening to iPS cell differentiation and live-cell imaging. We utilize a variety of model systems ranging from yeast to human cell culture to assure that the technologies we generate are applicable to a broad swath of the scientific community.

Our team places a strong emphasis on mentoring, and values the opportunity to be able to train the next generation of budding scientists.

Research Interests

  • Cancer
  • COVID-19
  • Genome Engineering
  • Genomics
  • Neurodegeneration
  • Synthetic Biology

Clinical Trials

COVID-19 STUDIES - Recruiting people who have recovered from COVID-19 (Coronavirus) to donate convalescent plasma.

Selected Publications

# denotes co-first author

^ denotes co-second author

* denotes co-senior author

  • 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(1):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. Synthetic immunomodulation with a CRISPR super-repressor in vivo. Nature Cell Biology. 2020; 22:1143-1154
  • 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; 29:843-847
  • Nobel, C., Min, J., Olejarz, J., Buchthal, J., Chavez, A., Smidler, A.L., DeBenedictis, E.A., Church, G.M., Nowak, M.A., 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
  • 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; 15:611-616
  • 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; 36:540-546. PMC5990468
  • 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. 2018; 10:31: PMC5909281
  • 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; 173:649-664.
  • *#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; 115:3669-3673: PMCID: PMC5889643
  • #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; 3:73-82: PMCID: PMC5832965
  • 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: PMCID: PMC5793212
  • 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.  PNAS. 2004; 101:6403-6408: PMCID: PMC404057