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Wendell Lim, PhD

Title(s)Professor, Cellular Molecular Pharmacology
SchoolSchool of Medicine
Phone415-502-8080
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    Other Positions
    Title(s)Howard Hughes Investigator


    Collapse Research 
    Collapse Research Activities and Funding
    UCSF Center for Synthetic Immunology: Tools to Reprogram the Immune System to Combat Cancer
    NIH/NCI U54CA244438Sep 24, 2019 - Aug 31, 2024
    Role: Principal Investigator
    Protein Recognition in Signal Transduction
    NIH/NCI R01CA220257Sep 1, 2018 - Jul 31, 2023
    Role: Principal Investigator
    Designer Tregs for restoring tolerance in patients with type 1 diabetes
    NIH/NIDDK UC4DK116264Sep 20, 2017 - Aug 31, 2021
    Role: Co-Principal Investigator
    Redesigning the T cell: Using Synthetic Biology to Engineer Therapeutic Cells
    NIH/NCI R01CA196277Sep 23, 2014 - Aug 31, 2019
    Role: Principal Investigator
    Harnessing CRISPR for Targeted and Inducible Epigenomic Reprogramming
    NIH/NIDA R01DA036858Sep 30, 2013 - May 31, 2018
    Role: Co-Principal Investigator
    Exploring Design Principles of Cellular Control Circuits
    NIH/NIGMS P50GM081879Aug 1, 2010 - Jul 31, 2018
    Role: Principal Investigator
    Cellular Control: Synthetic Signaling/Motility (RMI)
    NIH/NEI PN2EY016546Sep 30, 2004 - Jul 31, 2015
    Role: Principal Investigator
    Engineering Synthetic Cell Motility Systems (RMI)
    NIH/NEI PN1EY016546Sep 30, 2004 - Jul 31, 2005
    Role: Principal Investigator
    ASSEMBLY AND TARGETING OF NEURAL RECEPTORS AND CHANNELS
    NIH/NIMH P50MH063981Aug 15, 2001 - Jul 31, 2007
    Role: Co-Investigator
    Protein Interactions Regulating Cell Motility
    NIH/NIGMS R01GM062583Feb 1, 2001 - Apr 30, 2012
    Role: Principal Investigator
    Protein Recognition in Signal Transduction
    NIH/NIGMS R01GM055040Jan 1, 1997 - Jul 31, 2016
    Role: Principal Investigator
    Bio-Organic Biomedical Mass Spectrometry Resource
    NIH P41RR001614Mar 1, 1982 - May 31, 2015
    Role: Co-Investigator

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    Collapse In The News

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    Collapse 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. Yu W, Marshall WF, Metzger RJ, Brakeman PR, Morsut L, Lim W, Mostov KE. Simple Rules Determine Distinct Patterns of Branching Morphogenesis. Cell Syst. 2019 Sep 25; 9(3):221-227. PMID: 31557453.
      View in: PubMed
    2. Gerardin J, Reddy NR, Lim WA. The Design Principles of Biochemical Timers: Circuits that Discriminate between Transient and Sustained Stimulation. Cell Syst. 2019 Sep 25; 9(3):297-308.e2. PMID: 31521602.
      View in: PubMed
    3. Bugaj LJ, Lim WA. High-throughput multicolor optogenetics in microwell plates. Nat Protoc. 2019 07; 14(7):2205-2228. PMID: 31235951.
      View in: PubMed
    4. Toda S, Frankel NW, Lim WA. Engineering cell-cell communication networks: programming multicellular behaviors. Curr Opin Chem Biol. 2019 Oct; 52:31-38. PMID: 31150899.
      View in: PubMed
    5. Satoshi Toda, Jonathan M. Brunger, Wendell A. Lim. Synthetic Development: Learning to Program Multicellular Self-Organization. Current Opinion in Systems Biology. 2019 Apr 1; 14(Nature 459 2009):41-49.
      View in: Publisher Site
    6. Payal Watchmaker, Joseph Choe, Diego Carrera, Kira Downey, Maryam Shahin, Kole Roybal, Wendell Lim, Hideho Okada. IMMU-57. SEQUENTIAL TWO-RECEPTOR PRIMING CAR SYSTEM TO OVERCOME HETEROGENEOUS ANTIGEN EXPRESSION. Neuro-Oncology. 2018 Nov 5; 20(suppl_6):vi134-vi134.
      View in: Publisher Site
    7. Bugaj LJ, Sabnis AJ, Mitchell A, Garbarino JE, Toettcher JE, Bivona TG, Lim WA. Cancer mutations and targeted drugs can disrupt dynamic signal encoding by the Ras-Erk pathway. Science. 2018 08 31; 361(6405). PMID: 30166458.
      View in: PubMed
    8. Toda S, Blauch LR, Tang SKY, Morsut L, Lim WA. Programming self-organizing multicellular structures with synthetic cell-cell signaling. Science. 2018 07 13; 361(6398):156-162. PMID: 29853554.
      View in: PubMed
    9. Frankel NW, Lim WA. Building a Stable Relationship: Ensuring Homeostasis among Cell Types within a Tissue. Cell. 2018 02 08; 172(4):638-640. PMID: 29425483.
      View in: PubMed
    10. Zhang ZB, Wang QY, Ke YX, Liu SY, Ju JQ, Lim WA, Tang C, Wei P. Design of Tunable Oscillatory Dynamics in a Synthetic NF-?B Signaling Circuit. Cell Syst. 2017 11 22; 5(5):460-470.e5. PMID: 29102361.
      View in: PubMed
    11. Wilson MZ, Ravindran PT, Lim WA, Toettcher JE. Tracing Information Flow from Erk to Target Gene Induction Reveals Mechanisms of Dynamic and Combinatorial Control. Mol Cell. 2017 Sep 07; 67(5):757-769.e5. PMID: 28826673.
      View in: PubMed
    12. Roybal KT, Lim WA. Synthetic Immunology: Hacking Immune Cells to Expand Their Therapeutic Capabilities. Annu Rev Immunol. 2017 04 26; 35:229-253. PMID: 28446063.
      View in: PubMed
    13. Rupp LJ, Schumann K, Roybal KT, Gate RE, Ye CJ, Lim WA, Marson A. CRISPR/Cas9-mediated PD-1 disruption enhances anti-tumor efficacy of human chimeric antigen receptor T cells. Sci Rep. 2017 04 07; 7(1):737. PMID: 28389661.
      View in: PubMed
    14. Lim WA, June CH. The Principles of Engineering Immune Cells to Treat Cancer. Cell. 2017 02 09; 168(4):724-740. PMID: 28187291.
      View in: PubMed
    15. Bugaj LJ, O'Donoghue GP, Lim WA. Interrogating cellular perception and decision making with optogenetic tools. J Cell Biol. 2017 Jan 02; 216(1):25-28. PMID: 28003330.
      View in: PubMed
    16. Esensten JH, Bluestone JA, Lim WA. Engineering Therapeutic T Cells: From Synthetic Biology to Clinical Trials. Annu Rev Pathol. 2017 Jan 24; 12:305-330. PMID: 27959633.
      View in: PubMed
    17. Gordley RM, Williams RE, Bashor CJ, Toettcher JE, Yan S, Lim WA. Engineering dynamical control of cell fate switching using synthetic phospho-regulons. Proc Natl Acad Sci U S A. 2016 11 22; 113(47):13528-13533. PMID: 27821768.
      View in: PubMed
    18. Gao Y, Xiong X, Wong S, Charles EJ, Lim WA, Qi LS. Complex transcriptional modulation with orthogonal and inducible dCas9 regulators. Nat Methods. 2016 Dec; 13(12):1043-1049. PMID: 27776111.
      View in: PubMed
    19. Roybal KT, Williams JZ, Morsut L, Rupp LJ, Kolinko I, Choe JH, Walker WJ, McNally KA, Lim WA. Engineering T Cells with Customized Therapeutic Response Programs Using Synthetic Notch Receptors. Cell. 2016 Oct 06; 167(2):419-432.e16. PMID: 27693353.
      View in: PubMed
    20. Mitchell A, Lim W. Cellular perception and misperception: Internal models for decision-making shaped by evolutionary experience. Bioessays. 2016 09; 38(9):845-9. PMID: 27461864.
      View in: PubMed
    21. Gordley RM, Bugaj LJ, Lim WA. Modular engineering of cellular signaling proteins and networks. Curr Opin Struct Biol. 2016 08; 39:106-114. PMID: 27423114.
      View in: PubMed
    22. Xiong X, Chen M, Lim WA, Zhao D, Qi LS. CRISPR/Cas9 for Human Genome Engineering and Disease Research. Annu Rev Genomics Hum Genet. 2016 08 31; 17:131-54. PMID: 27216776.
      View in: PubMed
    23. Isaac RS, Jiang F, Doudna JA, Lim WA, Narlikar GJ, Almeida R. Nucleosome breathing and remodeling constrain CRISPR-Cas9 function. Elife. 2016 04 28; 5. PMID: 27130520.
      View in: PubMed
    24. Morsut L, Roybal KT, Xiong X, Gordley RM, Coyle SM, Thomson M, Lim WA. Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors. Cell. 2016 Feb 11; 164(4):780-91. PMID: 26830878.
      View in: PubMed
    25. Roybal KT, Rupp LJ, Morsut L, Walker WJ, McNally KA, Park JS, Lim WA. Precision Tumor Recognition by T Cells With Combinatorial Antigen-Sensing Circuits. Cell. 2016 Feb 11; 164(4):770-9. PMID: 26830879.
      View in: PubMed
    26. Coyle SM, Lim WA. Mapping the functional versatility and fragility of Ras GTPase signaling circuits through in vitro network reconstitution. Elife. 2016 Jan 14; 5. PMID: 26765565.
      View in: PubMed
    27. Chen B, Hu J, Almeida R, Liu H, Balakrishnan S, Covill-Cooke C, Lim WA, Huang B. Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci. Nucleic Acids Res. 2016 05 05; 44(8):e75. PMID: 26740581.
      View in: PubMed
    28. Dominguez AA, Lim WA, Qi LS. Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Nat Rev Mol Cell Biol. 2016 Jan; 17(1):5-15. PMID: 26670017.
      View in: PubMed
    29. Mitchell A, Wei P, Lim WA. Oscillatory stress stimulation uncovers an Achilles' heel of the yeast MAPK signaling network. Science. 2015 Dec 11; 350(6266):1379-83. PMID: 26586187.
      View in: PubMed
    30. Wu CY, Roybal KT, Puchner EM, Onuffer J, Lim WA. Remote control of therapeutic T cells through a small molecule-gated chimeric receptor. Science. 2015 Oct 16; 350(6258):aab4077. PMID: 26405231.
      View in: PubMed
    31. Wu CY, Rupp LJ, Roybal KT, Lim WA. Synthetic biology approaches to engineer T cells. Curr Opin Immunol. 2015 Aug; 35:123-30. PMID: 26218616.
      View in: PubMed
    32. Martin H, Shales M, Fernandez-Piñar P, Wei P, Molina M, Fiedler D, Shokat KM, Beltrao P, Lim W, Krogan NJ. Differential genetic interactions of yeast stress response MAPK pathways. Mol Syst Biol. 2015 Apr 17; 11(4):800. PMID: 25888283.
      View in: PubMed
    33. Zalatan JG, Lee ME, Almeida R, Gilbert LA, Whitehead EH, La Russa M, Tsai JC, Weissman JS, Dueber JE, Qi LS, Lim WA. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell. 2015 Jan 15; 160(1-2):339-50. PMID: 25533786.
      View in: PubMed
    34. Ji W, Lee D, Wong E, Dadlani P, Dinh D, Huang V, Kearns K, Teng S, Chen S, Haliburton J, Heimberg G, Heineike B, Ramasubramanian A, Stevens T, Helmke KJ, Zepeda V, Qi LS, Lim WA. Specific gene repression by CRISPRi system transferred through bacterial conjugation. ACS Synth Biol. 2014 Dec 19; 3(12):929-31. PMID: 25409531.
      View in: PubMed
    35. Youk H, Lim WA. Sending mixed messages for cell population control. Cell. 2014 Aug 28; 158(5):973-975. PMID: 25171399.
      View in: PubMed
    36. 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. PMID: 24711398.
      View in: PubMed
    37. Youk H, Lim WA. Secreting and sensing the same molecule allows cells to achieve versatile social behaviors. Science. 2014 Feb 07; 343(6171):1242782. PMID: 24503857.
      View in: PubMed
    38. Toettcher JE, Weiner OD, Lim WA. Using optogenetics to interrogate the dynamic control of signal transmission by the Ras/Erk module. Cell. 2013 Dec 05; 155(6):1422-34. PMID: 24315106.
      View in: PubMed
    39. Jagirdar K, Yin K, Harrison M, Lim W, Muscat GE, Sturm RA, Smith AG. The NR4A2 nuclear receptor is recruited to novel nuclear foci in response to UV irradiation and participates in nucleotide excision repair. PLoS One. 2013; 8(11):e78075. PMID: 24223135.
      View in: PubMed
    40. 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. PMID: 24032656.
      View in: PubMed
    41. 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. PMID: 24136345.
      View in: PubMed
    42. 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. PMID: 24062580.
      View in: PubMed
    43. 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 01; 110(40):16015-20. PMID: 24043832.
      View in: PubMed
    44. 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. PMID: 23953117.
      View in: PubMed
    45. 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. PMID: 23849981.
      View in: PubMed
    46. Lee S, Lim WA, Thorn KS. Improved blue, green, and red fluorescent protein tagging vectors for S. cerevisiae. PLoS One. 2013; 8(7):e67902. PMID: 23844123.
      View in: PubMed
    47. 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. PMID: 23636498.
      View in: PubMed
    48. Fischbach MA, Bluestone JA, Lim WA. Cell-based therapeutics: the next pillar of medicine. Sci Transl Med. 2013 Apr 03; 5(179):179ps7. PMID: 23552369.
      View in: PubMed
    49. Lee CM, Gong S, Tang C, Lim WA. Bridging cross-cultural gaps in scientific exchange through innovative team challenge workshops. Quant Biol. 2013 Mar; 1(1):3-8. PMID: 25339992.
      View in: PubMed
    50. 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. PMID: 23452860.
      View in: PubMed
    51. 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. PMID: 23352241.
      View in: PubMed
    52. Elias M. Puchner, Jessica M. Walter, Robert Kasper, Bo Huang, Wendell A. Lim. Probing Molecular Number Variability in Intracellular Structures using Photoswitchable Fluorescent Proteins. Biophysical Journal. 2013 Jan 1; 104(2):201a.
      View in: Publisher Site
    53. Lim WA, Alvania R, Marshall WF. Cell biology 2.0. Trends Cell Biol. 2012 Dec; 22(12):611-2. PMID: 23142093.
      View in: PubMed
    54. 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. PMID: 23039994.
      View in: PubMed
    55. Lim W. Wendell Lim: exploring the path not chosen. Interview by Caitlin Sedwick. J Cell Biol. 2012 Sep 17; 198(6):956-7. PMID: 22986491.
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    56. 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, Jiménez-Dalmaroni A, Joanny JF, Thiery JP, Erfle H, Parsons M, Mitchison TJ, Lim WA, Lennon-Duménil AM, Piel M, Théry M. The first World Cell Race. Curr Biol. 2012 Sep 11; 22(17):R673-5. PMID: 22974990.
      View in: PubMed
    57. 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. PMID: 22820255.
      View in: PubMed
    58. 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 07; 337(6099):1218-22. PMID: 22878499.
      View in: PubMed
    59. 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. PMID: 22817900.
      View in: PubMed
    60. 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. PMID: 22558529.
      View in: PubMed
    61. 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 03; 109(14):5277-82. PMID: 22403064.
      View in: PubMed
    62. Jared Toettcher, Delquin Gong, Wendell A. Lim, Orion Weiner. A Light-Based Feedback Control System for Generating User-Defined Intracelullar Signaling Dynamics. Biophysical Journal. 2012 Jan 1; 102(3):41a.
      View in: Publisher Site
    63. Toettcher JE, Gong D, Lim WA, Weiner OD. Light-based feedback for controlling intracellular signaling dynamics. Nat Methods. 2011 Sep 11; 8(10):837-9. PMID: 21909100.
      View in: PubMed
    64. 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. PMID: 21628578.
      View in: PubMed
    65. Good MC, Zalatan JG, Lim WA. Scaffold proteins: hubs for controlling the flow of cellular information. Science. 2011 May 06; 332(6030):680-6. PMID: 21551057.
      View in: PubMed
    66. 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. PMID: 21362156.
      View in: PubMed
    67. 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. PMID: 21601096.
      View in: PubMed
    68. 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. PMID: 21191370.
      View in: PubMed
    69. Elowitz M, Lim WA. Build life to understand it. Nature. 2010 Dec 16; 468(7326):889-90. PMID: 21164460.
      View in: PubMed
    70. Lim WA, Pawson T. Phosphotyrosine signaling: evolving a new cellular communication system. Cell. 2010 Sep 03; 142(5):661-7. PMID: 20813250.
      View in: PubMed
    71. Ahmad KF, Lim WA. The minimal autoinhibited unit of the guanine nucleotide exchange factor intersectin. PLoS One. 2010 Jun 24; 5(6):e11291. PMID: 20585582.
      View in: PubMed
    72. Lim WA. Designing customized cell signalling circuits. Nat Rev Mol Cell Biol. 2010 Jun; 11(6):393-403. PMID: 20485291.
      View in: PubMed
    73. 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. PMID: 20395511.
      View in: PubMed
    74. 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 Feb 16; 3(109):ra12. PMID: 20159853.
      View in: PubMed
    75. 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. PMID: 20192780.
      View in: PubMed
    76. 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. PMID: 19827767.
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    77. 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. PMID: 19917259.
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    78. 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. PMID: 19749742.
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    79. 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. PMID: 19703401.
      View in: PubMed
    80. Zeke A, Lukács M, Lim WA, Reményi A. Scaffolds: interaction platforms for cellular signalling circuits. Trends Cell Biol. 2009 Aug; 19(8):364-74. PMID: 19651513.
      View in: PubMed
    81. 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. PMID: 19589966.
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    82. 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. PMID: 19547744.
      View in: PubMed
    83. 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. PMID: 19303851.
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    84. Lim WA. Frederic M Richards 1925-2009. Nat Struct Mol Biol. 2009 Mar; 16(3):230-2. PMID: 19259121.
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    85. Wendell Lim. The Modular Logic of Cell Signaling Systems. Biophysical Journal. 2009 Feb 1; 96(3):3a.
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    86. 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. PMID: 18650806.
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    87. 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. PMID: 18599463.
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    88. 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. PMID: 18339942.
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    89. 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. PMID: 18273011.
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    90. Lee PJ, Helman NC, Lim WA, Hung PJ. A microfluidic system for dynamic yeast cell imaging. Biotechniques. 2008 Jan; 44(1):91-5. PMID: 18254385.
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    91. Yeh BJ, Lim WA. Synthetic biology: lessons from the history of synthetic organic chemistry. Nat Chem Biol. 2007 Sep; 3(9):521-5. PMID: 17710092.
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    92. 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. PMID: 17515921.
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    93. Dueber JE, Mirsky EA, Lim WA. Engineering synthetic signaling proteins with ultrasensitive input/output control. Nat Biotechnol. 2007 Jun; 25(6):660-2. PMID: 17515908.
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    94. 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. PMID: 17381089.
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    95. 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. PMID: 17229736.
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    96. Hammond MC, Harris BZ, Lim WA, Bartlett PA. Beta strand peptidomimetics as potent PDZ domain ligands. Chem Biol. 2006 Dec; 13(12):1247-51. PMID: 17185220.
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    97. Reményi A, Good MC, Lim WA. Docking interactions in protein kinase and phosphatase networks. Curr Opin Struct Biol. 2006 Dec; 16(6):676-85. PMID: 17079133.
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    98. 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. PMID: 16424299.
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    99. 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. PMID: 16756506.
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    100. 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. PMID: 16364919.
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    101. 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. PMID: 16147993.
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    102. 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. PMID: 15664188.
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    103. 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. PMID: 15582393.
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    104. 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. PMID: 15200959.
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    105. 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. PMID: 14668868.
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    106. 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. PMID: 14512628.
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    107. 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. PMID: 12704386.
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    108. Zarrinpar A, Bhattacharyya RP, Lim WA. The structure and function of proline recognition domains. Sci STKE. 2003 Apr 22; 2003(179):RE8. PMID: 12709533.
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    109. 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. PMID: 12627945.
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    110. Park SH, Zarrinpar A, Lim WA. Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms. Science. 2003 Feb 14; 299(5609):1061-4. PMID: 12511654.
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    111. 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. PMID: 12437929.
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    112. 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. PMID: 12379860.
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    113. 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. PMID: 12110687.
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    114. 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. PMID: 11891112.
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    115. 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. PMID: 11839491.
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    116. David Baker, Wendell A Lim. From folding towards function. Current Opinion in Structural Biology. 2002 Feb 1; 12(1):11-13.
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    117. 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. PMID: 11779504.
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    118. Harris BZ, Lim WA. Mechanism and role of PDZ domains in signaling complex assembly. J Cell Sci. 2001 Sep; 114(Pt 18):3219-31. PMID: 11591811.
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    119. Prehoda KE, Lim WA. The double life of PX domains. Nat Struct Biol. 2001 Jul; 8(7):570-2. PMID: 11427879.
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    120. Harris BZ, Hillier BJ, Lim WA. Energetic determinants of internal motif recognition by PDZ domains. Biochemistry. 2001 May 22; 40(20):5921-30. PMID: 11352727.
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    121. 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 02; 123(17):3986-94. PMID: 11457149.
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    122. 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. PMID: 11052943.
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    123. Zarrinpar A, Lim WA. Converging on proline: the mechanism of WW domain peptide recognition. Nat Struct Biol. 2000 Aug; 7(8):611-3. PMID: 10932238.
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    124. 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. PMID: 10903934.
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    125. 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. PMID: 10488080.
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    126. 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. PMID: 10338211.
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    127. 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. PMID: 10221915.
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    128. 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. PMID: 9851931.
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    129. Nguyen JT, Lim WA. How Src exercises self-restraint. Nat Struct Biol. 1997 Apr; 4(4):256-60. PMID: 9095189.
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    130. Lim WA. Reading between the lines: SH3 recognition of an intact protein. Structure. 1996 Jun 15; 4(6):657-9. PMID: 8805558.
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    131. 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. PMID: 7802869.
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    132. 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. PMID: 7987221.
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    133. 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. PMID: 7656049.
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    134. 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 04; 91(1):423-7. PMID: 8278404.
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    135. Richards FM, Lim WA. An analysis of packing in the protein folding problem. Q Rev Biophys. 1993 Nov; 26(4):423-98. PMID: 8058892.
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    136. Lim WA, Farruggio DC, Sauer RT. Structural and energetic consequences of disruptive mutations in a protein core. Biochemistry. 1992 May 05; 31(17):4324-33. PMID: 1567879.
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    137. 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. PMID: 2038061.
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    138. Lim WA, Sauer RT, Lander AD. Analysis of DNA-protein interactions by affinity coelectrophoresis. Methods Enzymol. 1991; 208:196-210. PMID: 1838134.
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    139. 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. PMID: 1779849.
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    140. 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. PMID: 2315699.
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    141. Lim WA, Sauer RT. Alternative packing arrangements in the hydrophobic core of lambda repressor. Nature. 1989 May 04; 339(6219):31-6. PMID: 2524006.
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