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Coauthors
Xiaowo Wang Tsinghua University
1 protocol

Honglei Liu Capital Medical University
1 protocol

Lei Stanley Qi
  • Stanford Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, USA, USA,
  • 1 Author merit

Education

PhD, UC Berkeley, United States, 2012

Current position

Assistant Professor, Bioengineering, Stanford University, United States

Publications

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. Wang, F. and Qi, L. S. (2016). Applications of CRISPR Genome Engineering in Cell Biology. Trends Cell Biol 26: 875-888. 
  6. 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.
  7. Wang, H., La Russa, M. and Qi, L. S. (2016). CRISPR/Cas9 in Genome Editing and Beyond. Annu Rev Biochem 85: 227-264.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. Liu, C. C., Qi, L. S., Yanofsky, C., Arkin, A. P. (2011). Regulation of transcription by unnatural amino acids. Nat Biotechnol 29: 164-168.
  34. 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.
1 Protocol published
Using CRISPR-ERA Webserver for sgRNA Design
Authors:  Honglei Liu, Xiaowo Wang and Lei S. Qi, date: 09/05/2017, view: 2349, Q&A: 0
The CRISPR-Cas9 system is emerging as a powerful technology for gene editing (modifying the genome sequence) and gene regulation (without modifying the genome sequence). Designing sgRNAs for specific genes or regions of interest is indispensable to ...