| Year |
Citation |
Score |
| 2024 |
Park Y, Metzger BPH, Thornton JW. The simplicity of protein sequence-function relationships. Nature Communications. 15: 7953. PMID 39261454 DOI: 10.1038/s41467-024-51895-5 |
0.324 |
|
| 2024 |
Metzger BPH, Park Y, Starr TN, Thornton JW. Epistasis facilitates functional evolution in an ancient transcription factor. Elife. 12. PMID 38767330 DOI: 10.7554/eLife.88737 |
0.324 |
|
| 2023 |
Park Y, Metzger BPH, Thornton JW. The simplicity of protein sequence-function relationships. Biorxiv : the Preprint Server For Biology. PMID 37732229 DOI: 10.1101/2023.09.02.556057 |
0.319 |
|
| 2022 |
Pillai AS, Hochberg GKA, Thornton JW. Simple mechanisms for the evolution of protein complexity. Protein Science : a Publication of the Protein Society. e4449. PMID 36107026 DOI: 10.1002/pro.4449 |
0.314 |
|
| 2022 |
Park Y, Metzger BPH, Thornton JW. Epistatic drift causes gradual decay of predictability in protein evolution. Science (New York, N.Y.). 376: 823-830. PMID 35587978 DOI: 10.1126/science.abn6895 |
0.307 |
|
| 2021 |
Xie VC, Pu J, Metzger BP, Thornton JW, Dickinson BC. Contingency and chance erase necessity in the experimental evolution of ancestral proteins. Elife. 10. PMID 34061027 DOI: 10.7554/eLife.67336 |
0.334 |
|
| 2020 |
Hochberg GKA, Liu Y, Marklund EG, Metzger BPH, Laganowsky A, Thornton JW. A hydrophobic ratchet entrenches molecular complexes. Nature. PMID 33299178 DOI: 10.1038/s41586-020-3021-2 |
0.318 |
|
| 2020 |
Pillai AS, Chandler SA, Liu Y, Signore AV, Cortez-Romero CR, Benesch JLP, Laganowsky A, Storz JF, Hochberg GKA, Thornton JW. Origin of complexity in haemoglobin evolution. Nature. 581: 480-485. PMID 32461643 DOI: 10.1038/S41586-020-2292-Y |
0.362 |
|
| 2019 |
Siddiq MA, Thornton JW. Fitness effects but no temperature-mediated balancing selection at the polymorphic gene of . Proceedings of the National Academy of Sciences of the United States of America. PMID 31594844 DOI: 10.1073/Pnas.1909216116 |
0.324 |
|
| 2019 |
Cheng S, Park Y, Kurleto JD, Jeon M, Zinn K, Thornton JW, Özkan E. Family of neural wiring receptors in bilaterians defined by phylogenetic, biochemical, and structural evidence. Proceedings of the National Academy of Sciences of the United States of America. PMID 31043568 DOI: 10.1073/Pnas.1818631116 |
0.37 |
|
| 2018 |
Liu Q, Onal P, Datta RR, Rogers JM, Schmidt-Ott U, Bulyk ML, Small S, Thornton JW. Ancient mechanisms for the evolution of the bicoid homeodomain's function in fly development. Elife. 7. PMID 30298815 DOI: 10.7554/Elife.34594 |
0.386 |
|
| 2018 |
Venkat A, Hahn MW, Thornton JW. Multinucleotide mutations cause false inferences of lineage-specific positive selection. Nature Ecology & Evolution. PMID 29967485 DOI: 10.1038/S41559-018-0584-5 |
0.371 |
|
| 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 |
0.419 |
|
| 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 |
0.745 |
|
| 2017 |
Siddiq MA, Hochberg GK, Thornton JW. Evolution of protein specificity: insights from ancestral protein reconstruction. Current Opinion in Structural Biology. 47: 113-122. PMID 28841430 DOI: 10.1016/J.Sbi.2017.07.003 |
0.428 |
|
| 2017 |
Siddiq MA, Loehlin DW, Montooth KL, Thornton JW. Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster. Nature Ecology & Evolution. 1: 25. PMID 28812605 DOI: 10.1038/S41559-016-0025 |
0.366 |
|
| 2017 |
Hochberg GK, Thornton JW. Reconstructing Ancient Proteins to Understand the Causes of Structure and Function. Annual Review of Biophysics. PMID 28301769 DOI: 10.1146/Annurev-Biophys-070816-033631 |
0.453 |
|
| 2017 |
Starr TN, Thornton JW. Exploring protein sequence-function landscapes. Nature Biotechnology. 35: 125-126. PMID 28178247 DOI: 10.1038/Nbt.3786 |
0.443 |
|
| 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 |
0.644 |
|
| 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 |
0.32 |
|
| 2016 |
Starr TN, Thornton JW. Epistasis in protein evolution. Protein Science : a Publication of the Protein Society. PMID 26833806 DOI: 10.1002/Pro.2897 |
0.422 |
|
| 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 |
0.736 |
|
| 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 |
0.747 |
|
| 2016 |
Lim SA, Bolin ER, Harms MJ, Hart KM, Thornton JW, Marqusee S. Ancestral Sequence Reconstruction Reveals the Evolutionary History of the Folding Pathway and Landscape of Ribonucleases H Biophysical Journal. 110: 391a. DOI: 10.1016/J.Bpj.2015.11.2111 |
0.619 |
|
| 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 |
0.373 |
|
| 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 |
0.385 |
|
| 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 |
0.599 |
|
| 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 |
0.339 |
|
| 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 |
0.63 |
|
| 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 |
0.408 |
|
| 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 |
0.566 |
|
| 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 |
0.622 |
|
| 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 |
0.605 |
|
| 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 |
0.734 |
|
| 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 |
0.746 |
|
| 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 |
0.624 |
|
| 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 |
0.504 |
|
| 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 |
0.367 |
|
| 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 |
0.631 |
|
| 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 |
0.609 |
|
| 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 |
0.759 |
|
| 2010 |
Kolaczkowski B, Thornton JW. Correction: Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics Plos One. 5. DOI: 10.1371/annotation/93635f70-47d7-4876-84f5-dd568434c9ae |
0.649 |
|
| 2010 |
Kolaczkowski B, Thornton JW. Correction: Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics Plos One. 5. DOI: 10.1371/Annotation/93635F70-47D7-4876-84F5-Dd568434C9Ae |
0.696 |
|
| 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 |
0.72 |
|
| 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 |
0.466 |
|
| 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 |
0.569 |
|
| 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 |
0.398 |
|
| 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 |
0.707 |
|
| 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 |
0.394 |
|
| 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 |
0.415 |
|
| 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 |
0.703 |
|
| 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 |
0.349 |
|
| 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 |
0.695 |
|
| 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 |
0.307 |
|
| 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 |
0.601 |
|
| 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 |
0.707 |
|
| 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 |
0.325 |
|
| 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 |
0.721 |
|
| 2004 |
Thornton JW. Resurrecting ancient genes: experimental analysis of extinct molecules. Nature Reviews. Genetics. 5: 366-75. PMID 15143319 DOI: 10.1038/Nrg1324 |
0.355 |
|
| 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 |
0.376 |
|
| 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 |
0.574 |
|
| 2003 |
Thornton JW. Nonmammalian nuclear receptors: Evolution and endocrine disruption Pure and Applied Chemistry. 75: 1827-1839. DOI: 10.1351/Pac200375111827 |
0.406 |
|
| 2003 |
Wu KH, Tobias ML, Thornton JW, Kelley DB. Erratum to “Estrogen receptors in Xenopus: duplicate genes, splice variants, and tissue-specific expression” [Gen. Comp. Endocrinol. 133 (2003) 38–49] General and Comparative Endocrinology. 134: 347. DOI: 10.1016/J.Ygcen.2003.09.008 |
0.544 |
|
| 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 |
0.577 |
|
| 2002 |
Thornton J. Gene family phylogenetics: tracing protein evolution on trees Exs. 191-207. PMID 11924497 |
0.343 |
|
| 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 |
0.355 |
|
| 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 |
0.557 |
|
| 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 |
0.575 |
|
| 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 |
0.352 |
|
| 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 |
0.597 |
|
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