Richard A. Goldstein, PhD - Publications

Affiliations: 
University College London, London, United Kingdom 
Area:
protein folding, phylogeny, virus evolution, chemotaxis

94 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
2019 Monit C, Morris ER, Ruis C, Szafran B, Thiltgen G, Tsai MC, Mitchison NA, Bishop KN, Stoye JP, Taylor IA, Fassati A, Goldstein RA. Positive selection in dNTPase SAMHD1 throughout mammalian evolution. Proceedings of the National Academy of Sciences of the United States of America. PMID 31451672 DOI: 10.1073/pnas.1908755116  0.6
2019 Cudini J, Roy S, Houldcroft CJ, Bryant JM, Depledge DP, Tutill H, Veys P, Williams R, Worth AJJ, Tamuri AU, Goldstein RA, Breuer J. Human cytomegalovirus haplotype reconstruction reveals high diversity due to superinfection and evidence of within-host recombination. Proceedings of the National Academy of Sciences of the United States of America. PMID 30819890 DOI: 10.1073/pnas.1818130116  0.88
2017 Goldstein RA, Pollock DD. Sequence entropy of folding and the absolute rate of amino acid substitutions. Nature Ecology & Evolution. PMID 29062121 DOI: 10.1038/s41559-017-0338-9  0.44
2016 Thiltgen G, Dos Reis M, Goldstein RA. Finding Direction in the Search for Selection. Journal of Molecular Evolution. PMID 27913840 DOI: 10.1007/s00239-016-9765-5  0.88
2016 Goldstein RA, Pollock DD. The tangled bank of amino acids. Protein Science : a Publication of the Protein Society. PMID 27028523 DOI: 10.1002/pro.2930  0.44
2015 Goldstein RA, Pollard ST, Shah SD, Pollock DD. Nonadaptive Amino Acid Convergence Rates Decrease over Time. Molecular Biology and Evolution. 32: 1373-81. PMID 25737491 DOI: 10.1093/molbev/msv041  1
2015 Khatri BS, Goldstein RA. A coarse-grained biophysical model of sequence evolution and the population size dependence of the speciation rate Journal of Theoretical Biology. 378: 56-64. DOI: 10.1016/j.jtbi.2015.04.027  1
2014 Pollock DD, Goldstein RA. Strong evidence for protein epistasis, weak evidence against it. Proceedings of the National Academy of Sciences of the United States of America. 111: E1450. PMID 24706894 DOI: 10.1073/pnas.1401112111  1
2013 Goldstein RA. Population size dependence of fitness effect distribution and substitution rate probed by biophysical model of protein thermostability Genome Biology and Evolution. 5: 1584-1593. PMID 23884461 DOI: 10.1093/gbe/evt110  1
2013 Kentzoglanakis K, García López D, Brown SP, Goldstein RA. The evolution of collective restraint: policing and obedience among non-conjugative plasmids. Plos Computational Biology. 9: e1003036. PMID 23637589 DOI: 10.1371/journal.pcbi.1003036  1
2012 Thiltgen G, Goldstein RA. Assessing Predictors of Changes in Protein Stability upon Mutation Using Self-Consistency Plos One. 7. PMID 23144695 DOI: 10.1371/journal.pone.0046084  1
2012 Coluzza I, MacDonald JT, Sadowski MI, Taylor WR, Goldstein RA. Analytic markovian rates for generalized protein structure evolution. Plos One. 7: e34228. PMID 22693543 DOI: 10.1371/journal.pone.0034228  1
2012 Pollock DD, Thiltgen G, Goldstein RA. Amino acid coevolution induces an evolutionary Stokes shift. Proceedings of the National Academy of Sciences of the United States of America. 109: E1352-9. PMID 22547823 DOI: 10.1073/pnas.1120084109  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, 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 Tamuri AU, dos Reis M, Goldstein RA. Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models Genetics. 190: 1101-1115. PMID 22209901 DOI: 10.1534/genetics.111.136432  1
2011 Soyer OS, Goldstein RA. Evolution of response dynamics underlying bacterial chemotaxis. Bmc Evolutionary Biology. 11: 240. PMID 21846396 DOI: 10.1186/1471-2148-11-240  1
2011 Goldstein RA. The evolution and evolutionary consequences of marginal thermostability in proteins Proteins: Structure, Function and Bioinformatics. 79: 1396-1407. PMID 21337623 DOI: 10.1002/prot.22964  1
2011 dos Reis M, Tamuri AU, Hay AJ, Goldstein RA. Charting the host adaptation of influenza viruses. Molecular Biology and Evolution. 28: 1755-67. PMID 21109586 DOI: 10.1093/molbev/msq317  1
2010 Fernando C, Goldstein R, Szathmáry E. The neuronal replicator hypothesis Neural Computation. 22: 2809-2857. PMID 20804380 DOI: 10.1162/NECO_a_00031  1
2010 Fernando C, Valiäjrvi RL, Goldstein RA. A model of the mechanisms of language extinction and revitalization strategies to save endangered languages Human Biology. 82: 47-75. PMID 20504171 DOI: 10.3378/027.082.0104  1
2010 Shah SD, Doorbar J, Goldstein RA. Analysis of host-parasite incongruence in papillomavirus evolution using importance sampling Molecular Biology and Evolution. 27: 1301-1314. PMID 20093429 DOI: 10.1093/molbev/msq015  1
2010 Fernando CT, Goldstein RA, Husbands P, Stekel DJ. In silico biology. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 477-80. PMID 19908399  1
2009 Tamuri AU, Dos Reis M, Hay AJ, Goldstein RA. Identifying changes in selective constraints: host shifts in influenza. Plos Computational Biology. 5: e1000564. PMID 19911053 DOI: 10.1371/journal.pcbi.1000564  1
2009 dos Reis M, Hay AJ, Goldstein RA. Using non-homogeneous models of nucleotide substitution to identify host shift events: application to the origin of the 1918 'Spanish' influenza pandemic virus. Journal of Molecular Evolution. 69: 333-45. PMID 19787384 DOI: 10.1007/s00239-009-9282-x  1
2008 Goldstein RA, Soyer OS. Evolution of taxis responses in virtual bacteria: non-adaptive dynamics. Plos Computational Biology. 4: e1000084. PMID 18483577 DOI: 10.1371/journal.pcbi.1000084  1
2008 Blackburne BP, Hay AJ, Goldstein RA. Changing selective pressure during antigenic changes in human influenza H3. Plos Pathogens. 4: e1000058. PMID 18451985 DOI: 10.1371/journal.ppat.1000058  1
2008 Goldstein RA. The structure of protein evolution and the evolution of protein structure Current Opinion in Structural Biology. 18: 170-177. PMID 18328690 DOI: 10.1016/j.sbi.2008.01.006  1
2008 Stadthagen-Gomez G, Helguera-Repetto AC, Cerna-Cortes JF, Goldstein RA, Cox RA, Gonzalez-y-Merchand JA. The organization of two rRNA (rrn) operons of the slow-growing pathogen Mycobacterium celatum provides key insights into mycobacterial evolution. Fems Microbiology Letters. 280: 102-12. PMID 18248431 DOI: 10.1111/j.1574-6968.2007.01050.x  1
2007 Goldstein RA. Amino-acid interactions in psychrophiles, mesophiles, thermophiles, and hyperthermophiles: Insights from the quasi-chemical approximation Protein Science. 16: 1887-1895. PMID 17766385 DOI: 10.1110/ps.072947007  1
2006 Williams PD, Pollock DD, Goldstein RA. SELECTIVE ADVANTAGE OF RECOMBINATION IN EVOLVING PROTEIN POPULATIONS: A LATTICE MODEL STUDY. International Journal of Modern Physics. C, Physics and Computers. 17: 75-90. PMID 25473139 DOI: 10.1142/S0129183106008959  1
2006 Williams PD, Pollock DD, Goldstein RA. Functionality and the evolution of marginal stability in proteins: inferences from lattice simulations. Evolutionary Bioinformatics Online. 2: 91-101. PMID 19455204  0.44
2006 Goldstein RA. Emergent robustness in competition between autocatalytic chemical networks Origins of Life and Evolution of the Biosphere. 36: 381-389. PMID 16972150 DOI: 10.1007/s11084-006-9014-9  1
2006 Williams PD, Pollock DD, Blackburne BP, Goldstein RA. Assessing the accuracy of ancestral protein reconstruction methods. Plos Computational Biology. 2: e69. PMID 16789817 DOI: 10.1371/journal.pcbi.0020069  1
2006 Goldstein RA, Pollock DD. Observations of amino acid gain and loss during protein evolution are explained by statistical bias. Molecular Biology and Evolution. 23: 1444-9. PMID 16698770 DOI: 10.1093/molbev/msl010  1
2005 Xu YO, Hall RW, Goldstein RA, Pollock DD. Divergence, recombination and retention of functionality during protein evolution. Human Genomics. 2: 158-67. PMID 16197733  1
2004 Soyer OS, Goldstein RA. Predicting functional sites in proteins: site-specific evolutionary models and their application to neurotransmitter transporters. Journal of Molecular Biology. 339: 227-42. PMID 15123434 DOI: 10.1016/j.jmb.2004.03.025  1
2004 Qian B, Goldstein RA. Performance of an iterated T-HMM for homology detection Bioinformatics. 20: 2175-2180. PMID 15044240 DOI: 10.1093/bioinformatics/bth181  1
2004 Goldstein RA. Evolutionary perspectives on protein thermo dynamics Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3039: 718-727.  1
2003 Soyer OS, Dimmic MW, Neubig RR, Goldstein RA. Dimerization in aminergic G-protein-coupled receptors: application of a hidden-site class model of evolution. Biochemistry. 42: 14522-31. PMID 14661965 DOI: 10.1021/bi035097r  1
2003 Goldberg NR, Beuming T, Soyer OS, Goldstein RA, Weinstein H, Javitch JA. Probing conformational changes in neurotransmitter transporters: a structural context. European Journal of Pharmacology. 479: 3-12. PMID 14612133 DOI: 10.1016/j.ejphar.2003.08.052  1
2003 Qian B, Soyer OS, Neubig RR, Goldstein RA. Depicting a protein's two faces: GPCR classification by phylogenetic tree-based HMMs. Febs Letters. 554: 95-9. PMID 14596921 DOI: 10.1016/S0014-5793(03)01112-8  1
2003 Qian B, Goldstein RA. Detecting distant homologs using phylogenetic tree-based HMMS Proteins: Structure, Function and Genetics. 52: 446-453. PMID 12866055 DOI: 10.1002/prot.10373  1
2003 Kann M, Goldstein RA. OPTIMA: A new score function for the detection of remote homologs Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2666: 99-108.  1
2002 Qian B, Goldstein RA. Optimization of a new score function for the generation of accurate alignments Proteins: Structure, Function and Genetics. 48: 605-610. PMID 12211027 DOI: 10.1002/prot.10132  1
2002 Dimmic MW, Rest JS, Mindell DP, Goldstein RA. rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. Journal of Molecular Evolution. 55: 65-73. PMID 12165843 DOI: 10.1007/s00239-001-2304-y  1
2002 Kann MG, Goldstein RA. Performance evaluation of a new algorithm for the detection of remote homologs with sequence comparison. Proteins. 48: 367-76. PMID 12112703 DOI: 10.1002/prot.10117  1
2002 Soyer O, Dimmic MW, Neubig RR, Goldstein RA. Using evolutionary methods to study G-protein coupled receptors. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 625-36. PMID 11928514  1
2002 Taverna DM, Goldstein RA. Why are proteins so robust to site mutations? Journal of Molecular Biology. 315: 479-484. PMID 11786027 DOI: 10.1006/jmbi.2001.5226  1
2002 Taverna DM, Goldstein RA. Why are proteins marginally stable? Proteins: Structure, Function and Genetics. 46: 105-109. PMID 11746707 DOI: 10.1002/prot.10016  1
2001 Qian B, Goldstein RA. Distribution of Indel lengths. Proteins. 45: 102-4. PMID 11536366 DOI: 10.1002/prot.1129  1
2001 Krueger BP, Kollman PA. Molecular dynamics simulations of a highly charged peptide from an SH3 domain: possible sequence-function relationship. Proteins. 45: 4-15. PMID 11536355 DOI: 10.1002/prot.1118  1
2001 Williams PD, Pollock DD, Goldstein RA. Evolution of functionality in lattice proteins. Journal of Molecular Graphics & Modelling. 19: 150-6. PMID 11381526 DOI: 10.1016/S1093-3263(00)00125-X  1
2001 Koshi JM, Goldstein RA. Analyzing site heterogeneity during protein evolution. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 191-202. PMID 11262940  1
2000 Kann M, Qian B, Goldstein RA. Optimization of a new score function for the detection of remote homologs Proteins: Structure, Function and Genetics. 41: 498-503. PMID 11056037 DOI: 10.1002/1097-0134(20001201)41:4<498::AID-PROT70>3.0.CO;2-3  1
2000 Chiu TL, Goldstein RA. How to generate improved potentials for protein tertiary structure prediction: A lattice model study Proteins: Structure, Function and Genetics. 41: 157-163. PMID 10966569 DOI: 10.1002/1097-0134(20001101)41:2<157::AID-PROT10>3.0.CO;2-W  1
2000 Dimmic MW, Mindell DP, Goldstein RA. Modeling evolution at the protein level using an adjustable amino acid fitness model. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 18-29. PMID 10902153  1
2000 Frishman D, Goldstein RA, Pollock DD. Protein evolution and structural genomics Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 3-5. PMID 10902151  0.44
2000 Taverna DM, Goldstein RA. The distribution of structures in evolving protein populations Biopolymers. 53: 1-8. PMID 10644946 DOI: 10.1002/(SICI)1097-0282(200001)53:1<1::AID-BIP1>3.0.CO;2-X  1
2000 Buchler NEG, Goldstein RA. Surveying determinants of protein structure designability across different energy models and amino-acid alphabets: A consensus Journal of Chemical Physics. 112: 2533-2547.  1
2000 Kann M, Goldstein RA. Optimizing for success: A new score function for distantly related protein sequence comparison Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 177-182.  1
1999 Govindarajan S, Recabarren R, Goldstein RA. Estimating the total number of protein folds. Proteins. 35: 408-14. PMID 10382668 DOI: 10.1002/(SICI)1097-0134(19990601)35:4<408::AID-PROT4>3.0.CO;2-A  1
1999 Buchler NE, Goldstein RA. Effect of alphabet size and foldability requirements on protein structure designability. Proteins. 34: 113-24. PMID 10336377 DOI: 10.1002/(SICI)1097-0134(19990101)34:1<113::AID-PROT9>3.0.CO;2-J  1
1999 Koshi JM, Mindell DP, Goldstein RA. Using physical-chemistry-based substitution models in phylogenetic analyses of HIV-1 subtypes. Molecular Biology and Evolution. 16: 173-9. PMID 10028285  1
1999 Buchler NEG, Goldstein RA. Universal correlation between energy gap and foldability for the random energy model and lattice proteins Journal of Chemical Physics. 111: 6599-6609.  1
1998 Chiu TL, Goldstein RA. Optimizing potentials for the inverse protein folding problem Protein Engineering. 11: 749-752. PMID 9796822  1
1998 Koshi JM, Goldstein RA. Models of natural mutations including site heterogeneity. Proteins. 32: 289-95. PMID 9715905 DOI: 10.1002/(SICI)1097-0134(19980815)32:3<289::AID-PROT4>3.0.CO;2-D  1
1998 Chiu TL, Goldstein RA. Optimizing energy potentials for success in protein tertiary structure prediction Folding and Design. 3: 223-228. PMID 9669880 DOI: 10.1016/S1359-0278(98)00030-3  1
1998 Govindarajan S, Goldstein RA. On the thermodynamic hypothesis of protein folding. Proceedings of the National Academy of Sciences of the United States of America. 95: 5545-9. PMID 9576919 DOI: 10.1073/pnas.95.10.5545  1
1997 Koshi JM, Mindell DP, Goldstein RA. Beyond Mutation Matrices: Physical-Chemistry Based Evolutionary Models. Genome Informatics. Workshop On Genome Informatics. 8: 80-89. PMID 11072308  1
1997 Govindarajan S, Goldstein RA. Evolution of model proteins on a foldability landscape. Proteins. 29: 461-6. PMID 9408943 DOI: 10.1002/(SICI)1097-0134(199712)29:4<461::AID-PROT6>3.0.CO;2-B  1
1997 Thompson MJ, Goldstein RA. Predicting protein secondary structure with probabilistic schemata of evolutionarily derived information Protein Science. 6: 1963-1975. PMID 9300496  1
1997 Govindarajan S, Goldstein RA. The foldability landscape of model proteins. Biopolymers. 42: 427-38. PMID 9283292 DOI: 10.1002/(SICI)1097-0282(19971005)42:4<427::AID-BIP6>3.0.CO;2-S  1
1997 Buchler NE, Zuiderweg ER, Wang H, Goldstein RA. Protein heteronuclear NMR assignments using mean-field simulated annealing. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 125: 34-42. PMID 9245358 DOI: 10.1006/jmre.1997.1106  1
1997 Koshi JM, Goldstein RA. Mutation matrices and physical-chemical properties: correlations and implications. Proteins. 27: 336-44. PMID 9094736 DOI: 10.1002/(SICI)1097-0134(199703)27:3<336::AID-PROT2>3.0.CO;2-B  1
1997 Chiu TL, Goldstein RA. Compaction and folding in model proteins Journal of Chemical Physics. 107: 4408-4415.  1
1996 Koshi JM, Goldstein RA. Correlating structure-dependent mutation matrices with physical-chemical properties. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 488-99. PMID 9390253  1
1996 Koshi JM, Goldstein RA. Probabilistic reconstruction of ancestral protein sequences. Journal of Molecular Evolution. 42: 313-20. PMID 8919883 DOI: 10.1007/BF02198858  1
1996 Thompson MJ, Goldstein RA. Predicting solvent accessibility: higher accuracy using Bayesian statistics and optimized residue substitution classes. Proteins. 25: 38-47. PMID 8727318 DOI: 10.1002/(SICI)1097-0134(199605)25:1<38::AID-PROT4>3.0.CO;2-G  1
1996 Thompson MJ, Goldstein RA. Constructing amino acid residue substitution classes maximally indicative of local protein structure. Proteins. 25: 28-37. PMID 8727317 DOI: 10.1002/(SICI)1097-0134(199605)25:1<28::AID-PROT3>3.0.CO;2-G  1
1996 Govindarajan S, Goldstein RA. Why are some proteins structures so common? Proceedings of the National Academy of Sciences of the United States of America. 93: 3341-5. PMID 8622938 DOI: 10.1073/pnas.93.8.3341  1
1995 Koshi JM, Goldstein RA. Context-dependent optimal substitution matrices. Protein Engineering. 8: 641-5. PMID 8577693  1
1995 Govindarajan S, Goldstein RA. Optimal local propensities for model proteins. Proteins. 22: 413-8. PMID 7479714 DOI: 10.1002/prot.340220411  1
1995 Govindarajan S, Goldstein RA. Searching for foldable protein structures using optimized energy functions Biopolymers. 36: 43-51. DOI: 10.1002/bip.360360105  1
1995 Goldstein RA, Luthey-Schulten ZA, Wolynes PG. Bayesian approach to sequence alignment algorithms for protein structure recognition Proceedings of the Hawaii International Conference On System Sciences. 5: 306-315.  1
1993 Goldstein RA, Katzenellenbogen JA, Luthey-Schulten ZA, Seielstad DA, Wolynes PG. Three-dimensional model for the hormone binding domains of steroid receptors. Proceedings of the National Academy of Sciences of the United States of America. 90: 9949-53. PMID 8234340  1
1992 Goldstein RA, Luthey-Schulten ZA, Wolynes PG. Optimal protein-folding codes from spin-glass theory. Proceedings of the National Academy of Sciences of the United States of America. 89: 4918-22. PMID 1594594  1
1992 Goldstein RA, Luthey-Schulten ZA, Wolynes PG. Protein tertiary structure recognition using optimized Hamiltonians with local interactions. Proceedings of the National Academy of Sciences of the United States of America. 89: 9029-33. PMID 1409599  1
1991 Friedrichs MS, Goldstein RA, Wolynes PG. Generalized protein tertiary structure recognition using associative memory Hamiltonians. Journal of Molecular Biology. 222: 1013-34. PMID 1762143 DOI: 10.1016/0022-2836(91)90591-S  1
1989 Goldstein RA, Boxer SG. The effect of very high magnetic fields on the reaction dynamics in bacterial reaction centers: Implications for the reaction mechanism Bba - Bioenergetics. 977: 78-86. DOI: 10.1016/S0005-2728(89)80011-8  1
1989 Goldstein RA, Boxer SG. The effect of very high magnetic fields on the delayed fluorescence from oriented bacterial reaction centers Bba - Bioenergetics. 977: 70-77. DOI: 10.1016/S0005-2728(89)80010-6  1
1989 Boxer SG, Goldstein RA, Lockhart DJ, Middendorf TR, Takiff L. Excited states, electron-transfer reactions, and intermediates in bacterial photosynthetic reaction centers Journal of Physical Chemistry. 93: 8280-8294.  1
1988 Goldstein RA, Takiff L, Steven G. B. Energetics of initial charge separation in bacterial photosynthesis: The triplet decay rate in very high magnetic fields Bba - Bioenergetics. 934: 253-263. DOI: 10.1016/0005-2728(88)90189-2  1
1987 Goldstein RA, Boxer SG. Effects of nuclear spin polarization on reaction dynamics in photosynthetic bacterial reaction centers. Biophysical Journal. 51: 937-46. PMID 19431700  1
1985 Chidsey CE, Takiff L, Goldstein RA, Boxer SG. Effect of magnetic fields on the triplet state lifetime in photosynthetic reaction centers: Evidence for thermal repopulation of the initial radical pair. Proceedings of the National Academy of Sciences of the United States of America. 82: 6850-4. PMID 16593615  1
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