Lim Lab | Papers By Interest

Areas of interest

  1. Mechanisms of Scaffold Proteins: Protein Interactions that Control the Flow of Information in Signaling Pathways
  2. Evolution and Evolvability of Cell Signaling Networks
  3. Synthetic Biology: Learning to Rewire Cell Signaling Pathways
  4. Exploring Design Principles of Regulatory Networks: Computationally Searching for the Core Algorithms of Cellular Decision-Making
  5. Novel Tools for Systematically Rewiring & Perturbing Cellular Networks
  6. CRISPRi
  7. Cellular Optogenetics
  8. Synthetic Biology: Engineering Therapeutic Cells

Mechanisms of Scaffold Proteins: Protein Interactions that Control the Flow of Information in Signaling Pathways

Scaffold proteins: hubs for controlling the flow of cellular information Matthew C. Good, Jesse G. Zalatan, Wendell A. Lim Science 332, 680-6 (2011) Abstract. PDF. Supplemental Video.

Conformational Control of the Ste5 Scaffold Protein Insulates Against MAP Kinase Misactivation. Jesse G. Zalatan*, Scott M. Coyle*, Saravanan Rajan, Sachdev S. Sidhu, Wendell A. Lim Science 337 (6099): 1218-1222 (2012) Abstract. PDF. Supplemental Data.

The Ste5 Scaffold Directs Mating Signaling by Catalytically Unlocking the Fus3 MAP Kinase for Activation Matthew C. Good, Grace Tang, Julie Singleton, Attila Reményi, and Wendell A. Lim Cell 136, 1085-97 (2009) Abstract. PDF. Supplemental Data. Commentary in Cell by Markus A. Seeliger and John Kuriyan (PDF)

Rewiring MAP Kinase Pathways Using Alternative Scaffold Assembly Mechanisms Sang-Hyun Park, Ali Zarrinpar, and Wendell A. Lim Science 299, 1061-1064 (2003)v Abstract. PDF. Supplemental Data. Commentary in Science by Mark Ptashne and Alexander Gann (PDF) Commentary in Molecular Cell by James E. Ferrell, Jr. and Karlene A. Cimprich (PDF)

The role of docking interactions in mediating signaling input, output, and discrimination in the yeast MAPK network Attila Reményi, Matthew C. Good, Roby P. Bhattacharyya, and Wendell A. Lim Molecular Cell 20, 951-962 (2005) Abstract. PDF. Supplemental Data.

The Ste5 Scaffold Allosterically Modulates Signaling Output of the Yeast Mating Pathway Roby P. Bhattacharyya*, Attila Reményi*, Matthew C. Good, Caleb J. Bashor, Arnold M. Falick, and Wendell A. Lim Science 311, 822-826 (2006) Abstract. PDF. Commentary in Science by Ashton Breitkreutz and Mike Tyers (PDF)

Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics Caleb J. Bashor, Noah C. Helman, Shude Yan, and Wendell A. Lim Science 319, 1539-43 (2008) Abstract. PDF. Supplemental Data. Commentary in Science by Peter M. Pryciak (PDF) Commentary in Nature Biotechnology by Patrick Guye and Ron Weiss (PDF)

Evolution and Evolvability of Cell Signaling Networks

Exploitation of Latent Allostery Enables the Evolution of New Modes of MAP Kinase Regulation Scott M. Coyle, Jonathan Flores, and Wendell A. Lim Cell 154, 875-887 (2013) Abstract. PDF. Supplemental Data.

Rapid diversification of cell signaling phenotypes by modular domain recombination Sergio G. Peisajovich, Joan E. Garbarino, Ping Wei, Wendell A. Lim Science 328, 368-372 (2010) Abstract. PDF. Supplemental Data. Commentary in Nature Reviews Genetics by Katharine H. Wrighton (PDF) Commentary in Nature Reviews Molecular Cell Biology by Katharine H. Wrighton (PDF)

Phosphotyrosine signaling: evolving a new cellular communication system Wendell A. Lim, Tony Pawson Cell 142, 661-667 (2010) Abstract. PDF.

Recruitment interactions can override catalytic interactions in determining the functional identity of a protein kinase Angela P. Won, Joan E. Garbarino, Wendell A. Lim Proceedings of the National Academy of Sciences 108, 9809-9814 (2011) Abstract. PDF. Supplemental Data.

Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species Pedro Beltrao, Jonathan C. Trinidad, Dorothea Fiedler, Assen Roguev, Wendell A. Lim, Kevan M. Shokat, Alma L. Burlingame, and Nevan J. Krogan PLoS Biology 7, e1000134 (2009). Abstract. PDF. Supplemental Data.

The pathogen protein EspF(U) hijacks actin polymerization using mimicry and multivalency Nathan A. Sallee, Gonzalo M. Rivera, John E. Dueber, Dan Vasilescu, R. Dyche Mullins, Bruce J. Mayer, and Wendell A. Lim Nature 454, 1005-8 (2008) Abstract. PDF. Supplemental Data.

Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages David Pincus, Ivica Letunic, Peer Bork, and Wendell A. Lim Proceedings of the National Academy of Sciences 105, 9680-4 (2008) Abstract. PDF. Supplemental Data. Commentary in Proceedings of the National Academy of Sciences by Bruce Mayer (PDF)

Optimization of specificity in a cellular protein interaction network by negative selection Ali Zarrinpar, Sang-Hyun Park, and Wendell A. Lim Nature 426, 676-680 (2003) Abstract. PDF. Supplemental Data. Commentary in Nature by Drew Endy and Michael B. Yaffe (PDF)

Synthetic Biology: Learning to Rewire Cell Signaling Pathways

Rewiring MAP Kinase Pathways Using Alternative Scaffold Assembly Mechanisms Sang-Hyun Park, Ali Zarrinpar, and Wendell A. Lim Science 299, 1061-1064 (2003)v Abstract. PDF. Supplemental Data. Commentary in Science by Mark Ptashne and Alexander Gann (PDF) Commentary in Molecular Cell by James E. Ferrell, Jr. and Karlene A. Cimprich (PDF)

Reprogramming Control of an Allosteric Signaling Switch Through Modular Recombination John E. Dueber, Brian J. Yeh, Kayam Chak, and Wendell A. Lim Science 301, 1904-1908 (2003) Abstract. PDF. Supplemental Data.

Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors Brian J. Yeh, Robert J. Rutigliano, Anrica Deb, Dafna Bar-Sagi, and Wendell A. Lim Nature 447, 596-600 (2007) Abstract. PDF. Supplemental Data. Supplemental Video. Commentary in Molecular Systems Biology by Philippe Bastiaens (PDF) Commentary in Developmental Cell by Christopher S. Chen (PDF)

Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics Caleb J. Bashor, Noah C. Helman, Shude Yan, and Wendell A. Lim Science 319, 1539-43 (2008) Abstract. PDF. Supplemental Data. Commentary in Science by Peter M. Pryciak (PDF) Commentary in Nature Biotechnology by Patrick Guye and Ron Weiss (PDF)

Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems Caleb J. Bashor, Andrew A. Horwitz, Sergio G. Peisajovich, and Wendell A. Lim Annual Review of Biophysics 39, 515-537 (2010) Abstract. PDF. (Copyright Annual Reviews)

Designing synthetic regulatory networks capable of self-organizing cell polarization. Angela H. Chau*, Jessica M. Walter*, Jaline Gerardin, Chao Tang, Wendell A. Lim Cell 151(2):320-32 (2012) Abstract. PDF. Supplemental Data. Supplemental Movie 1. Supplemental Movie 2. Simulation Code and Scripts.

Exploring Design Principles of Regulatory Networks: Computationally Searching for the Core Algorithms of Cellular Decision-Making

Design principles of regulatory networks: searching for the molecular algorithms of the cell. Wendell A. Lim, Connie M. Lee, Chao Tang Mol. Cell 49(2):202-12 (2013) Abstract. PDF.

Designing synthetic regulatory networks capable of self-organizing cell polarization. Angela H. Chau*, Jessica M. Walter*, Jaline Gerardin, Chao Tang, Wendell A. Lim Cell 151(2):320-32 (2012) Abstract. PDF. Supplemental Data. Supplemental Movie 1. Supplemental Movie 2. Simulation Code and Scripts.

Build life to understand it Michael Elowitz, Wendell A. Lim Nature 468, 889-890 (2010) Abstract. PDF.

Defining network topologies that can achieve biochemical adaptation Wenzhe Ma, Ala Trusina, Hana El-Samad, Wendell A. Lim, and Chao Tang Cell 138, 760-73 (2009) Abstract. PDF. Supplemental Data. PaperFlick video summary. Commentary in Cell by Alexander B. Artyukhin, Lani F. Wu, and Steven J. Altschuler (PDF)

Novel Tools for Systematically Rewiring & Perturbing Cellular Networks

CRISPRi

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes. Luke A. Gilbert, Matthew H. Larson, Leonardo Morsut, Zairan Liu, Gloria A. Brar, Sandra E. Torres, Noam Stern-Ginossar, Onn Brandman, Evan H. Whitehead, Jennifer A. Doudna, Wendell A. Lim, Jonathan S. Weissman, Lei S. Qi Cell (Resource) 154, 1-10 (2013) Abstract. PDF.

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression. Lei S. Qi, Matthew H. Larson, Luke A. Gilbert, Jennifer A. Doudna, Jonathan S. Weissman, Adam P. Arkin, Wendell A. Lim Cell 28;152(5):1173-83 (2013) Abstract. PDF. Supplemental Data. Supplemental Sequences.

Cellular Optogenetics

Spatiotemporal control of cell signalling using a light-switchable protein interaction Anselm Levskaya, Orion D. Weiner, Wendell A. Lim, and Christopher A. Voigt Nature 461, 997-1001 (2009) Abstract. PDF. Supplemental Data.

Light-based feedback for controlling intracellular signaling dynamics Jared E. Toettcher, Delquin Gong, Wendell A. Lim, Orion D. Weiner Nature Methods 8, 837-839 (2011) Abstract. PDF. Supplemental Data.

The promise of optogenetics in cell biology: interrogating molecular circuits in space and time Jared E. Toettcher, Christopher A. Voigt, Orion D. Weiner, Wendell A. Lim Nature Methods 1, 35-38 (2011) Abstract. PDF.

Using optogenetics to interrogate the dynamic control of signal transmission by the ras/erk module. Jared E. Toettcher, Orion D. Weiner, and Wendell A. Lim. Cell 155(6):1422-34 (2013) Abstract. PDF. Supplemental Data. Supplemental Movie 1. Supplemental Movie 2. RPPA data.

Synthetic Biology: Engineering Therapeutic Cells

Cell-based therapeutics: the next pillar of medicine. Michael A. Fischbach, Jeffrey A. Bluestone, Wendell A. Lim Science Translational Medicine 5(179) (2013) Abstract. PDF.

Bacterial virulence proteins as tools to rewire kinase pathways in yeast and immune cells. Ping Wei*, Wilson W. Wong*, Jason S. Park, Ethan E. Corcoran, Sergio G. Peisajovich, James J. Onuffer, Arthur Weiss, Wendell A. Lim Nature 488, 384-388 (2012) Abstract. PDF. Supplemental Data.

Designing customized cell signalling circuits Wendell A. Lim Nature Reviews Molecular Cell Biology 11, 393-403 (2010) Abstract. PDF.