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Enzymatic Labeling of Bacterial Proteins for Super-resolution Imaging in Live Cells.

Ho SH, Tirrell DA.

ACS Cent Sci. 2019 Dec 26;5(12):1911-1919. doi: 10.1021/acscentsci.9b00617. Epub 2019 Nov 21.


The dormancy-specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa.

Bergkessel M, Babin BM, VanderVelde D, Sweredoski MJ, Moradian A, Eggleston-Rangel R, Hess S, Tirrell DA, Artsimovitch I, Newman DK.

Mol Microbiol. 2019 Sep;112(3):992-1009. doi: 10.1111/mmi.14337. Epub 2019 Jul 10.


N-Myristoyl Transferase (NMT)-Catalyzed Labeling of Bacterial Proteins for Imaging in Fixed and Live Cells.

Ho SH, Tirrell DA.

Methods Mol Biol. 2019;2012:315-326. doi: 10.1007/978-1-4939-9546-2_16.


Mechanisms of Diffusion in Associative Polymer Networks: Evidence for Chain Hopping.

Rapp PB, Omar AK, Silverman BR, Wang ZG, Tirrell DA.

J Am Chem Soc. 2018 Oct 31;140(43):14185-14194. doi: 10.1021/jacs.8b07908. Epub 2018 Oct 22.


Incorporation of Non-Canonical Amino Acids into Proteins by Global Reassignment of Sense Codons.

Fang KY, Lieblich SA, Tirrell DA.

Methods Mol Biol. 2018;1798:173-186. doi: 10.1007/978-1-4939-7893-9_13.


Glucocorticoid Signaling Enhances Expression of Glucose-Sensing Molecules in Immature Pancreatic Beta-Like Cells Derived from Murine Embryonic Stem Cells In Vitro.

Ghazalli N, Wu X, Walker S, Trieu N, Hsin LY, Choe J, Chen C, Hsu J, LeBon J, Kozlowski MT, Rawson J, Tirrell DA, Yip MLR, Ku HT.

Stem Cells Dev. 2018 Jul 1;27(13):898-909. doi: 10.1089/scd.2017.0160. Epub 2018 Jun 6.


Cell-type-specific metabolic labeling of nascent proteomes in vivo.

Alvarez-Castelao B, Schanzenbächer CT, Hanus C, Glock C, Tom Dieck S, Dörrbaum AR, Bartnik I, Nassim-Assir B, Ciirdaeva E, Mueller A, Dieterich DC, Tirrell DA, Langer JD, Schuman EM.

Nat Biotechnol. 2017 Dec;35(12):1196-1201. doi: 10.1038/nbt.4016. Epub 2017 Nov 6.


Selective Proteomic Analysis of Antibiotic-Tolerant Cellular Subpopulations in Pseudomonas aeruginosa Biofilms.

Babin BM, Atangcho L, van Eldijk MB, Sweredoski MJ, Moradian A, Hess S, Tolker-Nielsen T, Newman DK, Tirrell DA.

mBio. 2017 Oct 24;8(5). pii: e01593-17. doi: 10.1128/mBio.01593-17.


Protein-Mediated Colloidal Assembly.

Obana M, Silverman BR, Tirrell DA.

J Am Chem Soc. 2017 Oct 11;139(40):14251-14256. doi: 10.1021/jacs.7b07798. Epub 2017 Sep 27.


4S-Hydroxylation of Insulin at ProB28 Accelerates Hexamer Dissociation and Delays Fibrillation.

Lieblich SA, Fang KY, Cahn JKB, Rawson J, LeBon J, Ku HT, Tirrell DA.

J Am Chem Soc. 2017 Jun 28;139(25):8384-8387. doi: 10.1021/jacs.7b00794. Epub 2017 Jun 20.


A Fluorescence in Situ Hybridization Method To Quantify mRNA Translation by Visualizing Ribosome-mRNA Interactions in Single Cells.

Burke KS, Antilla KA, Tirrell DA.

ACS Cent Sci. 2017 May 24;3(5):425-433. doi: 10.1021/acscentsci.7b00048. Epub 2017 May 3.


Analysis and Control of Chain Mobility in Protein Hydrogels.

Rapp PB, Omar AK, Shen JJ, Buck ME, Wang ZG, Tirrell DA.

J Am Chem Soc. 2017 Mar 15;139(10):3796-3804. doi: 10.1021/jacs.6b13146. Epub 2017 Mar 1.


Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) Enables Time-Resolved Analysis of Protein Synthesis in Native Plant Tissue.

Glenn WS, Stone SE, Ho SH, Sweredoski MJ, Moradian A, Hess S, Bailey-Serres J, Tirrell DA.

Plant Physiol. 2017 Mar;173(3):1543-1553. doi: 10.1104/pp.16.01762. Epub 2017 Jan 19.


Cell-selective proteomics for biological discovery.

Stone SE, Glenn WS, Hamblin GD, Tirrell DA.

Curr Opin Chem Biol. 2017 Feb;36:50-57. doi: 10.1016/j.cbpa.2016.12.026. Epub 2017 Jan 12. Review.


Chemoenzymatic Labeling of Proteins for Imaging in Bacterial Cells.

Ho SH, Tirrell DA.

J Am Chem Soc. 2016 Nov 23;138(46):15098-15101. Epub 2016 Nov 15.


Engineering the Dynamic Properties of Protein Networks through Sequence Variation.

Dooling LJ, Tirrell DA.

ACS Cent Sci. 2016 Nov 23;2(11):812-819. Epub 2016 Oct 18.


In Vitro Colony Assays for Characterizing Tri-potent Progenitor Cells Isolated from the Adult Murine Pancreas.

Tremblay JR, LeBon JM, Luo A, Quijano JC, Wedeken L, Jou K, Riggs AD, Tirrell DA, Ku HT.

J Vis Exp. 2016 Jun 10;(112). doi: 10.3791/54016.


Grand Challenges in Chemistry for 2016 and Beyond.

Bertozzi CR, Chang CJ, Davis BG, Olvera de la Cruz M, Tirrell DA, Zhao D.

ACS Cent Sci. 2016 Jan 27;2(1):1-3. doi: 10.1021/acscentsci.6b00010. No abstract available.


Programming Molecular Association and Viscoelastic Behavior in Protein Networks.

Dooling LJ, Buck ME, Zhang WB, Tirrell DA.

Adv Mater. 2016 Jun;28(23):4651-7. doi: 10.1002/adma.201506216. Epub 2016 Apr 9.


Engineered Aminoacyl-tRNA Synthetase for Cell-Selective Analysis of Mammalian Protein Synthesis.

Mahdavi A, Hamblin GD, Jindal GA, Bagert JD, Dong C, Sweredoski MJ, Hess S, Schuman EM, Tirrell DA.

J Am Chem Soc. 2016 Apr 6;138(13):4278-81. doi: 10.1021/jacs.5b08980. Epub 2016 Mar 25.


Time-resolved proteomic analysis of quorum sensing in Vibrio harveyi.

Bagert JD, van Kessel JC, Sweredoski MJ, Feng L, Hess S, Bassler BL, Tirrell DA.

Chem Sci. 2016 Mar 1;7(3):1797-1806. Epub 2015 Nov 23.


SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa.

Babin BM, Bergkessel M, Sweredoski MJ, Moradian A, Hess S, Newman DK, Tirrell DA.

Proc Natl Acad Sci U S A. 2016 Feb 2;113(5):E597-605. doi: 10.1073/pnas.1514412113. Epub 2016 Jan 19.


Cells with surface expression of CD133highCD71low are enriched for tripotent colony-forming progenitor cells in the adult murine pancreas.

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.

Stem Cell Res. 2016 Jan;16(1):40-53. doi: 10.1016/j.scr.2015.11.015. Epub 2015 Nov 30.


Bioorthogonal Chemoenzymatic Functionalization of Calmodulin for Bioconjugation Applications.

Kulkarni C, Lo M, Fraseur JG, Tirrell DA, Kinzer-Ursem TL.

Bioconjug Chem. 2015 Oct 21;26(10):2153-60. doi: 10.1021/acs.bioconjchem.5b00449. Epub 2015 Oct 2.


Two-Site Internally Cooperative Mechanism for Enzyme Kinetics in a Hydrogel Forming Recombinant Protein.

Zehner NA, Dietrick SM, Tirrell DA, Kennedy SB.

Biomacromolecules. 2015 Nov 9;16(11):3651-6. doi: 10.1021/acs.biomac.5b01110. Epub 2015 Oct 12.


Microbuckling of fibrin provides a mechanism for cell mechanosensing.

Notbohm J, Lesman A, Rosakis P, Tirrell DA, Ravichandran G.

J R Soc Interface. 2015 Jul 6;12(108):20150320. doi: 10.1098/rsif.2015.0320.


Quantifying cell-induced matrix deformation in three dimensions based on imaging matrix fibers.

Notbohm J, Lesman A, Tirrell DA, Ravichandran G.

Integr Biol (Camb). 2015 Oct;7(10):1186-95. doi: 10.1039/c5ib00013k. Epub 2015 May 29.


Postnatal Pancreas of Mice Contains Tripotent Progenitors Capable of Giving Rise to Duct, Acinar, and Endocrine Cells In Vitro.

Ghazalli N, Mahdavi A, Feng T, Jin L, Kozlowski MT, Hsu J, Riggs AD, Tirrell DA, Ku HT.

Stem Cells Dev. 2015 Sep 1;24(17):1995-2008. doi: 10.1089/scd.2015.0007. Epub 2015 Jun 9.


Direct visualization of newly synthesized target proteins in situ.

tom Dieck S, Kochen L, Hanus C, Heumüller M, Bartnik I, Nassim-Assir B, Merk K, Mosler T, Garg S, Bunse S, Tirrell DA, Schuman EM.

Nat Methods. 2015 May;12(5):411-4. doi: 10.1038/nmeth.3319. Epub 2015 Mar 16.


A photoreversible protein-patterning approach for guiding stem cell fate in three-dimensional gels.

DeForest CA, Tirrell DA.

Nat Mater. 2015 May;14(5):523-31. doi: 10.1038/nmat4219. Epub 2015 Feb 23.


Cell-specific proteomic analysis in Caenorhabditis elegans.

Yuet KP, Doma MK, Ngo JT, Sweredoski MJ, Graham RL, Moradian A, Hess S, Schuman EM, Sternberg PW, Tirrell DA.

Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):2705-10. doi: 10.1073/pnas.1421567112. Epub 2015 Feb 17.


A qrr noncoding RNA deploys four different regulatory mechanisms to optimize quorum-sensing dynamics.

Feng L, Rutherford ST, Papenfort K, Bagert JD, van Kessel JC, Tirrell DA, Wingreen NS, Bassler BL.

Cell. 2015 Jan 15;160(1-2):228-40. doi: 10.1016/j.cell.2014.11.051. Epub 2015 Jan 8.


Colony-forming progenitor cells in the postnatal mouse liver and pancreas give rise to morphologically distinct insulin-expressing colonies in 3D cultures.

Jin L, Feng T, Chai J, Ghazalli N, Gao D, Zerda R, Li Z, Hsu J, Mahdavi A, Tirrell DA, Riggs AD, Ku HT.

Rev Diabet Stud. 2014 Spring;11(1):35-50. doi: 10.1900/RDS.2014.11.35. Epub 2014 May 10.


Synthesis of bioactive protein hydrogels by genetically encoded SpyTag-SpyCatcher chemistry.

Sun F, Zhang WB, Mahdavi A, Arnold FH, Tirrell DA.

Proc Natl Acad Sci U S A. 2014 Aug 5;111(31):11269-74. doi: 10.1073/pnas.1401291111. Epub 2014 Jul 21.


Cell surface display yields evolvable, clickable antibody fragments.

Van Deventer JA, Yuet KP, Yoo TH, Tirrell DA.

Chembiochem. 2014 Aug 18;15(12):1777-81. doi: 10.1002/cbic.201402184. Epub 2014 Jul 17.


Contractile forces regulate cell division in three-dimensional environments.

Lesman A, Notbohm J, Tirrell DA, Ravichandran G.

J Cell Biol. 2014 Apr 28;205(2):155-62. doi: 10.1083/jcb.201309029.


In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry.

Hatzenpichler R, Scheller S, Tavormina PL, Babin BM, Tirrell DA, Orphan VJ.

Environ Microbiol. 2014 Aug;16(8):2568-90. doi: 10.1111/1462-2920.12436. Epub 2014 Apr 2.


Quantitative, time-resolved proteomic analysis by combining bioorthogonal noncanonical amino acid tagging and pulsed stable isotope labeling by amino acids in cell culture.

Bagert JD, Xie YJ, Sweredoski MJ, Qi Y, Hess S, Schuman EM, Tirrell DA.

Mol Cell Proteomics. 2014 May;13(5):1352-8. doi: 10.1074/mcp.M113.031914. Epub 2014 Feb 21.


Identification of secreted bacterial proteins by noncanonical amino acid tagging.

Mahdavi A, Szychowski J, Ngo JT, Sweredoski MJ, Graham RL, Hess S, Schneewind O, Mazmanian SK, Tirrell DA.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):433-8. doi: 10.1073/pnas.1301740111. Epub 2013 Dec 17.


Prometastatic GPCR CD97 is a direct target of tumor suppressor microRNA-126.

Lu YY, Sweredoski MJ, Huss D, Lansford R, Hess S, Tirrell DA.

ACS Chem Biol. 2014 Feb 21;9(2):334-8. doi: 10.1021/cb400704n. Epub 2013 Nov 25.


Brush-first and click: efficient synthesis of nanoparticles that degrade and release doxorubicin in response to light.

Burts AO, Liao L, Lu YY, Tirrell DA, Johnson JA.

Photochem Photobiol. 2014 Mar-Apr;90(2):380-5. doi: 10.1111/php.12182. Epub 2013 Nov 25.


Selective functionalization of the protein N terminus with N-myristoyl transferase for bioconjugation in cell lysate.

Kulkarni C, Kinzer-Ursem TL, Tirrell DA.

Chembiochem. 2013 Oct 11;14(15):1958-62. doi: 10.1002/cbic.201300453. Epub 2013 Sep 12.


Controlling macromolecular topology with genetically encoded SpyTag-SpyCatcher chemistry.

Zhang WB, Sun F, Tirrell DA, Arnold FH.

J Am Chem Soc. 2013 Sep 18;135(37):13988-97. doi: 10.1021/ja4076452. Epub 2013 Sep 9.


Chemical tools for temporally and spatially resolved mass spectrometry-based proteomics.

Yuet KP, Tirrell DA.

Ann Biomed Eng. 2014 Feb;42(2):299-311. doi: 10.1007/s10439-013-0878-3. Epub 2013 Aug 14. Review.


Self-assembly of elastin-mimetic double hydrophobic polypeptides.

Le DH, Hanamura R, Pham DH, Kato M, Tirrell DA, Okubo T, Sugawara-Narutaki A.

Biomacromolecules. 2013 Apr 8;14(4):1028-34. doi: 10.1021/bm301887m. Epub 2013 Mar 28.


Mutant methionyl-tRNA synthetase from bacteria enables site-selective N-terminal labeling of proteins expressed in mammalian cells.

Ngo JT, Schuman EM, Tirrell DA.

Proc Natl Acad Sci U S A. 2013 Mar 26;110(13):4992-7. doi: 10.1073/pnas.1216375110. Epub 2013 Mar 11.


Colony-forming cells in the adult mouse pancreas are expandable in Matrigel and form endocrine/acinar colonies in laminin hydrogel.

Jin L, Feng T, Shih HP, Zerda R, Luo A, Hsu J, Mahdavi A, Sander M, Tirrell DA, Riggs AD, Ku HT.

Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3907-12. doi: 10.1073/pnas.1301889110. Epub 2013 Feb 19.


A genetically encoded and gate for cell-targeted metabolic labeling of proteins.

Mahdavi A, Segall-Shapiro TH, Kou S, Jindal GA, Hoff KG, Liu S, Chitsaz M, Ismagilov RF, Silberg JJ, Tirrell DA.

J Am Chem Soc. 2013 Feb 27;135(8):2979-82. doi: 10.1021/ja400448f. Epub 2013 Feb 18.


A magnetic cell-based sensor.

Wang H, Mahdavi A, Tirrell DA, Hajimiri A.

Lab Chip. 2012 Nov 7;12(21):4465-71. doi: 10.1039/c2lc40392g.


Synthesis and cell adhesive properties of linear and cyclic RGD functionalized polynorbornene thin films.

Patel PR, Kiser RC, Lu YY, Fong E, Ho WC, Tirrell DA, Grubbs RH.

Biomacromolecules. 2012 Aug 13;13(8):2546-53. doi: 10.1021/bm300795y. Epub 2012 Jul 27.

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