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James A Lake - Publications

Affiliations: 
University of California, Los Angeles, Los Angeles, CA 
Area:
ribosome structure, phylogenetic trees
Website:
https://research.mcdb.ucla.edu/Lake/
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68 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 Lake JA, Larsen J, Tran DT, Sinsheimer JS. Uncovering the Genomic Origins of Life. Genome Biology and Evolution. PMID 29947758 DOI: 10.1093/Gbe/Evy129  0.567
2016 Lake JA, Larsen J, Sarna B, de la Haba RR, Pu Y, Koo H, Zhao J, Sinsheimer JS. Rings Reconcile Genotypic and Phenotypic Evolution within the Proteobacteria. Genome Biology and Evolution. 8: 578. PMID 26966240 DOI: 10.1093/gbe/evw030  0.43
2015 Lake JA, Larsen J, Sarna B, de la Haba RR, Pu Y, Koo H, Zhao J, Sinsheimer JS. Rings Reconcile Genotypic and Phenotypic Evolution within the Proteobacteria. Genome Biology and Evolution. PMID 26659922 DOI: 10.1093/Gbe/Evv221  0.609
2015 Simpson L, Douglass SM, Lake JA, Pellegrini M, Li F. Comparison of the Mitochondrial Genomes and Steady State Transcriptomes of Two Strains of the Trypanosomatid Parasite, Leishmania tarentolae. Plos Neglected Tropical Diseases. 9: e0003841. PMID 26204118 DOI: 10.1371/Journal.Pntd.0003841  0.378
2013 Lake JA, Sinsheimer JS. The deep roots of the rings of life. Genome Biology and Evolution. 5: 2440-8. PMID 24281049 DOI: 10.1093/Gbe/Evt194  0.571
2012 Sinsheimer JS, Little RJ, Lake JA. Rooting gene trees without outgroups: EP rooting. Genome Biology and Evolution. 4: 709-19. PMID 22593551 DOI: 10.1093/Gbe/Evs047  0.688
2009 Lake JA. Evidence for an early prokaryotic endosymbiosis Nature. 460: 967-971. PMID 19693078 DOI: 10.1038/Nature08183  0.324
2009 Lake JA, Skophammer RG, Herbold CW, Servin JA. Genome beginnings: Rooting the tree of life Philosophical Transactions of the Royal Society B: Biological Sciences. 364: 2177-2185. PMID 19571238 DOI: 10.1098/Rstb.2009.0035  0.341
2009 Ragan MA, McInerney JO, Lake JA. The network of life: genome beginnings and evolution. Introduction. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 364: 2169-75. PMID 19571237 DOI: 10.1098/Rstb.2009.0046  0.334
2008 Lake JA, Servin JA, Herbold CW, Skophammer RG. Evidence for a new root of the tree of life Systematic Biology. 57: 835-843. PMID 19085327 DOI: 10.1080/10635150802555933  0.35
2008 Lake JA. Reconstructing evolutionary graphs: 3D parsimony Molecular Biology and Evolution. 25: 1677-1682. PMID 18492661 DOI: 10.1093/Molbev/Msn117  0.378
2008 Servin JA, Herbold CW, Skophammer RG, Lake JA. Evidence excluding the root of the tree of life from the Actinobacteria Molecular Biology and Evolution. 25: 1-4. PMID 18003601 DOI: 10.1093/Molbev/Msm249  0.357
2007 Skophammer RG, Servin JA, Herbold CW, Lake JA. Evidence for a Gram-positive, eubacterial root of the tree of life Molecular Biology and Evolution. 24: 1761-1768. PMID 17513883 DOI: 10.1093/Molbev/Msm096  0.399
2007 Martin W, Dagan T, Koonin EV, Dipippo JL, Gogarten JP, Lake JA. The evolution of eukaryotes. Science (New York, N.Y.). 316: 542-3; author reply . PMID 17463271 DOI: 10.1126/Science.316.5824.542C  0.333
2007 Lake JA, Herbold CW, Rivera MC, Servin JA, Skophammer RG. Rooting the tree of life using nonubiquitous genes Molecular Biology and Evolution. 24: 130-136. PMID 17023560 DOI: 10.1093/Molbev/Msl140  0.396
2006 Skophammer RG, Herbold CW, Rivera MC, Servin JA, Lake JA. Evidence that the root of the tree of life is not within the Archaea Molecular Biology and Evolution. 23: 1648-1651. PMID 16801395 DOI: 10.1093/Molbev/Msl046  0.359
2005 Simonson AB, Servin JA, Skophammer RG, Herbold CW, Rivera MC, Lake JA. Decoding the genomic tree of life Proceedings of the National Academy of Sciences of the United States of America. 102: 6608-6613. PMID 15851667 DOI: 10.1073/Pnas.0501996102  0.397
2004 Rivera MC, Lake JA. The ring of life provides evidence for a genome fusion origin of eukaryotes Nature. 431: 152-155. PMID 15356622 DOI: 10.1038/Nature02848  0.385
2004 Lake JA, Rivera MC. Deriving the Genomic Tree of Life in the Presence of Horizontal Gene Transfer: Conditioned Reconstruction Molecular Biology and Evolution. 21: 681-690. PMID 14739244 DOI: 10.1093/Molbev/Msh061  0.39
2003 Moore JE, Lake JA. Gene structure prediction in syntenic DNA segments Nucleic Acids Research. 31: 7271-7279. PMID 14654703 DOI: 10.1093/Nar/Gkg905  0.354
2003 Jain R, Rivera MC, Moore JE, Lake JA. Horizontal gene transfer accelerates genome innovation and evolution. Molecular Biology and Evolution. 20: 1598-602. PMID 12777514 DOI: 10.1093/Molbev/Msg154  0.351
2003 Jain R, Rivera MC, Moore JE, Lake JA. Non-clonal evolution of microbes Biological Journal of the Linnean Society. 79: 27-32. DOI: 10.1046/J.1095-8312.2003.00174.X  0.408
2002 Jain R, Rivera MC, Moore JE, Lake JA. Horizontal gene transfer in microbial genome evolution. Theoretical Population Biology. 61: 489-95. PMID 12167368 DOI: 10.1006/Tpbi.2002.1596  0.321
2002 Simonson AB, Lake JA. The transorientation hypothesis for codon recognition during protein synthesis Nature. 416: 281-285. PMID 11907568 DOI: 10.1038/416281A  0.329
2001 Belova GI, Prasad R, Kozyavkin SA, Lake JA, Wilson SH, Slesarev AI. A type IB topoisomerase with DNA repair activities Proceedings of the National Academy of Sciences of the United States of America. 98: 6015-6020. PMID 11353838 DOI: 10.1073/Pnas.111040498  0.302
1999 Lake JA, Jain R, Rivera MC. Mix and match in the tree of life Science. 283: 2027-2028. PMID 10206909 DOI: 10.1126/Science.283.5410.2027  0.433
1999 Jain R, Rivera MC, Lake JA. Horizontal gene transfer among genomes: The complexity hypothesis Proceedings of the National Academy of Sciences of the United States of America. 96: 3801-3806. PMID 10097118 DOI: 10.1073/Pnas.96.7.3801  0.334
1998 Lake JA. Optimally recovering rate variation information from genomes and sequences: Pattern filtering Molecular Biology and Evolution. 15: 1224-1231. PMID 9729887 DOI: 10.1093/Oxfordjournals.Molbev.A026030  0.336
1998 Rivera MC, Jain R, Moore JE, Lake JA. Genomic evidence for two functionally distinct gene classes Proceedings of the National Academy of Sciences of the United States of America. 95: 6239-6244. PMID 9600949 DOI: 10.1073/Pnas.95.11.6239  0.362
1998 Aguinaldo AMA, Lake JA. Evolution of the Multicellular Animals Integrative and Comparative Biology. 38: 878-887. DOI: 10.1093/Icb/38.6.878  0.376
1998 Lake JA, Moore JE. Phylogenetic analysis and comparative genomics Trends in Biotechnology. 16: 22-23. DOI: 10.1016/S0167-7799(98)00132-2  0.323
1997 Aguinaldo AM, Turbeville JM, Linford LS, Rivera MC, Garey JR, Raff RA, Lake JA. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature. 387: 489-93. PMID 9168109 DOI: 10.1038/387489A0  0.362
1997 Sinsheimer JS, Lake JA, Little RJA. Inference for phylogenies under a hybrid parsimony method: Evolutionary- symmetric transversion parsimony Biometrics. 53: 23-38. PMID 9147592 DOI: 10.2307/2533094  0.544
1997 Lake JA. Phylogenetic inference: How much evolutionary history is knowable? Molecular Biology and Evolution. 14: 213-219. PMID 9066789 DOI: 10.1093/Oxfordjournals.Molbev.A025757  0.385
1996 Sinsheimer JS, Lake JA, Little RJA. Bayesian hypothesis testing of four-taxon topologies using molecular sequence data Biometrics. 52: 193-210. PMID 8934592 DOI: 10.2307/2533156  0.567
1996 Nölling J, Elfner A, Palmer JR, Steigerwald VJ, Pihl TD, Lake JA, Reeve JN. Phylogeny of Methanopyrus kandleri based on methyl coenzyme M reductase operons International Journal of Systematic Bacteriology. 46: 1170-1173. PMID 8863453 DOI: 10.1099/00207713-46-4-1170  0.329
1996 Rivera MC, Lake JA. The phylogeny of Methanopyrus kandleri International Journal of Systematic Bacteriology. 46: 348-351. PMID 8573519 DOI: 10.1099/00207713-46-1-348  0.378
1995 Halanych KM, Bacheller JD, Aguinaldo AM, Liva SM, Hillis DM, Lake JA. Evidence from 18S ribosomal DNA that the lophophorates are protostome animals. Science (New York, N.Y.). 267: 1641-3. PMID 7886451 DOI: 10.1126/Science.7886451  0.37
1995 Lake JA. Calculating the probability of multitaxon evolutionary trees: Bootstrappers Gambit Proceedings of the National Academy of Sciences of the United States of America. 92: 9662-9666. PMID 7568193 DOI: 10.1073/Pnas.92.21.9662  0.377
1994 Maslov DA, Avila HA, Lake JA, Simpson L. Evolution of RNA editing in kinetoplastid protozoa Nature. 368: 345-348. PMID 8127370 DOI: 10.1038/368345A0  0.358
1994 Lake JA. Reconstructing evolutionary trees from DNA and protein sequences: Paralinear distances Proceedings of the National Academy of Sciences of the United States of America. 91: 1455-1459. PMID 8108430 DOI: 10.1073/Pnas.91.4.1455  0.39
1992 Rivera MC, Lake JA. Evidence that eukaryotes and eocyte prokaryotes are immediate relatives Science. 257: 74-76. PMID 1621096 DOI: 10.1126/Science.1621096  0.346
1992 Scheinman A, Atha T, Aguinaldo AM, Kahan L, Shankweiler G, Lake JA. Mapping the three-dimensional locations of ribosomal RNA and proteins Biochimie. 74: 307-317. PMID 1379075 DOI: 10.1016/0300-9084(92)90108-Q  0.341
1991 Lake JA. Tracing origins with molecular sequences: metazoan and eukaryotic beginnings Trends in Biochemical Sciences. 16: 46-50. PMID 1858129 DOI: 10.1016/0968-0004(91)90020-V  0.42
1990 Lake JA. Origin of the Metazoa Proceedings of the National Academy of Sciences of the United States of America. 87: 763-766. PMID 2300560 DOI: 10.1073/Pnas.87.2.763  0.322
1990 Oakes MI, Kahan L, Lake JA. DNA-hybridization electron microscopy. Tertiary structure of 16 S rRNA Journal of Molecular Biology. 211: 907-918. PMID 2179567 DOI: 10.1016/0022-2836(90)90083-X  0.344
1990 Oakes MI, Lake JA. DNA-hybridization electron microscopy. Localization of five regions of 16 S rRNA on the surface of 30 S ribosomal subunits Journal of Molecular Biology. 211: 897-906. PMID 2156079 DOI: 10.1016/0022-2836(90)90082-W  0.327
1989 Lake JA. Origin of the eukaryotic nucleus: Eukaryotes and eocytes are genotypically related Canadian Journal of Microbiology. 35: 109-118. PMID 2720490 DOI: 10.1139/M89-017  0.381
1988 Lake JA. Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences Nature. 331: 184-186. PMID 3340165 DOI: 10.1038/331184A0  0.401
1988 Lake JA, de la Cruz VF, Ferreira PC, Morel C, Simpson L. Evolution of parasitism: kinetoplastid protozoan history reconstructed from mitochondrial rRNA gene sequences. Proceedings of the National Academy of Sciences of the United States of America. 85: 4779-83. PMID 3133662 DOI: 10.1073/Pnas.85.13.4779  0.374
1987 Lake JA. A rate-independent technique for analysis of nucleic acid sequences: Evolutionary parsimony Molecular Biology and Evolution. 4: 167-191. PMID 3447007 DOI: 10.1093/Oxfordjournals.Molbev.A040433  0.356
1987 Lake JA. Determining evolutionary distances from highly diverged nucleic acid sequences: Operator metrics Journal of Molecular Evolution. 26: 59-73. PMID 3125338 DOI: 10.1007/Bf02111282  0.328
1986 Oakes MI, Clark MW, Henderson E, Lake JA. DNA hybridization electron microscopy: Ribosomal RNA nucleotides 1392-1407 are exposed in the cleft of the small subunit Proceedings of the National Academy of Sciences of the United States of America. 83: 275-279. PMID 3510432 DOI: 10.1073/Pnas.83.2.275  0.389
1986 Lake JA, Henderson E, Clark MW, Scheinman A, Oakes MI. Mapping evolution with three dimensional ribosome structure Systematic and Applied Microbiology. 7: 131-136. DOI: 10.1016/S0723-2020(86)80135-7  0.353
1986 Oakes MI, Clark MW, Henderson E, Scheinman A, Lake JA. Evidence for a specific phylogenetic relationship between the methanogens Methanococcus thermolithotrophicus and Methanothermus fervidus, and the sulfur respiring Thermoproteus tenax Systematic and Applied Microbiology. 7: 190-193. DOI: 10.1016/S0723-2020(86)80004-2  0.351
1986 Lake JA. Mapping the early evolution of cells with rrna sequences and structure Origins of Life and Evolution of Biospheres. 16: 244-244. DOI: 10.1007/Bf02422004  0.308
1985 Lake JA, Clark MW, Henderson E, Fay SP, Oakes M, Scheinman A, Thornber JP, Mah RA. Eubacteria, halobacteria, and the origin of photosynthesis: The photocytes Proceedings of the National Academy of Sciences of the United States of America. 82: 3716-3720. PMID 3858845 DOI: 10.1073/Pnas.82.11.3716  0.341
1985 De la Cruz VF, Lake JA, Simpson AM, Simpson L. A minimal ribosomal RNA: Sequence and secondary structure of the 9S kinetoplast ribosomal RNA from Leishmania tarentolae Proceedings of the National Academy of Sciences of the United States of America. 82: 1401-1405. PMID 3856267 DOI: 10.1073/Pnas.82.5.1401  0.377
1985 de la Cruz VF, Simpson AM, Lake JA, Simpson L. Primary sequence and partial secondary structure of the 12S kinetoplast (mitochondrial) ribosomal RNA from Leishmania tarentolae: Conservation of peptidyl-transferase structural elements Nucleic Acids Research. 13: 2337-2356. PMID 2987850 DOI: 10.1093/Nar/13.7.2337  0.403
1984 Lake JA, Henderson E, Oakes M, Clark MW. Eocytes: A new ribosome structure indicates a kingdom with a close relationship to eukaryotes Proceedings of the National Academy of Sciences of the United States of America. 81: 3786-3790. PMID 6587394 DOI: 10.1073/Pnas.81.12.3786  0.376
1984 Henderson E, Oakes M, Clark MW, Lake JA, Matheson AT, Zillig W. A new ribosome structure Science. 225: 510-512. PMID 6429855 DOI: 10.1126/Science.6429855  0.344
1983 Lake JA. Ribosome evolution: the structural bases of protein synthesis in archaebacteria, eubacteria, and eukaryotes Progress in Nucleic Acid Research and Molecular Biology. 30: 163-194. PMID 6420842 DOI: 10.1016/S0079-6603(08)60686-8  0.326
1982 Lake JA, Henderson E, Clark MW, Matheson AT. Mapping evolution with ribosome structure: Intralineage constancy and interlineage variation Proceedings of the National Academy of Sciences of the United States of America. 79: 5948-5952. PMID 6764534 DOI: 10.1073/Pnas.79.19.5948  0.364
1982 Lake JA. Ribosomal subunit orientations determined in the monomeric ribosome by single and by double-labeling immune electron microscopy Journal of Molecular Biology. 161: 89-106. PMID 6759661 DOI: 10.1016/0022-2836(82)90280-7  0.334
1981 Studnicka GM, Eiserling FA, Lake JA. A unique secondary folding pattern for 5S RNA corresponds to the lowest energy homologous secondary structure in 17 different prokaryotes Nucleic Acids Research. 9: 1885-1904. PMID 6165963 DOI: 10.1093/Nar/9.8.1885  0.357
1979 Clark MW, Hammons M, Langer JA, Lake JA. Helical arrays of Escherichia coli small ribosomal subunits produced in vitro. Journal of Molecular Biology. 135: 507-12. PMID 395321 DOI: 10.1016/0022-2836(79)90450-9  0.313
1976 Lake JA. Ribosome structure determined by electron microscopy of Escherichia coli small subunits, large subunits and monomeric ribosomes Journal of Molecular Biology. 105: 131-159. PMID 792456 DOI: 10.1016/0022-2836(76)90200-X  0.32
1968 Lake JA, Beeman WW. On the conformation of yeast transfer RNA. Journal of Molecular Biology. 31: 115-25. PMID 5636878  0.615
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