2016

Zakas PM, Brown HC, Knight K, Meeks SL, Spencer HT, Gaucher EA & Doering CB. Enhancing the pharmaceutical properties of protein drugs by ancestral sequence reconstruction. Nature Biotechnology preprint, xx, doi:10.1038/nbt.3677 (2016).

Randall RN, Radford CE, Roof KA, Natarajan DK & Gaucher EA. An experimental phylogeny to benchmark ancestral sequence reconstruction. Nature Communications 7, 12847, doi:10.1038/ncomms12847 (2016).

Tan PK, Farrar JE, Gaucher EA & Miner JN. Coevolution of URAT1 and Uricase during Primate Evolution: Implications for Serum Urate Homeostasis and Gout. Mol. Biol. Evol. 33, 2193-2200, doi:10.1093/molbev/msw116 (2016).

Romero-Romero ML, Risso VA, Martinez-Rodriguez S, Gaucher EA, Ibarra-Molero B & Sanchez-Ruiz JM. Selection for Protein Kinetic Stability Connects Denaturation Temperatures to Organismal Temperatures and Provides Clues to Archaean Life. PLoS One 11, e0156657, doi:10.1371/journal.pone.0156657 (2016).

2015

Cox, V. E. & Gaucher E. A. Molecular Evolution Directs Protein Translation using Unnatural Amino Acids. Curr. Protoc. Chem. Biol. 7, 223-228, doi:10.1002/9780470559277.ch150115 (2015).

Risso, V. A., Manssour-Triedo, F., Delgado-Delgado, A., Arco, R., Barroso-delJesus, A., Ingles-Prieto, A., Godoy-Ruiz, R., Gavira, J. A., Gaucher, E. A., Ibarra-Molero, B. & Sanchez-Ruiz, J. M. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Mol. Biol. Evol. 32, 440-455, doi:10.1093/molbev/msu312 (2015).

2014

Cox, V. E. & Gaucher E. A. Engineering Proteins by Reconstructing Evolutionary Adaptive Paths. Methods in Molecular Biology 1179, 353-363, doi:10.1007/978-1-4939-1053-3_24 (2014).

Cicerchi, C., Li, N., Kratzer, J., Garcia, G., Roncal-Jimenez, C. A., Tanabe, K., Hunter, B., Rivard, C. J., Sautin, Y. Y., Gaucher, E. A., Johnson, R. J. & Lanaspa, M. A. Uric acid-dependent inhibition of AMP kinase induces hepatic glucose production in diabetes and starvation: evolutionary implications of the uricase loss in hominids. FASEB 28, 3339-3350 doi:10.1002/prot.24575. [doi] (2014).

Risso, V. A., Gavira, J. A., Gaucher, E. A. & Sanchez-Ruiz, J. M. Phenotypic comparisons of consensus variants versus laboratory resurrections of Precambrian proteins. Proteins 82, 887-896, doi:10.1002/prot.24575. [doi] (2014).

Veleva-Rotse, B. O., Smart, J. L., Baas, A. F., Edmonds, B., Zhao, Z. M., Brown, A., Klug, L. R., Hansen, K., Reilly, G., Gardner, A. P., Subbiah, K., Gaucher, E. A., Clevers, H. & Barnes, A. P. STRAD pseudokinases regulate exogenesis and LKB1 stability. Neural Dev 29, 5, doi:10.1186/1749-8104-9-5. [doi] (2014).

Kratzer, J. T., Lanaspa, M. A., Murphy, M. N., Cicerchi, C., Graves, C. L., Tipton, P. A., Ortlund, E. A., Johnson, R. J. & Gaucher E. A. Evolutionary history and metabolic insights of ancient mammalian uricases. Proc Natl Acad Sci U S A 111, 3763-3768, doi:10.1073/pnas.1320393111. [doi] (2014).

2013

Ingles-Prieto, A., Ibarra-Molero, B., Delgado-Delgado, A., Perez-Jimenez, R., Fernandez, J. M., Gaucher, E. A., Sanchez-Ruiz, J. M. & Gavira, J. A. Conservation of protein structure over four billion years. Structure 21, 1690-1697, doi:10.1016/j.str.2013.06.020 [doi] (2013).

Risso, V. A., Gavira, J. A., Mejia-Carmona, D. F., Gaucher, E. A. & Sanchez-Ruiz, J. M. Hyperstability and substrate promiscuity in laboratory resurrections of Precambrian beta-lactamases. J Am Chem Soc 135, 2899-2902, doi:10.1021/ja311630a [doi] (2013).

2012

Kacar, B. & Gaucher, E. A., Towards the Recapitulation of Ancient History in the Laboratory: Combining Synthetic Biology with Experimental Evolution Artificial Life 13, 11-18. (2012)

Abstract

Zhou, Y., Asahara, H., Gaucher, E. A. & Chong, S. Reconstitution of translation from Thermus thermophilus reveals a minimal set of components sufficient for protein synthesis at high temperatures and functional conservation of modern and ancient translation components. Nucleic Acids Res 40, 7932-7945, doi:gks568 (2012)

2011

Zhao, Z. M., Reynolds, A. B. & Gaucher, E. A. The evolutionary history of the catenin gene family during metazoan evolution. BMC Evol Biol 11, 198, doi:1471-2148-11-198 [pii]. 10.1186/1471-2148-11-198 [doi] (2011). 'Highly Accessed'

Perez-Jimenez, R. et al. Single-molecule paleoenzymology probes the chemistry of resurrected enzymes. Nat Struct Mol Biol 18, 592-596, doi:nsmb.2020 [pii]. 10.1038/nsmb.2020 [doi] (2011).

Johnson, R. J., Lanaspa, M. A. & Gaucher, E. A. Uric acid: a danger signal from the RNA world that may have a role in the epidemic of obesity, metabolic syndrome, and cardiorenal disease: evolutionary considerations. Semin Nephrol 31, 394-399, doi:S0270-9295(11)00119-7 [pii]. 10.1016/j.semnephrol.2011.08.002 [doi] (2011).

Cole, M. F. & Gaucher, E. A. Exploiting models of molecular evolution to efficiently direct protein engineering. J Mol Evol 72, 193-203, doi:10.1007/s00239-010-9415-2 [doi] (2011).

Cole, M. F. & Gaucher, E. A. Utilizing natural diversity to evolve protein function: applications towards thermostability. Curr Opin Chem Biol 15, 399-406, doi:S1367-5931(11)00040-8 [pii]. 10.1016/j.cbpa.2011.03.005 [doi] (2011).

2010

Chen, F. et al. Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection. Proc Natl Acad Sci U S A 107, 1948-1953, doi:0908463107 [pii] 10.1073/pnas.0908463107 [doi] (2010).

Carnahan, R. H., Rokas, A., Gaucher, E. A. & Reynolds, A. B. The molecular evolution of the p120-catenin subfamily and its functional associations. PLoS One 5, e15747, doi:10.1371/journal.pone.0015747 [doi] (2010).

2009

Perez-Jimenez, R. et al. Diversity of chemical mechanisms in thioredoxin catalysis revealed by single-molecule force spectroscopy. Nat Struct Mol Biol 16, 890-896, doi:nsmb.1627 [pii]. 10.1038/nsmb.1627 [doi] (2009).

2008

Johnson, R. J. et al. The planetary biology of ascorbate and uric acid and their relationship with the epidemic of obesity and cardiovascular disease. Med Hypotheses 71, 22-31, doi:S0306-9877(08)00043-1 [pii]. 10.1016/j.mehy.2008.01.017 [doi] (2008).

Gaucher, E. A., Govindarajan, S. & Ganesh, O. K. Palaeotemperature trend for Precambrian life inferred from resurrected proteins. Nature 451, 704-707, doi:nature06510 [pii]. 10.1038/nature06510 [doi] (2008).

2007

Gaucher, E. A., De Kee, D. W. & Benner, S. A. Application of DETECTER, an evolutionary genomic tool to analyze genetic variation, to the cystic fibrosis gene family. BMC Genomics 7, 44, doi:1471-2164-7-44 [pii] 10.1186/1471-2164-7-44 [doi] (2006).

Li, T. et al. Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics. BMC Evol Biol 6, 25, doi:1471-2148-6-25 [pii] 10.1186/1471-2148-6-25 [doi] (2006).

Phillips, S. E. et al. The diverse biological functions of phosphatidylinositol transfer proteins in eukaryotes. Crit Rev Biochem Mol Biol 41, 21-49, doi:U30272K385875671 [pii]
10.1080/10409230500519573 [doi] (2006).

2005

Gaucher, E. A. & Miyamoto, M. M. A call for likelihood phylogenetics even when the process of sequence evolution is heterogeneous. Mol Phylogenet Evol 37, 928-931, doi:S1055-7903(05)00104-1 [pii] 10.1016/j.ympev.2005.03.027 [doi] (2005).

Thomson, J. M. et al. Resurrecting ancestral alcohol dehydrogenases from yeast. Nat Genet 37, 630-635, doi:ng1553 [pii] 10.1038/ng1553 [doi] (2005).

2004

Gaucher, E. A., Graddy, L.G., Simmen, R. C. M., Simmen, F. A., Kowalski, A. A., Schreiber, D. R., Libereles, D. A., Zhao, G., Janis, C. M.,  & Benner, S. A. The planetary biology of cytochrome P450 aromatases. BMC Biol 2, 19, doi:10.1186/1741-7007-2-19 [doi]

West, C. M., Van Der Wel, H., Sassi, S. & Gaucher, E. A. Cytoplasmic glycosylation of protein-hydroxyproline and its relationship to other glycosylation pathways. Biochim Biophys Acta 1673, 29-44, doi:10.1016/j.bbagen.2004.04.007 [doi]S0304416504001035 [pii] (2004).

2003

Gaucher, E. A., Thomson, J. M., Burgan, M. F. & Benner, S. A. Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 425, 285-288, doi:10.1038/nature01977 [doi]
nature01977 [pii] (2003).

Gaucher, E. A., Miyamoto, M. M. & Benner, S. A. Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein. Genetics 163, 1549-1553 (2003).

2002

Gaucher, E. A., Gu, X., Miyamoto, M. M. & Benner, S. A. Predicting functional divergence in protein evolution by site-specific rate shifts. Trends Biochem Sci 27, 315-321, doi:S0968-0004(02)02094-7 [pii] (2002).

Benner, S. A., Caraco, M. D., Thomson, J. M. & Gaucher, E. A. Planetary biology--paleontological, geological, and molecular histories of life. Science 296, 864-868, doi:10.1126/science.1069863 [doi] 296/5569/864 [pii] (2002).

West, C. M., van der Wel, H. & Gaucher, E. A. Complex glycosylation of Skp1 in Dictyostelium: implications for the modification of other eukaryotic cytoplasmic and nuclear proteins. Glycobiology 12, 17R-27R (2002).

Gaucher, E. A., Das, U. K., Miyamoto, M. M. & Benner, S. A. The crystal structure of eEF1A refines the functional predictions of an evolutionary analysis of rate changes among elongation factors. Mol Biol Evol 19, 569-573 (2002).

2001

Gaucher, E. A., Miyamoto, M. M. & Benner, S. A. Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors. Proc Natl Acad Sci U S A 98, 548-552, doi:10.1073/pnas.98.2.548 [doi] 98/2/548 [pii] (2001).

Benner, S. A. & Gaucher, E. A. Evolution, language and analogy in functional genomics. Trends Genet 17, 414-418, doi:S0168-9525(01)02320-4 [pii] (2001).

1998

Laten, H. M., Majumdar, A. & Gaucher, E. A. SIRE-1, a copia/Ty1-like retroelement from soybean, encodes a retroviral envelope-like protein. Proc Natl Acad Sci U S A 95, 6897-6902 (1998).

2012

Cox, V, Cole, M. F., Gaucher, E. A. (2012) Bridging protein evolution and engineering. in Methods in Molecular Biology (Enzyme Engineering Edition) (Editor James Samuelson, Springer Press).

Kratzer, J. K., Cole, M. F., & Gaucher, E. A. (2012) Protein engineering guided by natural diversity. in Protein Engineering Handbook 3rd Edition (Eds Lutz and Bornscheuer, Wiley Press).

2011

Cole, M. F. & Gaucher, E. A. (2011) Proteins. in Encyclopedia of Astrobiology (Eds Gargaud, Amils, Cleaves, Irvine, Pinti and Viso, Springer Press).

2010

Gaucher, E. A., Kratzer, J. T. & Randall, R. N. Deep phylogeny--how a tree can help characterize early life on Earth. Cold Spring Harb Perspect Biol 2, a002238, doi:10.1101/cshperspect.a002238 [doi] (2010).

2007

Gaucher, E. A. (2007). Ancestral sequence reconstruction as a tool to understand natural history and guide synthetic biology: Realizing (and extending) the vision of Zukerkandl and Pauling. in Ancestral Sequence Reconstruction pp. 20-33 (Ed. David Liberles, Oxford University Press).

Gaucher, E. A. (2007). Experimental resurrection of ancient biomolecules: gene synthesis, heterologous protein expression, and functional assays. in Ancestral Sequence Reconstruction pp.153-163 (Ed. David Liberles, Oxford University Press).

Danchin, E. G. J., Gaucher, E. A., & P. Pontarotti (2007). Computational reconstruction of ancestral genomic regions from evolutionarily conserved gene clusters. in Ancestral Sequence Reconstruction pp. 139-152 (Ed. David Liberles, Oxford University Press).

Brooks, D. J. & Gaucher, E. A. (2007). Inferred thermophily of the last universal ancestor based on estimated amino acid composition. in Ancestral Sequence Reconstruction pp. 200-207 (Ed. David Liberles, Oxford University Press).