Wendell Lim, PhD
Professor
Cellular Molecular Pharmacology
School of Medicine

Education & Training

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• PhD Biochemistry & Biophysics Mass. Institute of Technology 1991
• AB Chemistry Harvard University 1986

Websites

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• Profile at limlab.ucsf.edu (limlab.ucsf.edu)
• UCSF Cell Design Institute (celldesigninstitute.org)

Grants and Projects

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• Synthetic circuits that drive infiltration of therapeutic T cells into immunologically cold tumors, NIH, 2021-2026
• Synthetic epigenetic circuits: tunable cell fate switches controlled by dynamic and combinatorial inputs, NIH, 2021-2026
• Recognizing the tumor ecosystem: Integrating stromal and cancer antigen signals to achieve precision recognition of solid tumors by CAR T cells, NIH, 2020-2025
• UCSF Center for Synthetic Immunology: Tools to Reprogram the Immune System to Combat Cancer, NIH, 2019-2024
• Protein Recognition in Signal Transduction, NIH, 2018-2023
• Designer Tregs for restoring tolerance in patients with type 1 diabetes, NIH, 2017-2021
• Redesigning the T cell: Using Synthetic Biology to Engineer Therapeutic Cells, NIH, 2014-2021
• Exploring Design Principles of Cellular Control Circuits, NIH, 2010-2019
• Protein Recognition in Signal Transduction, NIH, 1997-2018
• Harnessing CRISPR for Targeted and Inducible Epigenomic Reprogramming, NIH, 2013-2018
• Cellular Control: Synthetic Signaling/Motility (RMI), NIH, 2004-2015
• Bio-Organic Biomedical Mass Spectrometry Resource, NIH, 1982-2015
• Protein Interactions Regulating Cell Motility, NIH, 2001-2012
• Assembly and Targeting of Neural Receptors and Channels, NIH, 2001-2007
• Engineering Synthetic Cell Motility Systems (RMI), NIH, 2004-2005

Publications (175)

Top publication keywords:
Signal TransductionProtein EngineeringOptogeneticsImmunotherapy, AdoptiveFeedback, PhysiologicalT-LymphocytesSynthetic BiologyMitogen-Activated Protein KinasesSaccharomyces cerevisiae ProteinsInterleukin-2Cell EngineeringSaccharomyces cerevisiaeReceptors, NotchMAP Kinase Signaling SystemCell Communication

• Degron-based bioPROTACs for controlling signaling in CAR T cells.
  bioRxiv : the preprint server for biology 2024 Kim MS, Bhargava HK, Shavey GE, Lim WA, El-Samad H, Ng AH
• General Characteristics and Design Taxonomy of Chatbots for COVID-19: Systematic Review.
  Journal of medical Internet research 2024 Lim WA, Custodio R, Sunga M, Amoranto AJ, Sarmiento RF
• Golden age of immunoengineering.
  Immunological reviews 2023 Wong WW, Lim WA
• An immune-based tool platform for in vivo cell clearance.
  Life science alliance 2023 Zhang J, Tsukui T, Wu X, Brito A, Trumble JM, Caraballo JC, Allen GM, Zavala-Solorio J, Zhang C, Paw J, Lim WA, Geng J, Kutskova Y, Freund A, Kolumam G, Sheppard D, Cohen RL
• Instructional materials that control cellular activity through synthetic Notch receptors.
  Biomaterials 2023 Lee JC, Brien HJ, Walton BL, Eidman ZM, Toda S, Lim WA, Brunger JM

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• CAR-T Cell-Mediated B-Cell Depletion in Central Nervous System Autoimmunity.
  Neurology(R) neuroimmunology & neuroinflammation 2023 Gupta S, Simic M, Sagan SA, Shepherd C, Duecker J, Sobel RA, Dandekar R, Wu GF, Wu W, Pak JE, Hauser SL, Lim W, Wilson MR, Zamvil SS
• Harnessing synthetic biology to engineer organoids and tissues.
  Cell stem cell 2023 Trentesaux C, Yamada T, Klein OD, Lim WA
• Synthetic cytokine circuits that drive T cells into immune-excluded tumors.
  Science (New York, N.Y.) 2022 Allen GM, Frankel NW, Reddy NR, Bhargava HK, Yoshida MA, Stark SR, Purl M, Lee J, Yee JL, Yu W, Li AW, Garcia KC, El-Samad H, Roybal KT, Spitzer MH, Lim WA
• Programming multicellular assembly with synthetic cell adhesion molecules.
  Nature 2022 Stevens AJ, Harris AR, Gerdts J, Kim KH, Trentesaux C, Ramirez JT, McKeithan WL, Fattahi F, Klein OD, Fletcher DA, Lim WA
• Decoding CAR T cell phenotype using combinatorial signaling motif libraries and machine learning.
  Science (New York, N.Y.) 2022 Daniels KG, Wang S, Simic MS, Bhargava HK, Capponi S, Tonai Y, Yu W, Bianco S, Lim WA
• CAR-T Cell-Mediated B Cell Depletion in Central Nervous System Autoimmunity.
  Neurology 2022 Sasha Gupta, Milos Simic, Sharon Sagan, Jason Duecker, Chanelle Shepherd, Raymond Sobel, Stephen Hauser, Wendell Lim, Michael Wilson, Scott Zamvil
• The emerging era of cell engineering: Harnessing the modularity of cells to program complex biological function.
  Science (New York, N.Y.) 2022 Lim WA
• EXTH-33. PRIMING OF SYNNOTCH CAR T CELLS VIA CNS-SPECIFIC ANTIGEN ALLOWS SPATIAL AND TEMPORAL REGULATION OF CAR EXPRESSION, EFFECTIVE HOMING AND PERSISTENCE OF T CELLS IN THE CNS.
  Neuro-Oncology 2022 Payal Watchmaker, Milos Simic, David Diebold, Psalm Pineo-Cavanaugh, Jason Deucker, Wei Yu, Wendell Lim, Hideho Okada
• Rethinking cancer targeting strategies in the era of smart cell therapeutics.
  Nature reviews. Cancer 2022 Allen GM, Lim WA
• Deep-learning-based analysis of combinatorial synthetic T-cell receptor libraries.
  Biophysical Journal 2022 Shangying Wang, Kyle G. Daniels, Sara Capponi, Wendell Lim, Simone Bianco
• SynNotch-CAR T cells overcome challenges of specificity, heterogeneity, and persistence in treating glioblastoma.
  Science translational medicine 2021 Choe JH, Watchmaker PB, Simic MS, Gilbert RD, Li AW, Krasnow NA, Downey KM, Yu W, Carrera DA, Celli A, Cho J, Briones JD, Duecker JM, Goretsky YE, Dannenfelser R, Cardarelli L, Troyanskaya O, Sidhu SS…
• T cells selectively filter oscillatory signals on the minutes timescale.
  Proceedings of the National Academy of Sciences of the United States of America 2021 O'Donoghue GP, Bugaj LJ, Anderson W, Daniels KG, Rawlings DJ, Lim WA
• T cell circuits that sense antigen density with an ultrasensitive threshold.
  Science (New York, N.Y.) 2021 Hernandez-Lopez RA, Yu W, Cabral KA, Creasey OA, Lopez Pazmino MDP, Tonai Y, De Guzman A, Mäkelä A, Saksela K, Gartner ZJ, Lim WA
• Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.
  Cell 2021 Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA
• DNA scaffolds enable efficient and tunable functionalization of biomaterials for immune cell modulation.
  Nature nanotechnology 2020 Huang X, Williams JZ, Chang R, Li Z, Burnett CE, Hernandez-Lopez R, Setiady I, Gai E, Patterson DM, Yu W, Roybal KT, Lim WA, Desai TA
• Engineering cytokines and cytokine circuits.
  Science (New York, N.Y.) 2020 Li AW, Lim WA
• Precise T cell recognition programs designed by transcriptionally linking multiple receptors.
  Science (New York, N.Y.) 2020 Williams JZ, Allen GM, Shah D, Sterin IS, Kim KH, Garcia VP, Shavey GE, Yu W, Puig-Saus C, Tsoi J, Ribas A, Roybal KT, Lim WA
• IMMU-33. MULTI-ANTIGEN RECOGNITION CIRCUITS OVERCOME CHALLENGES OF SPECIFICITY, HETEROGENEITY, AND DURABILITY IN T-CELL THERAPY FOR GLIOBLASTOMA.
  Neuro-Oncology 2020 Payal Watchmaker, Joseph Choe, Milos Simic, Ryan Gilbert, Aileen li, Nira Krasnow, Diego Carrera, Wei Yu, Kira Downey, Anna Celli, Juhyun Cho, Jessica Briones, Ruth Dannenfelser, Lia Cardarelli, …
• Engineering synthetic morphogen systems that can program multicellular patterning.
  Science (New York, N.Y.) 2020 Toda S, McKeithan WL, Hakkinen TJ, Lopez P, Klein OD, Lim WA
• What is the Optimal Design-Build-Test Cycle for Clinically Relevant Synthetic CAR T Cell Therapies?
  Cell systems 2020 Chen YY, Lim W, Levings M, Blazar B, Krenciute G, Wong W, Lehner M
• Discriminatory Power of Combinatorial Antigen Recognition in Cancer T Cell Therapies.
  Cell systems 2020 Dannenfelser R, Allen GM, VanderSluis B, Koegel AK, Levinson S, Stark SR, Yao V, Tadych A, Troyanskaya OG, Lim WA
• DNA-scaffolded biomaterials enable modular and tunable presentation of proteins to control immune cell therapies.
  The Journal of Immunology 2020 Xiao Huang, Jasper Z. Williams, Ryan Chang, Zhongbo Li, Eric Gai, David M. Patterson, Yu Wei, Wendell A. Lim, Tejal Desai
• Engineering T Cells to Treat Cancer: The Convergence of Immuno-Oncology and Synthetic Biology.
  Annual Review of Cancer Biology 2020 Joseph H. Choe, Jasper Z. Williams, Wendell A. Lim
• IMMU-21. SEQUENTIAL TWO-RECEPTOR PRIMING CAR SYSTEM TO OVERCOME HETEROGENEOUS ANTIGEN EXPRESSION.
  Neuro-Oncology 2019 Payal Watchmaker, Joseph Choe, Diego Carrera, Ryan Gilbert, Wei Yu, Kira Downey, Kole Roybal, Wendell Lim, Hideho Okada
• Simple Rules Determine Distinct Patterns of Branching Morphogenesis.
  Cell systems 2019 Yu W, Marshall WF, Metzger RJ, Brakeman PR, Morsut L, Lim W, Mostov KE
• The Design Principles of Biochemical Timers: Circuits that Discriminate between Transient and Sustained Stimulation.
  Cell systems 2019 Gerardin J, Reddy NR, Lim WA
• High-throughput multicolor optogenetics in microwell plates.
  Nature protocols 2019 Bugaj LJ, Lim WA
• Engineering cell-cell communication networks: programming multicellular behaviors.
  Current opinion in chemical biology 2019 Toda S, Frankel NW, Lim WA
• Synthetic Development: Learning to Program Multicellular Self-Organization.
  Current Opinion in Systems Biology 2019 Satoshi Toda, Jonathan M. Brunger, Wendell A. Lim
• Abstract A031: Engineering antigen density sensors for T-cell immunotherapy.
  Cancer Immunology Research 2019 Rogelio A. Hernandez-Lopez, Wendell A. Lim, Wei Yu
• IMMU-57. SEQUENTIAL TWO-RECEPTOR PRIMING CAR SYSTEM TO OVERCOME HETEROGENEOUS ANTIGEN EXPRESSION.
  Neuro-Oncology 2018 Payal Watchmaker, Joseph Choe, Diego Carrera, Kira Downey, Maryam Shahin, Kole Roybal, Wendell Lim, Hideho Okada
• Cancer mutations and targeted drugs can disrupt dynamic signal encoding by the Ras-Erk pathway.
  Science (New York, N.Y.) 2018 Bugaj LJ, Sabnis AJ, Mitchell A, Garbarino JE, Toettcher JE, Bivona TG, Lim WA
• Programming self-organizing multicellular structures with synthetic cell-cell signaling.
  Science (New York, N.Y.) 2018 Toda S, Blauch LR, Tang SKY, Morsut L, Lim WA
• Building a Stable Relationship: Ensuring Homeostasis among Cell Types within a Tissue.
  Cell 2018 Frankel NW, Lim WA
• Design of Tunable Oscillatory Dynamics in a Synthetic NF-κB Signaling Circuit.
  Cell systems 2017 Zhang ZB, Wang QY, Ke YX, Liu SY, Ju JQ, Lim WA, Tang C, Wei P
• Tracing Information Flow from Erk to Target Gene Induction Reveals Mechanisms of Dynamic and Combinatorial Control.
  Molecular cell 2017 Wilson MZ, Ravindran PT, Lim WA, Toettcher JE
• Synthetic Immunology: Hacking Immune Cells to Expand Their Therapeutic Capabilities.
  Annual review of immunology 2017 Roybal KT, Lim WA
• CRISPR/Cas9-mediated PD-1 disruption enhances anti-tumor efficacy of human chimeric antigen receptor T cells.
  Scientific reports 2017 Rupp LJ, Schumann K, Roybal KT, Gate RE, Ye CJ, Lim WA, Marson A
• The Principles of Engineering Immune Cells to Treat Cancer.
  Cell 2017 Lim WA, June CH
• Interrogating cellular perception and decision making with optogenetic tools.
  The Journal of cell biology 2016 Bugaj LJ, O'Donoghue GP, Lim WA
• Engineering Therapeutic T Cells: From Synthetic Biology to Clinical Trials.
  Annual review of pathology 2016 Esensten JH, Bluestone JA, Lim WA
• Engineering dynamical control of cell fate switching using synthetic phospho-regulons.
  Proceedings of the National Academy of Sciences of the United States of America 2016 Gordley RM, Williams RE, Bashor CJ, Toettcher JE, Yan S, Lim WA
• Complex transcriptional modulation with orthogonal and inducible dCas9 regulators.
  Nature methods 2016 Gao Y, Xiong X, Wong S, Charles EJ, Lim WA, Qi LS
• Engineering T Cells with Customized Therapeutic Response Programs Using Synthetic Notch Receptors.
  Cell 2016 Roybal KT, Williams JZ, Morsut L, Rupp LJ, Kolinko I, Choe JH, Walker WJ, McNally KA, Lim WA
• Cellular perception and misperception: Internal models for decision-making shaped by evolutionary experience.
  BioEssays : news and reviews in molecular, cellular and developmental biology 2016 Mitchell A, Lim W
• Modular engineering of cellular signaling proteins and networks.
  Current opinion in structural biology 2016 Gordley RM, Bugaj LJ, Lim WA
• CRISPR/Cas9 for Human Genome Engineering and Disease Research.
  Annual review of genomics and human genetics 2016 Xiong X, Chen M, Lim WA, Zhao D, Qi LS
• CRISPR/Cas9-mediated PD-1 disruption enhances anti-tumor efficacy of human chimeric antigen receptor T cells.
  The Journal of Immunology 2016 Levi Rupp, Kathrin Schumann, Kole T Roybal, Alexander Marson, Wendell A Lim
• Nucleosome breathing and remodeling constrain CRISPR-Cas9 function.
  eLife 2016 Isaac RS, Jiang F, Doudna JA, Lim WA, Narlikar GJ, Almeida R
• Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors.
  Cell 2016 Morsut L, Roybal KT, Xiong X, Gordley RM, Coyle SM, Thomson M, Lim WA
• Precision Tumor Recognition by T Cells With Combinatorial Antigen-Sensing Circuits.
  Cell 2016 Roybal KT, Rupp LJ, Morsut L, Walker WJ, McNally KA, Park JS, Lim WA
• Mapping the functional versatility and fragility of Ras GTPase signaling circuits through in vitro network reconstitution.
  eLife 2016 Coyle SM, Lim WA
• Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci.
  Nucleic acids research 2016 Chen B, Hu J, Almeida R, Liu H, Balakrishnan S, Covill-Cooke C, Lim WA, Huang B
• Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation.
  Nature reviews. Molecular cell biology 2015 Dominguez AA, Lim WA, Qi LS
• Oscillatory stress stimulation uncovers an Achilles' heel of the yeast MAPK signaling network.
  Science (New York, N.Y.) 2015 Mitchell A, Wei P, Lim WA
• Remote control of therapeutic T cells through a small molecule-gated chimeric receptor.
  Science (New York, N.Y.) 2015 Wu CY, Roybal KT, Puchner EM, Onuffer J, Lim WA
• Synthetic biology approaches to engineer T cells.
  Current opinion in immunology 2015 Wu CY, Rupp LJ, Roybal KT, Lim WA
• Differential genetic interactions of yeast stress response MAPK pathways.
  Molecular systems biology 2015 Martin H, Shales M, Fernandez-Piñar P, Wei P, Molina M, Fiedler D, Shokat KM, Beltrao P, Lim W, Krogan NJ
• Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds.
  Cell 2014 Zalatan JG, Lee ME, Almeida R, Gilbert LA, Whitehead EH, La Russa M, Tsai JC, Weissman JS, Dueber JE, Qi LS, Lim WA
• Specific gene repression by CRISPRi system transferred through bacterial conjugation.
  ACS synthetic biology 2014 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
• Sending mixed messages for cell population control.
  Cell 2014 Youk H, Lim WA
• Synthetic control of mammalian-cell motility by engineering chemotaxis to an orthogonal bioinert chemical signal.
  Proceedings of the National Academy of Sciences of the United States of America 2014 Park JS, Rhau B, Hermann A, McNally KA, Zhou C, Gong D, Weiner OD, Conklin BR, Onuffer J, Lim WA
• Exploitation of latent allostery enables the evolution of new modes of MAP kinase regulation (609.5).
  The FASEB Journal 2014 Scott Coyle, Wendell Lim
• Secreting and sensing the same molecule allows cells to achieve versatile social behaviors.
  Science (New York, N.Y.) 2014 Youk H, Lim WA
• Using optogenetics to interrogate the dynamic control of signal transmission by the Ras/Erk module.
  Cell 2013 Toettcher JE, Weiner OD, Lim WA
• The NR4A2 nuclear receptor is recruited to novel nuclear foci in response to UV irradiation and participates in nucleotide excision repair.
  PloS one 2013 Jagirdar K, Yin K, Harrison M, Lim W, Muscat GE, Sturm RA, Smith AG
• Genetic sensor for strong methylating compounds.
  ACS synthetic biology 2013 Moser F, Horwitz A, Chen J, Lim W, Voigt CA
• CRISPR interference (CRISPRi) for sequence-specific control of gene expression.
  Nature protocols 2013 Larson MH, Gilbert LA, Wang X, Lim WA, Weissman JS, Qi LS
• Actin dynamics rapidly reset chemoattractant receptor sensitivity following adaptation in neutrophils.
  Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2013 Dandekar SN, Park JS, Peng GE, Onuffer JJ, Lim WA, Weiner OD
• Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Puchner EM, Walter JM, Kasper R, Huang B, Lim WA
• Exploitation of latent allostery enables the evolution of new modes of MAP kinase regulation.
  Cell 2013 Coyle SM, Flores J, Lim WA
• CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes.
  Cell 2013 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
• Improved blue, green, and red fluorescent protein tagging vectors for S. cerevisiae.
  PloS one 2013 Lee S, Lim WA, Thorn KS
• Signalling change: signal transduction through the decades.
  Nature reviews. Molecular cell biology 2013 Hynes NE, Ingham PW, Lim WA, Marshall CJ, Massagué J, Pawson T
• Cell-based therapeutics: the next pillar of medicine.
  Science translational medicine 2013 Fischbach MA, Bluestone JA, Lim WA
• Bridging cross-cultural gaps in scientific exchange through innovative team challenge workshops.
  Quantitative biology (Beijing, China) 2013 Lee CM, Gong S, Tang C, Lim WA
• Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.
  Cell 2013 Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA
• Design principles of regulatory networks: searching for the molecular algorithms of the cell.
  Molecular cell 2013 Lim WA, Lee CM, Tang C
• Probing Molecular Number Variability in Intracellular Structures using Photoswitchable Fluorescent Proteins.
  Biophysical Journal 2013 Elias M. Puchner, Jessica M. Walter, Robert Kasper, Bo Huang, Wendell A. Lim
• Cell biology 2.0.
  Trends in cell biology 2012 Lim WA, Alvania R, Marshall WF
• Designing synthetic regulatory networks capable of self-organizing cell polarization.
  Cell 2012 Chau AH, Walter JM, Gerardin J, Tang C, Lim WA
• Wendell Lim: exploring the path not chosen. Interview by Caitlin Sedwick.
  The Journal of cell biology 2012 Lim W
• The first World Cell Race.
  Current biology : CB 2012 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, WCR participants, Jiménez-…
• Bacterial virulence proteins as tools to rewire kinase pathways in yeast and immune cells.
  Nature 2012 Wei P, Wong WW, Park JS, Corcoran EE, Peisajovich SG, Onuffer JJ, Weiss A, Lim WA
• Conformational control of the Ste5 scaffold protein insulates against MAP kinase misactivation.
  Science (New York, N.Y.) 2012 Zalatan JG, Coyle SM, Rajan S, Sidhu SS, Lim WA
• Systematic functional prioritization of protein posttranslational modifications.
  Cell 2012 Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ
• SYNZIP protein interaction toolbox: in vitro and in vivo specifications of heterospecific coiled-coil interaction domains.
  ACS synthetic biology 2012 Thompson KE, Bashor CJ, Lim WA, Keating AE
• Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Kapp GT, Liu S, Stein A, Wong DT, Reményi A, Yeh BJ, Fraser JS, Taunton J, Lim WA, Kortemme T
• A Light-Based Feedback Control System for Generating User-Defined Intracelullar Signaling Dynamics.
  Biophysical Journal 2012 Jared Toettcher, Delquin Gong, Wendell A. Lim, Orion Weiner
• Light-based feedback for controlling intracellular signaling dynamics.
  Nature methods 2011 Toettcher JE, Gong D, Lim WA, Weiner OD
• Recruitment interactions can override catalytic interactions in determining the functional identity of a protein kinase.
  Proceedings of the National Academy of Sciences of the United States of America 2011 Won AP, Garbarino JE, Lim WA
• Scaffold proteins: hubs for controlling the flow of cellular information.
  Science (New York, N.Y.) 2011 Good MC, Zalatan JG, Lim WA
• Regulation of NR4A nuclear receptor expression by oncogenic BRAF in melanoma cells.
  Pigment cell & melanoma research 2011 Smith AG, Lim W, Pearen M, Muscat GE, Sturm RA
• Light control of plasma membrane recruitment using the Phy-PIF system.
  Methods in enzymology 2011 Toettcher JE, Gong D, Lim WA, Weiner OD
• The promise of optogenetics in cell biology: interrogating molecular circuits in space and time.
  Nature methods 2010 Toettcher JE, Voigt CA, Weiner OD, Lim WA
• Build life to understand it.
  Nature 2010 Elowitz M, Lim WA
• Phosphotyrosine signaling: evolving a new cellular communication system.
  Cell 2010 Lim WA, Pawson T
• The minimal autoinhibited unit of the guanine nucleotide exchange factor intersectin.
  PloS one 2010 Ahmad KF, Lim WA
• Designing customized cell signalling circuits.
  Nature reviews. Molecular cell biology 2010 Lim WA
• Rapid diversification of cell signaling phenotypes by modular domain recombination.
  Science (New York, N.Y.) 2010 Peisajovich SG, Garbarino JE, Wei P, Lim WA
• Defining network topologies that can achieve biochemical adaptation.
  The FASEB Journal 2010 Chao Tang, Wenzhe Ma, Ala Trusina, Hana El-Samad, Wendell Lim
• The Design Logic of Cell Signaling Systems.
  The FASEB Journal 2010 Wendell A Lim
• Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs.
  Science signaling 2010 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, …
• Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems.
  Annual review of biophysics 2010 Bashor CJ, Horwitz AA, Peisajovich SG, Lim WA
• Reengineering the signaling properties of a Src family kinase.
  Biochemistry 2009 Yadav SS, Yeh BJ, Craddock BP, Lim WA, Miller WT
• A reciprocal interdependence between Nck and PI(4,5)P(2) promotes localized N-WASp-mediated actin polymerization in living cells.
  Molecular cell 2009 Rivera GM, Vasilescu D, Papayannopoulos V, Lim WA, Mayer BJ
• Spatiotemporal control of cell signalling using a light-switchable protein interaction.
  Nature 2009 Levskaya A, Weiner OD, Lim WA, Voigt CA
• Defining network topologies that can achieve biochemical adaptation.
  Cell 2009 Ma W, Trusina A, El-Samad H, Lim WA, Tang C
• Scaffolds: interaction platforms for cellular signalling circuits.
  Trends in cell biology 2009 Zeke A, Lukács M, Lim WA, Reményi A
• Positive selection of tyrosine loss in metazoan evolution.
  Science (New York, N.Y.) 2009 Tan CS, Pasculescu A, Lim WA, Pawson T, Bader GD, Linding R
• Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species.
  PLoS biology 2009 Beltrao P, Trinidad JC, Fiedler D, Roguev A, Lim WA, Shokat KM, Burlingame AL, Krogan NJ
• The Ste5 scaffold directs mating signaling by catalytically unlocking the Fus3 MAP kinase for activation.
  Cell 2009 Good M, Tang G, Singleton J, Reményi A, Lim WA
• Frederic M Richards 1925-2009.
  Nature structural & molecular biology 2009 Lim WA
• The Modular Logic of Cell Signaling Systems.
  Biophysical Journal 2009 Wendell Lim
• The pathogen protein EspF(U) hijacks actin polymerization using mimicry and multivalency.
  Nature 2008 Sallee NA, Rivera GM, Dueber JE, Vasilescu D, Mullins RD, Mayer BJ, Lim WA
• Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages.
  Proceedings of the National Academy of Sciences of the United States of America 2008 Pincus D, Letunic I, Bork P, Lim WA
• Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics.
  Science (New York, N.Y.) 2008 Bashor CJ, Helman NC, Yan S, Lim WA
• The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans.
  Nature 2008 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…
• A microfluidic system for dynamic yeast cell imaging.
  BioTechniques 2008 Lee PJ, Helman NC, Lim WA, Hung PJ
• Synthetic biology: lessons from the history of synthetic organic chemistry.
  Nature chemical biology 2007 Yeh BJ, Lim WA
• Engineering synthetic signaling proteins with ultrasensitive input/output control.
  Nature biotechnology 2007 Dueber JE, Mirsky EA, Lim WA
• Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors.
  Nature 2007 Yeh BJ, Rutigliano RJ, Deb A, Bar-Sagi D, Lim WA
• Engineering modular protein interaction switches by sequence overlap.
  Journal of the American Chemical Society 2007 Sallee NA, Yeh BJ, Lim WA
• Multiple WASP-interacting protein recognition motifs are required for a functional interaction with N-WASP.
  The Journal of biological chemistry 2007 Peterson FC, Deng Q, Zettl M, Prehoda KE, Lim WA, Way M, Volkman BF
• Beta strand peptidomimetics as potent PDZ domain ligands.
  Chemistry & biology 2006 Hammond MC, Harris BZ, Lim WA, Bartlett PA
• Docking interactions in protein kinase and phosphatase networks.
  Current opinion in structural biology 2006 Reményi A, Good MC, Lim WA
• The Modular Logic of Cell Signaling Systems.
  The FASEB Journal 2006 Wendell A Lim
• The Ste5 scaffold allosterically modulates signaling output of the yeast mating pathway.
  Science (New York, N.Y.) 2006 Bhattacharyya RP, Reményi A, Good MC, Bashor CJ, Falick AM, Lim WA
• Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits.
  Annual review of biochemistry 2006 Bhattacharyya RP, Reményi A, Yeh BJ, Lim WA
• The role of docking interactions in mediating signaling input, output, and discrimination in the yeast MAPK network.
  Molecular cell 2005 Reményi A, Good MC, Bhattacharyya RP, Lim WA
• A general model for preferential hetero-oligomerization of LIN-2/7 domains: mechanism underlying directed assembly of supramolecular signaling complexes.
  The Journal of biological chemistry 2005 Petrosky KY, Ou HD, Löhr F, Dötsch V, Lim WA
• A polybasic motif allows N-WASP to act as a sensor of PIP(2) density.
  Molecular cell 2005 Papayannopoulos V, Co C, Prehoda KE, Snapper S, Taunton J, Lim WA
• Rewiring cell signaling: the logic and plasticity of eukaryotic protein circuitry.
  Current opinion in structural biology 2004 Dueber JE, Yeh BJ, Bhattacharyya RP, Lim WA
• Sho1 and Pbs2 act as coscaffolds linking components in the yeast high osmolarity MAP kinase pathway.
  Molecular cell 2004 Zarrinpar A, Bhattacharyya RP, Nittler MP, Lim WA
• Optimization of specificity in a cellular protein interaction network by negative selection.
  Nature 2003 Zarrinpar A, Park SH, Lim WA
• Reprogramming control of an allosteric signaling switch through modular recombination.
  Science (New York, N.Y.) 2003 Dueber JE, Yeh BJ, Chak K, Lim WA
• Activation of Ras by Grb2-SOS: Demonstrating an Assembly Role of SH3 Domains.
  Science Signaling 2003 Ali Zarrinpar, Roby P. Bhattacharyya, Wendell A. Lim, Nancy R. Gough
• Complex inheritance of familial hypercholanemia with associated mutations in TJP2 and BAAT.
  Nature genetics 2003 Carlton VE, Harris BZ, Puffenberger EG, Batta AK, Knisely AS, Robinson DL, Strauss KA, Shneider BL, Lim WA, Salen G, Morton DH, Bull LN
• The structure and function of proline recognition domains.
  Science's STKE : signal transduction knowledge environment 2003 Zarrinpar A, Bhattacharyya RP, Lim WA
• Role of electrostatic interactions in PDZ domain ligand recognition.
  Biochemistry 2003 Harris BZ, Lau FW, Fujii N, Guy RK, Lim WA
• Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms.
  Science (New York, N.Y.) 2003 Park SH, Zarrinpar A, Lim WA
• Shared receptors in axon guidance: SAX-3/Robo signals via UNC-34/Enabled and a Netrin-independent UNC-40/DCC function.
  Nature neuroscience 2002 Yu TW, Hao JC, Lim W, Tessier-Lavigne M, Bargmann CI
• Coordinated folding and association of the LIN-2, -7 (L27) domain. An obligate heterodimerization involved in assembly of signaling and cell polarity complexes.
  The Journal of biological chemistry 2002 Harris BZ, Venkatasubrahmanyam S, Lim WA
• How signaling proteins integrate multiple inputs: a comparison of N-WASP and Cdk2.
  Current opinion in cell biology 2002 Prehoda KE, Lim WA
• From folding towards function.
  Current opinion in structural biology 2002 Baker D, Lim WA
• From folding towards function.
  Current Opinion in Structural Biology 2002 David Baker, Wendell A Lim
• Structure of the SH3-guanylate kinase module from PSD-95 suggests a mechanism for regulated assembly of MAGUK scaffolding proteins.
  Molecular cell 2001 McGee AW, Dakoji SR, Olsen O, Bredt DS, Lim WA, Prehoda KE
• The double life of PX domains.
  Nature structural biology 2001 Prehoda KE, Lim WA
• Energetic determinants of internal motif recognition by PDZ domains.
  Biochemistry 2001 Harris BZ, Hillier BJ, Lim WA
• An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis.
  Journal of the American Chemical Society 2001 Wang W, Lim WA, Jakalian A, Wang J, Wang J, Luo R, Bayly CI, Kollman PA
• Integration of multiple signals through cooperative regulation of the N-WASP-Arp2/3 complex.
  Science (New York, N.Y.) 2000 Prehoda KE, Scott JA, Mullins RD, Lim WA
• Converging on proline: the mechanism of WW domain peptide recognition.
  Nature structural biology 2000 Zarrinpar A, Lim WA
• Improving SH3 domain ligand selectivity using a non-natural scaffold.
  Chemistry & biology 2000 Nguyen JT, Porter M, Amoui M, Miller WT, Zuckermann RN, Lim WA
• PSD-95 assembles a ternary complex with the N-methyl-D-aspartic acid receptor and a bivalent neuronal NO synthase PDZ domain.
  The Journal of biological chemistry 1999 Christopherson KS, Hillier BJ, Lim WA, Bredt DS
• Structure of the enabled/VASP homology 1 domain-peptide complex: a key component in the spatial control of actin assembly.
  Cell 1999 Prehoda KE, Lee DJ, Lim WA
• Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex.
  Science (New York, N.Y.) 1999 Hillier BJ, Christopherson KS, Prehoda KE, Bredt DS, Lim WA
• Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors.
  Science (New York, N.Y.) 1998 Nguyen JT, Turck CW, Cohen FE, Zuckermann RN, Lim WA
• How Src exercises self-restraint.
  Nature structural biology 1997 Nguyen JT, Lim WA
• Reading between the lines: SH3 recognition of an intact protein.
  Structure (London, England : 1993) 1996 Lim WA
• Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains.
  Nature 1994 Lim WA, Richards FM, Fox RO
• Stability and peptide binding affinity of an SH3 domain from the Caenorhabditis elegans signaling protein Sem-5.
  Protein science : a publication of the Protein Society 1994 Lim WA, Fox RO, Richards FM
• Critical residues in an SH3 domain from Sem-5 suggest a mechanism for proline-rich peptide recognition.
  Nature structural biology 1994 Lim WA, Richards FM
• The crystal structure of a mutant protein with altered but improved hydrophobic core packing.
  Proceedings of the National Academy of Sciences of the United States of America 1994 Lim WA, Hodel A, Sauer RT, Richards FM
• An analysis of packing in the protein folding problem.
  Quarterly reviews of biophysics 1993 Richards FM, Lim WA
• Structural and energetic consequences of disruptive mutations in a protein core.
  Biochemistry 1992 Lim WA, Farruggio DC, Sauer RT
• The role of internal packing interactions in determining the structure and stability of a protein.
  Journal of molecular biology 1991 Lim WA, Sauer RT
• Analysis of DNA-protein interactions by affinity coelectrophoresis.
  Methods in enzymology 1991 Lim WA, Sauer RT, Lander AD
• Random mutagenesis of protein sequences using oligonucleotide cassettes.
  Methods in enzymology 1991 Reidhaar-Olson JF, Bowie JU, Breyer RM, Hu JC, Knight KL, Lim WA, Mossing MC, Parsell DA, Shoemaker KR, Sauer RT
• Deciphering the message in protein sequences: tolerance to amino acid substitutions.
  Science (New York, N.Y.) 1990 Bowie JU, Reidhaar-Olson JF, Lim WA, Sauer RT
• Alternative packing arrangements in the hydrophobic core of lambda repressor.
  Nature 1989 Lim WA, Sauer RT