Selected Publication List
(*Corresponding Author, ^Graduate Student/Postdoc Trainee, &Undergraduate Trainee, +Authors contributed equally)
- 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
- Baumer ZT^, Whitehead TA* (2021) “The inner workings of an enzyme”, Science 373(6553):391-392 DOI:10.1126/science.abj8346
- Summary: http://science.sciencemag.org/cgi/content/summary/373/6553/391?ijkey=uFWlBw5P4lq9k&keytype=ref&siteid=sci
- Reprint: http://science.sciencemag.org/cgi/rapidpdf/373/6553/391?ijkey=uFWlBw5P4lq9k&keytype=ref&siteid=sci
- Full text: http://science.sciencemag.org/cgi/content/full/373/6553/391?ijkey=uFWlBw5P4lq9k&keytype=ref&siteid=sci
-
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
-
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
-
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
-
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 http://doi.org/10.1002/bit.28471
-
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 https://doi.org/10.1021/acs.biochem.2c00172
-
Leonard AC^, Whitehead TA* (2022), "Design and engineering of genetically encoded protein biosensors for small molecules", Current Opinion Biotechnology https://doi.org/10.1016/j.copbio.2022.102787
-
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
-
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 https://doi.org/10.1093/protein/gzac002
-
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
-
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
-
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
-
Baumer ZT^, Whitehead TA* (2021) “The inner workings of an enzyme”, Science 373(6553):391-392 DOI:10.1126/science.abj8346
-
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
-
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
-
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: 10.1016/j.celrep.2021.109771
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
Whitehead TA*, (2017) “A peptide mimic of an antibody” Science 358(6362):450-451 doi:10.1126/science.aap9608
-
Whitehead T*, Cutler S, Wheeldon I, (2017) “Plant Metabolic Engineering for Chemicals, Fuels, and Precursors”, Chemical Engineering Progress SBE Supplement (invited)
-
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
-
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
-
Cover of ACS Sustainable Chemistry & Engineering
-
-
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
-
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
-
Wrenbeck EE^, Faber M^, Whitehead TA* (2017) “Deep sequencing methods for protein engineering and design”, Current Opinion in Structural Biology 45:36-44
-
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
-
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
-
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
-
Documentation at Nature Protocols Exchange (doi:10.1038/protex.2016.061)
-
-
Klesmith JR^, Thorwall S&, Whitehead TA* (2016) “Interpreting deep mutational scanning data resulting from plate-based selections”, bioRxiv 087072
-
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
-
Khare S*, Whitehead TA* (2015), “Introduction to RosettaCON Special Collection”, PLoS ONE 10(12):e0144326
-
Klesmith JR^, Whitehead TA* (2015), “High-throughput evaluation of synthetic metabolic pathways”, Technology 4(01):9-14
-
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
-
Selected for ‘Introducing our Authors’ feature highlight.
-
-
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
-
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
-
Top 5 accessed article for J. Biol. Chem., Oct. 2015.
-
-
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
-
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
-
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
-
Selected for B&B video highlight.
-
-
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
-
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
-
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.
-
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
-
Cover of Nature Biotechnology; Featured in numerous popular press articles and radio interviews, including NPR.
-
-
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
-
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
-
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
-
Featured in numerous popular press articles and radio interviews, including NPR.
-
-
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
-
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
-
Slocik JM, Kim SN, Whitehead TA, Clark DS, Naik RR (2009), “Biotemplated metal nanowires using hyperthermophilic protein filaments”, Small 5 (18):2038-42
-
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
-
Inside cover of Angew Chem Int Ed Engl; feature story in Chemistry World
-
-
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
-
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
-
Spotlight article in Biotechnol Bioeng.
-
-
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
-
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
-
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
-
Laksanalamai P, Whitehead TA, Robb FT (2004), “Minimal protein-folding systems in hyperthermophilic archaea”, Nature Reviews Microbiology 2 (4): 315-324