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Recent Publications


Rapp PB, Omar AK, Shen JJ, Buck ME, Wang ZG, Tirrell DA.
Analysis and Control of Chain Mobility in Protein Hydrogels.
J Am Chem Soc. (2017). 
PMID: 28225256

Glenn WS, Stone SE, Ho SH, Sweredoski MJ, Moradian A, Hess S, Bailey-Serres J, Tirrell DA.
BONCAT enables time-resolved analysis of protein synthesis in native plant tissue.
Plant Physiol. 173(3): 1543-1553. (2017). 
PMID: 28104718

Stone SE, Glenn WS, Hamblin GD, Tirrell DA.
Cell-selective proteomics for biological discovery.
Curr Opin Chem Biol. 36:50-57. (2017).
PMID: 28088696

Ho SH, Tirrell DA.
Chemoenzymatic Labeling of Proteins for Imaging in Bacterial Cells.
J Am Chem Soc. 138(46):15098-15101. (2016). 
PMID: 27933886

Dooling LJ, Tirrell DA.
Engineering the Dynamic Properties of Protein Networks through Sequence Variation.
ACS Cent Sci. 2(11): 812-819. (2016).
PMID: 27924309

Tremblay JR, LeBon JM, Luo A, Quijano JC, Jou K, Riggs AD, Tirrell DA, Ku HT.
In Vitro Colony Assays for Characterizing Tri-potent Progenitor Cells Isolated from the Adult Murine Pancreas.
J Vis Exp. 112. (2016).
PMID: 27340914

Bertozzi CR, Chang CJ, Davis BG, Olvera de la Cruz M, Tirrell DA, Zhao D.
Grand Challenges in Chemistry for 2016 and Beyond.
ACS Cent. Sci. 27;2(1):1-3. (2016).
PMID: 27163017 

Dooling LJ, Buck ME, Zhang WB, Tirrell DA.
Programming Molecular Association and Viscoelastic Behavior in Protein Networks.
Adv Mat. 28(23):4651-7. (2016).
PMID: 27061171

Mahdavi A, Hamblin GD, Jindal GA, Bagert JD, Dong C, Sweredoski MJ, Hess S, Schuman EM, Tirrell DA.
An engineered aminoacyl-tRNA synthetase for cell-selective analysis of mammalian protein synthesis.
J Am Chem Soc. 138(13):4278-81. (2016).
PMID: 26991063

Bagert JD, van Kessel JC, Sweredoski MJ, Feng L, Hess S, Bassler BL, Tirrell DA. 
Time-resolved proteomic analysis of quorum sensing in Vibrio harveyi.
Chem Sci. 1;7(3):1797-1806. (2016).
PMID: 26925210

Babin BM, Bergkessel M, Sweredoski MJ, Moradian A, Hess S, Newman DK, Tirrell DA.
SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa.
Proc Natl Acad Sci USA. 113(5):E597-605. (2016).
PMID: 26787849

Jin L, Gao D, Feng T, Tremblay JR, Ghazalli N, Luo A, Rawson J, Quijano JC, Chai J, Wedeken L, Hsu J, LeBon J, Walker S, Shih HP, Mahdavi A, Tirrell DA, Riggs AD, Ku HT. 
Cells with surface expression of CD133highCD71low are enriched for tripotent colony-forming progenitor cells in the adult murine pancreas.
Stem Cell Res. 16(1): 40-53 (2015).
PMID: 26691820

Kulkarni C, Lo M, Fraseur JG, Tirrell DA, Kinzer-Ursem TL. 
Bioorthogonal Chemoenzymatic Functionalization of Calmodulin for Bioconjugation Applications.
Bioconjug Chem. 26(10): 2153-60. (2015). 
PMID: 26431265

Zehner NA, Dietrick SM, Tirrell DA, Kennedy SB.
Two-Site Internally Cooperative Mechanism for Enzyme Kinetics in a Hydrogel Forming Recombinant Protein.
Biomacromolecules, 6(11): 3651-6 (2015). 
PMID: 26402311

Notbohm J, Lesman A, Rosakis P, Tirrell DA, Ravichandran G.
Microbuckling of fibrin provides a mechanism for cell mechanosensing.
J R Soc Interface. 6;12(108):20150320 (2015).
PMID: 26040601

Notbohm J, Lesman A, Tirrell DA, Ravichandran G.
Quantifying cell-induced matrix deformation in three dimensions based on imaging matrix fibers.
Integr Biol (Camb). (10):1186-95. (2015).
PMID: 26021600

Ghazalli N, Mahdavi A, Feng T, Jin L, Kozlowski MT, Hsu J, Riggs AD, Tirrell DA, Ku HT.
Postnatal Pancreas of Mice Contains Tripotent Progenitors Capable of Giving Rise to Duct, Acinar, and Endocrine Cells In Vitro.
Stem Cells Dev. 24(17):1995-2008. (2015).
PMID: 25941840

tom Dieck S, Kochen L, Hanus C, Heumuller M, Bartnik I, Nassim-Assir B, Merk K, Mosler T, Garg S, Buse S, Tirrell DA, Schuman EM.
Direct visualization of newly synthesized target proteins in situ.
Nat. Meth. 12(5): 411-4 (2015).
PMID: 25775042

Deforest CA, Tirrell DA.
A photoreversible protein-patterning approach for guiding stem cell fate in three-dimensional gels.
Nat. Mat. 14(5): 523-31 (2015).
PMID: 25707020

Yuet KP, Doma MK, Ngo JT, Sweredoski MJ, Graham RLJ, Moradian A, Hess S, Schuman EM, Sternberg PW, Tirrell DA.
Cell-specific proteomic analysis in Caenorhabditis elegans.
Proc Natl Acad Sci USA. 112(9): 2705-10 (2015).
PMID: 25691744

Feng L, Rutherford ST, Papenfort K, Bagert JD, van Kessel JC, Tirrell DA, Wingreen NS, Bassler BL.
A Qrr Noncoding RNA Deploys Four Different Regulatory Mechnanisms to Optimize Quorum-Sensing Dynamics.
Cell. 160: 228-240 (2015).
PMID: 25579683

Jin L, Feng T, Chai J, Ghazalli N, Gao D, Zerda R, Li Z, Hsu J, Mahdavi A, Tirrell DA, Riggs AD, Ku HT. 
Colony-Forming Progenitor Cells in the Postnatal Mouse Liver and Pancreas Give Rise to Morphologically Distinct Insulin-Expressing Colonies in 3D Cultures.
Rev. Diabet. Stud. 11: 35-50 (2014).
PMID: 25148366

Sun F, Zhang W-B, Mahdavi A, Arnold FH, Tirrell DA.
Synthesis of bioactive protein hydrogels by genetically encoded SpyTag-SpyCatcher chemistry.
Proc Natl Acad Sci USA. 111: 11269-11274 (2014). 
PMID: 25049400

Van Deventer JA, Yuet KP, Yoo TH, Tirrell DA.
Cell Surface Display Yields Evolvable, Clickable Antibody Fragments.
Chembiochem. 15: 1777-1781 (2014).  
PMID: 25045032

Lesman A, Notbohm J, Tirrell DA, Ravichandran G.
Contractile forces regulate cell division in three-dimensional environments.
J. Cell Biol. 205(2):155-62. (2014).
PMID: 24778310

Hatzenpichler R, Scheller S, Tavormina PL, Babin BM, Tirrell DA, Orphan VJ.
In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry.
Environ Microbiol. 16: 2568-90 (2014).  
PMID: 24571640

Bagert JD, Xie Y, Sweredoski M, Qi Y, Hess S, Schuman E, Tirrell DA.
Quantitative, Time-Resolved Proteomic Analysis by Combining Bioorthogonal Noncanonical Amino Acid Tagging and Pulsed Stable Isotope Labeling by Amino Acids in Cell Culture.
Mol. Cell Prot. 13(5):1352-8. (2014).
PMID: 24563536

Tirrell DA.
The Wonder of Life in Its Chemical Aspect.
Advances in Polymer Science, 261: 199-210. (2013).

Mahdavi A, Szychowski J, Ngo JT, Sweredoski MJ, Graham RL, Hess S, Schneewind O, Mazmanian SK, Tirrell DA. 
Identification of secreted bacterial proteins by noncanonical amino acid tagging. 
Proc Natl Acad Sci USA. 111(1): 433-8. (2014).
PMID: 24347637

Lu Y-Y, Sweredoski M, Huss D, Lansford R, Hess S, Tirrell DA.
Prometastatic GPCR CD97 Is a Direct Target of Tumor Suppressor microRNA-126.
ACS Chem. Biol. 9: 334-338 (2014).
PMID: 24274104

Burts AO, Liao L, Lu Y-Y, Tirrell DA, Johnson JA.
Brush-first and click: efficient synthesis of nanoparticles that degrade and release doxorubicin in response to light.
Photochem. Photobiol. 90: 380-385 (2014).
PMID: 24117423

Yuet KP, Tirrell DA.
Chemical Tools for Temporally and Spatially Resolved Mass Spectrometry-Based Proteomics.
Ann. Biomed. Eng. 42: 299-311 (2014).
PMID: 23943069

Kulkarni C, Kinzer-Ursem TL, Tirrell DA.
Selective Functionalization of the Protein N Terminus with N-Myristoyl Transferase for Bioconjugation in Cell Lysate.
ChemBioChem. 14: 1958-1962 (2013).
PMID: 24030852

Zhang WB, Sun F, Tirrell DA, Arnold FH.
Controlling Macromolecular Topology with Genetically Encoded SpyTag-SpyCatcher Chemistry.
J. Am. Chem. Soc. 135: 13988-13997 (2013).
PMID: 23964715

Tzlil S, Tirrell DA.
Strain propagation in artificial extracellular matrix proteins can accelerate cell spreading and polarization.
Soft Matter. 9: 5602-5608 (2013).

Dooling LJ, Tirrell DA.
Peptide and Protein Hydrogels.
Polymeric and Self Assembled Hydrogels: From Fundamental Understanding to Applications. XJ Loh and OA Scherman, eds., RSC Publishing, Cambridge, (2013), pp. 93–124.

Le DH, Hanamura R, Pham DH, Kato M, Tirrell DA, Okubo T, Sugahara-Narutaki A.
Self-Assembly of Elastin-Mimetic Double Hydrophobic Polypeptides.
Biomacromolecules. 14: 1028-1034 (2013).

Ngo JT, Schuman EM, Tirrell DA.
Mutant Methionyl-tRNA Synthetase from Bacteria Enables Site-Selective N-terminal Labeling of Proteins Expressed in Mammalian Cells.
Proc Natl Acad Sci USA. 110: 4992-4997 (2013).

Jin L, Feng T, Shih HP, Zerda R, Luo A, Hsu J, Mahdavi A, Sander M, Tirrell DA, Riggs AD, Ku HT.
Colony-forming cells in the adult mouse pancreas are expandable in Matrigel and form endocrine/acinar colonies in laminin hydrogel.
Proc Natl Acad Sci USA. 110: 3907-3912 (2013).

Mahdavi A, Segall-Shapiro TH, Kou S, Jindal GA, Hoff KG, Liu S, Chitsaz M, Ismagilov RF, Silberg JJ, Tirrell DA.
A Genetically Encoded AND Gate for Cell-Targeted Metabolic Labeling of Proteins.
J. Am. Chem. Soc. 135: 2979-2982 (2013).

Wang H, Mahdavi A, Tirrell DA, Hajimiri A.
A magnetic cell-based sensor.
Lab Chip 12: 4465-4471 (2012).

Buck ME, Tirrell DA.
Artificial Proteins.
Polymer Science: A Comprehensive Reference, K. Matyjaszewski and M. Möller, eds., Elsevier BV, Amsterdam, (2012), Vol. 9,  pp. 117–136.

Patel PR, Kiser RC, Lu YY, Fong WC, Ho WC, Tirrell DA, Grubbs RH.
Synthesis and Cell Adhesive Properties of Linear and Cyclic RGD Functionalized Polynorbornene Thin Films.
Biomacromolecules 13: 2546-2553 (2012).

Hodas JJ, Nehring A, Höche N, Sweredoski MJ, Pielot R, Hess S, Tirrell DA, Dieterich DC, Schuman EM.
Dopaminergic modulation of the hippocampal neuropil proteome identified by bioorthogonal non-canonical amino-acid tagging (BONCAT).
Proteomics 12: 2464-2476 (2012).

Ngo JT, Babin BM, Champion JA, Schuman EM, Tirrell DA.
State-Selective Metabolic Labeling of Cellular Proteins.
ACS Chem. Biol. 7: 1326-1330 (2012).

Troung F, Yoo TH, Lampo TJ, Tirrell DA.
Two-Strain, Cell-Selective Protein Labeling in Mixed Bacterial Cultures.
J. Am. Chem. Soc. 134: 8551-8556 (2012).

Hinz FI, Dieteich DC, Tirrell DA, Schuman EM, Noncanonical amino acid labeling in vivo to visualize and affinity purify newly synthesized proteins in larval zebrafish.
ACS Chem. Neurosci. 3: 40-49 (2012).

Xia Y, Li Y, Burts AO, Ottaviani MF, Tirrell DA, Johnson JA, Turro NK, Grubss RH, EPR Study of Spin Labeled Brush Polymers in Organic Solvents.
J. Am. Chem. Soc. 133: 19953-19959 (2011).

Beatty KE, Szychowski J, Fisk JD, Tirrell DA, A BODIPY-Cyclooctyne for Protein Imaging in Live Cells.
ChemBioChem 12: 2137-2139 (2011).

Ngo JT, Tirrell DA, Noncanonical Amino Acids in the Interrogation of Cellular Protein Synthesis.
Acc. Chem. Res. 44: 677-685 (2011).

Franck C, Maskarinec S, Tirrell DA, Ravichandran G, Three-dimensional Traction Force Microscopy:  A New Tool for Quantifying Cell-Matrix Interactions.
PLoS One 6: e17833 (2011).

Van Deventer JA, Fisk JD, Tirrell DA, Homoisoleucine: A Translationally Active Leucine Surrogate of Expanded Hydrophobic Surface Area.
ChemBioChem 12: 700-702 (2011).

Johnson JA, Lu YY, Burts AO, Lim YH, Finn MG, Koberstein JT, Turro NJ, Tirrell DA. Core-Clickable PEG-Branch-Azide Bivalent-Bottle-Brush Polymers by ROMP: Grafting-Through and Clicking-To.
J. Am. Chem. Soc. 133: 559-566 (2011).

Olsen BD, Kornfield JA, Tirrell DA.
Yielding Behavior in Injectable Hydrogels from Telechelic Proteins.
Macromolecules. 2010;43(21):9094-9099.
PMID: 21221427

Johnson JA, Lu YY, Burts AO, Lim YH, Finn MG, Koberstein JT, Turro NJ, Tirrell DA, Grubbs RH. Core-Clickable PEG-Branch-Azide Bivalent-Bottle-Brush Polymers by ROMP: Grafting-Through and Clicking-To.
J Am Chem Soc. 2010; 133: 559-566
PMID: 21142161

Szychowski J, Mahdavi A, Hodas JJ, Bagert JD, Ngo JT, Landgraf P, Dieterich DC, Schuman EM, Tirrell DA.
Cleavable biotin probes for labeling of biomolecules via azide-alkyne cycloaddition.
J Am Chem Soc. 2010;132(51):18351-60.
PMID: 21141861

Johnson JA, Lu YY, Van Deventer JA, Tirrell DA.
Residue-specific incorporation of non-canonical amino acids into proteins: recent developments and applications.
Curr Opin Chem Biol. 2010;14(6):774-80.
PMID: 21071259

Fong E, Tzlil S, Tirrell DA.
Boundary crossing in epithelial wound healing.
Proc Natl Acad Sci U S A. 2010;107(45):19302-7.
PMID: 20974917

Fong E, Tirrell DA.
Collective cell migration on artificial extracellular matrix proteins containing full-length fibronectin domains.
Adv Mater. 2010;22(46):5271-5.
PMID: 20886461

Kwon OH, Yoo TH, Othon CM, Van Deventer JA, Tirrell DA, Zewail AH.
Hydration dynamics at fluorinated protein surfaces.
Proc Natl Acad Sci U S A. 2010;107(40):17101-6.
PMID: 20855583

Beatty KE, Fisk JD, Smart BP, Lu YY, Szychowski J, Hangauer MJ, Baskin JM, Bertozzi CR, Tirrell DA.
Live-cell imaging of cellular proteins by a strain-promoted azide-alkyne cycloaddition.
Chembiochem. 2010;11(15):2092-5.
PMID: 20836119

Dieterich DC, Hodas JJ, Gouzer G, Shadrin IY, Ngo JT, Triller A, Tirrell DA, Schuman EM.
In situ visualization and dynamics of newly synthesized proteins in rat hippocampal neurons.
Nat Neuroscience 2010;13(7):897-905.
PMID: 20543841