Selected Major Publications (Students and postdocs in Qi lab are underlined)

A full list of publications can be viewed Pubmed or Google Scholars.


73. Lin X#, Liu Y#, Liu S#, Zhu X, Wu L, Zhu Y, Zhao D, Xu X, Chemparathy A, Wang H, Cao Y, Nakamura M, Noordermeer JN, La Russa M, Wong WH, Zhao K, Qi LS*. ­­­­­Nested Epistasis Enhancer Networks for Robust Genome Regulation. Science. 2022 Aug 11. (#Equal Contribution)

          Free access link.

72. Kempton HR, Love KS, Guo LY, Qi LS*. Scalable Biological Signal Recording in Mammalian Cells Using Cas12a Base Editors­. Nat Chem Biol. 18(7): 742-750. 2022 Jul.

            Read Spotlight "A multifaceted signal recorder of cellular experiences using Cas12a base-editing", Trends in Biotechnology, 2022 Aug 3.

71. Zeng L#, Liu Y#, Nguyenla XH, Abbott TR, Han M, Zhu Y, Chemparathy A, Lin X, Chen X, Wang H, Rane DA, Spatz JM, Jain S, Rustagi A, Pinsky B, Zepeda AE, Kadina AP, Walker III JA, Holden K, Temperton N, Cochran JR, Barron AE, Connolly MD, Blish CA, Lewis DB, Stanley SA*, La Russa MF*, Qi LS*. Broad-spectrum CRISPR-mediated prophylaxis and treatment of SARS-CoV-2 variants and endemic coronavirusesNat Commun. 13(1):2766. 2022 May 19 (#Equal Contribution)

70.  Guo LY#*, Bian J#, Davis AE, Liu P, Kempton HR, Zhang X, Chemparathy A, Gu B, Lin X, Rane DA, Xu X, Jamiolkowski RM, Hu Y, Wang S*, Qi LS*. Multiplexed genome regulation in vivo with hyper-efficient Cas12a. Nat Cell Biol. 24(4): 590-600. 2022 Apr (#Equal Contribution)

             Read Stanford News. Free access to the paper is available here.

             Read the protocol used in this paper.

69. Shen WJ#, Still II C#, Han L, Yang P, Chen J, Wosczyna M, Salmon BJR, Perez KC, Li J, Cuevas PL, Liu B, Azhar S, Helms J, Qi LS*, Kraemer FB*. Hormone sensitive lipase ablation promotes bone regeneration. Biochim Biophys Acta Mol Basis Dis. 1868(9): 166449. 2022 May 23 (#Equal Contribution)

68. Dominguez AA#, Chavez M#, Urke A, Gao Y, Wang L*, Qi LS*. CRISPR-mediated Synergistic Epigenetic and Transcriptional Control. CRISPR J. 5(2): 264-275. 2022 Apr (#Equal Contribution)

67.  Wang J#, Han M#, Roy A, Wang H, Mockl L, Zeng L, Moerner WE*, Qi LS*. Multi-color super-resolution imaging to study human coronavirus RNA during cellular infection. Cell Rep Methods. 2(2): 100170. 2022 Feb 28 (#Equal Contribution)

66. Bock C, Datlinger P, Chardon F, Coelho MA, Dong MB, Lawson KA, Lu T, Maroc L, Norman TM, Song B, Stanley G, Chen S, Garnett M, Li W, Moffat J, Qi LS, Shapiro RS, Shendure J, Weissman JS, Zhuang X. High-content CRISPR screening. Nat Rev. Method Primers 2:8. 2022 Feb 10.

65. Nishiga M, Liu C, Qi LS, Wu JC. The use of new CRISPR tools in cardiovascular research and medicine. Nat Rev Cardiol. 19(8):505-521. 2022 Feb 10.

64. Cui X, Zhang C, Xu Z, Wang S, Li X, Stringer-Reasor E, Bea S, Zeng L, Zhao D, Liu R*, Qi LS*, Wang L*. Dual CRISPR Interference and Activation for Targeted Reactivation of X-linked Endogenous FOXP3 in Human Breast Cancer Cells. Mol Cancer. 21(1):38. 2022 Feb 7.


63. Xu X, Chemparathy A, Zeng L, Kempton HR, Shang S, Nakamura M, Qi LS*. Engineered Miniature CRISPR-Cas System for Mammalian Genome Regulation and Editing. Mol. Cell. S1097-2765(21)00648-1. 2021 September 3.

                 Read Stanford News, Cell Press, Nat. Rev. Mol. Cell Biol., Nat. Rev. Genetics, Fiercebiotech, Telegraph, etc.

62. Gao Y, Han M, Shang S, Wang H, Qi LS*. Interrogation of the Dynamic Properties of Higher-Order Heterochromatin Using CRISPR/dCas9. Mol. Cell. S1097-2765(21)00612-2. 2021 Aug 23.

61. Nakamura M, Ivec A, Gao Y, Qi LS*. Durable CRISPR-Based Epigenetic Silencing. Biodesign Research. 2021: 9815820. 2021 May.

60. Still II C#, Chang WT#, Sherman, SL, Sochacki KR, Dragoo JL, Qi LS*. Single-cell transcriptomic profiling reveals distinct mechanical responses between normal and diseased tendon progenitor cellsCell Rep Med. 2(7): 100343. 2021 July 20. (#Equal Contribution)

59. Nishiga M, Qi LS, Wu JC. CRISPRi/a Screening with Human iPSCs. Methods Mol Biol. 2320: 261-281. 2021

58. Lin X#, Liu Y#, Chemparathy A#, Pande T, La Russa M, Qi LS*. A comprehensive analysis and resource to use CRISPR-Cas13 for broad-spectrum targeting of RNA viruses. Cell Rep Med. 2(4): 100245.  2021 Apr 20. (# Equal contribution)

57. Wang H#Han M#, Qi LS*. Engineering 3D genome organizationNat. Rev. Genet. 2021 Feb 8 (Review). (#equal contribution)

56. Nakamura MGao YDominguez AA, Qi LS*. CRISPR technologies for precise epigenome editingNat. Cell Biol. 23(1):11-22. 2021 Jan (Review)

55. Magnusson JPRios ARWu L, Qi LS*. Enhanced Cas12a multi-gene regulation using a CRISPR array separator. eLife. 10: e66406. 2021 September 9. 


54. Abbott TR#, Dhamdhere G#, Liu Y#, Lin X#, Goudy L#, Zeng L, Chemparathy A, Chmura S, Heaton NS, Debs R, Pande T, Endy D, La Russa MF*, Lewis DB*, Qi LS*. Development of CRISPR as an antiviral strategy to combat SARS-CoV-2 and influenza. Cell. 181(4): 865-876. 2020 May 14. (#equal contribution).

                      Read Wired, Berkeley Lab, Fierce Biotech.

53. Lin XChemparathy ALa Russa MDaley T, Qi LS*. Computational methods for analysis of large-scale CRISPR screensAnnu. Rev. Biomed. Data Sci. 3:137–162. 2020 July 22. (Review) 

52. Sarkar TJ, Quarta M, Mukherjee S, Colville A, Paine P, Doan L, Tran CM, Chu CR, Horvath S, Qi LS, Bhutani N, Rando TA, Sebastiano V. Transient non-integrative expression of nuclear reprogramming factor promotes multifaceted amelioration of aging in human cells. Nat Commun. 11(1): 1545. 2020 Mar 24.

51. Bodapati S#, Daley TP#, Lin X, Zou J, Qi LS*. A benchmark of algorithms for the analysis of pooled CRISPR screens. Genome Biol. 21:62. 2020 Mar 9. (#Equal contribution) (Review)

50. Nishiga M, Qi LS, Wu JC. Therapeutic genome editing in cardiovascular diseases. Adv Drug Deliv Rev. 2020 Feb 21. (Review)

49. Kempton HR, Goudy LE, Love KS, Qi LS*. Multiple Input Sensing and Signal Integration Using a Split Cas12a System. Mol. Cell 78(1): 184-191. 2020 Feb 5.


48. Wang H, Nakamura M, Abbott TR, Zhao D, Luo K, Yu C, Nguyen CM, Lo A, Daley TP, La Russa M, Liu Y, Qi LS*. CRISPR-mediated live imaging of genome editing and transcription. Science 365(6459): 1301-1305. 2019 Sep 20.

                       Read Spectrum, Stanford news.

47. Chavez M, Qi LS*. Site-programmable transposition: shifting the paradigm for CRISPR-Cas systems. Mol. Cell 75(2): 206-208. 2019 Jul 25 (Perspective).

46. Shariati SA, Dominguez AA, Xie S, Wernig M, Qi LS, Skotheim JM. Reversible Disruption of Specific Transcription Factor-DNA Interactions Using CRISPR/Cas9. Mol. Cell 74(3):622-633.e4. 2019 May 2.

45. Lee JY, Chang JK, Dominguez AA, Chang HLJ, Varma S, Qi LS, West RB, Chaudhuri O. YAP-independent mechanotransduction drives breast cancer progression. Nat. Commun. 10(1):1848. 2019 Apr 23.

44. Kempton HR, Qi LS*. When genome editing goes off-target. Science 364(6437): 234-236. 2019 Apr 19 (Perspective).

43. Nakamura M, Srinivasan P, Chavez M, Carter MA, Dominguez AA, La Russa M, Lau MB, Abbott TR, Xu X, Zhao D, Gao Y, Kipniss NH, Smolke CD, Bondy-Denomy J, Qi LS*. Anti-CRISPR-mediated control of gene editing and synthetic circuits in eukaryotic cells. Nat. Commun. 10:194. 2019 Jan 14.


42. Wang H, Xu X, Nguyen CM, Liu Y, Gao Y, Lin X, Daley TP, Kipniss NH, La Russa M, Qi LS*. CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization. Cell 175(5): 1405–1417. 2018 Nov 15.

                      Read Science, Nature, Quanta Magazine, Stanford News.

41. Abbott TR, Qi LS*. Evolution at the Cutting Edge: CRISPR-Mediated Directed Evolution. Mol Cell 72(3): 402-403. 2018 Nov 1 (Perspective).

40. Liu Y#, Yu C#, Daley TP#, Wang F, Cao WS, Bhate S, Lin X, Still C, Liu H, Zhao D, Wang H, Xie XS, Ding S, Wong WH, Wernig M, Qi LS*. CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming. Cell Stem Cell 23(5): 758-771. 2018 Oct 11. (#Equal contribution)

                     Selected in Cell Stem Cell Best of 2018.

39.  Daley TP, Lin Z, Lin X, Liu Y, Wong WH, Qi LS. CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens. Genome Biol. 19:159. 2018 Oct 8.

38. Xu X, Qi LS*. A CRISPR-dCas Toolbox for Genetic Engineering and Synthetic Biology. J Mol. Biol. pii: S0022-2836(18)30666-1. 2018 Jun 26. (Review)

37.  Liu P, Chen M, Liu Y, Qi LS, Ding S. CRISPR-based chromatin remodeling of the endogenous Oct4 or Sox2 locus enables reprogramming to pluripotency. Cell Stem Cell 22: 252-261. 2018 Feb 1.


36. Kipniss NK#, Dingal PCDP#, Abbott TR, Gao Y, Wang H, Dominguez AA, Labanieh L, Qi LS*. Engineering cell sensing and responses using a GPCR-coupled CRISPR-Cas system. Nat. Commun. 8(1):2212. 2017 Dec 20. (#Equal contribution)

35. Lo A, Qi LS*. Genetic and epigenetic control of gene expression by CRISPR–Cas systems. F1000Res 6: 747. 2017 May 25. (Review)

34.  Zhou XX, Zou X, Chung HK, Gao Y, Liu Y, Qi LS, Lin MZ. A Single-Chain Photoswitchable CRISPR-Cas9 Architecture for Light-Inducible Gene Editing and Transcription. ACS Chem. Biol. 13(2):443-448. 2017 Sep 22.

33. Chen M, Qi LS. Repurposing CRISPR System for Transcriptional Activation. Adv. Exp. Med. Biol. 983:147-157. 2017 Jun 22. (Review)

32. Du D#, Roguez A#, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS*, Krogan NJ*. Genetic interaction mapping in mammalian cells using CRISPR interference. Nat Methods. 14(6): 577-580. 2017 May 8. (#Equal contribution)

31. Shen JP, Zhao D, Sasik R, Luebeck K, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguez A, Lewis NE, Chang AN, Kreisberg JF, Krogan NJ, Qi LS, Ideker T, Mali P. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods. 14(6): 573-576. 2017 Mar 20.

30. Takei Y, Shah S, Harvey S, Qi LS, Cai L. Multiplexed dynamic imaging of genomic loci in single cells by combined CRISPR imaging and DNA sequential FISH. Biophys J. 112: 1173-1176. 2017 Apr 17.


29. Gao Y#, Xiong X#, Wong S, Charles EJ, Lim WA, Qi LS*. Complex Transcriptional Modulation with Orthogonal and Inducible dCas9 Regulators. Nat. Methods. 13(12):1043-1049. 2016 Dec. (#Equal contribution)

28. Xiong X, Chen M, Lim WA, Zhao D, Qi LS*. Genome engineering and disease research. Annu. Rev. Genomics Hum. Genet. 17:131-154. 2016 Aug 31. (Review)

27. Peters JM, Colavin A, Shi H, Czarny ML, Larson MH, Wong S, Hawkins JS, Lu CHS, Koo BM, Marta E, Shiver AL, Whitehead EH, Weissman JS, Brown ED, Qi LS*, Huang KC*, Gross CA*. A comprehensive, CRISPR-based functional analysis of essential genes in bacteria. Cell 165: 1493-1506. 2016 Jun 2.

26. Wang H, La Russa M, Qi LS*. CRISPR-Cas9 in genome editing and beyond. Annu. Rev. Biochem. 85: 227-264. 2016 Jun 2. (Review)

                 The #1 cited article in the Annual Review Journals in 2016.

25. Mandegar MA, Huebsch N, Frolov EB, Shin E, Truong A, Chan AH, Olvera MP, Chan AH, Miyaoka Y, Holmes K, Spencer CI, Judge LM, Gordon DE, Eskildsen TV, Villalta JE, Horlbeck MA, Gilbert LA, Krogan NJ, Sheikh SP, Weissman JS, Qi LS, So PL, Conklin BR. CRISPR interference efficiently induces specific and reversible gene silencing in human iPSCs. Cell Stem Cell. 18: 541–553. 2016 Apr 7.

24. Dominguze AA, Lim WA*, Qi LS*. Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Nat. Rev. Mol. Cell. Biol. 17: 5-15. 2016 Jan. (Review)

23. Du D, Qi LS*. An Introduction to CRISPR Technology for Genome Activation and Repression in Mammalian Cells. Cold Spring Harb Protoc 2016: pdb.top086835. 2016 Jan 4. (Protocol)


22. La Russa MF, Qi LS*. The new state of the art: Cas9 for gene activation and repression. Mol. Cell Biol. 35: 3800-3809. 2015 Nov 15. (Review)

21. Liu H, Wei Z, Dominguez AA, Li Y, Wang X*, Qi LS*. CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation. Bioinformatics 31: 3676-3678. 2015 Nov 15.

20. Peters JM, Silvis MR, Zhao D, Hawkins JS, Gross CA*, Qi LS*. Bacterial CRISPR: accomplishments and prospects. Curr. Opin. Microbiol. 27: 121–126. 2015 Sep 9. (Review)

19. Sokolik, Liu Y, Bauer D, McPherson J, Broeker M, Heimberg G, Qi LS, Sivak DA, Thomson M. Transcription factor competition allows embryonic stem cells to distinguish authentic signals from noise. Cell Syst. 1(2): 117-129. 2015 Aug 26.

18. Hawkins JS, Wong S, Peters JM, Almeida R, Qi LS*. Targeted transcriptional repression in bacteria using CRISPR interference (CRISPRi). Methods Mol. Biol. 1311: 349-362. 2015 May. (Protocol)

17. Yu C#, Liu Y#, Ma T, Xu S, Liu K, Zhang Y, La Russa MF, Xie M, Ding S*, Qi LS*. Small molecules enhance CRISPR genome editing in pluripotent stem cells. Cell Stem Cell 16: 142-147. 2015 Feb 5. (#Equal contribution)

16. Zalatan JG, Lee ME, Gilbert LA, Almeida R, Tsai JC, Whitehead EH, La Russa MF, Weissman JS, Dueber JE, Qi LS*, Lim WA*. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160: 339-350. 2015 Jan 15. (Cover article)


15. 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 KJ, Zepeda V, Qi LS, Lim WA. Specific gene repression by CRISPRi system transferred through bacterial conjugation. ACS Synth. Biol. 3(12): 929-931. 2014 Dec 19.

14. Tanenbaum ME, Gilbert LA, Qi LS, Weissman JS, Vale RD. A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159(3): 635-646. 2014 Oct 23.

13. Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y, Whitehead EH, Guimaraes C, Panning B, Ploegh HL, Bassik MC, Qi LS, Kampmann M, Weissman JS. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159(3): 647-661. 2014 Oct 23.

12. Qi LS*, Arkin AP*. A versatile platform for microbial engineering using synthetic noncoding RNAs. Nat. Rev. Microbiol. 12: 341-354. 2014 May. (Review)


11. Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS*, Huang B*. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155: 1479-1491. 2013 Dec 19.

10. Larson MH, Gilbert LA, Wang X, Lim WA, Weissman JS, Qi LS*. CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nat. Protoc. 8: 2108-2196. 2013 Nov. (Protocol)

9. Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, Lim WA, Weissman JS, Qi LS. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154: 442-451. 2013 Jul 18.

8. Qi LS*, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152: 1173-1183. 2013 Feb 28. (*Corresponding author)

                 The Top 10 downloaded article in Cell 2013.

Before independence (2012 and before):

7. Liu CC#, Qi LS#, Lucks JB, Segall-Shapiro TH, Wang D, Mutalik VM, Arkin AP. An adaptor from translational to transcriptional control enables predictable assembly of complex regulation. Nat. Methods 9: 1088-1094. 2012 Nov. (#Equal contribution)

6. Qi LS, Haurwitz RE, Shao WJ, Doudna JA, Arkin AP. RNA processing enables predictable programming of gene expression. Nat. Biotechnol. 30: 1002-1006. 2012 Oct.

5. Qi LS, Lucks JB, Liu CC, Mutalik VK, Arkin AP. Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Res. 40: 5775-5786. 2012 Jul.

4. Mutalik VK#, Qi LS#, Guimaraes JC, Lucks JB, Arkin AP. Rationally designed families of orthogonal RNA regulators of translation. Nat. Chem. Biol. 8: 447-454. 2012 Mar 25. (#Equal contribution)

3. Lucks JB#, Qi LS#, Mutalik VK, Wang D, Arkin AP. Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proc. Natl Acad. Sci. USA 108:8617-8822. 2011 May 24. (#Equal contribution)

2. Liu CC, Qi LS, Yanofsky C, Arkin AP. Regulation of transcription by unnatural amino acids. Nat. Biotechnol. 29:164-168. 2011 Feb.

1. Lucks JB, Qi LS, Whitaker WR, Arkin AP. Toward scalable parts families for predictable design of biological circuits. Curr. Opin. Microbiol. 11:567-573. 2008 Dec. (Review)