Education
PhD, UC Berkeley, United States, 2012
Current position
Assistant Professor, Bioengineering, Stanford University, United States
Publications
-
Du, D., Roguev, A., Gordon, D. E., Chen, M., Chen, S. H., Shales, M., Shen, J. P., Ideker, T., Mali, P., Qi, L. S. and Krogan, N. J. (2017). Genetic interaction mapping in mammalian cells using CRISPR interference. Nat Methods 14(6): 577-580.
-
Takei, Y., Shah, S., Harvey, S., Qi, L. S. and Cai, L. (2017). Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH. Biophys J 112(9): 1773-1776.
-
Shen, J. P., Zhao, D., Sasik, R., Luebeck, J., Birmingham, A., Bojorquez-Gomez, A., Licon, K., Klepper, K., Pekin, D., Beckett, A. N., Sanchez, K. S., Thomas, A., Kuo, C. C., Du, D., Roguev, A., Lewis, N. E., Chang, A. N., Kreisberg, J. F., Krogan, N., Qi, L., Ideker, T. and Mali, P. (2017). Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods 14(6): 573-576.
-
Gao, Y., Xiong, X., Wong, S., Charles, E. J., Lim, W. A. and Qi, L. S. (2016). Complex transcriptional modulation with orthogonal and inducible dCas9 regulators. Nat Methods 13(12): 1043-1049.
-
Wang, F. and Qi, L. S. (2016). Applications of CRISPR Genome Engineering in Cell Biology. Trends Cell Biol 26: 875-888.
-
Xiong, X., Chen, M., Lim, W. A., Zhao, D. and Qi, L. S. (2016). CRISPR/Cas9 for Human Genome Engineering and Disease Research. Annu Rev Genomics Hum Genet 17: 131-154.
-
Wang, H., La Russa, M. and Qi, L. S. (2016). CRISPR/Cas9 in Genome Editing and Beyond. Annu Rev Biochem 85: 227-264.
-
Peters, J. M., Colavin, A., Shi, H., Czarny, T. L., Larson, M. H., Wong, S., Hawkins, J. S., Lu, C. H. S., Koo, B. M., Marta, E., Shiver, A. L., Whitehead, E. H., Weissman, J. S., Brown, E. D., Qi, L. S., Huang, K. C. and Gross, C. A. (2016). A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria. Cell 165(6): 1493-1506.
-
Mandegar, M. A., Huebsch, N., Frolov, E. B., Shin, E., Truong, A., Olvera, M. P., Chan, A. H., Miyaoka, Y., Holmes, K., Spencer, C. I., Judge, L. M., Gordon, D. E., Eskildsen, T. V., Villalta, J. E., Horlbeck, M. A., Gilbert, L. A., Krogan, N. J., Sheikh, S. P., Weissman, J. S., Qi, L. S., So, P. L. and Conklin, B. R. (2016). CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs. Cell Stem Cell 18(4): 541-553.
-
Qin, H., Hejna, M., Liu, Y., Percharde, M., Wossidlo, M., Blouin, L., Durruthy-Durruthy, J., Wong, P., Qi, Z., Yu, J., Qi, L. S., Sebastiano, V., Song, J. S. and Ramalho-Santos, M. (2016). YAP Induces Human Naive Pluripotency. Cell Rep 14(10): 2301-2312.
-
Dominguez, A. A., Lim, W. A. and Qi, L. S. (2016). Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Nat Rev Mol Cell Biol 17(1): 5-15.
-
Du, D. and Qi, L. S. (2016). CRISPR Technology for Genome Activation and Repression in Mammalian Cells. Cold Spring Harb Protoc 2016(1): pdb prot090175.
-
La Russa, M. F. and Qi, L. S. (2015). The New State of the Art: Cas9 for Gene Activation and Repression. Mol Cell Biol 35(22): 3800-3809.
-
Liu, H., Wei, Z., Dominguez, A., Li, Y., Wang, X. and Qi, L. S. (2015). CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation. Bioinformatics 31(22): 3676-3678.
-
Peters, J. M., Silvis, M. R., Zhao, D., Hawkins, J. S., Gross, C. A. and Qi, L. S. (2015). Bacterial CRISPR: accomplishments and prospects. Curr Opin Microbiol 27: 121-126.
-
Sokolik, C., Liu, Y., Bauer, D., McPherson, J., Broeker, M., Heimberg, G., Qi, L. S., Sivak, D. A. and Thomson, M. (2015). Transcription factor competition allows embryonic stem cells to distinguish authentic signals from noise. Cell Syst 1(2): 117-129.
-
Hawkins, J. S., Wong, S., Peters, J. M., Almeida, R. and Qi, L. S. (2015). Targeted Transcriptional Repression in Bacteria Using CRISPR Interference (CRISPRi). Methods Mol Biol 1311: 349-362.
-
Yu, C., Liu, Y., Ma, T., Liu, K., Xu, S., Zhang, Y., Liu, H., La Russa, M., Xie, M., Ding, S. and Qi, L. S. (2015). Small molecules enhance CRISPR genome editing in pluripotent stem cells. Cell Stem Cell 16(2): 142-147.
-
Zalatan, J. G., Lee, M. E., Almeida, R., Gilbert, L. A., Whitehead, E. H., La Russa, M., Tsai, J. C., Weissman, J. S., Dueber, J. E., Qi, L. S. and Lim, W. A. (2015). Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160(1-2): 339-350.
-
Ji, W., Lee, D., Wong, E., Dadlani, P., Dinh, D., Huang, V., Kearns, K., Teng, S., Chen, S., Haliburton, J., Heimberg, G., Heineike, B., Ramasubramanian, A., Stevens, T., Helmke, K. J., Zepeda, V., Qi, L. S. and Lim, W. A. (2014). Specific gene repression by CRISPRi system transferred through bacterial conjugation. ACS Synth Biol 3(12): 929-931.
-
Tanenbaum, M. E., Gilbert, L. A., Qi, L. S., Weissman, J. S. and Vale, R. D. (2014). A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159(3): 635-646.
-
Gilbert, L. A., Horlbeck, M. A., Adamson, B., Villalta, J. E., Chen, Y., Whitehead, E. H., Guimaraes, C., Panning, B., Ploegh, H. L., Bassik, M. C., Qi, L. S., Kampmann, M. and Weissman, J. S. (2014). Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. Cell 159(3): 647-661.
-
Qi, L. S. and Arkin, A. P. (2014). A versatile framework for microbial engineering using synthetic non-coding RNAs. Nat Rev Microbiol 12(5): 341-354.
-
Chen, B., Gilbert, L. A., Cimini, B. A., Schnitzbauer, J., Zhang, W., Li, G. W., Park, J., Blackburn, E. H., Weissman, J. S., Qi, L. S. and Huang, B. (2013). Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155(7): 1479-1491.
-
Larson, M. H., Gilbert, L. A., Wang, X., Lim, W. A., Weissman, J. S. and Qi, L. S. (2013). CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nat Protoc 8(11): 2180-2196.
-
Gilbert, L. A., Larson, M. H., Morsut, L., Liu, Z., Brar, G. A., Torres, S. E., Stern-Ginossar, N., Brandman, O., Whitehead, E. H., Doudna, J. A., Lim, W. A., Weissman, J. S. and Qi, L. S. (2013). CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154(2): 442-451.
-
Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P. and Lim, W. A. (2013). Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152(5): 1173-1183.
-
Liu, C. C., Qi, L., Lucks, J. B., Segall-Shapiro, T. H., Wang, D., Mutalik, V. K. and Arkin, A. P. (2012). An adaptor from translational to transcriptional control enables predictable assembly of complex regulation. Nat Methods 9(11): 1088-1094.
-
Qi, L., Haurwitz, R. E., Shao, W., Doudna, J. A. and Arkin, A. P. (2012). RNA processing enables predictable programming of gene expression. Nat Biotechnol 30(10): 1002-1006.
-
Qi, L. S., Lucks, J. B., Liu, C. C., Mutalik, V. K. and Arkin, A. P. (2012). Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Res 40: 5775-5786.
-
Mutalik, V. K., Qi, L., Guimaraes, J. C., Lucks, J. B. and Arkin, A. P. (2012). Rationally designed families of orthogonal RNA regulators of translation. Nat Chem Biol 8(5): 447-454.
-
Lucks, J. B., Qi, L., Mutalik, V. K., Wang, D. and Arkin, A. P. (2011). Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proc Natl Acad Sci U S A 108(21): 8617-8622.
-
Liu, C. C., Qi, L. S., Yanofsky, C., Arkin, A. P. (2011). Regulation of transcription by unnatural amino acids. Nat Biotechnol 29: 164-168.
-
Lucks, J. B., Qi, L., Whitaker, W. R. and Arkin, A. P. (2008). Toward scalable parts families for predictable design of biological circuits. Curr Opin Microbiol 11(6): 567-573.