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Timothy Andrew Whitehead

TitleAssociate Professor
InstitutionUniversity of Colorado Boulder
DepartmentChemical & Biological Engin

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. 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 Jun; 86(6). PMID: 29581192.
      View in: PubMed
    2. 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 Aug; 115(8):1925-1937. PMID: 29663315.
      View in: PubMed
    3. 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.
      View in: PubMed
    4. Whitehead TA. A peptide mimic of an antibody. Science. 2017 10 27; 358(6362):450-451. PMID: 29074756.
      View in: PubMed
    5. 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.
      View in: PubMed
    6. 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.
      View in: PubMed
    7. 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.
      View in: PubMed
    8. 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.
      View in: PubMed
    9. 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.
      View in: PubMed
    10. 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.
      View in: PubMed
    11. 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.
      View in: PubMed
    12. 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; PMCID: PMC4720449.
    13. Khare SD, Whitehead TA. Introduction to the Rosetta Special Collection. PLoS One. 2015; 10(12):e0144326. PMID: 26714017; PMCID: PMC4700992.
    14. Klesmith JR, Whitehead TA. High-throughput evaluation of synthetic metabolic pathways. Technology (Singap World Sci). 2016 Mar; 4(1):9-14. PMID: 27453919.
      View in: PubMed
    15. 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.
      View in: PubMed
    16. 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; PMCID: PMC4646320 [Available on 10/30/16].
    17. 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; PMCID: PMC4646304 [Available on 10/30/16].
    18. 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; PMCID: PMC4534290.
    19. 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; PMCID: PMC4366243.
    20. 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; PMCID: PMC4272552.
    21. 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.
      View in: PubMed
    22. 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; PMCID: PMC4186888.
    23. Whitehead TA, Baker D, Fleishman SJ. Computational design of novel protein binders and experimental affinity maturation. Methods Enzymol. 2013; 523:1-19. PMID: 23422423.
      View in: PubMed
    24. 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; PMCID: PMC3638900.
    25. 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, Azé J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-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-Rodríguez 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; PMCID: PMC3839241.
    26. 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; PMCID: PMC4144197.
    27. 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; PMCID: PMC3164876.
    28. 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; PMCID: PMC2952713.
    29. 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.
      View in: PubMed
    30. 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.
      View in: PubMed
    31. 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.
      View in: PubMed
    32. 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.
      View in: PubMed
    33. 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.
      View in: PubMed
    34. 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.
      View in: PubMed
    35. Whitehead TA, Boonyaratanakornkit BB, Höllrigl 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; PMCID: PMC2203346.
    36. 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.
      View in: PubMed
    37. Laksanalamai P, Whitehead TA, Robb FT. Minimal protein-folding systems in hyperthermophilic archaea. Nat Rev Microbiol. 2004 Apr; 2(4):315-24. PMID: 15031730.
      View in: PubMed
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