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    Wendell Lim, PhD

    TitleProfessor
    SchoolUCSF School of Medicine
    DepartmentCMP (Cellular Molecular Pha)
    Address600 16th Street
    San Francisco CA 94158
    Phone415-502-8080
      Other Positions
      TitleHoward Hughes Investigator


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       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Youk H, Lim WA. Sending mixed messages for cell population control. Cell. 2014 Aug 28; 158(5):973-5.
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      2. Park JS, Rhau B, Hermann A, McNally KA, Zhou C, Gong D, Weiner OD, Conklin BR, Onuffer J, Lim WA. Synthetic control of mammalian-cell motility by engineering chemotaxis to an orthogonal bioinert chemical signal. Proc Natl Acad Sci U S A. 2014 Apr 22; 111(16):5896-901.
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      3. Youk H, Lim WA. Secreting and sensing the same molecule allows cells to achieve versatile social behaviors. Science. 2014 Feb 7; 343(6171):1242782.
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      4. Toettcher JE, Weiner OD, Lim WA. Using optogenetics to interrogate the dynamic control of signal transmission by the ras/erk module. Cell. 2013 Dec 5; 155(6):1422-34.
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      5. Moser F, Horwitz A, Chen J, Lim W, Voigt CA. Genetic sensor for strong methylating compounds. ACS Synth Biol. 2013 Oct 18; 2(10):614-24.
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      6. Larson MH, Gilbert LA, Wang X, Lim WA, Weissman JS, Qi LS. CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nat Protoc. 2013 Nov; 8(11):2180-96.
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      7. Dandekar SN, Park JS, Peng GE, Onuffer JJ, Lim WA, Weiner OD. Actin dynamics rapidly reset chemoattractant receptor sensitivity following adaptation in neutrophils. Philos Trans R Soc Lond B Biol Sci. 2013; 368(1629):20130008.
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      8. Puchner EM, Walter JM, Kasper R, Huang B, Lim WA. Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory. Proc Natl Acad Sci U S A. 2013 Oct 1; 110(40):16015-20.
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      9. Coyle SM, Flores J, Lim WA. Exploitation of latent allostery enables the evolution of new modes of MAP kinase regulation. Cell. 2013 Aug 15; 154(4):875-87.
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      10. 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. 2013 Jul 18; 154(2):442-51.
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      11. Lee S, Lim WA, Thorn KS. Improved blue, green, and red fluorescent protein tagging vectors for S. cerevisiae. PLoS One. 2013; 8(7):e67902.
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      12. Hynes NE, Ingham PW, Lim WA, Marshall CJ, Massagué J, Pawson T. Signalling change: signal transduction through the decades. Nat Rev Mol Cell Biol. 2013 Jun; 14(6):393-8.
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      13. Fischbach MA, Bluestone JA, Lim WA. Cell-based therapeutics: the next pillar of medicine. Sci Transl Med. 2013 Apr 3; 5(179):179ps7.
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      14. 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. 2013 Feb 28; 152(5):1173-83.
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      15. Lim WA, Lee CM, Tang C. Design principles of regulatory networks: searching for the molecular algorithms of the cell. Mol Cell. 2013 Jan 24; 49(2):202-12.
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      16. Lim WA, Alvania R, Marshall WF. Cell biology 2.0. Trends Cell Biol. 2012 Dec; 22(12):611-2.
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      17. Chau AH, Walter JM, Gerardin J, Tang C, Lim WA. Designing synthetic regulatory networks capable of self-organizing cell polarization. Cell. 2012 Oct 12; 151(2):320-32.
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      18. Lim W. Wendell Lim: exploring the path not chosen. Interview by Caitlin Sedwick. J Cell Biol. 2012 Sep 17; 198(6):956-7.
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      19. Maiuri P, Terriac E, Paul-Gilloteaux P, Vignaud T, McNally K, Onuffer J, Thorn K, Nguyen PA, Georgoulia N, Soong D, Jayo A, Beil N, Beneke J, Lim JC, Sim CP, Chu YS. The first World Cell Race. Curr Biol. 2012 Sep 11; 22(17):R673-5.
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      20. Wei P, Wong WW, Park JS, Corcoran EE, Peisajovich SG, Onuffer JJ, Weiss A, Lim WA. Bacterial virulence proteins as tools to rewire kinase pathways in yeast and immune cells. Nature. 2012 Aug 16; 488(7411):384-8.
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      21. Zalatan JG, Coyle SM, Rajan S, Sidhu SS, Lim WA. Conformational control of the Ste5 scaffold protein insulates against MAP kinase misactivation. Science. 2012 Sep 7; 337(6099):1218-22.
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      22. Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ. Systematic functional prioritization of protein posttranslational modifications. Cell. 2012 Jul 20; 150(2):413-25.
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      23. Thompson KE, Bashor CJ, Lim WA, Keating AE. SYNZIP protein interaction toolbox: in vitro and in vivo specifications of heterospecific coiled-coil interaction domains. ACS Synth Biol. 2012 Apr 20; 1(4):118-29.
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      24. Kapp GT, Liu S, Stein A, Wong DT, Reményi A, Yeh BJ, Fraser JS, Taunton J, Lim WA, Kortemme T. Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair. Proc Natl Acad Sci U S A. 2012 Apr 3; 109(14):5277-82.
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      25. Toettcher JE, Gong D, Lim WA, Weiner OD. Light-based feedback for controlling intracellular signaling dynamics. Nat Methods. 2011; 8(10):837-9.
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      26. Won AP, Garbarino JE, Lim WA. Recruitment interactions can override catalytic interactions in determining the functional identity of a protein kinase. Proc Natl Acad Sci U S A. 2011 Jun 14; 108(24):9809-14.
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      27. Good MC, Zalatan JG, Lim WA. Scaffold proteins: hubs for controlling the flow of cellular information. Science. 2011 May 6; 332(6030):680-6.
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      28. Smith AG, Lim W, Pearen M, Muscat GE, Sturm RA. Regulation of NR4A nuclear receptor expression by oncogenic BRAF in melanoma cells. Pigment Cell Melanoma Res. 2011 Jun; 24(3):551-63.
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      29. Toettcher JE, Gong D, Lim WA, Weiner OD. Light control of plasma membrane recruitment using the Phy-PIF system. Methods Enzymol. 2011; 497:409-23.
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      30. Toettcher JE, Voigt CA, Weiner OD, Lim WA. The promise of optogenetics in cell biology: interrogating molecular circuits in space and time. Nat Methods. 2011 Jan; 8(1):35-8.
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      31. Elowitz M, Lim WA. Build life to understand it. Nature. 2010 Dec 16; 468(7326):889-90.
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      32. Lim WA, Pawson T. Phosphotyrosine signaling: evolving a new cellular communication system. Cell. 2010 Sep 3; 142(5):661-7.
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      33. Ahmad KF, Lim WA. The minimal autoinhibited unit of the guanine nucleotide exchange factor intersectin. PLoS One. 2010; 5(6):e11291.
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      34. Lim WA. Designing customized cell signalling circuits. Nat Rev Mol Cell Biol. 2010 Jun; 11(6):393-403.
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      35. Peisajovich SG, Garbarino JE, Wei P, Lim WA. Rapid diversification of cell signaling phenotypes by modular domain recombination. Science. 2010 Apr 16; 328(5976):368-72.
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      36. Mok J, Kim PM, Lam HY, Piccirillo S, Zhou X, Jeschke GR, Sheridan DL, Parker SA, Desai V, Jwa M, Cameroni E, Niu H, Good M, Remenyi A, Ma JL, Sheu YJ, Sassi HE, Sopko R, Chan CS, De Virgilio C, Hollingsworth NM, Lim WA, Stern DF, Stillman B, Andrews BJ, Gerstein MB, Snyder M, Turk BE. Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci Signal. 2010; 3(109):ra12.
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      37. Bashor CJ, Horwitz AA, Peisajovich SG, Lim WA. Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems. Annu Rev Biophys. 2010; 39:515-37.
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      38. Yadav SS, Yeh BJ, Craddock BP, Lim WA, Miller WT. Reengineering the signaling properties of a Src family kinase. Biochemistry. 2009 Nov 24; 48(46):10956-62.
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      39. Rivera GM, Vasilescu D, Papayannopoulos V, Lim WA, Mayer BJ. A reciprocal interdependence between Nck and PI(4,5)P(2) promotes localized N-WASp-mediated actin polymerization in living cells. Mol Cell. 2009 Nov 13; 36(3):525-35.
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      40. Levskaya A, Weiner OD, Lim WA, Voigt CA. Spatiotemporal control of cell signalling using a light-switchable protein interaction. Nature. 2009 Oct 15; 461(7266):997-1001.
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      41. Ma W, Trusina A, El-Samad H, Lim WA, Tang C. Defining network topologies that can achieve biochemical adaptation. Cell. 2009 Aug 21; 138(4):760-73.
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      42. Zeke A, Lukács M, Lim WA, Reményi A. Scaffolds: interaction platforms for cellular signalling circuits. Trends Cell Biol. 2009 Aug; 19(8):364-74.
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      43. Tan CS, Pasculescu A, Lim WA, Pawson T, Bader GD, Linding R. Positive selection of tyrosine loss in metazoan evolution. Science. 2009 Sep 25; 325(5948):1686-8.
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      44. Beltrao P, Trinidad JC, Fiedler D, Roguev A, Lim WA, Shokat KM, Burlingame AL, Krogan NJ. Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. PLoS Biol. 2009 Jun 16; 7(6):e1000134.
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      45. Good M, Tang G, Singleton J, Reményi A, Lim WA. The Ste5 scaffold directs mating signaling by catalytically unlocking the Fus3 MAP kinase for activation. Cell. 2009 Mar 20; 136(6):1085-97.
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      46. Lim WA. Frederic M Richards 1925-2009. Nat Struct Mol Biol. 2009 Mar; 16(3):230-2.
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      47. Sallee NA, Rivera GM, Dueber JE, Vasilescu D, Mullins RD, Mayer BJ, Lim WA. The pathogen protein EspF(U) hijacks actin polymerization using mimicry and multivalency. Nature. 2008 Aug 21; 454(7207):1005-8.
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      48. Pincus D, Letunic I, Bork P, Lim WA. Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages. Proc Natl Acad Sci U S A. 2008 Jul 15; 105(28):9680-4.
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      49. Bashor CJ, Helman NC, Yan S, Lim WA. Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Science. 2008 Mar 14; 319(5869):1539-43.
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      50. King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I, Marr M, Pincus D, Putnam N, Rokas A, Wright KJ, Zuzow R, Dirks W, Good M, Goodstein D, Lemons D, Li W, Lyons JB, Morris A, Nichols S, Richter DJ, Salamov A, Sequencing JG, Bork P, Lim WA, Manning G, Miller WT, McGinnis W, Shapiro H, Tjian R, Grigoriev IV, Rokhsar D. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature. 2008 Feb 14; 451(7180):783-8.
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      51. Lee PJ, Helman NC, Lim WA, Hung PJ. A microfluidic system for dynamic yeast cell imaging. Biotechniques. 2008 Jan; 44(1):91-5.
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      52. Yeh BJ, Lim WA. Synthetic biology: lessons from the history of synthetic organic chemistry. Nat Chem Biol. 2007 Sep; 3(9):521-5.
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      53. Yeh BJ, Rutigliano RJ, Deb A, Bar-Sagi D, Lim WA. Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors. Nature. 2007 May 31; 447(7144):596-600.
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      54. Dueber JE, Mirsky EA, Lim WA. Engineering synthetic signaling proteins with ultrasensitive input/output control. Nat Biotechnol. 2007 Jun; 25(6):660-2.
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      55. Sallee NA, Yeh BJ, Lim WA. Engineering modular protein interaction switches by sequence overlap. J Am Chem Soc. 2007 Apr 18; 129(15):4606-11.
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      56. Peterson FC, Deng Q, Zettl M, Prehoda KE, Lim WA, Way M, Volkman BF. Multiple WASP-interacting protein recognition motifs are required for a functional interaction with N-WASP. J Biol Chem. 2007 Mar 16; 282(11):8446-53.
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      57. Hammond MC, Harris BZ, Lim WA, Bartlett PA. Beta strand peptidomimetics as potent PDZ domain ligands. Chem Biol. 2006 Dec; 13(12):1247-51.
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      58. Reményi A, Good MC, Lim WA. Docking interactions in protein kinase and phosphatase networks. Curr Opin Struct Biol. 2006 Dec; 16(6):676-85.
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      59. Bhattacharyya RP, Reményi A, Good MC, Bashor CJ, Falick AM, Lim WA. The Ste5 scaffold allosterically modulates signaling output of the yeast mating pathway. Science. 2006 Feb 10; 311(5762):822-6.
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      60. Bhattacharyya RP, Reményi A, Yeh BJ, Lim WA. Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annu Rev Biochem. 2006; 75:655-80.
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      61. Reményi A, Good MC, Bhattacharyya RP, Lim WA. The role of docking interactions in mediating signaling input, output, and discrimination in the yeast MAPK network. Mol Cell. 2005 Dec 22; 20(6):951-62.
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      62. Petrosky KY, Ou HD, Löhr F, Dötsch V, Lim WA. A general model for preferential hetero-oligomerization of LIN-2/7 domains: mechanism underlying directed assembly of supramolecular signaling complexes. J Biol Chem. 2005 Nov 18; 280(46):38528-36.
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      63. Papayannopoulos V, Co C, Prehoda KE, Snapper S, Taunton J, Lim WA. A polybasic motif allows N-WASP to act as a sensor of PIP(2) density. Mol Cell. 2005 Jan 21; 17(2):181-91.
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      64. Dueber JE, Yeh BJ, Bhattacharyya RP, Lim WA. Rewiring cell signaling: the logic and plasticity of eukaryotic protein circuitry. Curr Opin Struct Biol. 2004 Dec; 14(6):690-9.
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      65. Zarrinpar A, Bhattacharyya RP, Nittler MP, Lim WA. Sho1 and Pbs2 act as coscaffolds linking components in the yeast high osmolarity MAP kinase pathway. Mol Cell. 2004 Jun 18; 14(6):825-32.
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      66. Zarrinpar A, Park SH, Lim WA. Optimization of specificity in a cellular protein interaction network by negative selection. Nature. 2003 Dec 11; 426(6967):676-80.
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      67. Dueber JE, Yeh BJ, Chak K, Lim WA. Reprogramming control of an allosteric signaling switch through modular recombination. Science. 2003 Sep 26; 301(5641):1904-8.
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      68. Carlton VE, Harris BZ, Puffenberger EG, Batta AK, Knisely AS, Robinson DL, Strauss KA, Shneider BL, Lim WA, Salen G, Morton DH, Bull LN. Complex inheritance of familial hypercholanemia with associated mutations in TJP2 and BAAT. Nat Genet. 2003 May; 34(1):91-6.
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      69. Zarrinpar A, Bhattacharyya RP, Lim WA. The structure and function of proline recognition domains. Sci STKE. 2003 Apr 22; 2003(179):RE8.
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      70. Harris BZ, Lau FW, Fujii N, Guy RK, Lim WA. Role of electrostatic interactions in PDZ domain ligand recognition. Biochemistry. 2003 Mar 18; 42(10):2797-805.
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      71. Park SH, Zarrinpar A, Lim WA. Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms. Science. 2003 Feb 14; 299(5609):1061-4.
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      72. Volkman BF, Prehoda KE, Scott JA, Peterson FC, Lim WA. Structure of the N-WASP EVH1 domain-WIP complex: insight into the molecular basis of Wiskott-Aldrich Syndrome. Cell. 2002 Nov 15; 111(4):565-76.
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      73. Yu TW, Hao JC, Lim W, Tessier-Lavigne M, Bargmann CI. Shared receptors in axon guidance: SAX-3/Robo signals via UNC-34/Enabled and a Netrin-independent UNC-40/DCC function. Nat Neurosci. 2002 Nov; 5(11):1147-54.
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      74. Harris BZ, Venkatasubrahmanyam S, Lim WA. Coordinated folding and association of the LIN-2, -7 (L27) domain. An obligate heterodimerization involved in assembly of signaling and cell polarity complexes. J Biol Chem. 2002 Sep 20; 277(38):34902-8.
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      75. Prehoda KE, Lim WA. How signaling proteins integrate multiple inputs: a comparison of N-WASP and Cdk2. Curr Opin Cell Biol. 2002 Apr; 14(2):149-54.
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      76. Lim WA. The modular logic of signaling proteins: building allosteric switches from simple binding domains. Curr Opin Struct Biol. 2002 Feb; 12(1):61-8.
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      77. McGee AW, Dakoji SR, Olsen O, Bredt DS, Lim WA, Prehoda KE. Structure of the SH3-guanylate kinase module from PSD-95 suggests a mechanism for regulated assembly of MAGUK scaffolding proteins. Mol Cell. 2001 Dec; 8(6):1291-301.
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      78. Harris BZ, Lim WA. Mechanism and role of PDZ domains in signaling complex assembly. J Cell Sci. 2001 Sep; 114(Pt 18):3219-31.
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      79. Prehoda KE, Lim WA. The double life of PX domains. Nat Struct Biol. 2001 Jul; 8(7):570-2.
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      80. Harris BZ, Hillier BJ, Lim WA. Energetic determinants of internal motif recognition by PDZ domains. Biochemistry. 2001 May 22; 40(20):5921-30.
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      81. Wang W, Lim WA, Jakalian A, Wang J, Wang J, Luo R, Bayly CI, Kollman PA. An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis. J Am Chem Soc. 2001 May 2; 123(17):3986-94.
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      82. Prehoda KE, Scott JA, Mullins RD, Lim WA. Integration of multiple signals through cooperative regulation of the N-WASP-Arp2/3 complex. Science. 2000 Oct 27; 290(5492):801-6.
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      83. Zarrinpar A, Lim WA. Converging on proline: the mechanism of WW domain peptide recognition. Nat Struct Biol. 2000 Aug; 7(8):611-3.
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      84. Nguyen JT, Porter M, Amoui M, Miller WT, Zuckermann RN, Lim WA. Improving SH3 domain ligand selectivity using a non-natural scaffold. Chem Biol. 2000 Jul; 7(7):463-73.
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      85. Christopherson KS, Hillier BJ, Lim WA, Bredt DS. PSD-95 assembles a ternary complex with the N-methyl-D-aspartic acid receptor and a bivalent neuronal NO synthase PDZ domain. J Biol Chem. 1999 Sep 24; 274(39):27467-73.
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      86. Prehoda KE, Lee DJ, Lim WA. Structure of the enabled/VASP homology 1 domain-peptide complex: a key component in the spatial control of actin assembly. Cell. 1999 May 14; 97(4):471-80.
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      87. Hillier BJ, Christopherson KS, Prehoda KE, Bredt DS, Lim WA. Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex. Science. 1999 Apr 30; 284(5415):812-5.
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      88. Nguyen JT, Turck CW, Cohen FE, Zuckermann RN, Lim WA. Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors. Science. 1998 Dec 11; 282(5396):2088-92.
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      89. Nguyen JT, Lim WA. How Src exercises self-restraint. Nat Struct Biol. 1997 Apr; 4(4):256-60.
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      90. Lim WA. Reading between the lines: SH3 recognition of an intact protein. Structure. 1996 Jun 15; 4(6):657-9.
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      91. Lim WA, Richards FM, Fox RO. Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains. Nature. 1994 Nov 24; 372(6504):375-9.
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      92. Lim WA, Fox RO, Richards FM. Stability and peptide binding affinity of an SH3 domain from the Caenorhabditis elegans signaling protein Sem-5. Protein Sci. 1994 Aug; 3(8):1261-6.
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      93. Lim WA, Richards FM. Critical residues in an SH3 domain from Sem-5 suggest a mechanism for proline-rich peptide recognition. Nat Struct Biol. 1994 Apr; 1(4):221-5.
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      94. Lim WA, Hodel A, Sauer RT, Richards FM. The crystal structure of a mutant protein with altered but improved hydrophobic core packing. Proc Natl Acad Sci U S A. 1994 Jan 4; 91(1):423-7.
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      95. Richards FM, Lim WA. An analysis of packing in the protein folding problem. Q Rev Biophys. 1993 Nov; 26(4):423-98.
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      96. Lim WA, Farruggio DC, Sauer RT. Structural and energetic consequences of disruptive mutations in a protein core. Biochemistry. 1992 May 5; 31(17):4324-33.
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      97. Lim WA, Sauer RT. The role of internal packing interactions in determining the structure and stability of a protein. J Mol Biol. 1991 May 20; 219(2):359-76.
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      98. Reidhaar-Olson JF, Bowie JU, Breyer RM, Hu JC, Knight KL, Lim WA, Mossing MC, Parsell DA, Shoemaker KR, Sauer RT. Random mutagenesis of protein sequences using oligonucleotide cassettes. Methods Enzymol. 1991; 208:564-86.
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      99. Lim WA, Sauer RT, Lander AD. Analysis of DNA-protein interactions by affinity coelectrophoresis. Methods Enzymol. 1991; 208:196-210.
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      100. Bowie JU, Reidhaar-Olson JF, Lim WA, Sauer RT. Deciphering the message in protein sequences: tolerance to amino acid substitutions. Science. 1990 Mar 16; 247(4948):1306-10.
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      101. Lim WA, Sauer RT. Alternative packing arrangements in the hydrophobic core of lambda repressor. Nature. 1989 May 4; 339(6219):31-6.
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