Joseph W. Thornton, Ph.D. - Publications

Affiliations: 
2002-2014 University of Oregon, Eugene, OR, United States 
 2012- University of Chicago, Chicago, IL 
Area:
protein evolution
Website:
https://genes.uchicago.edu/admin/person/joe-thornton-phd

69 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Starr TN, Flynn JM, Mishra P, Bolon DNA, Thornton JW. Pervasive contingency and entrenchment in a billion years of Hsp90 evolution. Proceedings of the National Academy of Sciences of the United States of America. PMID 29626131 DOI: 10.1073/Pnas.1718133115  0.44
2017 Starr TN, Picton LK, Thornton JW. Alternative evolutionary histories in the sequence space of an ancient protein. Nature. PMID 28902834 DOI: 10.1038/Nature23902  0.44
2017 Starr TN, Thornton JW. Exploring protein sequence-function landscapes. Nature Biotechnology. 35: 125-126. PMID 28178247 DOI: 10.1038/Nbt.3786  0.44
2016 Eick GN, Bridgham JT, Anderson DP, Harms MJ, Thornton JW. Robustness of reconstructed ancestral protein functions to statistical uncertainty. Molecular Biology and Evolution. PMID 27795231 DOI: 10.1093/Molbev/Msw223  0.92
2016 Katsu Y, Cziko PA, Chandsawangbhuwana C, Thornton JW, Sato R, Oka K, Takei Y, Baker ME, Iguchi T. A second estrogen receptor from Japanese lamprey (Lethenteron japonicum) does not have activities for estrogen binding and transcription. General and Comparative Endocrinology. PMID 27432813 DOI: 10.1016/J.Ygcen.2016.07.014  1
2016 Starr TN, Thornton JW. Epistasis in protein evolution. Protein Science : a Publication of the Protein Society. PMID 26833806 DOI: 10.1002/Pro.2897  0.44
2016 Anderson DP, Whitney DS, Hanson-Smith V, Woznica A, Campodonico-Burnett W, Volkman BF, King N, Thornton JW, Prehoda KE. Correction: Evolution of an ancient protein function involved in organized multicellularity in animals. Elife. 5. PMID 26790885 DOI: 10.7554/Elife.14311  0.92
2016 Anderson DP, Whitney DS, Hanson-Smith V, Woznica A, Campodonico-Burnett W, Volkman BF, King N, Prehoda KE, Thornton JW. Evolution of an ancient protein function involved in organized multicellularity in animals. Elife. 5. PMID 26740169 DOI: 10.7554/Elife.10147  1
2015 Hudson WH, Kossmann BR, de Vera IM, Chuo SW, Weikum ER, Eick GN, Thornton JW, Ivanov IN, Kojetin DJ, Ortlund EA. Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space. Proceedings of the National Academy of Sciences of the United States of America. PMID 26715749 DOI: 10.1073/Pnas.1518960113  1
2015 Anderson DW, McKeown AN, Thornton JW. Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its DNA binding sites. Elife. 4. PMID 26076233 DOI: 10.7554/Elife.07864  1
2014 Hart KM, Harms MJ, Schmidt BH, Elya C, Thornton JW, Marqusee S. Thermodynamic system drift in protein evolution. Plos Biology. 12: e1001994. PMID 25386647 DOI: 10.1371/Journal.Pbio.1001994  1
2014 McKeown AN, Bridgham JT, Anderson DW, Murphy MN, Ortlund EA, Thornton JW. Evolution of DNA specificity in a transcription factor family produced a new gene regulatory module. Cell. 159: 58-68. PMID 25259920 DOI: 10.1016/J.Cell.2014.09.003  1
2014 Ibebuogu UN, Khouzam RN, Sharma G, Thornton JW, Robati R, Silverman D. A thrombus in transit through a patent foramen ovale. Jaapa : Official Journal of the American Academy of Physician Assistants. 27: 32-5. PMID 25251652 DOI: 10.1097/01.JAA.0000446233.16049.01  0.01
2014 Harms MJ, Thornton JW. Historical contingency and its biophysical basis in glucocorticoid receptor evolution. Nature. 512: 203-7. PMID 24930765 DOI: 10.1038/Nature13410  1
2014 Bridgham JT, Keay J, Ortlund EA, Thornton JW. Vestigialization of an allosteric switch: genetic and structural mechanisms for the evolution of constitutive activity in a steroid hormone receptor. Plos Genetics. 10: e1004058. PMID 24415950 DOI: 10.1371/Journal.Pgen.1004058  1
2013 Harms MJ, Thornton JW. Evolutionary biochemistry: revealing the historical and physical causes of protein properties. Nature Reviews. Genetics. 14: 559-71. PMID 23864121 DOI: 10.1038/Nrg3540  1
2013 Harms MJ, Eick GN, Goswami D, Colucci JK, Griffin PR, Ortlund EA, Thornton JW. Biophysical mechanisms for large-effect mutations in the evolution of steroid hormone receptors. Proceedings of the National Academy of Sciences of the United States of America. 110: 11475-80. PMID 23798447 DOI: 10.1073/Pnas.1303930110  1
2012 Eick GN, Colucci JK, Harms MJ, Ortlund EA, Thornton JW. Evolution of minimal specificity and promiscuity in steroid hormone receptors. Plos Genetics. 8: e1003072. PMID 23166518 DOI: 10.1371/Journal.Pgen.1003072  1
2012 Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, ... ... Thornton JW, et al. The interface of protein structure, protein biophysics, and molecular evolution. Protein Science : a Publication of the Protein Society. 21: 769-85. PMID 22528593 DOI: 10.1002/Pro.2071  1
2012 Finnigan GC, Hanson-Smith V, Stevens TH, Thornton JW. Evolution of increased complexity in a molecular machine. Nature. 481: 360-4. PMID 22230956 DOI: 10.1038/Nature10724  1
2011 Carroll SM, Ortlund EA, Thornton JW. Mechanisms for the evolution of a derived function in the ancestral glucocorticoid receptor. Plos Genetics. 7: e1002117. PMID 21698144 DOI: 10.1371/Journal.Pgen.1002117  1
2011 DeRemer CE, Gujral JS, Thornton JW, Sorrentino RA. Dabigatran falsely elevates point of care international normalized ratio results. The American Journal of Medicine. 124: e5-6. PMID 21640327 DOI: 10.1016/j.amjmed.2011.02.009  0.01
2011 Thornton JW, Carroll SM. Lamprey endocrinology is not ancestral. Proceedings of the National Academy of Sciences of the United States of America. 108: E5; author reply E6. PMID 21209326 DOI: 10.1073/Pnas.1014896108  1
2011 Eick GN, Thornton JW. Evolution of steroid receptors from an estrogen-sensitive ancestral receptor. Molecular and Cellular Endocrinology. 334: 31-8. PMID 20837101 DOI: 10.1016/J.Mce.2010.09.003  1
2010 Bridgham JT, Eick GN, Larroux C, Deshpande K, Harms MJ, Gauthier ME, Ortlund EA, Degnan BM, Thornton JW. Protein evolution by molecular tinkering: diversification of the nuclear receptor superfamily from a ligand-dependent ancestor. Plos Biology. 8. PMID 20957188 DOI: 10.1371/Journal.Pbio.1000497  1
2010 Harms MJ, Thornton JW. Analyzing protein structure and function using ancestral gene reconstruction. Current Opinion in Structural Biology. 20: 360-6. PMID 20413295 DOI: 10.1016/J.Sbi.2010.03.005  1
2010 Hanson-Smith V, Kolaczkowski B, Thornton JW. Robustness of ancestral sequence reconstruction to phylogenetic uncertainty. Molecular Biology and Evolution. 27: 1988-99. PMID 20368266 DOI: 10.1093/Molbev/Msq081  1
2009 Kolaczkowski B, Thornton JW. Long-branch attraction bias and inconsistency in Bayesian phylogenetics. Plos One. 4: e7891. PMID 20011052 DOI: 10.1371/Journal.Pone.0007891  1
2009 Bridgham JT, Ortlund EA, Thornton JW. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature. 461: 515-9. PMID 19779450 DOI: 10.1038/Nature08249  1
2009 Keay J, Thornton JW. Hormone-activated estrogen receptors in annelid invertebrates: implications for evolution and endocrine disruption. Endocrinology. 150: 1731-8. PMID 19036877 DOI: 10.1210/En.2008-1338  1
2008 Carroll SM, Bridgham JT, Thornton JW. Evolution of hormone signaling in elasmobranchs by exploitation of promiscuous receptors. Molecular Biology and Evolution. 25: 2643-52. PMID 18799714 DOI: 10.1093/Molbev/Msn204  1
2008 Bridgham JT, Brown JE, Rodríguez-Marí A, Catchen JM, Thornton JW. Evolution of a new function by degenerative mutation in cephalochordate steroid receptors. Plos Genetics. 4: e1000191. PMID 18787702 DOI: 10.1371/Journal.Pgen.1000191  1
2008 Ibebuogu UN, Salah AK, Malhotra S, Calkins JB, Thornton JW, Mandawat M, Robinson VJ. The D-dimer assay: a possible tool in the evaluation of atrial thrombosis. The Canadian Journal of Cardiology. 24: 517-9. PMID 18548152  0.01
2008 Salah AK, Ahmed A, Bodiwala KN, Manaloor EJ, Thornton JW, Moliterno DJ. Cardiac amyloidosis. The Canadian Journal of Cardiology. 24: e35. PMID 18464954  0.01
2008 Patel D, Robinson VJ, Arteaga RB, Thornton JW. Diastolic filling parameters derived from myocardial perfusion imaging can predict left ventricular end-diastolic pressure at subsequent cardiac catheterization. Journal of Nuclear Medicine : Official Publication, Society of Nuclear Medicine. 49: 746-51. PMID 18413386 DOI: 10.2967/jnumed.107.049395  0.01
2008 Ibebuogu UN, Thornton JW, Reed GL. An unrecognized cause of acute abdomen in peripartum cardiomyopathy. Southern Medical Journal. 101: 447-8. PMID 18360323 DOI: 10.1097/SMJ.0b013e318167d678  0.01
2008 Robinson VJ, Patel RN, Nalamolu VR, Kaminski RJ, Dias JK, Thornton JW, Kersey TW, Mandawat MK. Encircling reperfusion pattern on the stress-minus-delay bull's-eye map improves sensitivity of myocardial perfusion scans. Nuclear Medicine Communications. 29: 222-9. PMID 18349792 DOI: 10.1097/MNM.0b013e3282f3d02e  0.01
2008 Kolaczkowski B, Thornton JW. A mixed branch length model of heterotachy improves phylogenetic accuracy. Molecular Biology and Evolution. 25: 1054-66. PMID 18319244 DOI: 10.1093/Molbev/Msn042  1
2008 Thornton JW, Bridgham JT. Using ancestral gene resurrection to unravel the evolution of protein function Ancestral Sequence Reconstruction. DOI: 10.1093/acprof:oso/9780199299188.003.0016  1
2007 Ibebuogu UN, Thornton JW, Reed GL. An unusual case of peripartum cardiomyopathy manifesting with multiple thrombo-embolic phenomena. Thrombosis Journal. 5: 18. PMID 17967197 DOI: 10.1186/1477-9560-5-18  0.01
2007 Patel RN, Arteaga RB, Mandawat MK, Thornton JW, Robinson VJ. Pharmacologic stress myocardial perfusion imaging. Southern Medical Journal. 100: 1006-14; quiz 1004. PMID 17943047 DOI: 10.1097/SMJ.0b013e318153f9c6  0.01
2007 Dean AM, Thornton JW. Mechanistic approaches to the study of evolution: the functional synthesis. Nature Reviews. Genetics. 8: 675-88. PMID 17703238 DOI: 10.1038/Nrg2160  1
2007 Ortlund EA, Bridgham JT, Redinbo MR, Thornton JW. Crystal structure of an ancient protein: evolution by conformational epistasis. Science (New York, N.Y.). 317: 1544-8. PMID 17702911 DOI: 10.1126/Science.1142819  1
2007 Kolaczkowski B, Thornton JW. Effects of branch length uncertainty on Bayesian posterior probabilities for phylogenetic hypotheses. Molecular Biology and Evolution. 24: 2108-18. PMID 17636043 DOI: 10.1093/Molbev/Msm141  1
2007 Fox JE, Bridgham JT, Bovee TF, Thornton JW. An evolvable oestrogen receptor activity sensor: development of a modular system for integrating multiple genes into the yeast genome. Yeast (Chichester, England). 24: 379-90. PMID 17345582 DOI: 10.1002/Yea.1466  1
2006 Kolaczkowski B, Thornton JW. Is there a star tree paradox? Molecular Biology and Evolution. 23: 1819-23. PMID 16837562 DOI: 10.1093/Molbev/Msl059  1
2006 Keay J, Bridgham JT, Thornton JW. The Octopus vulgaris estrogen receptor is a constitutive transcriptional activator: evolutionary and functional implications. Endocrinology. 147: 3861-9. PMID 16690796 DOI: 10.1210/En.2006-0363  1
2006 Bridgham JT, Carroll SM, Thornton JW. Evolution of hormone-receptor complexity by molecular exploitation. Science (New York, N.Y.). 312: 97-101. PMID 16601189 DOI: 10.1126/Science.1123348  1
2005 Krieger N, Löwy I, Aronowitz R, Bigby J, Dickersin K, Garner E, Gaudillière JP, Hinestrosa C, Hubbard R, Johnson PA, Missmer SA, Norsigian J, Pearson C, Rosenberg CE, Rosenberg L, ... ... Thornton J, et al. Hormone replacement therapy, cancer, controversies, and women's health: historical, epidemiological, biological, clinical, and advocacy perspectives. Journal of Epidemiology and Community Health. 59: 740-8. PMID 16100311 DOI: 10.1136/Jech.2005.033316  1
2005 Thornton JW, Kolaczkowski B. No magic pill for phylogenetic error. Trends in Genetics : Tig. 21: 310-1. PMID 15922825 DOI: 10.1016/J.Tig.2005.04.002  1
2005 Krylova IN, Sablin EP, Moore J, Xu RX, Waitt GM, MacKay JA, Juzumiene D, Bynum JM, Madauss K, Montana V, Lebedeva L, Suzawa M, Williams JD, Williams SP, Guy RK, ... Thornton JW, et al. Structural analyses reveal phosphatidyl inositols as ligands for the NR5 orphan receptors SF-1 and LRH-1. Cell. 120: 343-55. PMID 15707893 DOI: 10.1016/J.Cell.2005.01.024  1
2004 Wilson VS, Cardon MC, Thornton J, Korte JJ, Ankley GT, Welch J, Gray LE, Hartig PC. Cloning and in vitro expression and characterization of the androgen receptor and isolation of estrogen receptor α from the fathead minnow (Pimephales promelas) Environmental Science and Technology. 38: 6314-6321. PMID 15597887 DOI: 10.1021/es049771j  1
2004 Kolaczkowski B, Thornton JW. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature. 431: 980-4. PMID 15496922 DOI: 10.1038/Nature02917  1
2004 Thornton JW. Resurrecting ancient genes: experimental analysis of extinct molecules. Nature Reviews. Genetics. 5: 366-75. PMID 15143319 DOI: 10.1038/Nrg1324  1
2003 Thornton JW, Need E, Crews D. Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling. Science (New York, N.Y.). 301: 1714-7. PMID 14500980 DOI: 10.1126/Science.1086185  1
2003 Wu KH, Tobias ML, Thornton JW, Kelley DB. Estrogen receptors in Xenopus: duplicate genes, splice variants, and tissue-specific expression. General and Comparative Endocrinology. 133: 38-49. PMID 12899845 DOI: 10.1016/S0016-6480(03)00148-5  1
2003 Thornton JW. Nonmammalian nuclear receptors: Evolution and endocrine disruption Pure and Applied Chemistry. 75: 1827-1839. DOI: 10.1351/Pac200375111827  1
2002 Thornton JW, McCally M, Houlihan J. Biomonitoring of industrial pollutants: health and policy implications of the chemical body burden. Public Health Reports (Washington, D.C. : 1974). 117: 315-23. PMID 12477912 DOI: 10.1016/S0033-3549(04)50167-X  1
2002 Sarkar IN, Thornton JW, Planet PJ, Figurski DH, Schierwater B, DeSalle R. An automated phylogenetic key for classifying homeoboxes. Molecular Phylogenetics and Evolution. 24: 388-99. PMID 12220982 DOI: 10.1016/S1055-7903(02)00259-2  1
2002 Thornton J. Gene family phylogenetics: tracing protein evolution on trees Exs. 191-207. PMID 11924497  1
2001 Thornton JW. Evolution of vertebrate steroid receptors from an ancestral estrogen receptor by ligand exploitation and serial genome expansions. Proceedings of the National Academy of Sciences of the United States of America. 98: 5671-6. PMID 11331759 DOI: 10.1073/Pnas.091553298  1
2001 Thornton J. Implementing green chemistry. An environmental policy for sustainability Pure and Applied Chemistry. 73: 1231-1236. DOI: 10.1351/Pac200173081231  1
2000 Thornton JW, DeSalle R. A new method to localize and test the significance of incongruence: detecting domain shuffling in the nuclear receptor superfamily. Systematic Biology. 49: 183-201. PMID 12118404 DOI: 10.1093/Sysbio/49.2.183  1
2000 Thornton JW, DeSalle R. Gene family evolution and homology: genomics meets phylogenetics. Annual Review of Genomics and Human Genetics. 1: 41-73. PMID 11701624 DOI: 10.1146/Annurev.Genom.1.1.41  1
2000 Thornton J. Beyond risk: An ecological paradigm to prevent global chemical pollution International Journal of Occupational and Environmental Health. 6: 318-330. PMID 11114125 DOI: 10.1179/Oeh.2000.6.4.318  1
2000 Hawkins MB, Thornton JW, Crews D, Skipper JK, Dotte A, Thomas P. Identification of a third distinct estrogen receptor and reclassification of estrogen receptors in teleosts. Proceedings of the National Academy of Sciences of the United States of America. 97: 10751-6. PMID 11005855 DOI: 10.1073/Pnas.97.20.10751  1
1998 Thornton JW, Kelley DB. Evolution of the androgen receptor: structure-function implications. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 20: 860-9. PMID 9819573 DOI: 10.1002/(Sici)1521-1878(199810)20:10<860::Aid-Bies12>3.0.Co;2-S  1
1996 Thornton J, McCally M, Orris P, Weinberg J. Hospitals and plastics. Dioxin prevention and medical waste incinerators Public Health Reports (Washington, D.C. : 1974). 111: 298-313. PMID 8711095  1
1996 Thornton J, McCally M, Orris P, Weinberg J. Dioxin prevention and me dical waste incinerators Public Health Reports. 111: 299-313.  1
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