Timothy Andrew Whitehead
Title | Professor |
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Institution | University of Colorado Boulder |
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Department | Chemical & Biological Engin |
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Research R21GM129559 (GURUMURTHY, CHANNABASAVAIAH)Jul 1, 2019 - Jun 30, 2021 NIH Engineering Long ssDNA for Genome Editing Applications Role: Co-Principal Investigator |
| R01AI141452 (WHITEHEAD, TIMOTHY ANDREW)Jan 24, 2019 - Dec 31, 2024 NIH The influence of evolutionary landscapes on protective antibody development Role: Principal Investigator |
| R21CA176854 (CHAN, CHRISTINA)Apr 1, 2013 - Mar 31, 2016 NIH Deep Sequencing to Screen Functional Antibody Epitopes Role: Co-Principal Investigator |
Bibliographic
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Whitehead TA. Deep screening of antibody-antigen affinities. Nat Biomed Eng. 2024 Mar; 8(3):203-204. PMID: 38151637.
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Park SY, Qiu J, Wei S, Peterson FC, Beltr?n J, Medina-Cucurella AV, Vaidya AS, Xing Z, Volkman BF, Nusinow DA, Whitehead TA, Wheeldon I, Cutler SR. An orthogonalized PYR1-based CID module with reprogrammable ligand-binding specificity. Nat Chem Biol. 2024 Jan; 20(1):103-110. PMID: 37872402.
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Daffern N, Francino-Urdaniz IM, Baumer ZT, Whitehead TA. Standardizing cassette-based deep mutagenesis by Golden Gate assembly. Biotechnol Bioeng. 2024 01; 121(1):281-290. PMID: 37750676.
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Li Z, Shen Y, Beltr?n J, Tian H, Bedewitz M, Wheeldon I, Whitehead TA, Cutler SR, Zhong W. High-Performance Cannabinoid Sensor Empowered by Plant Hormone Receptors and Antifouling Magnetic Nanorods. ACS Sens. 2023 10 27; 8(10):3914-3922. PMID: 37737572.
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Strawn IK, Steiner PJ, Newton MS, Baumer ZT, Whitehead TA. A method for generating user-defined circular single-stranded DNA from plasmid DNA using Golden Gate intramolecular ligation. Biotechnol Bioeng. 2023 10; 120(10):3057-3066. PMID: 37366288.
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Leonard AC, Whitehead TA. Design and engineering of genetically encoded protein biosensors for small molecules. Curr Opin Biotechnol. 2022 Dec; 78:102787. PMID: 36058141.
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Zhao F, Keating C, Ozorowski G, Shaabani N, Francino-Urdaniz IM, Barman S, Limbo O, Burns A, Zhou P, Ricciardi MJ, Woehl J, Tran Q, Turner HL, Peng L, Huang D, Nemazee D, Andrabi R, Sok D, Teijaro JR, Whitehead TA, Ward AB, Burton DR, Jardine JG. Engineering SARS-CoV-2 neutralizing antibodies for increased potency and reduced viral escape pathways. iScience. 2022 Sep 16; 25(9):104914. PMID: 35971553.
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Beltr?n J, Steiner PJ, Bedewitz M, Wei S, Peterson FC, Li Z, Hughes BE, Hartley Z, Robertson NR, Medina-Cucurella AV, Baumer ZT, Leonard AC, Park SY, Volkman BF, Nusinow DA, Zhong W, Wheeldon I, Cutler SR, Whitehead TA. Rapid biosensor development using plant hormone receptors as reprogrammable scaffolds. Nat Biotechnol. 2022 12; 40(12):1855-1861. PMID: 35726092.
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Steiner PJ, Swift SD, Bedewitz M, Wheeldon I, Cutler SR, Nusinow DA, Whitehead TA. A Closed Form Model for Molecular Ratchet-Type Chemically Induced Dimerization Modules. Biochemistry. 2023 01 17; 62(2):281-291. PMID: 35675717.
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Leonard AC, Weinstein JJ, Steiner PJ, Erbse AH, Fleishman SJ, Whitehead TA. Stabilization of the SARS-CoV-2 receptor binding domain by protein core redesign and deep mutational scanning. Protein Eng Des Sel. 2022 02 17; 35. PMID: 35325236.
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Kirby MB, Whitehead TA. Facile Assembly of Combinatorial Mutagenesis Libraries Using Nicking Mutagenesis. Methods Mol Biol. 2022; 2461:85-109. PMID: 35727445.
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Leonard AC, Weinstein JJ, Steiner PJ, Erbse AH, Fleishman SJ, Whitehead TA. Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. bioRxiv. 2021 Nov 24. PMID: 34845448.
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Francino-Urdaniz IM, Whitehead TA. An overview of methods for the structural and functional mapping of epitopes recognized by anti-SARS-CoV-2 antibodies. RSC Chem Biol. 2021 Dec 02; 2(6):1580-1589. PMID: 34977572.
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Banach BB, Cerutti G, Fahad AS, Shen CH, Oliveira De Souza M, Katsamba PS, Tsybovsky Y, Wang P, Nair MS, Huang Y, Francino-Urd?niz IM, Steiner PJ, Guti?rrez-Gonz?lez M, Liu L, L?pez Acevedo SN, Nazzari AF, Wolfe JR, Luo Y, Olia AS, Teng IT, Yu J, Zhou T, Reddem ER, Bimela J, Pan X, Madan B, Laflin AD, Nimrania R, Yuen KY, Whitehead TA, Ho DD, Kwong PD, Shapiro L, DeKosky BJ. Paired heavy- and light-chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses. Cell Rep. 2021 10 05; 37(1):109771. PMID: 34587480.
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Petersen BM, Ulmer SA, Rhodes ER, Gutierrez-Gonzalez MF, Dekosky BJ, Sprenger KG, Whitehead TA. Regulatory Approved Monoclonal Antibodies Contain Framework Mutations Predicted From Human Antibody Repertoires. Front Immunol. 2021; 12:728694. PMID: 34646268.
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Haas CM, Francino-Urdaniz IM, Steiner PJ, Whitehead TA. Identification of SARS-CoV-2?S RBD escape mutants using yeast screening and deep mutational scanning. STAR Protoc. 2021 12 17; 2(4):100869. PMID: 34568839.
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Francino-Urdaniz IM, Steiner PJ, Kirby MB, Zhao F, Haas CM, Barman S, Rhodes ER, Leonard AC, Peng L, Sprenger KG, Jardine JG, Whitehead TA. One-shot identification of SARS-CoV-2?S RBD escape mutants using yeast screening. Cell Rep. 2021 08 31; 36(9):109627. PMID: 34416153.
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Baumer ZT, Whitehead TA. The inner workings of an enzyme. Science. 2021 07 23; 373(6553):391-392. PMID: 34437105.
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Urdaniz IF, Steiner PJ, Kirby MB, Zhao F, Haas CM, Barman S, Rhodes ER, Peng L, Sprenger KG, Jardine JG, Whitehead TA. One-shot identification of SARS-CoV-2 S RBD escape mutants using yeast screening. bioRxiv. 2021 Mar 15. PMID: 33758848.
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Kirby MB, Medina-Cucurella AV, Baumer ZT, Whitehead TA. Optimization of multi-site nicking mutagenesis for generation of large, user-defined combinatorial libraries. Protein Eng Des Sel. 2021 02 15; 34. PMID: 34341824.
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Banach BB, Cerutti G, Fahad AS, Shen CH, de Souza MO, Katsamba PS, Tsybovsky Y, Wang P, Nair MS, Huang Y, Urd?niz IMF, Steiner PJ, Guti?rrez-Gonz?lez M, Liu L, L?pez Acevedo SN, Nazzari A, Wolfe JR, Luo Y, Olia AS, Teng IT, Yu J, Zhou T, Reddem ER, Bimela J, Pan X, Madan B, Laflin AD, Nimrania R, Yuen KT, Whitehead TA, Ho DD, Kwong PD, Shapiro L, DeKosky BJ. Paired heavy and light chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses. bioRxiv. 2021 Jan 03. PMID: 33442681.
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Steiner PJ, Baumer ZT, Whitehead TA. A Method for User-defined Mutagenesis by Integrating Oligo Pool Synthesis Technology with Nicking Mutagenesis. Bio Protoc. 2020 Aug 05; 10(15):e3697. PMID: 33659364.
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Medina-Cucurella AV, Bammert GF, Dunkle W, Javens C, Zhu Y, Mutchler VT, Teel JT, Stein CA, Dunham SA, Whitehead TA. Feline Interleukin-31 Shares Overlapping Epitopes with the Oncostatin M Receptor and IL-31RA. Biochemistry. 2020 06 16; 59(23):2171-2181. PMID: 32459958.
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Whitehead TA, Banta S, Bentley WE, Betenbaugh MJ, Chan C, Clark DS, Hoesli CA, Jewett MC, Junker B, Koffas M, Kshirsagar R, Lewis A, Li CT, Maranas C, Terry Papoutsakis E, Prather KLJ, Schaffer S, Segatori L, Wheeldon I. The importance and future of biochemical engineering. Biotechnol Bioeng. 2020 08; 117(8):2305-2318. PMID: 32343367.
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Faber MS, Van Leuven JT, Ederer MM, Sapozhnikov Y, Wilson ZL, Wichman HA, Whitehead TA, Miller CR. Saturation Mutagenesis Genome Engineering of Infective FX174 Bacteriophage via Unamplified Oligo Pools and Golden Gate Assembly. ACS Synth Biol. 2020 01 17; 9(1):125-131. PMID: 31825605.
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Faber MS, Wrenbeck EE, Azouz LR, Steiner PJ, Whitehead TA. Impact of In Vivo Protein Folding Probability on Local Fitness Landscapes. Mol Biol Evol. 2019 12 01; 36(12):2764-2777. PMID: 31400199.
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Medina-Cucurella AV, Steiner PJ, Faber MS, Beltr?n J, Borelli AN, Kirby MB, Cutler SR, Whitehead TA. User-defined single pot mutagenesis using unamplified oligo pools. Protein Eng Des Sel. 2019 09 10; 32(1):41-45. PMID: 31297523.
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Faber MS, Whitehead TA. Data-driven engineering of protein therapeutics. Curr Opin Biotechnol. 2019 12; 60:104-110. PMID: 30822697.
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Wrenbeck EE, Bedewitz MA, Klesmith JR, Noshin S, Barry CS, Whitehead TA. An Automated Data-Driven Pipeline for Improving Heterologous Enzyme Expression. ACS Synth Biol. 2019 03 15; 8(3):474-481. PMID: 30721031.
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Acquaye-Seedah E, Reczek EE, Russell HH, DiVenere AM, Sandman SO, Collins JH, Stein CA, Whitehead TA, Maynard JA. Characterization of Individual Human Antibodies That Bind Pertussis Toxin Stimulated by Acellular Immunization. Infect Immun. 2018 06; 86(6). PMID: 29581192.
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Medina-Cucurella AV, Zhu Y, Bowen SJ, Bergeron LM, Whitehead TA. Pro region engineering of nerve growth factor by deep mutational scanning enables a yeast platform for conformational epitope mapping of anti-NGF monoclonal antibodies. Biotechnol Bioeng. 2018 08; 115(8):1925-1937. PMID: 29663315.
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Medina-Cucurella AV, Whitehead TA. Characterizing Protein-Protein Interactions Using Deep Sequencing Coupled to Yeast Surface Display. Methods Mol Biol. 2018; 1764:101-121. PMID: 29605911.
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Whitehead TA. A peptide mimic of an antibody. Science. 2017 10 27; 358(6362):450-451. PMID: 29074756.
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Wrenbeck EE, Azouz LR, Whitehead TA. Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded. Nat Commun. 2017 06 06; 8:15695. PMID: 28585537.
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Wang X, Stapleton JA, Klesmith JR, Hewlett EL, Whitehead TA, Maynard JA. Fine Epitope Mapping of Two Antibodies Neutralizing the Bordetella Adenylate Cyclase Toxin. Biochemistry. 2017 03 07; 56(9):1324-1336. PMID: 28177609.
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Klesmith JR, Bacik JP, Wrenbeck EE, Michalczyk R, Whitehead TA. Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning. Proc Natl Acad Sci U S A. 2017 02 28; 114(9):2265-2270. PMID: 28196882.
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Wrenbeck EE, Faber MS, Whitehead TA. Deep sequencing methods for protein engineering and design. Curr Opin Struct Biol. 2017 08; 45:36-44. PMID: 27886568.
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Haarmeyer CN, Smith MD, Chundawat SP, Sammond D, Whitehead TA. Insights into cellulase-lignin non-specific binding revealed by computational redesign of the surface of green fluorescent protein. Biotechnol Bioeng. 2017 04; 114(4):740-750. PMID: 27748522.
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Kowalsky CA, Whitehead TA. Determination of binding affinity upon mutation for type I dockerin-cohesin complexes from Clostridium thermocellum and Clostridium cellulolyticum using deep sequencing. Proteins. 2016 12; 84(12):1914-1928. PMID: 27699856.
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Wrenbeck EE, Klesmith JR, Stapleton JA, Adeniran A, Tyo KE, Whitehead TA. Plasmid-based one-pot saturation mutagenesis. Nat Methods. 2016 Nov; 13(11):928-930. PMID: 27723752.
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Stapleton JA, Kim J, Hamilton JP, Wu M, Irber LC, Maddamsetti R, Briney B, Newton L, Burton DR, Brown CT, Chan C, Buell CR, Whitehead TA. Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing. PLoS One. 2016; 11(1):e0147229. PMID: 26789840.
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Khare SD, Whitehead TA. Introduction to the Rosetta Special Collection. PLoS One. 2015; 10(12):e0144326. PMID: 26714017.
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Klesmith JR, Whitehead TA. High-throughput evaluation of synthetic metabolic pathways. Technology (Singap World Sci). 2016 Mar; 4(1):9-14. PMID: 27453919.
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Klesmith JR, Bacik JP, Michalczyk R, Whitehead TA. Comprehensive Sequence-Flux Mapping of a Levoglucosan Utilization Pathway in E. coli. ACS Synth Biol. 2015 Nov 20; 4(11):1235-43. PMID: 26369947.
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Bacik JP, Klesmith JR, Whitehead TA, Jarboe LR, Unkefer CJ, Mark BL, Michalczyk R. Producing glucose 6-phosphate from cellulosic biomass: structural insights into levoglucosan bioconversion. J Biol Chem. 2015 Oct 30; 290(44):26638-48. PMID: 26354439.
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Kowalsky CA, Faber MS, Nath A, Dann HE, Kelly VW, Liu L, Shanker P, Wagner EK, Maynard JA, Chan C, Whitehead TA. Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing. J Biol Chem. 2015 Oct 30; 290(44):26457-70. PMID: 26296891.
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Stapleton JA, Whitehead TA, Nanda V. Computational redesign of the lipid-facing surface of the outer membrane protein OmpA. Proc Natl Acad Sci U S A. 2015 Aug 04; 112(31):9632-7. PMID: 26199411.
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Kowalsky CA, Klesmith JR, Stapleton JA, Kelly V, Reichkitzer N, Whitehead TA. High-resolution sequence-function mapping of full-length proteins. PLoS One. 2015; 10(3):e0118193. PMID: 25790064.
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Gao D, Haarmeyer C, Balan V, Whitehead TA, Dale BE, Chundawat SP. Lignin triggers irreversible cellulase loss during pretreated lignocellulosic biomass saccharification. Biotechnol Biofuels. 2014; 7(1):175. PMID: 25530803.
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Tomek KJ, Saldarriaga CR, Velasquez FP, Liu T, Hodge DB, Whitehead TA. Removal and upgrading of lignocellulosic fermentation inhibitors by in situ biocatalysis and liquid-liquid extraction. Biotechnol Bioeng. 2015 Mar; 112(3):627-32. PMID: 25311910.
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Bienick MS, Young KW, Klesmith JR, Detwiler EE, Tomek KJ, Whitehead TA. The interrelationship between promoter strength, gene expression, and growth rate. PLoS One. 2014; 9(10):e109105. PMID: 25286161.
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Whitehead TA, Baker D, Fleishman SJ. Computational design of novel protein binders and experimental affinity maturation. Methods Enzymol. 2013; 523:1-19. PMID: 23422423.
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Whitehead TA, Chevalier A, Song Y, Dreyfus C, Fleishman SJ, De Mattos C, Myers CA, Kamisetty H, Blair P, Wilson IA, Baker D. Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Nat Biotechnol. 2012 May 27; 30(6):543-8. PMID: 22634563.
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Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Az? J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, P?rez-Cano L, Pons C, Fern?ndez-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodr?guez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol. 2011 Nov 25; 414(2):289-302. PMID: 22001016.
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Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Karanicolas J, Baker D. Hotspot-centric de novo design of protein binders. J Mol Biol. 2011 Nov 11; 413(5):1047-62. PMID: 21945116.
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Fleishman SJ, Whitehead TA, Ekiert DC, Dreyfus C, Corn JE, Strauch EM, Wilson IA, Baker D. Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science. 2011 May 13; 332(6031):816-21. PMID: 21566186.
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Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Andre I, Thompson J, Havranek JJ, Das R, Bradley P, Baker D. Rosetta in CAPRI rounds 13-19. Proteins. 2010 Nov 15; 78(15):3212-8. PMID: 20597089.
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Slocik JM, Kim SN, Whitehead TA, Clark DS, Naik RR. Biotemplated metal nanowires using hyperthermophilic protein filaments. Small. 2009 Sep; 5(18):2038-42. PMID: 19517487.
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Whitehead TA, Bergeron LM, Clark DS. Tying up the loose ends: circular permutation decreases the proteolytic susceptibility of recombinant proteins. Protein Eng Des Sel. 2009 Oct; 22(10):607-13. PMID: 19622546.
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Whitehead TA, Je E, Clark DS. Rational shape engineering of the filamentous protein gamma prefoldin through incremental gene truncation. Biopolymers. 2009 Jun; 91(6):496-503. PMID: 19189379.
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Bergeron LM, Gomez L, Whitehead TA, Clark DS. Self-renaturing enzymes: design of an enzyme-chaperone chimera as a new approach to enzyme stabilization. Biotechnol Bioeng. 2009 Apr 01; 102(5):1316-22. PMID: 19170240.
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Bruns N, Pustelny K, Bergeron LM, Whitehead TA, Clark DS. Mechanical nanosensor based on FRET within a thermosome: damage-reporting polymeric materials. Angew Chem Int Ed Engl. 2009; 48(31):5666-9. PMID: 19402088.
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Whitehead TA, Meadows AL, Clark DS. Controlling the self-assembly of a filamentous hyperthermophilic chaperone by an engineered capping protein. Small. 2008 Jul; 4(7):956-60. PMID: 18576281.
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Whitehead TA, Boonyaratanakornkit BB, H?llrigl V, Clark DS. A filamentous molecular chaperone of the prefoldin family from the deep-sea hyperthermophile Methanocaldococcus jannaschii. Protein Sci. 2007 Apr; 16(4):626-34. PMID: 17384227.
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Boonyaratanakornkit BB, Simpson AJ, Whitehead TA, Fraser CM, El-Sayed NM, Clark DS. Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock. Environ Microbiol. 2005 Jun; 7(6):789-97. PMID: 15892698.
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Faffe DS, Flynt L, Mellema M, Moore PE, Silverman ES, Subramaniam V, Jones MR, Mizgerd JP, Whitehead T, Imrich A, Panettieri RA, Shore SA. Oncostatin M causes eotaxin-1 release from airway smooth muscle: synergy with IL-4 and IL-13. J Allergy Clin Immunol. 2005 Mar; 115(3):514-20. PMID: 15753898.
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Laksanalamai P, Whitehead TA, Robb FT. Minimal protein-folding systems in hyperthermophilic archaea. Nat Rev Microbiol. 2004 Apr; 2(4):315-24. PMID: 15031730.
This graph shows the total number of publications by year, by first, middle/unknown, or last author.
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Year | Publications |
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2004 | 1 | 2005 | 2 | 2007 | 1 | 2008 | 1 | 2009 | 5 | 2010 | 1 | 2011 | 3 | 2012 | 1 | 2013 | 1 | 2014 | 3 | 2015 | 7 | 2016 | 5 | 2017 | 4 | 2018 | 3 | 2019 | 4 | 2020 | 4 | 2021 | 10 | 2022 | 6 | 2023 | 4 | 2024 | 1 |
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