Publications

  1. Structure and Engineering of Francisella novicida Cas9.
    Hirano H, Gootenberg JS, Horii T, Abudayyeh OO, Kimura M, Hsu PD, Nakane T, Ishitani R, Hatada I, Zhang F, Nishimasu H, Nureki O. Cell. Feb 10. (2016). pii: S0092-8674(16)30053-8.

  2. In vivo gene editing in dystrophic mouse muscle and muscle stem cells.
    Tabebordbar M, Zhu K, Cheng JK, Chew WL, Widrick JJ, Yan WX, Maesner C, Wu EY, Xiao R, Ran FA, Cong L, Zhang F, Vandenberghe LH, Church GM, Wagers AJ. Science. Jan 22. (2016). 351(6271):407-11.

  3. In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy.
    Nelson CE, Hakim CH, Ousterout DG, Thakore PI, Moreb EA, Castellanos Rivera RM, Madhavan S, Pan X, Ran FA, Yan WX, Asokan A, Zhang F, Duan D, Gersbach CA. Science. Jan 22. (2016). 351(6271):403-7.

  4. Mice with Shank3 Mutations Associated with ASD and Schizophrenia Display Both Shared and Distinct Defects.
    Zhou Y, Kaiser T, Monteiro P, Zhang X, Van der Goes MS, Wang D, Barak B, Zeng M, Li C, Lu C, Wells M, Amaya A, Nguyen S, Lewis M, Sanjana N, Zhou Y, Zhang M, Zhang F, Fu Z, Feng G. Neuron. Jan 6. (2016). 89(1):147-62.

  5. Applications of CRISPR-Cas systems in neuroscience.
    Heidenreich M, Zhang F. Nat Rev Neurosci. Jan (2016). 17(1):36-44.

  6. Rationally engineered Cas9 nucleases with improved specificity.
    Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F. Science. Jan 1. (2016). 351(6268):84-8.

  7. Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems.
    Shmakov S, Abudayyeh OO, Makarova KS, Wolf YI, Gootenberg JS, Semenova E, Minakhin L, Joung J, Konermann S, Severinov K, Zhang F, Koonin EV. Mol Cell. Nov 5. (2015). 60(3):385-97.

  8. Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease.
    Dahlman JE, Abudayyeh OO, Joung J, Gootenberg JS, Zhang F, Konermann S. Nat Biotechnol. Oct 5. (2015). 33(11):1159-1161.

  9. Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System.
    Zetsche B, Gootenberg J, Abudayyeh O, Slaymaker I, Makarova K, Essletzbichler P, Volz S, Joung J, Oost J, Regev A, Koonin E, Zhang F. Cell Sep 25. (2015).

  10. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis.
    Canver MC, Smith EC, Sher F, Pinello L, Sanjana NE, Shalem O, Chen DD, Schupp PG, Vinjamur DS, Garcia SP, Luc S, Kurita R, Nakamura Y, Fujiwara Y, Maeda T, Yuan GC, Zhang F, Orkin SH, Bauer DE. Nature Sep 16. (2015).

  11. Crystal Structure of Staphylococcus aureus Cas9.
    Nishimasu H, Cong L, Yan WX, Ran FA, Zetsche B, Li Y, Kurabayashi A, Ishitani R, Zhang F, Nureki O. Cell. Aug 27. (2015). 162(5):1113-26. doi: 10.1016/j.cell.2015.08.007.

  12. A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks.
    Parnas O., Jovanovic M., Eisenhaure TM., Herbst RH., Dixit A., Ye CJ., Przybylski D., Platt RJ., Tirosh I., Sanjana NE., Shalem O., Satija R., Raychowdhury R., Mertins P., Carr SA., Zhang F., Hacohen N., Regev A. Cell Jul 15. (2015). pii: S0092-8674(15)00829-6.

  13. CRISPR-Cas9: Prospects and Challenges.
    Zhang F. Hum Gene Ther.Jul;26(7):409-10.(2015).

  14. Sequence determinants of improved CRISPR sgRNA design.
    Xu H., Xiao T., Chen CH., Li W., Meyer CA., Wu Q., Wu D., Cong L., Zhang F., Liu JS., Brown M., Liu XS. Genome Res. Jun 10. (2015).

  15. CRISPR/Cas9 cleavage of viral DNA efficiently suppresses hepatitis B virus.
    Ramanan V., Shlomai A., Cox DB., Schwartz RE., Michailidis E., Bhatta A., Scott DA., Zhang F., Rice CM., Bhatia SN. Sci Rep. Jun 2;5:10833. (2015).

  16. High-throughput functional genomics using CRISPR-Cas9.
    Shalem O., Sanjana NE., Zhang F. Nat Rev Genet. May;16(5):299-311. (2015).

  17. CRISPR germline engineering-the community speaks.
    Bosley KS., Botchan M., Bredenoord AL., Carroll D., Charo RA., Charpentier E., Cohen R., Corn J., Doudna J., Feng G., Greely HT., Isasi R., Ji W., Kim JS., Knoppers B., Lanphier E., Li J., Lovell-Badge R., Martin GS., Moreno J., Naldini L., Pera M., Perry AC., Venter JC., Zhang F., Zhou Q. Nat Biotechnol. May 12;33(5):478-86. (2015).

  18. Brains, Genes, and Primates.
    Belmonte JC., Callaway EM., Churchland P., Caddick SJ., Feng G., Homanics GE., Lee KF., Leopold DA., Miller CT., Mitchell JF., Mitalipov S., Moutri AR., Movshon JA., Okano H, Reynolds JH., Ringach D., Sejnowski TJ., Silva AC., Strick PL., Wu J., Zhang F. Neuron May 6;86(3):617-631. (2015).

  19. In vivo genome editing using Staphylococcus aureus Cas9.
    Ran FA.*, Cong L.*, Yan WX.*, Scott DA., Gootenberg JS., Kriz AJ., Zetsche B., Shalem O., Wu X., Makarova KS., Koonin EV., Sharp PA., Zhang F. Nature Apr 1. (2015).

  20. Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis.
    Chen S.*, Sanjana NE.*, Zheng K., Shalem O., Lee K., Shi X., Scott DA., Song J., Pan JQ., Weissleder R., Lee H., Zhang F., Sharp PA. Cell Mar 12;160(6):1246-60. (2015).

  21. Therapeutic genome editing: prospects and challenges.
    Cox DB., Platt RJ., Zhang F. Nature Medicine Feb 5;21(2):121-131. (2015).

  22. A split-Cas9 architecture for inducible genome editing and transcription modulation.
    Zetsche B., Volz SE., Zhang F. Nat Biotechnol Feb 2;33(2):139-42. (2015).

  23. Genome Engineering Using CRISPR-Cas9 System.
    Cong L., Zhang F. Methods Mol Biol 1239:197-217. (2015).

  24. Locus-specific epigenetic remodeling controls addiction- and depression-related behaviors.
    Heller EA., Cates HM., Peña CJ., Sun H., Shao N., Feng J., Golden SA., Herman JP., Walsh JJ., Mazei-Robison M., Ferguson D., Knight S., Gerber MA., Nievera C., Han MH., Russo SJ., Tamminga CS., Neve RL., Shen L., Zhang HS., Zhang F., Nestler EJ. Nat Neurosci. Dec;17(12):1720-7. (2014).

  25. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex.
    Konermann S.*, Brigham MD.*, Trevino AE., Joung J., Abudayyeh OO., Barcena C., Hsu PD., Habib N., Gootenberg JS., Nishimasu H., Nureki O., Zhang F. Nature Dec 10. (2014).

  26. Genome Engineering Using CRISPR-Cas9 System.
    Trevino AE,. Zhang F. Methods Enzymol. 546:161-74. (2014).

  27. In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9.
    Swiech L.*, Heidenreich M.*, Banerjee A., Habib N., Li Y., Trombetta J., Sur M., Zhang F. Nat Biotechnol Oct 19. (2014).

  28. CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling.
    Platt, RJ.*, Chen, S.*, Zhou, Y., Yim, MJ., Swiech, L., Kempton, HR., Dahlman, JE., Parnas, O., Eisenhaure, TM., Jovanovic, M., Graham, DB., Jhunjhunwala, S., Heidenreich, M., Xavier, RJ., Langer, R., Anderson, DG., Hacohen, N., Regev, A., Feng, G., Sharp, PA., Zhang, F. Cell Sep 24. pii: S0092-8674(14)01163-5. (2014).
    [ featured in Cell, cover art by Anna Hupalowska]

  29. CRISPR-mediated direct mutation of cancer genes in the mouse liver.
    Xue, W.*, Chen, S.*, Yin, H.*, Tammela, T., Papagiannakopoulos, T., Joshi, NS., Cai, W., Yang, G., Bronson, R., Crowley, DG., Zhang, F., Anderson, DG., Sharp, PA., Jacks, T. Nature Aug 6. (2014).

  30. Efficient CRISPR-Cas9-mediated genome editing in Plasmodium falciparum.
    Wagner, JC., Platt, RJ., Goldfless, SJ., Zhang, F., Niles, JC. Nat Methods Sep;11(9):915-8. (2014).

  31. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites.
    Schwartz, S.*, Mumbach, MR.*, Jovanovic, M., Wang, T., Maciag, K., Bushkin, GG., Mertins, P., Ter-Ovanesyan, D., Habib, N., Cacchiarelli, D., Sanjana, NE., Freinkman, E., Pacold, ME., Satija, R., Mikkelsen, TS., Hacohen, N., Zhang, F., Carr, SA., Lander, ES., Regev, A. Cell Rep Jul 10;8(1):284-96. (2014).

  32. Improved vectors and genome-wide libraries for CRISPR screening.
    Sanjana, N., Shalem, O., Zhang, F. Nat Methods 11, 783–784 (2014).

  33. Development and Applications of CRISPR-Cas9 for Genome Engineering.
    Hsu PD., Lander ES., Zhang F. Cell Jun 5;157(6):1262-1278. (2014).

  34. Global microRNA depletion suppresses tumor angiogenesis.
    Chen S,. Xue Y,. Wu X,. Le C,. Bhutkar A,. Bell EL,. Zhang F,. Langer R,. Sharp PA. Genes Dev. May 15;28(10):1054-67. (2014).

  35. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells.
    Wu X., Scott DA., Kriz AJ., Chiu AC., Hsu PD., Dadon DB., Cheng AW., Trevino AE., Konermann S., Chen S., Jaenisch R., Zhang F., Sharp PA. Nat Biotechnol. Apr 20. (2014).

  36. Common genetic variants modulate pathogen-sensing responses in human dendritic cells.
    Lee, MN., Ye, C., Villani, AC., Raj, T., Li, W., Eisenhaure, TM., Imboywa, SH., Chipendo, PI., Ran, FA., Slowikowski, K., Ward, LD., Raddassi, K., McCabe, C., Lee, MH., Frohlich, IY., Hafler, DA., Kellis, M., Raychaudhuri, S., Zhang, F., Stranger, BE., Benoist, CO., De Jager, PL., Regev, A., Hacohen, N. Science Mar 7. 7;343(6175):1246980. (2014).

  37. RNA-Guided Genome Editing of Mammalian Cells.
    Pyzocha, NK., Ran, FA., Hsu, PD., Zhang, F. Methods Mol Biol. 2014;1114:269-77. (2014).

  38. Crystal structure of cas9 in complex with guide RNA and target DNA.
    Nishimasu, H., Ran, FA., Hsu, PD., Konermann, S., Shehata, SI., Dohmae, N., Ishitani, R., Zhang, F., Nureki, O. Cell Feb 27. 156(5):935-49. (2014).

  39. Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells.
    Shalem, O.*, Sanjana, NE.*, Hartenian, E., Shi, X., Scott, DA., Mikkelson, T., Heckl, D., Ebert, BL., Root, DE., Doench, JG., Zhang, F. Science Jan 3;343(6166):84-7. (2014).

  40. Genome engineering using the CRISPR-Cas9 system.
    Ran, FA.*, Hsu, PD.*, Wright, J., Agarwala, V., Scott, DA., Zhang, F. Nature Protocols Nov;8(11):2281-308. (2013).

  41. Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity.
    Ran, FA.*, Hsu, PD.*, Lin, CY., Gootenberg, JS., Konermann, S., Trevino, AE., Scott, DA., Inoue, A., Matoba, S., Zhang, Y., & Zhang, F. Cell Aug 28. pii: S0092-8674(13)01015-5. (2013).

  42. Optical control of mammalian endogenous transcription and epigenetic states.
    Konermann, S.*, Brigham, MD.*, Trevino A., Hsu, PD., Heidenreich, M., Cong, L., Platt, RJ., Scott, D., Church, GM., & Zhang, F. Nature (2013).

  43. DNA targeting specificity of RNA-guided Cas9 nucleases.
    Hsu, P.*, Scott, D.*, Weinstein, J., Ran, FA., Konermann, S., Agarwala, V., Li, Y., Fine, E., Wu, X., Shalem, O., Cradick, TJ., Marraffini, LA., Bao, G., & Zhang, F. Nat Biotechnol (2013).
    [ featured in Nature Biotechnology, cover art by Marina Spence]

  44. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system.
    Bikard D., Jiang W., Samai P., Hochschild A., Zhang F., Marraffini LA. NAR Jun 12. (2013).

  45. One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering.
    Wang H., Yang H., Shivalila CS., Dawlaty MM., Cheng AW., Zhang F., Jaenisch R. Cell May 9;153(4):910-8 (2013).

  46. RNA-guided editing of bacterial genomes using CRISPR-Cas systems.
    Jiang W., Bikard D., Cox D., Zhang F, Marraffini LA. Nat Biotechnol Mar;31(3):233-9 (2013).

  47. Multiplex genome engineering using CRISPR/Cas systems.
    Cong, L.*, Ran, F.A.*, Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P.D., Wu, X., Jiang, W., Marraffini, L.A., & Zhang, F. Science Feb 15;339(6121):819-23 (2013).

  48. Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains.
    Cong, L., Zhou, R., Kuo, Y.C., Cunniff, M., & Zhang, F. Nat Commun. Jul 24;3:968 (2012).

  49. Dissecting neural function using targeted genome engineering technologies.
    Hsu PD., & Zhang, F. ACS Chem Neurosci. Aug 15;3(8):603-10 (2012).

  50. A transcription activator-like effector toolbox for genome engineering.
    Sanjana, N., Cong, L., Zhou, Y., Cunniff, M., Feng, G. & Zhang, F. Nat Protoc. Jan 5;7(1):171-92 (2012).

  51. Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers.
    Briggs, A., Rios, X., Chari, R., Yang, L., Zhang, F., Mali, P., Church, G. NAR Aug;40(15):e117 (2012).

  52. Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription.
    Zhang, F.*, Cong, L.*, Lodato, S., Kosuri, S., Church, G.M. & Arlotta, P. Nat Biotechnol 29, 149-153 (2011).

  53. Crystal structure of the channelrhodopsin light-gated cation channel.
    Kato, H.E., Zhang, F., Yizhar, O., Ramakrishnan, C., Nishizawa, T., Hirata, K., Ito, J., Aita, Y., Tsukazaki, T., Hayashi, S., Hegemann, P., Maturana, A.D., Ishitani, R., Deisseroth, K., Nureki, O. Nature Jan 22. (2012).

  54. Molecular Tools and Approaches for Optogenetics.
    Mei, Y., Zhang, F. Biological Psychiatry 12, 1033–1038 (2012).

  55. The microbial opsin family of optogenetic tools.
    Zhang, F., Vierock, J., Yizhar, O., Fenno, L.E., Tsunoda, S., Kianianmomeni, A., Prigge, M., Berndt, A., Cushman, J., Polle, J., Magnuson, J., Hegemann, P. & Deisseroth, K. Cell 147, 1446-1457 (2011).

  56. Excitatory transmission from the amygdala to nucleus accumbens facilitates reward seeking.
    Stuber, G.D., Sparta, D.R., Stamatakis, A.M., van Leeuwen, W.A., Hardjoprajitno, J.E., Cho, S., Tye, K.M., Kempadoo, K.A., Zhang, F., Deisseroth, K. & Bonci, A. Nature 475, 377-380 (2011).

  57. Tracking stem cell differentiation in the setting of automated optogenetic stimulation.
    Stroh, A., Tsai, H.C., Wang, L.P., Zhang, F., Kressel, J., Aravanis, A., Santhanam, N., Deisseroth, K., Konnerth, A. & Schneider, M.B. Stem Cells 29, 78-88 (2011).

  58. In vivo optogenetic stimulation of neocortical excitatory neurons drives brain-state-dependent inhibition.
    Mateo, C., Avermann, M., Gentet, L.J., Zhang, F., Deisseroth, K. & Petersen, C.C. Curr Biol 21, 1593-1602 (2011).

  59. Optogenetic interrogation of dopaminergic modulation of the multiple phases of reward-seeking behavior.
    Adamantidis, A.R., Tsai, H.C., Boutrel, B., Zhang, F., Stuber, G.D., Budygin, E.A., Tourino, C., Bonci, A., Deisseroth, K. & de Lecea, L. J Neurosci 31, 10829-10835 (2011).

  60. Optogenetic interrogation of neural circuits: technology for probing mammalian brain structures.
    Zhang, F., Gradinaru, V., Adamantidis, A.R., Durand, R., Airan, R.D., de Lecea, L. & Deisseroth, K. Nature Protocols 5, 439-456 (2010).

  61. Global and local fMRI signals driven by neurons defined optogenetically by type and wiring.
    Lee, J.H., Durand, R., Gradinaru, V., Zhang, F., Goshen, I., Kim, D.S., Fenno, L.E., Ramakrishnan, C. & Deisseroth, K. Nature 465, 788-792 (2010).

  62. Molecular and cellular approaches for diversifying and extending optogenetics.
    Gradinaru, V., Zhang, F., Ramakrishnan, C., Mattis, J., Prakash, R., Diester, I., Goshen, I., Thompson, K.R. & Deisseroth, K. Cell 141, 154-165 (2010).

  63. Targeted optogenetic stimulation and recording of neurons in vivo using cell-type-specific expression of Channelrhodopsin-2.
    Cardin, J.A., Carlen, M., Meletis, K., Knoblich, U., Zhang, F., Deisseroth, K., Tsai, L.H. & Moore, C.I. Nature Protocols 5, 247-254 (2010).

  64. Manipulation of an innate escape response in Drosophila: photoexcitation of acj6 neurons induces the escape response.
    Zimmermann, G., Wang, L.P., Vaughan, A.G., Manoli, D.S., Zhang, F., Deisseroth, K., Baker, B.S. & Scott, M.P. PLoS One 4, e5100 (2009).

  65. Integrated device for optical stimulation and spatiotemporal electrical recording of neural activity in light-sensitized brain tissue.
    Zhang, J., Laiwalla, F., Kim, J.A., Urabe, H., Van Wagenen, R., Song, Y.K., Connors, B.W., Zhang, F., Deisseroth, K. & Nurmikko, A.V. J Neural Eng 6, 055007 (2009).

  66. Phasic firing in dopaminergic neurons is sufficient for behavioral conditioning.
    Tsai, H.C., Zhang, F., Adamantidis, A., Stuber, G.D., Bonci, A., de Lecea, L. & Deisseroth, K. Science 324, 1080-1084 (2009).

  67. Parvalbumin neurons and gamma rhythms enhance cortical circuit performance.
    Sohal, V.S., Zhang, F., Yizhar, O. & Deisseroth, K. Nature 459, 698-702 (2009).

  68. Driving fast-spiking cells induces gamma rhythm and controls sensory responses.
    Cardin, J.A., Carlen, M., Meletis, K., Knoblich, U., Zhang, F., Deisseroth, K., Tsai, L.H. & Moore, C.I. Nature 459, 663-667 (2009).

  69. Improved expression of halorhodopsin for light-induced silencing of neuronal activity.
    Zhao, S., Cunha, C., Zhang, F., Liu, Q., Gloss, B., Deisseroth, K., Augustine, G.J. & Feng, G. Brain Cell Biol 36, 141-154 (2008).

  70. Red-shifted optogenetic excitation: a tool for fast neural control derived from Volvox carteri.
    Zhang, F., Prigge, M., Beyriere, F., Tsunoda, S.P., Mattis, J., Yizhar, O., Hegemann, P. & Deisseroth, K. Nat Neurosci 11, 631-633 (2008).

  71. Controlling neuronal activity.
    Schneider, M.B., Gradinaru, V., Zhang, F. & Deisseroth, K. Am J Psychiatry 165, 562 (2008).

  72. Multimodal fast optical interrogation of neural circuitry.
    Zhang, F., Wang, L.P., Brauner, M., Liewald, J.F., Kay, K., Watzke, N., Wood, P.G., Bamberg, E., Nagel, G., Gottschalk, A. & Deisseroth, K. Nature 446, 633-639 (2007).

  73. Circuit-breakers: optical technologies for probing neural signals and systems.
    Zhang, F., Aravanis, A.M., Adamantidis, A., de Lecea, L. & Deisseroth, K. Nat Rev Neurosci 8, 577-581 (2007).

  74. High-speed mapping of synaptic connectivity using photostimulation in Channelrhodopsin-2 transgenic mice.
    Wang, H., Peca, J., Matsuzaki, M., Matsuzaki, K., Noguchi, J., Qiu, L., Wang, D., Zhang, F., Boyden, E., Deisseroth, K., Kasai, H., Hall, W.C., Feng, G. & Augustine, G.J. Proc Natl Acad Sci U S A 104, 8143-8148 (2007).

  75. Nociceptive neurons protect Drosophila larvae from parasitoid wasps. Hwang, R.Y., Zhong, L., Xu, Y., Johnson, T., Zhang, F., Deisseroth, K. & Tracey, W.D. Curr Biol 17, 2105-2116 (2007).

  76. Targeting and readout strategies for fast optical neural control in vitro and in vivo.
    Gradinaru, V., Thompson, K.R., Zhang, F., Mogri, M., Kay, K., Schneider, M.B. & Deisseroth, K. J Neurosci 27, 14231-14238 (2007).

  77. An optical neural interface: in vivo control of rodent motor cortex with integrated fiberoptic and optogenetic technology.
    Aravanis, A.M., Wang, L.P., Zhang, F., Meltzer, L.A., Mogri, M.Z., Schneider, M.B. & Deisseroth, K. J Neural Eng 4, S143-156 (2007).

  78. Neural substrates of awakening probed with optogenetic control of hypocretin neurons.
    Adamantidis, A.R., Zhang, F., Aravanis, A.M., Deisseroth, K. & de Lecea, L. Nature 450, 420-424 (2007).

  79. Channelrhodopsin-2 and optical control of excitable cells.
    Zhang, F., Wang, L.P., Boyden, E.S. & Deisseroth, K. Nat Methods 3, 785-792 (2006).

  80. Millisecond-timescale, genetically targeted optical control of neural activity.
    Boyden, E.S., Zhang, F., Bamberg, E., Nagel, G. & Deisseroth, K. Nat Neurosci 8, 1263-1268 (2005).