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Design of Tunable Oscillatory Dynamics in a Synthetic NF-kB Signaling Circuit.

Zhi-Bo Zhang, Qiu-Yue Wang, Yu-Xi Ke, Shi-Yu Liu, Jian-Qi Ju, Wendell A Lim, Chao Tang, Ping Wei.

Cell Syst.. 2017 Nov 22

Abstract. PDF.

Tracing Information Flow from Erk to Target Gene Induction Reveals Mechanisms of Dynamic and Combinatorial Control.

Maxwell Z. Wilson, Pavithran T. Ravindran, Wendell A. Lim, Jared E. Toettcher.

Mol Cell. 2017 Sep 7

Abstract. PDF.

Engineering Therapeutic T cells: From Synthetic Biology to Clinical Trials.

Jonathan H. Esensten, Jeffrey A. Bluestone, Wendell A. Lim.

Annu Rev Pathol. 2017 Jan

Abstract. PDF.

Interrogating cellular perception and decision making with optogenetic tools.

Lukasz J. Bugaj, Geoff P. O'Donoghue, Wendell A. Lim.

J Cell Biol. 2017 April 7

Abstract. PDF.

CRISPR/Cas9-mediated PD-1 disruption enhances anti-tumor efficacy of human chimeric antigen receptor T cells.

Levi J. Rupp, Kathrin Schumann, Kole T. Roybal, Rachel E. Gate, Chun J. Ye, Wendell A. Lim, Alexander Marson.

Scientific Reports. 2017 April 7

Abstract. PDF.

The Principles of Engineering Immune Cells to Treat Cancer.

Wendell A. Lim and Carl H. June.

Cell. 2017 February 9

Abstract. PDF.

Complex transcriptional modulation with orthogonal and inducible dCas9 regulators.

Yuchen Gao, Xin Xiong, Spencer Wong, Emeric J Charles, Wendell A. Lim, Lei S Qi.

Nat Methods. 2016 December

Abstract. PDF.

Engineering dynamical control of cell fate switching using synthetic phospho-regulons.

Russell M. Gordley, Reid E. Williams, Caleb J. Bashor, Jared E. Toettcher, Shude Yan, Wendell A. Lim.

Proceedings of the National Academy of Sciences. 2016 November 22

Abstract. PDF.

Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of mutiple genomic loci.

Baohui Chen, Jeffrey Hu, Ricardo Almeida, Harrison Liu, Sanjeev Balakrishnan, Christian Covill-Cooke, Wendell A. Lim, and Bo Huang.

Nucleic Acids Research. 2016 January 5

Abstract. PDF.

Engineering T cells with Customized Therapeutic Response Programs Using Synthetic Notch Receptors.

Kole T. Roybal, Jasper Z. Williams, Leonardo Morsut, Levi J. Rupp, Whitney J. Walker, Krista A. McNally, Wendell A. Lim.

Cell. 2016 October 6

Abstract. PDF.

Cellular perception and misperception: Internal models for decision-making shaped by evolutionary experience.

Amir Mitchell, Wendell A. Lim.

Bioessays. 2016 July 27

Abstract. PDF.

Modular engineering of cellular signaling proteins and networks.

Russell M. Gordley, Lukasz J. Bugaj, Wendell A. Lim.

Curr Opin Struct Biol. 2016 July 13

Abstract. PDF.

CRISPR/Cas9 for Human Genome Engineering and Disease Research.

Xin Xiong, Meng Chen, Wendell A. Lim, Dehua Zhao, Lei S. Qi.

Annu Rev Genomics Hum Genet. 2016 May 23

Abstract. PDF.

Nucleosome breathing and remodeling constrain CRISPR-Cas9 function.

R. Stefan Isaac, Fuguo Jiang, Jennifer A. Doudna, Geeta J. Narlikar, Wendell A. Lim, Ricardo Almeida.

eLife. 2016; 5:e13450 Apr 28

Abstract. PDF.

Precision tumor recognition by T cells with combinatorial antigen-sensing circuits.

Kole T. Roybal, Levi J. Rupp, Leonardo Morsut, Whitney J. Walker, Krista A. McNally, Jason S. Park, Wendell A. Lim.

Cell. 2016 Feb. 11

Abstract. PDF. Supplemental Info.

Engineering customized cell sensing and response behaviors using synthetic notch receptors.

Leonardo Morsut*, Kole T. Roybal*, Xin Xiong, Russell M. Gordley, Scott M. Coyle, Matthew Thomson, Wendell A. Lim.

Cell. 2016 Feb. 11

*These authors contributed equally to this work.

Abstract. PDF. Supplemental Info. Addgene.

Mapping the functional versatility and fragility of Ras GTPase signaling circuits through in vitro network reconstitution.

Scott Coyle, Wendell A. Lim.

eLife. 2016;5:12435 Jan. 14

Abstract. PDF.

Beyond editing: Repurposing CRISPR-Cas9 for precision genome regulation and interrogation

Antonia A. Dominguez, Wendell A. Lim, Lei S. Qi.

Nature Reviews Molecular Cell Biology. 2015 Dec 16

Abstract. PDF.

Oscillatory stress stimulation uncovers an Achilles' heel of the yeast MAPK signaling network

Amir Mitchell, Ping Wei, Wendell A. Lim.

Science. 2015 Nov 19

Abstract. PDF.

Remote control of therapeutic T cells through a small molecule-gated chimeric receptor

Chia-Yung Wu, Kole T. Roybal, Elias M. Puchner, James Onuffer, Wendell A. Lim.

Science. 2015 Sep 24

Abstract. PDF.

Synthetic biology approaches to engineer T cells

Chia-Yung Wu, Levi J. Rupp, Kole T. Roybal, Wendell A. Lim.

Current Opinion in Immunology. 2015; 35:123-130

Abstract. PDF.

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds

Zalatan JG, Lee ME, Almeida R, Gilbert LA, Whitehead EH, La Russa M, Tsai JC, Weissman JS, Dueber JE, Qi LS, Lim WA.

Cell. 2015 Jan 15;160(1-2):339-50.

Abstract. PDF.

Specific Gene Repression by CRISPRi System Transferred through Bacterial Conjugation

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.

ACS Synth Biol. 2014 Dec 19;3(12):929-31.

Abstract. PDF. Supplemental Data.

Sending mixed messages for cell population control.

Hyun Youk and Wendell A. Lim

Cell (Preview) 158 : 973-975 (2014)

Abstract. PDF.

Synthetic control of mammalian-cell motility by engineering chemotaxis to an orthogonal bioinert chemical signal.

Jason S. Park, Benjamin Rhau, Aynur Hermann, Krista A. McNally, Carmen Zhou, Delquin Gong, Orion D. Weiner, Bruce R. Conklin, James Onuffer, and Wendell A. Lim

Proceedings of the National Academy of Sciences (April 2014)

Abstract. PDF. Supplemental Data. Supplemental Movie 1. Supplemental Movie 2. Supplemental Movie 3.Supplemental Movie 4. Supplemental Movie 5Supplemental Movie 6.

Secreting and sensing the same molecule allows cells to achieve versatile social behaviors.

Hyun Youk and Wendell A. Lim

Science 343 (6171): 1242782 (2014)

Abstract. PDF. Supplemental Data.

Using optogenetics to interrogate the dynamic control of signal transmission by the ras/erk module.

Jared E. Toettcher, Orion D. Weiner, and Wendell A. Lim.

Cell 155(6):1422-34 (2013)

Abstract. PDF. Supplemental Data. Supplemental Movie 1. Supplemental Movie 2. RPPA data.

Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory.

Elias M. Puchner, Jessica M. Walter, Robert Kasper, Bo Huang, and Wendell A. Lim.

Proceedings of the National Academy of Sciences 110(40):16015-16020 (2013)

Abstract. PDF. Supplemental Data.

Exploitation of Latent Allostery Enables the Evolution of New Modes of MAP Kinase Regulation.

Scott M. Coyle, Jonathan Flores, and Wendell A. Lim

Cell 154, 875-887 (2013)

Abstract. PDF. Supplemental Data.

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes.

Luke A. Gilbert, Matthew H. Larson, Leonardo Morsut, Zairan Liu, Gloria A. Brar, Sandra E. Torres, Noam Stern-Ginossar, Onn Brandman, Evan H. Whitehead, Jennifer A. Doudna, Wendell A. Lim, Jonathan S. Weissman, Lei S. Qi

Cell (Resource) 154, 1-10 (2013)

Abstract. PDF.

Cell-based therapeutics: the next pillar of medicine.

Michael A. Fischbach, Jeffrey A. Bluestone, Wendell A. Lim

Science Translational Medicine 5(179) (2013)

Abstract. PDF.

Cell biology 2.0.

Wendell A. Lim, Rebecca Alvania, Wallace F. Marshall

Trends Cell Biol. 22(12):611-2 (2013)

Abstract. PDF.

Design principles of regulatory networks: searching for the molecular algorithms of the cell.

Wendell A. Lim, Connie M. Lee, Chao Tang

Mol. Cell 49(2):202-12 (2013)

Abstract. PDF.

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression.

Lei S. Qi, Matthew H. Larson, Luke A. Gilbert, Jennifer A. Doudna, Jonathan S. Weissman, Adam P. Arkin, Wendell A. Lim

Cell 28;152(5):1173-83 (2013)

Abstract. PDF. Supplemental Data. Supplemental Sequences.

Designing synthetic regulatory networks capable of self-organizing cell polarization.

Angela H. Chau*, Jessica M. Walter*, Jaline Gerardin, Chao Tang, Wendell A. Lim

Cell 151(2):320-32 (2012)

Abstract. PDF. Supplemental Data. Supplemental Movie 1. Supplemental Movie 2. Simulation Code and Scripts.

Conformational Control of the Ste5 Scaffold Protein Insulates Against MAP Kinase Misactivation.

Jesse G. Zalatan*, Scott M. Coyle*, Saravanan Rajan, Sachdev S. Sidhu, Wendell A. Lim

Science 337 (6099): 1218-1222 (2012)

Abstract. PDF. Supplemental Data.

Bacterial virulence proteins as tools to rewire kinase pathways in yeast and immune cells.

Ping Wei*, Wilson W. Wong*, Jason S. Park, Ethan E. Corcoran, Sergio G. Peisajovich, James J. Onuffer, Arthur Weiss, Wendell A. Lim

Nature 488, 384-388 (2012)

Abstract. PDF. Supplemental Data.

Systematic functional prioritization of protein posttranslational modifications.

Pedro Beltrao, Veronique Albanese, Lillian R. Kenner, Danielle L. Swaney, Alma Burlingame, Judit Villen, Wendell A. Lim, James S. Fraser, Judith Frydman, Nevan J. Krogan

Cell 150(2):413-25 (2012)

Abstract. PDF. Article + Supplemental Data. Supplemental Tables.

SYNZIP Protein Interaction Toolbox: in Vitro and in Vivo Specifications of Heterospecific Coiled-Coil Interaction Domains.

Kenneth Evan Thompson, Caleb J. Bashor, Wendell A. Lim, Amy E. Keating

ACS Synth Biol. 1(4): 118-129 (2012)

Abstract. PDF. Supplemental Data.

Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair.

Gregory T. Kapp, Sen Liu, Amelie Stein, Derek T. Wong, Attila Remenyi, Brian J. Yeh, James S. Fraser, Jack Taunton, Wendell A. Lim, Tanja Kortemme

Proceedings of the National Academy of Sciences 109(14): 5277-5282 (2012)

Abstract. PDF. Supplemental Data.

Light-based feedback for controlling intracellular signaling dynamics

Jared E. Toettcher, Delquin Gong, Wendell A. Lim, Orion D. Weiner

Nature Methods 8, 837-839 (2011)

Abstract. PDF. Supplemental Data.

Recruitment interactions can override catalytic interactions in determining the functional identity of a protein kinase

Angela P. Won, Joan E. Garbarino, Wendell A. Lim

Proceedings of the National Academy of Sciences 108, 9809-9814 (2011)

Abstract. PDF. Supplemental Data.

Light Control of Plasma Membrane Recruitment Using the Phy-PIF System

Jared E. Toettcher, Delquin Gong, Wendell A. Lim, Orion D. Weiner

Methods Enzymology 497, 409-23 (2011)

Abstract. PDF.

Scaffold proteins: hubs for controlling the flow of cellular information

Matthew C. Good, Jesse G. Zalatan, Wendell A. Lim

Science 332, 680-6 (2011)

Abstract. PDF. Supplemental Video.

The promise of optogenetics in cell biology: interrogating molecular circuits in space and time

Jared E. Toettcher, Christopher A. Voigt, Orion D. Weiner, Wendell A. Lim

Nature Methods 1, 35-38 (2011)

Abstract. PDF.

Build life to understand it

Michael Elowitz, Wendell A. Lim

Nature 468, 889-890 (2010)

Abstract. PDF.

Phosphotyrosine signaling: evolving a new cellular communication system

Wendell A. Lim, Tony Pawson

Cell 142, 661-667 (2010)

Abstract. PDF.

The minimal autoinhibited unit of the guanine nucleotide exchange factor intersectin

K. Farid Ahmad, Wendell A. Lim

PLos ONE 5, e11291 (2010)

Abstract. PDF.

Designing customized cell signalling circuits

Wendell A. Lim

Nature Reviews Molecular Cell Biology 11, 393-403 (2010)

Abstract. PDF.

Rapid diversification of cell signaling phenotypes by modular domain recombination

Sergio G. Peisajovich, Joan E. Garbarino, Ping Wei, Wendell A. Lim

Science 328, 368-372 (2010)

Abstract. PDF. Supplemental Data.

Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems

Caleb J. Bashor, Andrew A. Horwitz, Sergio G. Peisajovich, and Wendell A. Lim

Annual Review of Biophysics 39, 515-537 (2010)

Abstract. PDF.

Reengineering the signaling properties of a Src family kinase

Shalini S. Yadav, Brian J. Yeh, Barbara P. Craddock, Wendell A. Lim, and W. Todd Miller

Biochemistry 48, 10956-10962 (2009)

Abstract. PDF. Supplemental Data.

Spatiotemporal control of cell signalling using a light-switchable protein interaction

Anselm Levskaya, Orion D. Weiner, Wendell A. Lim, and Christopher A. Voigt

Nature 461, 997-1001 (2009)

Abstract. PDF. Supplemental Data.

Defining network topologies that can achieve biochemical adaptation

Wenzhe Ma, Ala Trusina, Hana El-Samad, Wendell A. Lim, and Chao Tang

Cell 138, 760-73 (2009)

Abstract. PDF. Supplemental Data. PaperFlick video summary.

Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species

Pedro Beltrao, Jonathan C. Trinidad, Dorothea Fiedler, Assen Roguev, Wendell A. Lim, Kevan M. Shokat, Alma L. Burlingame, and Nevan J. Krogan

PLoS Biology 7, e1000134 (2009).

Abstract. PDF. Supplemental Data.

The Ste5 Scaffold Directs Mating Signaling by Catalytically Unlocking the Fus3 MAP Kinase for Activation

Matthew C. Good, Grace Tang, Julie Singleton, Attila Reményi, and Wendell A. Lim

Cell 136, 1085-97 (2009)

Abstract. PDF. Supplemental Data.

The pathogen protein EspF(U) hijacks actin polymerization using mimicry and multivalency

Nathan A. Sallee, Gonzalo M. Rivera, John E. Dueber, Dan Vasilescu, R. Dyche Mullins, Bruce J. Mayer, and Wendell A. Lim

Nature 454, 1005-8 (2008)

Abstract. PDF. Supplemental Data.

Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages

David Pincus, Ivica Letunic, Peer Bork, and Wendell A. Lim

Proceedings of the National Academy of Sciences 105, 9680-4 (2008)

Abstract. PDF. Supplemental Data.

Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics

Caleb J. Bashor, Noah C. Helman, Shude Yan, and Wendell A. Lim

Science 319, 1539-43 (2008)

Abstract. PDF. Supplemental Data.

Synthetic biology: lessons from the history of synthetic organic chemistry

Brian J. Yeh and Wendell A. Lim

Nature Chemical Biology 3, 521-5 (2007)

Abstract. PDF.

Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors

Brian J. Yeh, Robert J. Rutigliano, Anrica Deb, Dafna Bar-Sagi, and Wendell A. Lim

Nature 447, 596-600 (2007)

Abstract. PDF. Supplemental Data. Supplemental Video.

Engineering synthetic signaling proteins with ultrasensitive input/output control

John E. Dueber, Ethan A. Mirsky, and Wendell A. Lim

Nature Biotechnology 25, 660-662 (2007)

Abstract. PDF. Supplemental Data.

Engineering modular protein interaction switches by sequence overlap

Nathan A. Sallee, Brian J. Yeh, and Wendell A. Lim

Journal of the American Chemical Society 129, 4606-4611 (2007)

Abstract. PDF. Supplemental Data.

Docking interactions in protein kinase and phosphatase networks

Attila Reményi, Matthew C. Good, and Wendell A. Lim

Current Opinion in Structural Biology 16, 676-685 (2006)

Abstract. PDF.

Domains, Motifs, and Scaffolds: The Role of Modular Interactions in the Evolution and Wiring of Cell Signaling Circuits

Roby P. Bhattacharyya, Attila Reményi, Brian J. Yeh, and Wendell A. Lim

Annual Review of Biochemistry 75, 655-680 (2006)

Abstract. PDF.

The Ste5 Scaffold Allosterically Modulates Signaling Output of the Yeast Mating Pathway

Roby P. Bhattacharyya*, Attila Reményi*, Matthew C. Good, Caleb J. Bashor, Arnold M. Falick, and Wendell A. Lim

Science 311, 822-826 (2006)

Abstract. PDF.

The role of docking interactions in mediating discrimination in the yeast MAPK network

Attila Reményi, Matthew C. Good, Roby P. Bhattacharyya, and Wendell A. Lim

Molecular Cell 20, 951-962 (2005)

Abstract. PDF. Supplemental Data.

A general model for preferential hetero-oligomerization of Lin-2/7 domains: Mechanism underlying directed assembly of supramolecular signaling complexes

Keiko Y. Petrosky, Horng D. Ou, Frank Löhr, Volker Dötsch, and Wendell A. Lim

Journal of Biological Chemistry 280, 38528-38536 (2005)

Abstract. PDF.

A Polybasic Motif Allows N-WASP to Act as a Sensor of PIP2 Density

Venizelos Papayannopoulos, Carl Co, Kenneth E. Prehoda, Scott Snapper, Jack Taunton, and Wendell A. Lim

Molecular Cell 17, 181-191 (2005)

Abstract. PDF. Supplemental Data.

Rewiring cell signaling: the logic and plasticity of eukaryotic protein circuitry

John E. Dueber, Brian J. Yeh, Roby P. Bhattacharyya, and Wendell A. Lim

Current Opinion in Structural Biology 14, 690-699 (2004)

Abstract. PDF.

Sho1 and Pbs2 Act as Coscaffolds Linking Components in the Yeast High Osmolarity MAP Kinase Pathway

Ali Zarrinpar, Roby P. Bhattacharyya, M. Paige Nittler, and Wendell A. Lim

Molecular Cell 14, 825–832 (2004)

Abstract. PDF. Supplemental Data.

Optimization of specificity in a cellular protein interaction network by negative selection

Ali Zarrinpar, Sang-Hyun Park, and Wendell A. Lim

Nature 426, 676-680 (2003)

Abstract. PDF. Supplemental Data.

Reprogramming Control of an Allosteric Signaling Switch Through Modular Recombination

John E. Dueber, Brian J. Yeh, Kayam Chak, and Wendell A. Lim

Science 301, 1904-1908 (2003)

Abstract. PDF. Supplemental Data.

The Structure and Function of Proline Recognition Domains

Ali Zarrinpar, Roby P. Bhattacharyya, and Wendell A. Lim

Science STKE 2003, re8 (2003)

Abstract. PDF. Structure Animations.

Role of Electrostatic Interactions in PDZ Domain Ligand Recognition

Baruch Z. Harris, Francis W. Lau, Naoaki Fujii, R. Kiplin Guy, and Wendell A. Lim

Biochemistry 42, 2797-2805 (2003)

Abstract. PDF.

Rewiring MAP Kinase Pathways Using Alternative Scaffold Assembly Mechanisms

Sang-Hyun Park, Ali Zarrinpar, and Wendell A. Lim

Science 299, 1061-1064 (2003)v

Abstract. PDF. Supplemental Data.

Structure of the N-WASP EVH1 Domain-WIP Complex: Insight into the Molecular Basis of Wiskott-Aldrich Syndrome

Brian F. Volkman, Kenneth E. Prehoda, Jessica A. Scott, Francis C. Peterson, and Wendell A. Lim

Cell 111, 565–576 (2002)

Abstract. PDF. Supplemental Data.

Coordinated folding and association of the LIN-2, -7 (L27) domain: An obligate heterodimerization involved in assembly of signaling and cell polarity complexes

Baruch Z. Harris, Shivkumar Venkatasubrahmanyam, and Wendell A. Lim

Journal of Biological Chemistry 277, 34902-34908 (2002)

Abstract. PDF.

How signaling proteins integrate multiple inputs: a comparison of N-WASP and Cdk2

Kenneth E. Prehoda and Wendell A. Lim

Current Opinion in Cell Biology14, 149-154 (2002)

Abstract. PDF.

The modular logic of signaling proteins: building allosteric switches from simple binding domains

Wendell A. Lim

Current Opinion in Structural Biology 12, 61-68 (2002)

Abstract. PDF.

Structure of the SH3-Guanylate Kinase Module from PSD-95 Suggests a Mechanism for Regulated Assembly of MAGUK Scaffolding Proteins

Aaron W. McGee, Srikanth R. Dakoji, Olav Olsen, David S. Bredt, Wendell A. Lim, and Kenneth E. Prehoda

Molecular Cell 8, 1291-1301 (2001)

Abstract. PDF.

Mechanism and role of PDZ domains in signaling complex assembly

Baruch Z. Harris and Wendell A. Lim

Journal of Cell Science 114, 3219-3231 (2001)

Abstract. PDF.

The double life of PX domains

Kenneth E. Prehoda and Wendell A. Lim

Nature Structural Biology 8, 570-572 (2001)

Abstract. PDF.

Energetic Determinants of Internal Motif Recognition by PDZ Domains

Baruch Z. Harris, Brian J. Hillier, and Wendell A. Lim

Biochemistry 40, 5921-5930 (2001)

Abstract. PDF.

Integration of Multiple Signals Through Cooperative Regulation of the N-WASP-Arp2/3 Complex

Kenneth E. Prehoda, Jessica A. Scott, R. Dyche Mullins, and Wendell A. Lim

Science 290, 801-806 (2000)

Abstract. PDF. Supplemental Data.

Converging on proline: the mechanism of WW domain peptide recognition

Ali Zarrinpar and Wendell A. Lim

Nature Structural Biology 7, 611-613 (2000)

Abstract. PDF.

Improving SH3 domain ligand selectivity using a non-natural scaffold

Jack T. Nguyen, Margaret Porter, Mehran Amoui, W. Todd Miller, Ronald N. Zuckermann and Wendell A. Lim

Chemistry & Biology 7, 463-473 (2000)

Abstract. PDF.

PSD-95 Assembles a Ternary Complex with the N-Methyl-D-aspartic Acid Receptor and a Bivalent Neuronal NO Synthase PDZ Domain

Karen S. Christopherson, Brian J. Hillier, Wendell A. Lim, and David S. Bredt

Journal of Biological Chemistry 274, 27467-27473 (1999)

Abstract. PDF.

Structure of the Enabled/VASP Homology 1 Domain–Peptide Complex: A Key Component in the Spatial Control of Actin Assembly

Kenneth E. Prehoda, Do. J. Lee, and Wendell A. Lim

Cell 97, 471-480 (1999)

Abstract. PDF.

Unexpected Modes of PDZ Domain Scaffolding Revealed by Structure of nNOS-Syntrophin Complex

Brian J. Hillier, Karen S. Christopherson, Kenneth E. Prehoda, David S. Bredt, and Wendell A. Lim

Science 284, 812-815 (1999)

Abstract. PDF.

Exploiting the Basis of Proline Recognition by SH3 and WW Domains: Design of N-Substituted Inhibitors

Jack T. Nguyen, Christoph W. Turck, Fred E. Cohen, Ronald N. Zuckermann, and Wendell A. Lim

Science 282, 2088-2092 (1998)

Abstract. PDF.
CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing.

Moreno-Mateos MA, Fernandez JP, Rouet R, Vejnar CE, Lane MA, Mis E, Khokha MK, Doudna JA, Giraldez AJ.
Nat Commun. 2017 Dec 8;8(1):2024. doi: 10.1038/s41467-017-01836-2.

Widespread Translational Remodeling during Human Neuronal Differentiation.

Blair JD, Hockemeyer D, Doudna JA, Bateup HS, Floor SN.
Cell Rep. 2017 Nov 14;21(7):2005-2016. doi: 10.1016/j.celrep.2017.10.095.

A thermostable Cas9 with increased lifetime in human plasma.

Harrington LB, Paez-Espino D, Staahl BT, Chen JS, Ma E, Kyrpides NC, Doudna JA
Nat Commun. 2017 Nov 10;8(1):1424. doi: 10.1038/s41467-017-01408-4.

GENOMES IN FOCUS: DEVELOPMENT AND APPLICATIONS OF CRISPR-CAS9 IMAGING TECHNOLOGIES.

Knight S, Tjian R, Doudna J.
Angew Chem Int Ed Engl. 2017 Oct 27. doi: 10.1002/anie.201709201. [Epub ahead of print]

Enhanced proofreading governs CRISPR-Cas9 targeting accuracy.

Chen JS, Dagdas YS, Kleinstiver BP, Welch MM, Sousa AA, Harrington LB, Sternberg SH, Joung JK, Yildiz A, Doudna JA.
Nature. 2017 Sep 20. doi: 10.1038/nature24268. [Epub ahead of print]

Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme.

Knott GJ, East-Seletsky A, Cofsky JC, Holton JM, Charles E, O'Connell MR, Doudna JA.
Nat Struct Mol Biol. 2017 Sep 11. doi: 10.1038/nsmb.3466. [Epub ahead of print]

A Broad-Spectrum Inhibitor of CRISPR-Cas9.

Harrington LB, Doxzen KW, Ma E, Liu JJ, Knott GJ, Edraki A, Garcia B, Amrani N, Chen JS, Cofsky JC, Kranzusch PJ, Sontheimer EJ, Davidson AR, Maxwell KL, Doudna JA.
Cell. 2017 Aug 23. pii: S0092-8674(17)30873-5. doi: 10.1016/j.cell.2017.07.037. [Epub ahead of print]

A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9.

Dagdas YS, Chen JS, Sternberg SH, Doudna JA, Yildiz A.
Sci Adv. 2017 Aug 4;3(8):eaao0027. doi: 10.1126/sciadv.aao0027. eCollection 2017 Aug.

Structures of the CRISPR genome integration complex.

Wright AV, Liu JJ, Knott GJ, Doxzen KW, Nogales E, Doudna JA.
Science. 2017 Jul 20. pii: eaao0679. doi: 10.1126/science.aao0679. [Epub ahead of print]

Disabling Cas9 by an anti-CRISPR DNA mimic.

Shin J, Jiang F, Liu JJ, Bray NL, Rauch BJ, Baik SH, Nogales E, Bondy-Denomy J, Corn JE, Doudna JA.
Science Advances 2017 Jul 12;3(7):e1701620. doi: 10.1126/sciadv.1701620. eCollection 2017 Jul.

DNA recognition by an RNA-guided bacterial Argonaute.

Doxzen KW, Doudna JA.
PLoS One. 2017 May 17;12(5):e0177097. doi: 10.1371/journal.pone.0177097. eCollection 2017.

High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding.

Boyle EA, Andreasson JOL, Chircus LM, Sternberg SH, Wu MJ, Guegler CK, Doudna JA, Greenleaf WJ.
Proc Natl Acad Sci U S A. 2017 May 11. pii: 201700557. doi: 10.1073/pnas.1700557114. [Epub ahead of print]

RNA Targeting by Functionally Orthogonal Type VI-A CRISPR-Cas Enzymes.

East-Seletsky A, O'Connell MR, Burstein D, Knott GJ, Doudna JA.
Mol Cell. 2017 May 4;66(3):373-383.e3. doi: 10.1016/j.molcel.2017.04.008.

CRISPR-Cas9 Structures and Mechanisms.

Jiang F, Doudna JA.
Annu Rev Biophys. 2017 Mar 30. doi: 10.1146/annurev-biophys-062215-010822. [Epub ahead of print]

Targeted gene knock-in by homology-directed genome editing using Cas9 ribonucleoprotein and AAV donor delivery.

Gaj T, Staahl BT, Rodrigues GM, Limsirichai P, Ekman FK, Doudna JA, Schaffer DV.
Nucleic Acids Res. 2017 Mar 2. doi: 10.1093/nar/gkx154. [Epub ahead of print]

Selective stalling of human translation through small-molecule engagement of the ribosome nascent chain.

Lintner NG, McClure KF, Petersen D, Londregan AT, Piotrowski DW, Wei L, Xiao J, Bolt M, Loria PM, Maguire B, Geoghegan KF, Huang A, Rolph T, Liras S, Doudna JA, Dullea RG, Cate JH.
PLoS Biol. 2017 Mar 21;15(3):e2001882. doi: 10.1371/journal.pbio.2001882. eCollection 2017.

RNA-based recognition and targeting: sowing the seeds of specificity.

Gorski SA, Vogel J, Doudna JA.
Nat Rev Mol Cell Biol. 2017 Feb 15. doi: 10.1038/nrm.2016.174. [Epub ahead of print]

Efficient genome editing in the mouse brain by local delivery of engineered Cas9 ribonucleoprotein complexes.

Staahl BT, Benekareddy M, Coulon-Bainier C, Banfal AA, Floor SN, Sabo JK, Urnes C, Munares GA, Ghosh A Doudna JA.
Nat Biotechnol. 2017 Feb 13. doi: 10.1038/nbt.3806. [Epub ahead of print]

RNA and DNA Targeting by a Reconstituted Thermus thermophiles Type III-A CRISPR-Cas System.

Liu TY, Iavarone AT, Doudna JA.
PLoS One. 2017 Jan 23;12(1):e0170552. doi: 10.1371/journal.pone.0170552. eCollection 2017.

Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response.

Heler R, Wright AV, Vucelja M, Bikard D, Doudna JA, Marraffini LA.
Mol Cell. 2017 Jan 5;65(1):168-175. doi: 10.1016/j.molcel.2016.11.031. Epub 2016 Dec 22.

Cornerstones of CRISPR-Cas in drug discovery and therapy.

Fellmann C, Gowen BG, Lin PC, Doudna JA, Corn JE.
Nat Rev Drug Discov. 2016 Dec 23. doi: 10.1038/nrd.2016.238. [Epub ahead of print]

New CRISPR-Cas systems from uncultivated microbes.

Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K, Thomas BC, Doudna JA, Banfield JF.
Nature. 2016 Dec 22. doi: 10.1038/nature21059. [Epub ahead of print]

RNA scanning of a molecular machine with a built-in ruler.

Koh HR, Kidwell MA, Doudna JA, Myong S.
J Am Chem Soc. 2016 Dec 13. [Epub ahead of print]

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing.

Chen X, Shen Y, Draper W, Buenrostro JD, Litzenburger U, Cho SW, Satpathy AT, Carter AC, Ghosh RP, East-Seletsky A, Doudna JA, Greenleaf WJ, Liphardt JT, Chang HY.
Nat Methods. 2016 Oct 17. doi: 10.1038/nmeth.4031. [Epub ahead of print]

A Cas9 Ribonucleoprotein Platform for Functional Genetic Studies of HIV-Host Interactions in Primary Human T Cells.

Hultquist JF, Schumann K, Woo JM, Manganaro L, McGregor MJ, Doudna J, Simon V, Krogan NJ, Marson A.
Cell Rep. 2016 Oct 25;17(5):1438-1452. doi: 10.1016/j.celrep.2016.09.080.

Insights into HIV-1 proviral transcription from the structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex.

Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna JA, Zhou Q, Sali A, Hurley JH.
Elife.2016 Oct 12;5. pii: e15910. doi: 10.7554/eLife.15910. [Epub ahead of print]

Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection.

East-Seletsky A, O'Connell MR, Knight SC, Burstein D, Cate JH, Tjian R, Doudna JA.
Nature. 2016 Sep 26. doi: 10.1038/nature19802. [Epub ahead of print]

Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9.

Singh D, Sternberg SH, Fei J, Doudna JA, Ha T.
Nat Commun. 2016 Sep 14;7:12778. doi: 10.1038/ncomms12778.

Applications of CRISPR technologies in research and beyond.

Barrangou R, Doudna JA.
Nat Biotechnol. 2016 Sep 8:933-941. doi: 10.1038/nbt.3659. [Epub ahead of print]

Protecting genome integrity during CRISPR immune adaptation.

Wright AV, Doudna JA.
Nat Struct Mol Biol.2016 Sep 5. doi: 10.1038/nsmb.3289. [Epub ahead of print]

DNA Targeting by a Minimal CRISPR RNA-Guided Cascade.

Hochstrasser ML, Taylor DW, Kornfeld JE, Nogales E, Doudna JA.
Mol Cell. 2016 Sep 1;63(5):840-51. doi: 10.1016/j.molcel.2016.07.027.

eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation.

Lee AS, Kranzusch PJ, Doudna JA, Cate JH.
Nature. 2016 Jul 27. doi: 10.1038/nature18954. [Epub ahead of print]

Reconstitution of selective HIV-1 RNA packaging in vitro by membrane-bound Gag assemblies.

Carlson LA, Bai Y, Keane SC, Doudna JA, Hurley JH.
Elife 2016 Jun 25;pii: e14663. doi: 10.7554/eLife.14663. [Epub ahead of print]

CRISPR Immunological Memory Requires a Host Factor for Specificity.

Nuñez JK, Bai L, Harrington LB, Hinder TL, Doudna JA.
Mol Cell 2016 Jun 16;62(6):824-33.

Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch.

Oakes BL, Nadler DC, Flamholz A, Fellmann C, Staahl BT, Doudna JA Savage DF.
Nat Biotechnol. 2016 Jun;34(6):646-51.

Nucleosome breathing and remodeling constrain CRISPR-Cas9 function.

Isaac RS, Jiang F, Doudna JA, Lim WA, Narlikar GJ, Almeida RA
Elife 2016 Apr 28;5. pii: e13450.

Programmable RNA Tracking in Live Cells with CRISPR/Cas9.

Nelles DA, Fang MY, O'Connell MR, Xu JL, Markmiller SJ, Doudna JA, Yeo GW
Cell 2016 Apr 7;165(2):488-96.

Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress.

Oh S, Flynn RA, Floor SN, Purzner J, Martin L, Do BT, Schubert S, Vaka D, Morrissy S, Li Y, Kool M, Hovestadt V, Jones DT, Northcott PA, Risch T, Warnatz HJ, Yaspo ML, Adams CM, Leib RD, Breese M, Marra MA, Malkin D, Lichter P, Doudna JA, Pfister SM, Taylor MD, Chang HY, Cho YJ.
Oncotarget 2016 Apr 5

A bacterial Argonaute with noncanonical guide RNA specificity.

Kaya E, Doxzen KW, Knoll KR, Wilson RC, Strutt SC, Kranzusch PJ, Doudna JA.
Proc Natl Acad Sci U S A 2016 Mar 30

Programmable RNA Tracking in Live Cells with CRISPR/Cas9.

Nelles DA, Fang MY, O'Connell MR, Xu JL, Markmiller SJ, Doudna JA, Yeo GW.
Cell 2016 Mar 16

Chemical and Biophysical Modulation of Cas9 for Tunable Genome Engineering.

Nuñez JK, Harrington LB, Doudna JA.
ACS Chem Biol 2016 Feb 9

Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage.

Jiang F, Taylor DW, Chen JS, Kornfeld JE, Zhou K, Thompson AJ, Nogales E, Doudna JA
Science 2016 Jan 14. pii: aad8282.

Biology and Applications of CRISPR Systems: Harnessing Nature's Toolbox for Genome Engineering.

Wright AV, Nuñez JK, Doudna JA
Cell 2016 Jan 14;164(1-2):29-44.

Tunable protein synthesis by transcript isoforms in human cells.

Floor SN, Doudna JA
eLife 2016 Jan 6;5. pii: e10921

Genome-editing revolution: My whirlwind year with CRISPR.

Doudna JA
Nature 2015 Dec 24;528(7583):469-71

Genome editing: the end of the beginning.

Doudna JA, Gersbach CA
Genome Biol 2015 Dec 23;16(1):292

Analog sensitive chemical inhibition of the DEAD-box protein DDX3.

Floor SN, Barkovich KJ, Condon KJ, Shokat KM, Doudna JA
Protein Sci 2015 Dec 9;

Get in LINE: Competition for Newly Minted Retrotransposon Proteins at the Ribosome.

Floor SN, Doudna JA
Mol Cell 2015 Dec 3;60(5):712-4

Perspective: Embryo editing needs scrutiny.

Doudna J
Nature 2015 Dec 3;528(7580):S6

Autoinhibitory Interdomain Interactions and Subfamily-Specific Extensions Redefine the Catalytic Core of the Human DEAD-box Protein DDX3.

Floor SN, Condon KJ, Sharma D, Jankowsky E, Doudna JA
J Biol Chem 2015 Nov 23;

Dynamics of CRISPR-Cas9 genome interrogation in living cells.

Knight SC, Xie L, Deng W, Guglielmi B, Witkowsky LB, Bosanac L, Zhang ET, El Beheiry M, Masson JB, Dahan M, Liu Z, Doudna JA, Tjian R
Science 2015 Nov 13;350(6262):823-6

Single-Stranded DNA Cleavage by Divergent CRISPR-Cas9 Enzymes.

Ma E, Harrington LB, O'Connell MR, Zhou K, Doudna JA
Mol Cell 2015 Nov 5;60(3):398-407 PMCID: PMC4636735

Conformational control of DNA target cleavage by CRISPR-Cas9.

Sternberg SH, LaFrance B, Kaplan M, Doudna JA
Nature 2015 Nov 5;527(7576):110-3

Surveillance and Processing of Foreign DNA by the Escherichia coli CRISPR-Cas System.

Redding S, Sternberg SH, Marshall M, Gibb B, Bhat P, Guegler CK, Wiedenheft B, Doudna JA, Greene EC
Cell 2015 Nov 5;163(4):854-65 PMCID: PMC4636941

Foreign DNA capture during CRISPR-Cas adaptive immunity.

Nuñez JK, Harrington LB, Kranzusch PJ, Engelman AN, Doudna JA
Nature 2015 Nov 26;527(7579):535-8 PMCID: PMC4662619

Ancient Origin of cGAS-STING Reveals Mechanism of Universal 2',3' cGAMP Signaling.

Kranzusch PJ, Wilson SC, Lee AS, Berger JM, Doudna JA, Vance RE
Mol Cell 2015 Sep 17;59(6):891-903 PMCID: PMC4575873

Generation of knock-in primary human T cells using Cas9 ribonucleoproteins.

Schumann K, Lin S, Boyer E, Simeonov DR, Subramaniam M, Gate RE, Haliburton GE, Ye CJ, Bluestone JA, Doudna JA, Marson A
Proc Natl Acad Sci U S A 2015 Aug 18;112(33):10437-42 PMCID: PMC4547290

STRUCTURAL BIOLOGY. A Cas9-guide RNA complex preorganized for target DNA recognition.

Jiang F, Zhou K, Ma L, Gressel S, Doudna JA
Science 2015 Jun 26;348(6242):1477-81

Expanding the Biologist's Toolkit with CRISPR-Cas9.

Sternberg SH, Doudna JA
Mol Cell 2015 May 21;58(4):568-74

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 2015 May;33(5):478-86

Structural biology. Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning.

Taylor DW, Zhu Y, Staals RH, Kornfeld JE, Shinkai A, van der Oost J, Nogales E, Doudna JA
Science 2015 May 1;348(6234):581-5 PMCID: PMC4582657

Biotechnology. A prudent path forward for genomic engineering and germline gene modification. (Free Full Text) (Free PDF)

Baltimore D, Berg P, Botchan M, Carroll D, Charo RA, Church G, Corn JE, Daley GQ, Doudna JA, Fenner M, Greely HT, Jinek M, Martin GS, Penhoet E, Puck J, Sternberg SH, Weissman JS, Yamamoto KR
Science 2015 Apr 3;348(6230):36-8 PMCID: PMC4394183

The structural biology of CRISPR-Cas systems.

Jiang F, Doudna JA
Curr Opin Struct Biol 2015 Feb;30:100-11 PMCID: PMC4417044

Rational design of a split-Cas9 enzyme complex.

Wright AV, Sternberg SH, Taylor DW, Staahl BT, Bardales JA, Kornfeld JE, Doudna JA
Proc Natl Acad Sci U S A 2015 Mar 10;112(10):2984-9 PMCID: PMC4364227

Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity.

Nuñez JK, Lee AS, Engelman A, Doudna JA
Nature 2015 Mar 12;519(7542):193-8 PMCID: PMC4359072

Dicer-TRBP complex formation ensures accurate mammalian microRNA biogenesis.

Wilson RC, Tambe A, Kidwell MA, Noland CL, Schneider CP, Doudna JA
Mol Cell 2015 Feb 5;57(3):397-407 PMCID: PMC4320653

Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery.

Lin S, Staahl BT, Alla RK, Doudna JA
Elife 2014 Dec 15;3:e04766 PMCID: PMC4383097

Cutting it close: CRISPR-associated endoribonuclease structure and function.

Hochstrasser ML, Doudna JA
Trends Biochem Sci 2015 Jan;40(1):58-66

RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus.

Staals RH, Zhu Y, Taylor DW, Kornfeld JE, Sharma K, Barendregt A, Koehorst JJ, Vlot M, Neupane N, Varossieau K, Sakamoto K, Suzuki T, Dohmae N, Yokoyama S, Schaap PJ, Urlaub H, Heck AJ, Nogales E, Doudna JA, Shinkai A, van der Oost J
Mol Cell 2014 Nov 20;56(4):518-30 PMCID: PMC4342149

Genome editing. The new frontier of genome engineering with CRISPR-Cas9. (Free Full Text)

Doudna JA, Charpentier E
Science 2014 Nov 28;346(6213):1258096

New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.

Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS
Nucleic Acids Res 2014 Nov 10;42(20):12833-46 PMCID: PMC4227795

Programmable RNA recognition and cleavage by CRISPR/Cas9.

O'Connell MR, Oakes BL, Sternberg SH, East-Seletsky A, Kaplan M, Doudna JA
Nature 2014 Dec 11;516(7530):263-6 PMCID: PMC4268322

RNA-guided assembly of Rev-RRE nuclear export complexes.

Bai Y, Tambe A, Zhou K, Doudna JA
Elife 2014 Aug 27;3:e03656 PMCID: PMC4142337

Evolutionarily conserved roles of the dicer helicase domain in regulating RNA interference processing.

Kidwell MA, Chan JM, Doudna JA
J Biol Chem 2014 Oct 10;289(41):28352-62 PMCID: PMC4192488

Structure-guided reprogramming of human cGAS dinucleotide linkage specificity.

Kranzusch PJ, Lee AS, Wilson SC, Solovykh MS, Vance RE, Berger JM, Doudna JA
Cell 2014 Aug 28;158(5):1011-21 PMCID: PMC4157622

Insights into RNA structure and function from genome-wide studies.

Mortimer SA, Kidwell MA, Doudna JA
Nat Rev Genet 2014 Jul;15(7):469-79

Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity.

Nuñez JK, Kranzusch PJ, Noeske J, Wright AV, Davies CW, Doudna JA
Nat Struct Mol Biol 2014 Jun;21(6):528-34 PMCID: PMC4075942

CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference.

Hochstrasser ML, Taylor DW, Bhat P, Guegler CK, Sternberg SH, Nogales E, Doudna JA
Proc Natl Acad Sci U S A 2014 May 6;111(18):6618-23 PMCID: PMC4020112

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9.

Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA
Nature 2014 Mar 6;507(7490):62-7 PMCID: PMC4106473

Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases.

Niewoehner O, Jinek M, Doudna JA
Nucleic Acids Res 2014 Jan;42(2):1341-53 PMCID: PMC3902920

Precise and heritable genome editing in evolutionarily diverse nematodes using TALENs and CRISPR/Cas9 to engineer insertions and deletions.

Lo TW, Pickle CS, Lin S, Ralston EJ, Gurling M, Schartner CM, Bian Q, Doudna JA, Meyer BJ
Genetics 2013 Oct;195(2):331-48 PMCID: PMC3781963

High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity.

Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna JA, Liu DR
Nat Biotechnol 2013 Sep;31(9):839-43 PMCID: PMC3782611

CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes.

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
Cell 2013 Jul 18;154(2):442-51

Hepatitis C virus 3'UTR regulates viral translation through direct interactions with the host translation machinery.

Bai Y, Zhou K, Doudna JA
Nucleic Acids Res 2013 Sep;41(16):7861-74 PMCID: PMC3763534

Two RNA-binding motifs in eIF3 direct HCV IRES-dependent translation.

Sun C, Querol-Audí J, Mortimer SA, Arias-Palomo E, Doudna JA, Nogales E, Cate JH
Nucleic Acids Res 2013 Aug;41(15):7512-21 PMCID: PMC3753635

Structure of human cGAS reveals a conserved family of second-messenger enzymes in innate immunity.

Kranzusch PJ, Lee AS, Berger JM, Doudna JA
Cell Rep 2013 May 30;3(5):1362-8 PMCID: PMC3800681

Differential roles of human Dicer-binding proteins TRBP and PACT in small RNA processing.

Lee HY, Zhou K, Smith AM, Noland CL, Doudna JA
Nucleic Acids Res 2013 Jul;41(13):6568-76 PMCID: PMC3711433

Substrate-specific structural rearrangements of human Dicer.

Taylor DW, Ma E, Shigematsu H, Cianfrocco MA, Noland CL, Nagayama K, Nogales E, Doudna JA, Wang HW
Nat Struct Mol Biol 2013 Jun;20(6):662-70 PMCID: PMC3676429

Multiple sensors ensure guide strand selection in human RNAi pathways.

Noland CL, Doudna JA
RNA 2013 May;19(5):639-48 PMCID: PMC3677279

RNA-protein analysis using a conditional CRISPR nuclease.

Lee HY, Haurwitz RE, Apffel A, Zhou K, Smart B, Wenger CD, Laderman S, Bruhn L, Doudna JA
Proc Natl Acad Sci U S A 2013 Apr 2;110(14):5416-21 PMCID: PMC3619310

Unconventional miR-122 binding stabilizes the HCV genome by forming a trimolecular RNA structure.

Mortimer SA, Doudna JA
Nucleic Acids Res 2013 Apr;41(7):4230-40 PMCID: PMC3627571

RNA-programmed genome editing in human cells.

Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J
Elife 2013 Jan 29;2:e00471 PMCID: PMC3557905

TRBP alters human precursor microRNA processing in vitro.

Lee HY, Doudna JA
RNA 2012 Nov;18(11):2012-9 PMCID: PMC3479391

RNA processing enables predictable programming of gene expression.

Qi L, Haurwitz RE, Shao W, Doudna JA, Arkin AP
Nat Biotechnol 2012 Oct;30(10):1002-6

A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.

Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E
Science 2012 Aug 17;337(6096):816-21

Coordinated activities of human dicer domains in regulatory RNA processing.

Ma E, Zhou K, Kidwell MA, Doudna JA
J Mol Biol 2012 Sep 28;422(4):466-76 PMCID: PMC3461841

Biochemistry. Guided tour to the heart of RISC.

Kaya E, Doudna JA
Science 2012 May 25;336(6084):985-6

Csy4 relies on an unusual catalytic dyad to position and cleave CRISPR RNA.

Haurwitz RE, Sternberg SH, Doudna JA
EMBO J 2012 Jun 13;31(12):2824-32 PMCID: PMC3380207

Mechanism of foreign DNA selection in a bacterial adaptive immune system.

Sashital DG, Wiedenheft B, Doudna JA
Mol Cell 2012 Jun 8;46(5):606-15 PMCID: PMC3397241

Mechanism of substrate selection by a highly specific CRISPR endoribonuclease.

Sternberg SH, Haurwitz RE, Doudna JA
RNA 2012 Apr;18(4):661-72 PMCID: PMC3312554

Reassortment and mutation of the avian influenza virus polymerase PA subunit overcome species barriers.

Mehle A, Dugan VG, Taubenberger JK, Doudna JA
J Virol 2012 Feb;86(3):1750-7 PMCID: PMC3264373

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