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Selected Publication List

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

1. Beltrán J+,��Steiner PJ^{^}+, Bedewitz M^{^}+, Wei S+, Peterson F, Li Z, Hughes BE, Hartley Z, Robertson NR, Volkman BF, Medina-Cucurella AV^{^}, Baumer ZT^{^}, Leonard AC^{^}, Park SY, Volkman BF, Nusinow DA, Wheeldon I, Cutler SR, Whitehead TA* (2022), “Rapid biosensor development using plant hormone receptors as reprogrammable scaffolds”, Nature Biotechnology��https://doi.org/10.1038/s41587-022-01364-5
2. Baumer ZT^{^}, Whitehead TA*��(2021) “The inner workings of an enzyme”, Science 373(6553):391-392��DOI:10.1126/science.abj8346
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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. Strawn IK^, Steiner PJ^, Newton MS^, Baumer ZT^, Whitehead TA* (2023), "A method for generating user-defined circular single-stranded DNA from plasmid DNA using Golden Gate intramolecular ligation", Biotechnology and Bioengineering��

2. Steiner PJ^, Swift SD^, Bedewitz M^, Wheeldon I, Cutler SR, Nusinow DA, Whitehead TA* (2023), "A closed form model for molecular ratchet-type chemically induced dimerization modules", Biochemistry��

3. Leonard AC^, Whitehead TA* (2022), "Design and engineering of genetically encoded protein biosensors for small molecules", Current Opinion Biotechnology��

4. Beltrán J+,��Steiner PJ^{^}+, Bedewitz M^{^}+, Wei S+, Peterson F, Li Z, Hughes BE, Hartley Z, Robertson NR, Volkman BF, Medina-Cucurella AV^{^}, Baumer ZT^{^}, Leonard AC^{^}, Park SY, Volkman BF, Nusinow DA, Wheeldon I, Cutler SR, Whitehead TA* (2022), “Rapid biosensor development using plant hormone receptors as reprogrammable scaffolds”, Nature Biotechnology��https://doi.org/10.1038/s41587-022-01364-5

5. Leonard AC^{^}, Weinstein JJ, Steiner PJ^{^}, Erbse AH, Fleishman SJ, Whitehead TA* (2022), "Stabilization of the SARS-CoV-2 receptor binding domain by protein core redesign and deep mutational scanning", Protein Engineering, Design, and Selection 35:gzac002��

6. Kirby MB^{^},��Whitehead TA*,��(2022)��“Facile��Assembly��of Combinatorial Mutagenesis Libraries using Nicking Mutagenesis”,��Methods in Molecular Biology vol 2461��https://link.springer.com/protocol/10.1007/978-1-0716-2152-3_6

7. 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

8. 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��

   • Full article: https://www.frontiersin.org/article/10.3389/fimmu.2021.728694 �� ����

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

10. 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

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11. 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

12. Bailey B. Banach, Gabriele Cerutti, Ahmed S. Fahad, Chen-Hsiang Shen, Matheus Olivera de Souza, Phinikoula 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 F. Nazzari, Jacy R. Wolfe, Yang Luo, Adam S. Olia, I-Ting Teng, Jian Yu, Tongqing Zhou, Eswar R. 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 37(1) 109771��doi:��

13. 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

14. 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

15. 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

16. 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

17. 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

18. 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

19. 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

20. 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

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

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

23. 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

24. 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

25. 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

26. 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

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

28. 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

29. 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

30. 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)

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

32. 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

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

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

35. 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.

36. 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

37. 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.

38. 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

39. 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

40. 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.

41. 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

42. Bienick MS&, Young KW&, Klesmith JR^, Detwiler EE^, Tomek KJ&, Whitehead TA*, (2014) “”, PLoS ONE, DOI: 10.1371/journal.pone.0109105

43. 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.

44. 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.

45. 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

46. 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

47. 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.

48. 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

49. 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

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

51. 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;

52. 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

53. 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.

54. 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

55. 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

56. 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

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