Publications

  1. 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. (2014). 7;343(6175):1246980.

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

  3. 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. (2014). 156(5):935-49.

  4. 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 Dec 12. (2013). [Epub ahead of print].

  5. 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).

  6. 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).

  7. 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 doi:10.1038/nature12466 (2013).

  8. 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 doi:10.1038/nbt.2647 (2013).
    [ featured in Nature Biotechnology ]

  9. 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. doi: 10.1093/nar/gkt520 (2013).

  10. 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).

  11. 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).

  12. 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).

  13. 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).

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

  15. 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).

  16. 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).

  17. 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).

  18. 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. doi: 10.1038/nature10870 (2012).

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

  20. 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).

  21. 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).

  22. 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).

  23. 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).

  24. 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).

  25. 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).

  26. 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).

  27. 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).

  28. 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).

  29. 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).

  30. 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).

  31. 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).

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

  33. 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).

  34. 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).

  35. 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).

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

  37. 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).

  38. 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).

  39. 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).

  40. 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).

  41. 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).

  42. 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).

  43. 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).

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

  45. 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).