Jeffrey L. Boore, Ph.D. - Publications

Integrative Biology University of California, Berkeley, Berkeley, CA 
Comparative genomics, molecular evolution, systematics, organelle genomics, high-throughput DNA sequencing

112 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 Sharbrough J, Luse M, Boore JL, Logsdon JM, Neiman M. Radical amino acid mutations persist longer in the absence of sex. Evolution; International Journal of Organic Evolution. PMID 29520921 DOI: 10.1111/Evo.13465  0.6
2017 Bankers LA, Fields P, McElroy KE, Boore JL, Logsdon JM, Neiman M. Genomic evidence for population-specific responses to coevolving parasites in a New Zealand freshwater snail. Molecular Ecology. PMID 28429458 DOI: 10.1111/Mec.14146  0.6
2014 Bell NE, Boore JL, Mishler BD, Hyvönen J. Organellar genomes of the four-toothed moss, Tetraphis pellucida. Bmc Genomics. 15: 383. PMID 24884426 DOI: 10.1186/1471-2164-15-383  1
2013 Rice DW, Alverson AJ, Richardson AO, Young GJ, Sanchez-Puerta MV, Munzinger J, Barry K, Boore JL, Zhang Y, dePamphilis CW, Knox EB, Palmer JD. Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella. Science (New York, N.Y.). 342: 1468-73. PMID 24357311 DOI: 10.1126/Science.1246275  1
2013 Schartl M, Walter RB, Shen Y, Garcia T, Catchen J, Amores A, Braasch I, Chalopin D, Volff JN, Lesch KP, Bisazza A, Minx P, Hillier L, Wilson RK, Fuerstenberg S, ... Boore J, et al. The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. Nature Genetics. 45: 567-72. PMID 23542700 DOI: 10.1038/Ng.2604  1
2013 Simakov O, Marletaz F, Cho SJ, Edsinger-Gonzales E, Havlak P, Hellsten U, Kuo DH, Larsson T, Lv J, Arendt D, Savage R, Osoegawa K, de Jong P, Grimwood J, Chapman JA, ... ... Boore JL, et al. Insights into bilaterian evolution from three spiralian genomes. Nature. 493: 526-31. PMID 23254933 DOI: 10.1038/Nature11696  1
2012 Radakovits R, Jinkerson RE, Fuerstenberg SI, Tae H, Settlage RE, Boore JL, Posewitz MC. Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropis gaditana. Nature Communications. 3: 686. PMID 22353717 DOI: 10.1038/Ncomms1688  1
2012 Price DC, Chan CX, Yoon HS, Yang EC, Qiu H, Weber AP, Schwacke R, Gross J, Blouin NA, Lane C, Reyes-Prieto A, Durnford DG, Neilson JA, Lang BF, Burger G, ... ... Boore J, et al. Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science (New York, N.Y.). 335: 843-7. PMID 22344442 DOI: 10.1126/Science.1213561  1
2012 Murtagh VJ, O'Meally D, Sankovic N, Delbridge ML, Kuroki Y, Boore JL, Toyoda A, Jordan KS, Pask AJ, Renfree MB, Fujiyama A, Graves JA, Waters PD. Evolutionary history of novel genes on the tammar wallaby Y chromosome: Implications for sex chromosome evolution. Genome Research. 22: 498-507. PMID 22128133 DOI: 10.1101/Gr.120790.111  1
2011 Zhan S, Merlin C, Boore JL, Reppert SM. The monarch butterfly genome yields insights into long-distance migration. Cell. 147: 1171-85. PMID 22118469 DOI: 10.1016/J.Cell.2011.09.052  1
2011 O'Quin KE, Smith D, Naseer Z, Schulte J, Engel SD, Loh YH, Streelman JT, Boore JL, Carleton KL. Divergence in cis-regulatory sequences surrounding the opsin gene arrays of African cichlid fishes. Bmc Evolutionary Biology. 11: 120. PMID 21554730 DOI: 10.1186/1471-2148-11-120  1
2011 Medina M, Lal S, Vallès Y, Takaoka TL, Dayrat BA, Boore JL, Gosliner T. Crawling through time: Transition of snails to slugs dating back to the Paleozoic, based on mitochondrial phylogenomics. Marine Genomics. 4: 51-9. PMID 21429465 DOI: 10.1016/J.Margen.2010.12.006  1
2011 Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Cáceres CE, Carmel L, Casola C, Choi JH, ... ... Boore JL, et al. The ecoresponsive genome of Daphnia pulex. Science (New York, N.Y.). 331: 555-61. PMID 21292972 DOI: 10.1126/Science.1197761  1
2011 Guisinger MM, Kuehl JV, Boore JL, Jansen RK. Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage. Molecular Biology and Evolution. 28: 583-600. PMID 20805190 DOI: 10.1093/Molbev/Msq229  1
2010 Baxter L, Tripathy S, Ishaque N, Boot N, Cabral A, Kemen E, Thines M, Ah-Fong A, Anderson R, Badejoko W, Bittner-Eddy P, Boore JL, Chibucos MC, Coates M, Dehal P, et al. Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome. Science (New York, N.Y.). 330: 1549-51. PMID 21148394 DOI: 10.1126/Science.1195203  1
2010 Karol KG, Arumuganathan K, Boore JL, Duffy AM, Everett KD, Hall JD, Hansen SK, Kuehl JV, Mandoli DF, Mishler BD, Olmstead RG, Renzaglia KS, Wolf PG. Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages. Bmc Evolutionary Biology. 10: 321. PMID 20969798 DOI: 10.1186/1471-2148-10-321  1
2010 Nardi F, Carapelli A, Boore JL, Roderick GK, Dallai R, Frati F. Domestication of olive fly through a multi-regional host shift to cultivated olives: comparative dating using complete mitochondrial genomes. Molecular Phylogenetics and Evolution. 57: 678-86. PMID 20723608 DOI: 10.1016/J.Ympev.2010.08.008  1
2010 Stone CL, Buitrago ML, Boore JL, Frederick RD. Analysis of the complete mitochondrial genome sequences of the soybean rust pathogens phakopsora pachyrhizi and p. meibomiae. Mycologia. 102: 887-97. PMID 20648755 DOI: 10.3852/09-198  1
2010 Rawlings TA, MacInnis MJ, Bieler R, Boore JL, Collins TM. Sessile snails, dynamic genomes: gene rearrangements within the mitochondrial genome of a family of caenogastropod molluscs. Bmc Genomics. 11: 440. PMID 20642828 DOI: 10.1186/1471-2164-11-440  1
2010 Lévesque CA, Brouwer H, Cano L, Hamilton JP, Holt C, Huitema E, Raffaele S, Robideau GP, Thines M, Win J, Zerillo MM, Beakes GW, Boore JL, Busam D, Dumas B, et al. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biology. 11: R73. PMID 20626842 DOI: 10.1186/Gb-2010-11-7-R73  1
2010 Rota-Stabelli O, Kayal E, Gleeson D, Daub J, Boore JL, Telford MJ, Pisani D, Blaxter M, Lavrov DV. Ecdysozoan mitogenomics: evidence for a common origin of the legged invertebrates, the Panarthropoda. Genome Biology and Evolution. 2: 425-40. PMID 20624745 DOI: 10.1093/Gbe/Evq030  1
2010 Oliver MJ, Murdock AG, Mishler BD, Kuehl JV, Boore JL, Mandoli DF, Everett KD, Wolf PG, Duffy AM, Karol KG. Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes. Bmc Genomics. 11: 143. PMID 20187961 DOI: 10.1186/1471-2164-11-143  1
2010 Guisinger MM, Chumley TW, Kuehl JV, Boore JL, Jansen RK. Implications of the plastid genome sequence of typha (typhaceae, poales) for understanding genome evolution in poaceae. Journal of Molecular Evolution. 70: 149-66. PMID 20091301 DOI: 10.1007/S00239-009-9317-3  1
2010 Torricelli G, Carapelli A, Convey P, Nardi F, Boore JL, Frati F. High divergence across the whole mitochondrial genome in the "pan-Antarctic" springtail Friesea grisea: evidence for cryptic species? Gene. 449: 30-40. PMID 19782734 DOI: 10.1016/J.Gene.2009.09.006  1
2009 Baker RH, Morgan J, Wang X, Boore JL, Wilkinson GS. Genomic analysis of a sexually-selected character: EST sequencing and microarray analysis of eye-antennal imaginal discs in the stalk-eyed fly Teleopsis dalmanni (Diopsidae). Bmc Genomics. 10: 361. PMID 19656405 DOI: 10.1186/1471-2164-10-361  1
2009 McNeal JR, Kuehl JV, Boore JL, Leebens-Mack J, dePamphilis CW. Parallel loss of plastid introns and their maturase in the genus Cuscuta. Plos One. 4: e5982. PMID 19543388 DOI: 10.1371/Journal.Pone.0005982  1
2009 Masta SE, Longhorn SJ, Boore JL. Arachnid relationships based on mitochondrial genomes: asymmetric nucleotide and amino acid bias affects phylogenetic analyses. Molecular Phylogenetics and Evolution. 50: 117-28. PMID 18992830 DOI: 10.1016/J.Ympev.2008.10.010  1
2008 Anderson SJ, Stone CL, Posada-Buitrago ML, Boore JL, Neelam BA, Stephens RM, Luster DG, Frederick RD, Pedley KF. Development of simple sequence repeat markers for the soybean rust fungus, Phakopsora pachyrhizi. Molecular Ecology Resources. 8: 1310-2. PMID 21586030 DOI: 10.1111/J.1755-0998.2008.02272.X  1
2008 Cai Z, Guisinger M, Kim HG, Ruck E, Blazier JC, McMurtry V, Kuehl JV, Boore J, Jansen RK. Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions. Journal of Molecular Evolution. 67: 696-704. PMID 19018585 DOI: 10.1007/S00239-008-9180-7  1
2008 Guisinger MM, Kuehl JV, Boore JL, Jansen RK. Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions. Proceedings of the National Academy of Sciences of the United States of America. 105: 18424-9. PMID 19011103 DOI: 10.1073/Pnas.0806759105  1
2008 Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, et al. The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology. 26: 541-7. PMID 18464787 DOI: 10.1038/Nbt1360  1
2008 McCoy SR, Kuehl JV, Boore JL, Raubeson LA. The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates. Bmc Evolutionary Biology. 8: 130. PMID 18452621 DOI: 10.1186/1471-2148-8-130  1
2008 Haberle RC, Fourcade HM, Boore JL, Jansen RK. Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes. Journal of Molecular Evolution. 66: 350-61. PMID 18330485 DOI: 10.1007/S00239-008-9086-4  1
2008 Mueller RL, Gregory TR, Gregory SM, Hsieh A, Boore JL. Genome size, cell size, and the evolution of enucleated erythrocytes in attenuate salamanders. Zoology (Jena, Germany). 111: 218-30. PMID 18328681 DOI: 10.1016/J.Zool.2007.07.010  1
2008 Masta SE, Boore JL. Parallel evolution of truncated transfer RNA genes in arachnid mitochondrial genomes. Molecular Biology and Evolution. 25: 949-59. PMID 18296699 DOI: 10.1093/Molbev/Msn051  1
2008 Vallès Y, Halanych KM, Boore JL. Group II introns break new boundaries: presence in a bilaterian's genome. Plos One. 3: e1488. PMID 18213396 DOI: 10.1371/Journal.Pone.0001488  1
2008 Boore JL, Fuerstenberg SI. Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 363: 1445-51. PMID 18192190 DOI: 10.1098/Rstb.2007.2234  1
2008 Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, ... ... Boore JL, et al. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science (New York, N.Y.). 319: 64-9. PMID 18079367 DOI: 10.1126/Science.1150646  1
2008 Wickett NJ, Zhang Y, Hansen SK, Roper JM, Kuehl JV, Plock SA, Wolf PG, DePamphilis CW, Boore JL, Goffinet B. Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort Aneura mirabilis. Molecular Biology and Evolution. 25: 393-401. PMID 18056074 DOI: 10.1093/Molbev/Msm267  1
2008 Boore JL. Detecting evolutionary transfer of genes using PhIGs Journal of Phycology. 44: 19-22. DOI: 10.1111/j.1529-8817.2007.00436.x  1
2007 Timme RE, Kuehl JV, Boore JL, Jansen RK. A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats. American Journal of Botany. 94: 302-12. PMID 21636403 DOI: 10.3732/Ajb.94.3.302  1
2007 McNeal JR, Arumugunathan K, Kuehl JV, Boore JL, Depamphilis CW. Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae). Bmc Biology. 5: 55. PMID 18078516 DOI: 10.1186/1741-7007-5-55  1
2007 Jansen RK, Cai Z, Raubeson LA, Daniell H, Depamphilis CW, Leebens-Mack J, Müller KF, Guisinger-Bellian M, Haberle RC, Hansen AK, Chumley TW, Lee SB, Peery R, McNeal JR, Kuehl JV, ... Boore JL, et al. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proceedings of the National Academy of Sciences of the United States of America. 104: 19369-74. PMID 18048330 DOI: 10.1073/Pnas.0709121104  1
2007 McNeal JR, Kuehl JV, Boore JL, de Pamphilis CW. Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta. Bmc Plant Biology. 7: 57. PMID 17956636 DOI: 10.1186/1471-2229-7-57  1
2007 Fujita MK, Boore JL, Moritz C. Multiple origins and rapid evolution of duplicated mitochondrial genes in parthenogenetic geckos (Heteronotia binoei; Squamata, Gekkonidae). Molecular Biology and Evolution. 24: 2775-86. PMID 17921488 DOI: 10.1093/Molbev/Msm212  1
2007 Hoegg S, Boore JL, Kuehl JV, Meyer A. Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni. Bmc Genomics. 8: 317. PMID 17845724 DOI: 10.1186/1471-2164-8-317  1
2007 Hansen DR, Dastidar SG, Cai Z, Penaflor C, Kuehl JV, Boore JL, Jansen RK. Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae). Molecular Phylogenetics and Evolution. 45: 547-63. PMID 17644003 DOI: 10.1016/J.Ympev.2007.06.004  1
2007 Raubeson LA, Peery R, Chumley TW, Dziubek C, Fourcade HM, Boore JL, Jansen RK. Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. Bmc Genomics. 8: 174. PMID 17573971 DOI: 10.1186/1471-2164-8-174  1
2007 Martin FN, Bensasson D, Tyler BM, Boore JL. Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. sojae. Current Genetics. 51: 285-96. PMID 17310332 DOI: 10.1007/S00294-007-0121-6  1
2007 Roper JM, Hansen SK, Wolf PG, Karol KG, Mandoli DF, Everett KDE, Kuehl J, Boore JL. The complete plastid genome sequence of Angiopteris evecta (G. Forst.) Hoffm. (Marattiaceae) American Fern Journal. 97: 95-106. DOI: 10.1640/0002-8444(2007)97[95:Tcpgso]2.0.Co;2  1
2006 Vallès Y, Boore JL. Lophotrochozoan mitochondrial genomes. Integrative and Comparative Biology. 46: 544-57. PMID 21672765 DOI: 10.1093/Icb/Icj056  1
2006 Krampis K, Tyler BM, Boore JL. Extensive variation in nuclear mitochondrial DNA content between the genomes of Phytophthora sojae and Phytophthora ramorum. Molecular Plant-Microbe Interactions : Mpmi. 19: 1329-36. PMID 17153917 DOI: 10.1094/Mpmi-19-1329  1
2006 Cai Z, Penaflor C, Kuehl JV, Leebens-Mack J, Carlson JE, dePamphilis CW, Boore JL, Jansen RK. Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. Bmc Evolutionary Biology. 6: 77. PMID 17020608 DOI: 10.1186/1471-2148-6-77  1
2006 Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CM, Dorrance AE, Dou D, Dickerman AW, ... ... Boore JL, et al. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science (New York, N.Y.). 313: 1261-6. PMID 16946064 DOI: 10.1126/Science.1128796  1
2006 Podsiadlowski L, Carapelli A, Nardi F, Dallai R, Koch M, Boore JL, Frati F. The mitochondrial genomes of Campodea fragilis and Campodea lubbocki (Hexapoda: Diplura): High genetic divergence in a morphologically uniform taxon. Gene. 381: 49-61. PMID 16919404 DOI: 10.1016/J.Gene.2006.06.009  1
2006 Chumley TW, Palmer JD, Mower JP, Fourcade HM, Calie PJ, Boore JL, Jansen RK. The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Molecular Biology and Evolution. 23: 2175-90. PMID 16916942 DOI: 10.1093/Molbev/Msl089  1
2006 Boore JL. Requirements and standards for organelle genome databases. Omics : a Journal of Integrative Biology. 10: 119-26. PMID 16901216 DOI: 10.1089/Omi.2006.10.119  1
2006 McNeal JR, Leebens-Mack JH, Arumuganathan K, Kuehl JV, Boore JL, DePamphilis CW. Using partial genomic fosmid libraries for sequencing complete organellar genomes. Biotechniques. 41: 69-73. PMID 16869516 DOI: 10.2144/000112202  1
2006 Boore JL. The complete sequence of the mitochondrial genome of Nautilus macromphalus (Mollusca: Cephalopoda). Bmc Genomics. 7: 182. PMID 16854241 DOI: 10.1186/1471-2164-7-182  1
2006 Carapelli A, Vannini L, Nardi F, Boore JL, Beani L, Dallai R, Frati F. The mitochondrial genome of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera). Gene. 376: 248-59. PMID 16766140 DOI: 10.1016/J.Gene.2006.04.005  1
2006 Boore JL. The use of genome-level characters for phylogenetic reconstruction. Trends in Ecology & Evolution. 21: 439-46. PMID 16762445 DOI: 10.1016/J.Tree.2006.05.009  1
2006 Medina M, Collins AG, Takaoka TL, Kuehl JV, Boore JL. Naked corals: skeleton loss in Scleractinia. Proceedings of the National Academy of Sciences of the United States of America. 103: 9096-100. PMID 16754865 DOI: 10.1073/Pnas.0602444103  1
2006 Dehal PS, Boore JL. A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database. Bmc Bioinformatics. 7: 201. PMID 16608522 DOI: 10.1186/1471-2105-7-201  1
2006 Parham JF, Feldman CR, Boore JL. The complete mitochondrial genome of the enigmatic bigheaded turtle (Platysternon): description of unusual genomic features and the reconciliation of phylogenetic hypotheses based on mitochondrial and nuclear DNA. Bmc Evolutionary Biology. 6: 11. PMID 16464263 DOI: 10.1186/1471-2148-6-11  1
2006 Simison WB, Lindberg DR, Boore JL. Rolling circle amplification of metazoan mitochondrial genomes. Molecular Phylogenetics and Evolution. 39: 562-7. PMID 16360323 DOI: 10.1016/J.Ympev.2005.11.006  1
2006 Parham JF, Macey JR, Papenfuss TJ, Feldman CR, Türkozan O, Polymeni R, Boore J. The phylogeny of Mediterranean tortoises and their close relatives based on complete mitochondrial genome sequences from museum specimens. Molecular Phylogenetics and Evolution. 38: 50-64. PMID 16150614 DOI: 10.1016/J.Ympev.2005.07.015  1
2006 Timme RE, Kuehl JV, Boore JL, Jansen RK. A Comparison of the First Two Sequenced Chloroplast Genomes in Asteraceae: Lettuce and Sunflower Lawrence Berkeley National Laboratory. DOI: 10.2172/960402  0.84
2005 Dehal P, Boore JL. Two rounds of whole genome duplication in the ancestral vertebrate. Plos Biology. 3: e314. PMID 16128622 DOI: 10.1371/Journal.Pbio.0030314  1
2005 Mueller RL, Boore JL. Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders. Molecular Biology and Evolution. 22: 2104-12. PMID 15987876 DOI: 10.1093/Molbev/Msi204  1
2005 Leebens-Mack J, Raubeson LA, Cui L, Kuehl JV, Fourcade MH, Chumley TW, Boore JL, Jansen RK, depamphilis CW. Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone. Molecular Biology and Evolution. 22: 1948-63. PMID 15944438 DOI: 10.1093/Molbev/Msi191  1
2005 Macey JR, Fong JJ, Kuehl JV, Shafiei S, Ananjeva NB, Papenfuss TJ, Boore JL. The complete mitochondrial genome of a gecko and the phylogenetic position of the Middle Eastern Teratoscincus keyserlingii. Molecular Phylogenetics and Evolution. 36: 188-93. PMID 15904865 DOI: 10.1016/J.Ympev.2005.03.025  1
2005 Jansen RK, Raubeson LA, Boore JL, dePamphilis CW, Chumley TW, Haberle RC, Wyman SK, Alverson AJ, Peery R, Herman SJ, Fourcade HM, Kuehl JV, McNeal JR, Leebens-Mack J, Cui L. Methods for obtaining and analyzing whole chloroplast genome sequences. Methods in Enzymology. 395: 348-84. PMID 15865976 DOI: 10.1016/S0076-6879(05)95020-9  1
2005 Boore JL, Macey JR, Medina M. Sequencing and comparing whole mitochondrial genomes of animals. Methods in Enzymology. 395: 311-48. PMID 15865975 DOI: 10.1016/S0076-6879(05)95019-2  1
2005 Wolf PG, Karol KG, Mandoli DF, Kuehl J, Arumuganathan K, Ellis MW, Mishler BD, Kelch DG, Olmstead RG, Boore JL. The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae). Gene. 350: 117-28. PMID 15788152 DOI: 10.1016/J.Gene.2005.01.018  1
2005 Swinstrom K, Caldwell R, Fourcade HM, Boore JL. The First Complete Mitochondrial Genome Sequences for Stomatopod Crustaceans: Implications for Phylogeny Lawrence Berkeley National Laboratory. DOI: 10.2172/960399  0.72
2005 Place AR, Feng X, Steven CR, Fourcade HM, Boore JL. Genetic markers in blue crabs (Callinectes sapidus) II. Complete mitochondrial genome sequence and characterization of genetic variation Journal of Experimental Marine Biology and Ecology. 319: 15-27. DOI: 10.1016/J.Jembe.2004.03.024  1
2005 Place AR, Feng X, Steven CR, Fourcade HM, Boore JL. Genetic markers in blue crabs (Callinectes sapidus) II. Complete mitochondrial genome sequence and characterization of genetic variation Journal of Experimental Marine Biology and Ecology. 319: 15-27. DOI: 10.1016/j.jembe.2004.03.024  0.72
2004 Boore JL. Complete mitochondrial genome sequence of Urechis caupo, a representative of the phylum Echiura. Bmc Genomics. 5: 67. PMID 15369601 DOI: 10.1186/1471-2164-5-67  1
2004 Mueller RL, Macey JR, Jaekel M, Wake DB, Boore JL. Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes. Proceedings of the National Academy of Sciences of the United States of America. 101: 13820-5. PMID 15365171 DOI: 10.1073/Pnas.0405785101  1
2004 Ruiz-Trillo I, Riutort M, Fourcade HM, Baguñà J, Boore JL. Mitochondrial genome data support the basal position of Acoelomorpha and the polyphyly of the Platyhelminthes. Molecular Phylogenetics and Evolution. 33: 321-32. PMID 15336667 DOI: 10.1016/J.Ympev.2004.06.002  1
2004 Macey JR, Papenfuss TJ, Kuehl JV, Fourcade HM, Boore JL. Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences. Molecular Phylogenetics and Evolution. 33: 22-31. PMID 15324836 DOI: 10.1016/J.Ympev.2004.05.003  1
2004 Helfenbein KG, Fourcade HM, Vanjani RG, Boore JL. The mitochondrial genome of Paraspadella gotoi is highly reduced and reveals that chaetognaths are a sister group to protostomes. Proceedings of the National Academy of Sciences of the United States of America. 101: 10639-43. PMID 15249679 DOI: 10.1073/Pnas.0400941101  1
2004 Wyman SK, Jansen RK, Boore JL. Automatic annotation of organellar genomes with DOGMA. Bioinformatics (Oxford, England). 20: 3252-5. PMID 15180927 DOI: 10.1093/Bioinformatics/Bth352  1
2004 Bensasson D, Boore JL, Nielsen KM. Genes without frontiers? Heredity. 92: 483-9. PMID 15162114 DOI: 10.1038/Sj.Hdy.6800451  1
2004 Lavrov DV, Brown WM, Boore JL. Phylogenetic position of the Pentastomida and (pan)crustacean relationships. Proceedings. Biological Sciences / the Royal Society. 271: 537-44. PMID 15129965 DOI: 10.1098/Rspb.2003.2631  1
2004 Masta SE, Boore JL. The complete mitochondrial genome sequence of the spider Habronattus oregonensis reveals rearranged and extremely truncated tRNAs. Molecular Biology and Evolution. 21: 893-902. PMID 15014167 DOI: 10.1093/Molbev/Msh096  1
2004 Boore JL, Medina M, Rosenberg LA. Complete sequences of the highly rearranged molluscan mitochondrial genomes of the Scaphopod Graptacme eborea and the bivalve Mytilus edulis. Molecular Biology and Evolution. 21: 1492-503. PMID 15014161 DOI: 10.1093/Molbev/Msh090  1
2004 Helfenbein KG, Boore JL. The mitochondrial genome of Phoronis architecta--comparisons demonstrate that phoronids are lophotrochozoan protostomes. Molecular Biology and Evolution. 21: 153-7. PMID 14595093 DOI: 10.1093/Molbev/Msh011  1
2003 Passamonti M, Boore JL, Scali V. Molecular evolution and recombination in gender-associated mitochondrial DNAs of the Manila clam Tapes philippinarum. Genetics. 164: 603-11. PMID 12807780  1
2003 Santini S, Boore JL, Meyer A. Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters. Genome Research. 13: 1111-22. PMID 12799348 DOI: 10.1101/Gr.700503  1
2003 Nardi F, Spinsanti G, Boore JL, Carapelli A, Dallai R, Frati F. Hexapod origins: monophyletic or paraphyletic? Science (New York, N.Y.). 299: 1887-9. PMID 12649480 DOI: 10.1126/Science.1078607  1
2002 Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, Harafuji N, Hastings KE, Ho I, Hotta K, Huang W, ... ... Boore J, et al. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science (New York, N.Y.). 298: 2157-67. PMID 12481130 DOI: 10.1126/Science.1080049  1
2002 Lavrov DV, Boore JL, Brown WM. Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: duplication and nonrandom loss. Molecular Biology and Evolution. 19: 163-9. PMID 11801744 DOI: 10.1093/Oxfordjournals.Molbev.A004068  1
2002 Boore JL, Staton JL. The mitochondrial genome of the Sipunculid Phascolopsis gouldii supports its association with Annelida rather than Mollusca. Molecular Biology and Evolution. 19: 127-37. PMID 11801741 DOI: 10.1093/Oxfordjournals.Molbev.A004065  1
2001 Helfenbein KG, Brown WM, Boore JL. The complete mitochondrial genome of the articulate brachiopod Terebratalia transversa. Molecular Biology and Evolution. 18: 1734-44. PMID 11504853 DOI: 10.1093/Oxfordjournals.Molbev.A003961  1
2001 Boore JL. Complete mitochondrial genome sequence of the polychaete annelid Platynereis dumerilii [1] Molecular Biology and Evolution. 18: 1413-1416. PMID 11420379 DOI: 10.1093/Oxfordjournals.Molbev.A003925  1
2001 von Nickisch-Rosenegk M, Brown WM, Boore JL. Complete sequence of the mitochondrial genome of the tapeworm Hymenolepis diminuta: gene arrangements indicate that Platyhelminths are Eutrochozoans. Molecular Biology and Evolution. 18: 721-30. PMID 11319256 DOI: 10.1093/Oxfordjournals.Molbev.A003854  1
2001 EviWollscheid-Lengeling, Boore J, Brown W, Wägele H. The phylogeny of nudibranchia (opisthobranchia, gastropoda, mollusca) reconstructed by three molecular markers Organisms Diversity and Evolution. 1: 241-256. DOI: 10.1078/1439-6092-00022  1
2000 Lavrov DV, Brown WM, Boore JL. A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus. Proceedings of the National Academy of Sciences of the United States of America. 97: 13738-42. PMID 11095730 DOI: 10.1073/Pnas.250402997  1
2000 Lavrov DV, Boore JL, Brown WM. The complete mitochondrial DNA sequence of the horseshoe crab Limulus polyphemus. Molecular Biology and Evolution. 17: 813-24. PMID 10779542 DOI: 10.1093/Oxfordjournals.Molbev.A026360  1
2000 Boore JL, Brown WM. Mitochondrial genomes of Galathealinum, Helobdella, and Platynereis: sequence and gene arrangement comparisons indicate that Pogonophora is not a phylum and Annelida and Arthropoda are not sister taxa. Molecular Biology and Evolution. 17: 87-106. PMID 10666709 DOI: 10.1093/Oxfordjournals.Molbev.A026241  1
1999 Boore JL, Fuerstenberg SI. Entamoeba histolytica: a derived, mitochondriate eukaryote? Trends in Microbiology. 7: 426-8. PMID 10542417 DOI: 10.1016/S0966-842X(99)01606-6  1
1999 Boore JL, Daehler LL, Brown WM. Complete sequence, gene arrangement, and genetic code of mitochondrial DNA of the cephalochordate Branchiostoma floridae (Amphioxus) Molecular Biology and Evolution. 16: 410-8. PMID 10331267 DOI: 10.1093/Oxfordjournals.Molbev.A026122  1
1999 Boore JL. Animal mitochondrial genomes Nucleic Acids Research. 27: 1767-1780. PMID 10101183 DOI: 10.1093/Nar/27.8.1767  1
1998 Boore JL, Brown WM. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Current Opinion in Genetics & Development. 8: 668-74. PMID 9914213 DOI: 10.1016/S0959-437X(98)80035-X  1
1998 Boore JL, Lavrov DV, Brown WM. Gene translocation links insects and crustaceans. Nature. 392: 667-8. PMID 9565028 DOI: 10.1038/33577  1
1997 Boore JL. Transmission of mitochondrial DNA - Playing favorites? Bioessays. 19: 751-753. PMID 9297965 DOI: 10.1002/Bies.950190904  1
1995 Boore JL, Brown WM. Complete sequence of the mitochondrial DNA of the annelid worm Lumbricus terrestris. Genetics. 141: 305-19. PMID 8536978  1
1995 Boore JL, Collins TM, Stanton D, Daehler LL, Brown WM. Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Nature. 376: 163-5. PMID 7603565 DOI: 10.1038/376163A0  1
1995 Yost HJ, Phillips CR, Boore JL, Bertman J, Whalon B, Danilchik MV. Relocation of mitochondria to the prospective dorsal marginal zone during Xenopus embryogenesis. Developmental Biology. 170: 83-90. PMID 7601317 DOI: 10.1006/dbio.1995.1197  1
1994 Boore JL, Brown WM. Complete DNA sequence of the mitochondrial genome of the black chiton, Katharina tunicata. Genetics. 138: 423-43. PMID 7828825  1
1992 Hoffmann RJ, Boore JL, Brown WM. A novel mitochondrial genome organization for the blue mussel, Mytilus edulis. Genetics. 131: 397-412. PMID 1386586  1
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