Wendell Lim, PhD

Professor and Chair
Cellular Molecular Pharmacology
+1 415 502-8080
Publications: 

Programming self-organizing multicellular structures with synthetic cell-cell signaling.

Science (New York, N.Y.)

Toda S, Blauch LR, Tang SKY, Morsut L, Lim WA

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

Cell systems

Zhang ZB, Wang QY, Ke YX, Liu SY, Ju JQ, Lim WA, Tang C, Wei P

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

Scientific reports

Rupp LJ, Schumann K, Roybal KT, Gate RE, Ye CJ, Lim WA, Marson A

Interrogating cellular perception and decision making with optogenetic tools.

The Journal of cell biology

Bugaj LJ, O'Donoghue GP, Lim WA

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

Annual review of pathology

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

Gordley RM, Williams RE, Bashor CJ, Toettcher JE, Yan S, Lim WA

Complex transcriptional modulation with orthogonal and inducible dCas9 regulators.

Nature methods

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

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

Mitchell A, Lim W

Modular engineering of cellular signaling proteins and networks.

Current opinion in structural biology

Gordley RM, Bugaj LJ, Lim WA

CRISPR/Cas9 for Human Genome Engineering and Disease Research.

Annual review of genomics and human genetics

Xiong X, Chen M, Lim WA, Zhao D, Qi LS

Nucleosome breathing and remodeling constrain CRISPR-Cas9 function.

eLife

Isaac RS, Jiang F, Doudna JA, Lim WA, Narlikar GJ, Almeida R

Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors.

Cell

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

Roybal KT, Rupp LJ, Morsut L, Walker WJ, McNally KA, Park JS, Lim WA

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

Nucleic acids research

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

Dominguez AA, Lim WA, Qi LS

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

Science (New York, N.Y.)

Wu CY, Roybal KT, Puchner EM, Onuffer J, Lim WA

Synthetic biology approaches to engineer T cells.

Current opinion in immunology

Wu CY, Rupp LJ, Roybal KT, Lim WA

Differential genetic interactions of yeast stress response MAPK pathways.

Molecular systems biology

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

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

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

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

Park JS, Rhau B, Hermann A, McNally KA, Zhou C, Gong D, Weiner OD, Conklin BR, Onuffer J, Lim WA

Genetic sensor for strong methylating compounds.

ACS synthetic biology

Moser F, Horwitz A, Chen J, Lim W, Voigt CA

CRISPR interference (CRISPRi) for sequence-specific control of gene expression.

Nature protocols

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

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

Puchner EM, Walter JM, Kasper R, Huang B, Lim WA

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

Cell

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

Signalling change: signal transduction through the decades.

Nature reviews. Molecular cell biology

Hynes NE, Ingham PW, Lim WA, Marshall CJ, Massagué J, Pawson T

Cell-based therapeutics: the next pillar of medicine.

Science translational medicine

Fischbach MA, Bluestone JA, Lim WA

Bridging cross-cultural gaps in scientific exchange through innovative team challenge workshops.

Quantitative biology (Beijing, China)

Lee CM, Gong S, Tang C, Lim WA

Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.

Cell

Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA

Cell biology 2.0.

Trends in cell biology

Lim WA, Alvania R, Marshall WF

The first World Cell Race.

Current biology : CB

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

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

Nature

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.)

Zalatan JG, Coyle SM, Rajan S, Sidhu SS, Lim WA

Systematic functional prioritization of protein posttranslational modifications.

Cell

Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ

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

Kapp GT, Liu S, Stein A, Wong DT, Reményi A, Yeh BJ, Fraser JS, Taunton J, Lim WA, Kortemme T

Light-based feedback for controlling intracellular signaling dynamics.

Nature methods

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

Won AP, Garbarino JE, Lim WA

Scaffold proteins: hubs for controlling the flow of cellular information.

Science (New York, N.Y.)

Good MC, Zalatan JG, Lim WA

Regulation of NR4A nuclear receptor expression by oncogenic BRAF in melanoma cells.

Pigment cell & melanoma research

Smith AG, Lim W, Pearen M, Muscat GE, Sturm RA

Light control of plasma membrane recruitment using the Phy-PIF system.

Methods in enzymology

Toettcher JE, Gong D, Lim WA, Weiner OD

Build life to understand it.

Nature

Elowitz M, Lim WA

Designing customized cell signalling circuits.

Nature reviews. Molecular cell biology

Lim WA

Rapid diversification of cell signaling phenotypes by modular domain recombination.

Science (New York, N.Y.)

Peisajovich SG, Garbarino JE, Wei P, Lim WA

Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs.

Science signaling

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

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

Annual review of biophysics

Bashor CJ, Horwitz AA, Peisajovich SG, Lim WA

Reengineering the signaling properties of a Src family kinase.

Biochemistry

Yadav SS, Yeh BJ, Craddock BP, Lim WA, Miller WT

Defining network topologies that can achieve biochemical adaptation.

Cell

Ma W, Trusina A, El-Samad H, Lim WA, Tang C

Scaffolds: interaction platforms for cellular signalling circuits.

Trends in cell biology

Zeke A, Lukács M, Lim WA, Reményi A

Positive selection of tyrosine loss in metazoan evolution.

Science (New York, N.Y.)

Tan CS, Pasculescu A, Lim WA, Pawson T, Bader GD, Linding R

Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species.

PLoS biology

Beltrao P, Trinidad JC, Fiedler D, Roguev A, Lim WA, Shokat KM, Burlingame AL, Krogan NJ

Frederic M Richards 1925-2009.

Nature structural & molecular biology

Lim WA

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

Nature

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

Pincus D, Letunic I, Bork P, Lim WA

Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics.

Science (New York, N.Y.)

Bashor CJ, Helman NC, Yan S, Lim WA

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans.

Nature

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

A microfluidic system for dynamic yeast cell imaging.

BioTechniques

Lee PJ, Helman NC, Lim WA, Hung PJ

Engineering modular protein interaction switches by sequence overlap.

Journal of the American Chemical Society

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

Peterson FC, Deng Q, Zettl M, Prehoda KE, Lim WA, Way M, Volkman BF

Beta strand peptidomimetics as potent PDZ domain ligands.

Chemistry & biology

Hammond MC, Harris BZ, Lim WA, Bartlett PA

Docking interactions in protein kinase and phosphatase networks.

Current opinion in structural biology

Reményi A, Good MC, Lim WA

The Ste5 scaffold allosterically modulates signaling output of the yeast mating pathway.

Science (New York, N.Y.)

Bhattacharyya RP, Reményi A, Good MC, Bashor CJ, Falick AM, Lim WA

A polybasic motif allows N-WASP to act as a sensor of PIP(2) density.

Molecular cell

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

Dueber JE, Yeh BJ, Bhattacharyya RP, Lim WA

Reprogramming control of an allosteric signaling switch through modular recombination.

Science (New York, N.Y.)

Dueber JE, Yeh BJ, Chak K, Lim WA

Complex inheritance of familial hypercholanemia with associated mutations in TJP2 and BAAT.

Nature genetics

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

Zarrinpar A, Bhattacharyya RP, Lim WA

Role of electrostatic interactions in PDZ domain ligand recognition.

Biochemistry

Harris BZ, Lau FW, Fujii N, Guy RK, Lim WA

Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms.

Science (New York, N.Y.)

Park SH, Zarrinpar A, Lim WA