selected publications


  1. Enhancer Discovery Reveals a New Model of Enhancer Organization Cerda-Smith, C. G., Hutchinson, H. M., Liu, A., Goel, V. Y., Sept, C., Kim, H., n, S., Burkman, K. G., Bassil, C. F., Hansen, A. S., Aryee, M. J., Johnstone, S. E., Eyler, C. E., and Wood, K. C. bioRxiv 2023
  2. Spatial transcriptomics reveals distinct tissue niches linked with steroid responsiveness in acute gastrointestinal GVHD Patel, B. K., Raabe, M. J., Lang, E. R., Song, Y., Lu, C., Deshpande, V., Nieman, L. T., Aryee, M. J., Chen, Y. B., Ting, D. T., and DeFilipp, Z. Blood 2023
  3. High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion dynamics Sept, Corriene E., Tak, Y. Esther, Cerda-Smith, Christian G., Hutchinson, Haley M., Goel, Viraat, Blanchette, Marco, Bhakta, Mital S., Hansen, Anders S., Joung, J. Keith, Johnstone, Sarah, Eyler, Christine E., and Aryee, Martin J. bioRxiv 2023 [Abs] [HTML]


  1. Epigenetic clocks, aging, and cancer Johnstone, Sarah E, Gladyshev, Vadim N, Aryee, Martin J, and Bernstein, Bradley E Science 2022 [Abs]
  2. Polycomb-lamina antagonism partitions heterochromatin at the nuclear periphery Siegenfeld, Allison P, Roseman, Shelby A, Roh, Heejin, Lue, Nicholas Z, Wagen, Corin C, Zhou, Eric, Johnstone, Sarah E, Aryee, Martin J, and Liau, Brian B Nat. Commun. 2022 [Abs]


  1. Augmenting and directing long-range CRISPR-mediated activation in human cells Tak, Y Esther, Horng, Joy E, Perry, Nicholas T, Schultz, Hayley T, Iyer, Sowmya, Yao, Qiuming, Zou, Luli S, Aryee, Martin J, Pinello, Luca, and Joung, J Keith Nat. Methods 2021 [Abs]


  1. Large-scale topological changes restrain malignant progression in colorectal cancer Johnstone, S. E., Reyes, A., Qi, Y., Adriaens, C., Hegazi, E., Pelka, K., Chen, J. H., Zou, L. S., Drier, Y., Hecht, V., Shoresh, N., Selig, M. K., Lareau, C. A., Iyer, S., Nguyen, S. C., Joyce, E. F., Hacohen, N., Irizarry, R. A., Zhang, B., Aryee, M. J., and Bernstein, B. E. Cell 2020 [Abs]
  2. A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing Grünewald, J., Zhou, R., Lareau, C. A., Garcia, S. P., Iyer, S., Miller, B. R., Langner, L. M., Hsu, J. Y., Aryee, M. J., and Joung, J. K. Nat. Biotechnol. 2020


  1. CRISPR DNA base editors with reduced RNA off-target and self-editing activities Grünewald, J., Zhou, R., Iyer, S., Lareau, C. A., Garcia, S. P., Aryee, M. J., and Joung, J. K. Nat. Biotechnol. 2019
  2. Stromal Microenvironment Shapes the Intratumoral Architecture of Pancreatic Cancer Ligorio, M., Sil, S., Malagon-Lopez, J., Nieman, L. T., Misale, S., Di Pilato, M., Ebright, R. Y., Karabacak, M. N., Kulkarni, A. S., Liu, A., Vincent Jordan, N., Franses, J. W., Philipp, J., Kreuzer, J., Desai, N., Arora, K. S., Rajurkar, M., Horwitz, E., Neyaz, A., Tai, E., Magnus, N. K. C., Vo, K. D., Yashaswini, C. N., Marangoni, F., Boukhali, M., Fatherree, J. P., Damon, L. J., Xega, K., Desai, R., Choz, M., Bersani, F., Langenbucher, A., Thapar, V., Morris, R., Wellner, U. F., Schilling, O., Lawrence, M. S., Liss, A. S., Rivera, M. N., Deshpande, V., Benes, C. H., Maheswaran, S., Haber, D. A., Fernandez-Del-Castillo, C., Ferrone, C. R., Haas, W., Aryee, M. J.*, and Ting, D. T.* Cell 2019
  3. Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors Grünewald, J., Zhou, R., Garcia, S. P., Iyer, S., Lareau, C. A., Aryee, M. J., and Joung, J. K. Nature 2019
  4. A (fire)cloud-based DNA methylation data preprocessing and quality control platform Kangeyan, D., Dunford, A., Iyer, S., Stewart, C., Hanna, M., Getz, G., and Aryee, M. J. BMC Bioinformatics 2019
  5. Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics Ludwig, L. S., Lareau, C. A., Ulirsch, J. C., Christian, E., Muus, C., Li, L. H., Pelka, K., Ge, W., Oren, Y., Brack, A., Law, T., Rodman, C., Chen, J. H., Boland, G. M., Hacohen, N., Rozenblatt-Rosen, O., Aryee, M. J., Buenrostro, J. D., Regev, A., and Sankaran, V. G. Cell 2019
  6. Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing Kleinstiver, B. P., Sousa, A. A., Walton, R. T., Tak, Y. E., Hsu, J. Y., Clement, K., Welch, M. M., Horng, J. E., Malagon-Lopez, J., Scarf?, I., Maus, M. V., Pinello, L., Aryee, M. J., and Joung, J. K. Nat. Biotechnol. 2019


  1. In vivo CRISPR editing with no detectable genome-wide off-target mutations Akcakaya, P., Bobbin, M. L., Guo, J. A., Malagon-Lopez, J., Clement, K., Garcia, S. P., Fellows, M. D., Porritt, M. J., Firth, M. A., Carreras, A., Baccega, T., Seeliger, F., Bjursell, M., Tsai, S. Q., Nguyen, N. T., Nitsch, R., Mayr, L. M., Pinello, L., Bohlooly-Y, M., Aryee, M. J., Maresca, M., and Joung, J. K. Nature 2018
  2. hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data Lareau, C. A., and Aryee, M. J. Nat. Methods 2018
  3. diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data Lareau, C. A., and Aryee, M. J. Bioinformatics 2018


  1. The early pregnancy placenta foreshadows DNA methylation alterations of solid tumors Nordor, A. V., Nehar-Belaid, D., Richon, S., Klatzmann, D., Bellet, D., Dangles-Marie, V., Fournier, T., and Aryee, M. J. Epigenetics 2017 [Abs]
  2. CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets Tsai, S. Q., Nguyen, N. T., Malagon-Lopez, J., Topkar, V. V., Aryee, M. J., and Joung, J. K. Nat. Methods 2017
  3. Diverse repetitive element RNA expression defines epigenetic and immunologic features of colon cancer Desai, N., Sajed, D., Arora, K. S., Solovyov, A., Rajurkar, M., Bledsoe, J. R., Sil, S., Amri, R., Tai, E., MacKenzie, O. C., Mino-Kenudson, M., Aryee, M. J., Ferrone, C. R., Berger, D. L., Rivera, M. N., Greenbaum, B. D., Deshpande, V., and Ting, D. T. JCI Insight 2017


  1. Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells Kleinstiver, B. P., Tsai, S. Q., Prew, M. S., Nguyen, N. T., Welch, M. M., Lopez, J. M., McCaw, Z. R., Aryee, M. J., and Joung, J. K. Nat. Biotechnol. 2016
  2. Open-source guideseq software for analysis of GUIDE-seq data Tsai, S. Q., Topkar, V. V., Joung, J. K., and Aryee, M. J. Nat. Biotechnol. 2016


  1. Engineered CRISPR-Cas9 nucleases with altered PAM specificities Kleinstiver, B. P., Prew, M. S., Tsai, S. Q., Topkar, V. V., Nguyen, N. T., Zheng, Z., Gonzales, A. P., Li, Z., Peterson, R. T., Yeh, J. R., Aryee, M. J., and Joung, J. K. Nature 2015
  2. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases Tsai, S. Q., Zheng, Z., Nguyen, N. T., Liebers, M., Topkar, V. V., Thapar, V., Wyvekens, N., Khayter, C., Iafrate, A. J., Le, L. P., Aryee, M. J., and Joung, J. K. Nat. Biotechnol. 2015
  3. Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing Ziller, M. J., Hansen, K. D., Meissner, A., and Aryee, M. J. Nat. Methods 2015


  1. EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma Riggi, N., Knoechel, B., Gillespie, S. M., Rheinbay, E., Boulay, G., Suv?, M. L., Rossetti, N. E., Boonseng, W. E., Oksuz, O., Cook, E. B., Formey, A., Patel, A., Gymrek, M., Thapar, V., Deshpande, V., Ting, D. T., Hornicek, F. J., Nielsen, G. P., Stamenkovic, I., Aryee, M. J., Bernstein, B. E., and Rivera, M. N. Cancer Cell 2014
  2. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing Tsai, S. Q., Wyvekens, N., Khayter, C., Foden, J. A., Thapar, V., Reyon, D., Goodwin, M. J., Aryee, M. J., and Joung, J. K. Nat. Biotechnol. 2014
  3. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays Aryee, M. J., Jaffe, A. E., Corrada-Bravo, H., Ladd-Acosta, C., Feinberg, A. P., Hansen, K. D., and Irizarry, R. A. Bioinformatics 2014