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Xie, Y., Cao, Z., Wong, E. W., Guan, Y., Ma, W., Zhang, J. Q., Walczak, E. G., Murphy, D., Ran, L., Sirota, I., Wang, S., Shukla, S., Gao, D., Knott, S. R., Chang, K., Leu, J., Wongvipat, J., Antonescu, C. R., Hannon, G., Chi, P., Chen, Y. (April 2018) COP1-DET1-ETS axis regulates ERK transcriptome and sensitivity to MAPK inhibitors. J Clin Invest, 128 (4). pp. 1442-1457. ISSN 0021-9738

Xie, Y., Cao, Z., Wong, E. W., Guan, Y., Ma, W., Zhang, J. Q., Walczak, E. G., Murphy, D., Ran, L., Sirota, I., Wang, S., Shukla, S., Gao, D., Knott, S. R., Chang, K., Leu, J., Wongvipat, J., Antonescu, C. R., Hannon, G., Chi, P., Chen, Y. (April 2018) COP1/DET1/ETS axis regulates ERK transcriptome and sensitivity to MAPK inhibitors. J Clin Invest, 128 (4). pp. 1442-1457. ISSN 0021-9738 (Print)0021-9738

Knott, S. R. V., Wagenblast, E., Khan, S., Kim, S. Y., Soto, M., Wagner, M., Turgeon, M. O., Fish, L., Erard, N., Gable, A. L., Maceli, A. R., Dickopf, S., Papachristou, E. K., D'Santos, C. S., Carey, L. A., Wilkinson, J. E., Harrell, J. C., Perou, C. M., Goodarzi, H., Poulogiannis, G., Hannon, G. J. (February 2018) Asparagine bioavailability governs metastasis in a model of breast cancer. Nature, 554 (7692). pp. 378-381. ISSN 0028-0836

Xie, Y. Y., Cao, Z., Wong, W. P., Guan, Y. X., Zhang, J., Walczak, E., Murphy, D., Ran, L., Sirota, I., Wang, S. Q., Shukla, S., Gao, D., Wongvipat, J., Knott, S., Chang, K., Antonescu, C., Hannon, G., Chi, P., Chen, Y. (January 2018) COP1-ETS axis regulates ERK transcriptional output and modulates sensitivity to MAPK inhibitors. Clinical Cancer Research, 24 (2 Supp). p. 61. ISSN 1078-0432

Delas, M. J., Sabin, L. R., Dolzhenko, E., Knott, S. R., Munera Maravilla, E., Jackson, B. T., Wild, S. A., Kovacevic, T., Stork, E. M., Zhou, M., Erard, N., Lee, E., Kelley, D. R., Roth, M., Barbosa, I. S. A., Zuber, J., Rinn, J. L., Smith, A. D., Hannon, G. J. (September 2017) lncRNA requirements for mouse acute myeloid leukemia and normal differentiation. Elife, 6. e25607. ISSN 2050-084x

Erard, Nicolas, Knott, Simon R. V., Hannon, Gregory J. (2017) A CRISPR Resource for Individual, Combinatorial, or Multiplexed Gene Knockout. Molecular Cell, 67 (2). 348-354.e3. ISSN 1097-2765

Wasik, K. A., Tam, O. H., Knott, S. R., Falciatori, I., Hammell, M., Vagin, V. V., Hannon, G. J. (June 2015) RNF17 blocks promiscuous activity of PIWI proteins in mouse testes. Genes Dev, 29 (13). pp. 1403-1415. ISSN 1549-5477 (Electronic)0890-9369 (Linking)

Wagenblast, E., Soto, M., Gutierrez-Angel, S., Hartl, C. A., Gable, A. L., Maceli, A. R., Erard, N., Williams, A. M., Kim, S. Y., Dickopf, S., Harrell, J. C., Smith, A. D., Perou, C. M., Wilkinson, J. E., Hannon, G. J., Knott, S. R. (April 2015) A model of breast cancer heterogeneity reveals vascular mimicry as a driver of metastasis. Nature, 520 (7547). pp. 358-362. ISSN 0028-0836

Knott, S. R., Maceli, A. R., Erard, N., Chang, K., Marran, K., Zhou, X., Gordon, A., El Demerdash, O., Wagenblast, E., Kim, S., Fellmann, C., Hannon, G. J. (December 2014) A Computational Algorithm to Predict shRNA Potency. Mol Cell, 56 (6). pp. 796-807. ISSN 1097-2765

Ostrow, A. Z., Nellimoottil, T., Knott, S. R., Fox, C. A., Tavare, S., Aparicio, O. M. (2014) Fkh1 and Fkh2 bind multiple chromosomal elements in the S. cerevisiae genome with distinct specificities and cell cycle dynamics. PLoS One, 9 (2). e87647. ISSN 1932-6203

Dalton, J. E., Fear, J. M., Knott, S., Baker, B. S., McIntyre, L. M., Arbeitman, M. N. (September 2013) Male-specific Fruitless isoforms have different regulatory roles conferred by distinct zinc finger DNA binding domains. BMC Genomics, 14. ISSN 1471-2164 (Public Dataset)

Zhong, Y., Nellimoottil, T., Peace, J. M., Knott, S. R., Villwock, S. K., Yee, J. M., Jancuska, J. M., Rege, S., Tecklenburg, M., Sclafani, R. A., Tavare, S., Aparicio, O. M. (April 2013) The level of origin firing inversely affects the rate of replication fork progression. J Cell Biol, 201 (3). pp. 373-83. ISSN 0021-9525

Knott, S. R. V., Peace, J. M., Ostrow, A. Z., Gan, Y., Rex, A. E., Viggiani, C. J., Tavaré, S., Aparicio, O. M. (January 2012) Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae. Cell, 148 (1-2). pp. 99-111. ISSN 00928674 (ISSN)

Ipsaro, J. J., Haase, A. D., Knott, S. R., Joshua-Tor, L., Hannon, G. J. (2012) The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis. Nature, 491 (7423). pp. 279-282. ISSN 00280836 (ISSN) (Public Dataset)

Viggiani, C. J., Knott, S. R., Aparicio, O. M. (February 2010) Genome-wide analysis of DNA synthesis by BrdU immunoprecipitation on tiling microarrays (BrdU-IP-chip) in Saccharomyces cerevisiae. Cold Spring Harb Protoc, 2010 (2). ISSN 1559-6095

Dalton, J. E., Kacheria, T. S., Knott, S. R., Lebo, M. S., Nishitani, A., Sanders, L. E., Stirling, E. J., Winbush, A., Arbeitman, M. N. (2010) Dynamic, mating-induced gene expression changes in female head and brain tissues of Drosophila melanogaster. BMC Genomics, 11. p. 541. ISSN 1471-2164

Knott, S., Mostafavi, S., Mousavi, P. (2010) A neural network based modeling and validation approach for identifying gene regulatory networks. Neurocomputing, 73 (13-15). pp. 2419-2429.

Knott, S. R., Viggiani, C. J., Aparicio, O. M. (August 2009) To promote and protect: coordinating DNA replication and transcription for genome stability. Epigenetics, 4 (6). pp. 362-5. ISSN 1559-2294

Knott, S. R., Viggiani, C. J., Tavare, S., Aparicio, O. M. (May 2009) Genome-wide replication profiles indicate an expansive role for Rpd3L in regulating replication initiation timing or efficiency, and reveal genomic loci of Rpd3 function in Saccharomyces cerevisiae. Genes Dev, 23 (9). pp. 1077-90. ISSN 0890-9369

Knott, S. R., Viggiani, C. J., Aparicio, O. M., Tavare, S. (2009) Strategies for analyzing highly enriched IP-chip datasets. BMC Bioinformatics, 10. p. 305. ISSN 1471-2105

Szyjka, S. J., Aparicio, J. G., Viggiani, C. J., Knott, S., Xu, W., Tavare, S., Aparicio, O. M. (July 2008) Rad53 regulates replication fork restart after DNA damage in Saccharomyces cerevisiae. Genes Dev, 22 (14). pp. 1906-20. ISSN 0890-9369 (Print)0890-9369

Fernald, G. H., Knott, S., Pachner, A., Caillier, S. J., Narayan, K., Oksenberg, J. R., Mousavi, P., Baranzini, S. E. (April 2007) Genome-wide network analysis reveals the global properties of IFN-beta immediate transcriptional effects in humans. J Immunol, 178 (8). pp. 5076-85. ISSN 0022-1767 (Print)0022-1767