Selected Publication List

(*Corresponding Author, ^Graduate Student/Postdoc Trainee, &Undergraduate Trainee, +Authors contributed equally)

  1. Baumer ZT^, Whitehead TA* (2021) “The inner workings of an enzyme”, Science 373(6553):391-392 DOI:10.1126/science.abj8346
  2. Wrenbeck EE^, Azouz LR&, Whitehead TA* (2017), “Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded”, Nature Communications 8:15695 doi:10.1038/ncomms15695

  3. Klesmith JR^, Bacik JP, Wrenbeck EE^, Michalczyk R, Whitehead TA* (2017) “Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning”, PNAS 114(9):2265-2270 doi:10.1073/pnas.1614437114

  4. Wrenbeck EE^, Klesmith JR^, Adeniran A, Stapleton JA^, Tyo KJ, Whitehead TA*, (2016) “Plasmid-based single-pot saturation mutagenesis”, Nature Methods 13(11):928-930 doi:10.1038/nmeth.4029

  5. Whitehead TA+, Chevalier A+, Song Y et al. (2012) “Optimization of affinity, specificity, and function of designed Influenza inhibitors using deep sequencing”, Nature Biotechnology 30(6):543-8. doi: 10.1038/nbt.2214

Complete Publication List

  1. Francino-Urdaniz, IM^, Whitehead TA* (2021) "An overview of methods for the structural and functional mapping of epitopes recognized by anti-SARS-CoV-2 antibodies", RCS Chemical Biology DOI:10.1039/D1CB00169H

  2. Petersen BM^, Ulmer SA&, Rhodes ER^, Gutierrez Gonzalez MF, Dekosky BJ, Sprenger KG*, Whitehead TA* (2021) “Regulatory approved monoclonal antibodies contain framework mutations predicted from human antibody repertoires”, Frontiers in Immunology 12:3855 DOI:10.3389/fimmu.2021.728694 

  3. Baumer ZT^, Whitehead TA* (2021) “The inner workings of an enzyme”, Science 373(6553):391-392 DOI:10.1126/science.abj8346

  4. Beltrán J, Steiner PJ^, Bedewitz M^, Wei S, Peterson F, Hughes BE, Hartley Z, Volkman BF, Nusinow DA, Wheeldon I, Cutler SR, Whitehead TA* (2021), “Cannabinoid biosensors from a plant hormone receptor”, under review

  5. Kirby MB^, Medina-Cucurella AV^, Baumer ZT^, Whitehead TA*, (2021) “Optimization of multi-site nicking mutagenesis for generation of large, user-defined combinatorial libraries”, Protein Engineering, Design, and Selection 34:gzab017 DOI:10.1093/protein/gzab017

  6. Francino-Urdaniz I^, Steiner PJ^, Kirby MB^, Zhao F, Haas CM&, Barman S, Rhodes ER^, Leonard AC^, Peng L, Sprenger K, Jardine JG, Whitehead TA* (2021) “One-shot identification of SARS-CoV-2 S RBD escape mutants using yeast screening”, Cell Reports 36(9):109627 doi:10.1016/j.celrep.2021.10962

  7. Bailey B. Banach, Gabriele Cerutti, Ahmed S. Fahad, Chen-Hsiang Shen, Matheus Olivera de Souza, Phini Katsamba, Yaroslav Tsybovsky, Pengfei Wang, Manoj S. Nair, Yaoxing Huang, Irene M. Francino Urdániz^, Paul J. Steiner^, Matias Gutiérrez-González, Lihong Liu, Sheila N. Lopez Acevedo, Alexandra Nazzari, Jacy R. Wolfe, Yang Luo, Adam S. Olia, I-Ting Teng, Jian Yu, Tongqing Zhou, Eswar Reddem, Jude Bimela, Xiaoli Pan, Bharat Madan, Amy D. Laflin, Rajani Madan, Kwok-Yung Yuen, Timothy A. Whitehead, David D. Ho, Peter D. Kwong, Lawrence Shapiro & Brandon J. DeKosky, (2021) “Paired heavy and light chain signatures contribute to potent SARS-CoV-2 neutralization in IGHV3-53/3-66 public antibody responses”, Cell Reports, accepted

  8. Kirby MB^, Whitehead TA*, (2021) “Facile Assembly of Combinatorial Mutagenesis Libraries using Nicking Mutagenesis”, Methods in Molecular Biology, in press

  9. Steiner PJ^, Baumer ZT^, Whitehead TA*, (2020) “A method for user-defined mutagenesis by integrating oligo pool synthesis technology with nicking mutagenesis”, Bio-protocol 10(15):e3697

  10. Medina-Cucurella A^, Gary F. Bammert, William Dunkle, Christopher Javens, Yaqi Zhu, Veronica T. Mutchler, Janet T. Teel, Caitlin A. Stein^, Steve A. Dunham, Whitehead TA* (2020)  “Feline Interleukin-31 shares overlapping epitopes with Oncostatin M receptor and IL-31RA”, Biochemistry 59(23):2171-2181 doi:10.1021/acs.biochem.0c00176

  11. Timothy A. Whitehead,*, Scott Banta, William E. Bentley, Michael J. Betenbaugh, Christina Chan, Douglas S. Clark, Corinne Hoesli, Michael C. Jewett, Beth Junker, Mattheos Koffas, Rashmi Kshirsagar, Amanda Lewis, Chien-Ting Li, Costas Maranas, E. Terry Papoutsakis, Kris J. Prather, Steffen Schaffer, Laura Segatori, Ian Wheeldon (2020) “The Importance and future of Biochemical Engineering”, Biotechnology & Bioengineering 117: 2305–2318 doi:10.1002/bit.27364

  12. Faber MS^, Van Leuven JT, Whitehead TA, Miller CR* “Saturation mutagenesis genome engineering of infective ΦX174 bacteriophage via unamplified oligo pools and golden gate assembly”, (2020) ACS Synthetic Biology 9(1):125-131 doi:10.1021/acssynbio.9b00411

  13. Leman JK, Weitzner BD, Renfrew DP, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Rosetta Commons Consortium, et al (2020) “Better together: Elements of successful scientific software development in a distributed collaborative community”, PLOS Computational Biology 16(5):e1007507 doi: 10.1371/journal.pcbi.1007507

  14. Medina-Cucurella A^, Zhu Y, Bowen SJ, Bergeron LM, Whitehead TA* (2018) “Pro region engineering of nerve growth factor by deep mutational scanning enables a yeast platform for conformational epitope mapping of anti-NGF monoclonal antibodies”, Biotechnology & Bioengineering 115(8):1925-1937 DOI:10.1002/bit.26706

  15. Acquaye-Seedah E, Reczek E, Russell H, Sandman SO&, Collins JH&, Stein CA^, DiVenere A, Whitehead TA, Maynard JA (2018) “Characterization of Individual Human Antibodies that Bind Pertussis Toxin Stimulated by Acellular Immunization”, Infection & Immunity 86(6):e00004-18 DOI:10.1128/IAI.00004-18

  16. Medina-Cucurella A^, Whitehead TA* (2018) “Characterizing Protein-Protein Interactions Using Deep Sequencing Coupled to Yeast Surface Display”, Methods in Molecular Biology in Protein Complex Assembly, 101-121

  17. Whitehead TA*, (2017) “A peptide mimic of an antibody” Science 358(6362):450-451 doi:10.1126/science.aap9608

  18. Whitehead T*, Cutler S, Wheeldon I, (2017) “Plant Metabolic Engineering for Chemicals, Fuels, and Precursors”, Chemical Engineering Progress SBE Supplement (invited)

  19. Wrenbeck EE^, Azouz LR&, Whitehead TA* (2017), “Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded”, Nature Communications 8:15695 doi:10.1038/ncomms15695

  20. Whitehead TA*, Bandi CK, Berger M, Park J, Chundawat S* (2017) “Negatively supercharging cellulases render them lignin-resistant”, ACS Sustainable Chemistry & Engineering in press doi:10.1021/acssuschemeng.7b01202

    1. Cover of ACS Sustainable Chemistry & Engineering

  21. Wang X, Stapleton JA^, Klesmith JR^, Hewlett E, Whitehead TA, Maynard J (2017) “Fine epitope mapping of two antibodies neutralizing the Bordetella adenylate cyclase toxin”, Biochemistry 56:1324-1336 doi: 10.1021/acs.biochem.6b01163

  22. Klesmith JR^, Bacik JP, Wrenbeck EE^, Michalczyk R, Whitehead TA* (2017) “Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning”, PNAS 114:2265-2270 doi: 10.1073/pnas.1614437114

  23. Wrenbeck EE^, Faber M^, Whitehead TA* (2017) “Deep sequencing methods for protein engineering and design”, Current Opinion in Structural Biology 45:36-44

  24. Haarmeyer C^, Smith MD&, Chundawat S, Sammond D, Whitehead TA*, (2017) “Insights into cellulase-lignin non-specific binding revealed by computational redesign of the surface of green fluorescent protein”, Biotechnology & Bioengineering 114:740-750 doi:10.1002/bit.26201

  25. Kowalsky CA^, Whitehead TA*, (2016) “Determination of binding affinity upon mutation for type I dockerin-cohesin complexes from Clostridium thermocellum and Clostridium cellulolyticum using deep sequencing”, Proteins 84(12): 1914-1928 doi:10.1002/prot.25175

  26. Wrenbeck EE^, Klesmith JR^, Adeniran A, Stapleton JA^, Tyo KJ, Whitehead TA*, (2016) “Plasmid-based single-pot saturation mutagenesis”, Nature Methods 13(11): 928-930 doi:10.1038/nmeth.4029

    1. Documentation at Nature Protocols Exchange (doi:10.1038/protex.2016.061)

  27. Klesmith JR^, Thorwall S&, Whitehead TA* (2016) “Interpreting deep mutational scanning data resulting from plate-based selections”, bioRxiv 087072

  28. 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* (2016) “Haplotype-phased synthetic long reads from short-read sequencing”, PLoS ONE 11(1):e0147229

  29. Khare S*, Whitehead TA* (2015), “Introduction to RosettaCON Special Collection”, PLoS ONE 10(12):e0144326

  30. Klesmith JR^, Whitehead TA* (2015), “High-throughput evaluation of synthetic metabolic pathways”, Technology 4(01):9-14

  31. Klesmith JR^, Bacik JP, Michalczyk R, Whitehead TA* (2015) “High-resolution sequence function mapping of a levoglucosan utilization pathway in E. coli”, ACS Synthetic Biology 4 (11), 1235-1243 DOI: 10.1021/acssynbio.5b00131

    1. Selected for ‘Introducing our Authors’ feature highlight.

  32. Bacik JP, Klesmith JR^, Whitehead TA, Jarboe LR, Unkefer CJ, Mark BL, Michalczyk R (2015) “Structural insights into bioconversion of the biomass pyrolysis product levoglucosan”, Journal of Biological Chemistry 290 (44), 26638-26648

  33. Kowalsky CA^, Faber M^, Nath A, Dann H&, Kelly VW&, Liu L, Shanker P, Wagner EK, Maynard J, Chan C, Whitehead TA* (2015) “Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing”, Journal of Biological Chemistry 290 (44), 26457-26470 doi:10.1074/jbc.M115.676635

    1. Top 5 accessed article for J. Biol. Chem., Oct. 2015.

  34. Stapleton JA^, Whitehead TA, Nanda V (2015) “Computational redesign of the lipid-facing surface of the outer membrane protein OmpA”, PNAS 112(31):9632-9637

  35. Kowalsky CA^, Klesmith JR^, Stapleton JA^, Kelly VW&, Reichkitzer N&, Whitehead TA* (2015) “High-resolution sequence-function mapping of full proteins”, PLoS ONE, 10(3): e0118193. doi:10.1371/journal.pone.0118193

  36. Tomek KJ&, Saldarriaga CRC&, Velasquez FPC, Liu T, Hodge DB, Whitehead TA*, (2015) “Removal and upgrading of lignocellulosic fermentation inhibitors by in situ biocatalysis and liquid-liquid extraction”, Biotechnology & Bioengineering, 112(3):627-632. http://onlinelibrary.wiley.com/doi/10.1002/bit.25473/abstract

    1. Selected for B&B video highlight.

  37. Gao D, Haarmeyer C^, Balan V, Whitehead TA, Dale BE, Chundawat SPS (2014) “Lignin triggers irreversible cellulase loss during pretreated lignocellulosic biomass saccarification”, Biotechnology for Biofuels, 7:175

  38. Bienick MS&, Young KW&, Klesmith JR^, Detwiler EE^, Tomek KJ&, Whitehead TA*, (2014) “The interrelationship between promoter strength, gene expression, and growth rate”, PLoS ONE, DOI: 10.1371/journal.pone.0109105

  39. Whitehead TA*, Baker D, Fleishman SJ* (2013) “Computational design of novel protein binders and experimental affinity maturation”, Methods Enzymology, 523:1-19. doi: 10.1016/B978-0-12-394292-0.00001-1.

  40. Whitehead TA+, Chevalier A+, Song Y et al. (2012) “Optimization of affinity, specificity, and function of designed Influenza inhibitors using deep sequencing”, Nature Biotechnology 30(6):543-8. doi: 10.1038/nbt.2214 + authors contributed equally

    1. Cover of Nature Biotechnology; Featured in numerous popular press articles and radio interviews, including NPR.

  41. Fleishman SJ, Whitehead TA, Strauch EM et al. (2011) “Community-wide assessment of protein-interface modeling suggests improvements to design methodology”, J Mol Biol 414(2):289

  42. Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Karanicolas J, Baker D (2011) “Hotspot-centric de novo design of protein binders”, J Mol Biol 413(5):1047

  43. Fleishman SJ+, Whitehead TA+, Ekiert D+, Dreyfus C, Corn JE, Strauch EM, Wilson IA, Baker D (2011) “Computational design of proteins targeting the conserved stem region of Influenza hemagglutinin”, Science 332(6031):816-21 +authors contributed equally

    1. Featured in numerous popular press articles and radio interviews, including NPR.

  44. Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Andre I, Thompson J, Havranek JJ, Das R, Bradley P, Baker D (2010), “Rosetta in CAPRI rounds 13-19” Proteins 78(15):3212

  45. Whitehead TA, Bergeron LM, Clark DS (2009), “Tying up the loose ends: circular permutation decreases the proteolytic susceptibility of recombinant proteins” Protein Eng Des Sel 22 (10):607-13

  46. Slocik JM, Kim SN, Whitehead TA, Clark DS, Naik RR (2009), “Biotemplated metal nanowires using hyperthermophilic protein filaments”, Small 5 (18):2038-42

  47. Bruns N, Pustelny K, Bergeron LM, Whitehead TA, Clark DS (2009), “Mechanical nanosensor based on FRET within a thermosome: damage-reporting polymeric materials”, Angew Chem Int Ed Engl 48 (31):5666-9

    1. Inside cover of Angew Chem Int Ed Engl; feature story in Chemistry World

  48. Whitehead TA, Je E, Clark DS (2009), “Rational shape engineering of the filamentous protein gamma prefoldin through incremental gene truncation”, Biopolymers 91 (6):496-503

  49. Bergeron LM, Gomez L, Whitehead TA, Clark DS (2009), “Self-renaturing enzymes: design of an enzyme-chaperone chimera as a new approach to enzyme stabilization”, Biotechnol Bioeng 102 (5):1316-22

    1. Spotlight article in Biotechnol Bioeng.

  50. Whitehead TA, Meadows AL, Clark DS (2008), “Controlling the self-assembly of a filamentous hyperthermophilic chaperone by an engineered capping protein”, Small 4 (7):956-60

  51. Whitehead TA, Boonyaratanakornkit BB, Hoellrigl V, Clark DS (2007), “A filamentous molecular chaperone of the prefoldin family from the deep-sea hyperthermophile Methanocaldococcus jannaschii”, Protein Science 16 (4): 626-634

  52. Boonyaratanakornkit BB, Simpson AJ, Whitehead TA, Fraser CM, El-Sayed NMA, Clark DS (2005), “Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock”, Environmental Microbiology 7 (6): 789-797

  53. Laksanalamai P, Whitehead TA, Robb FT (2004), “Minimal protein-folding systems in hyperthermophilic archaea”, Nature Reviews Microbiology 2 (4): 315-324