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Papers authored by Jansen RK

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Phylogeny of Barnadesioideae (Asteraceae) inferred from DNA sequence data and morphology.

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Gruenstaeudl M, Urtubey E, Jansen RK, Samuel R, Barfuss MH, and Stuessy TF

Molecular phylogenetics and evolution 51(3):572-87, 2009 Jun - Who cited this? | PubMed ID: 19264147 | Fulltext

Response to.

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Alverson AJ, Jansen RK, and Theriot EC

Molecular phylogenetics and evolution 50(2):409-10, 2009 Feb - Who cited this? | PubMed ID: 19056503 | Fulltext

Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions.

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Cai Z, Guisinger M, Kim HG, Ruck E, Blazier JC, McMurtry V, Kuehl JV, Boore J, and Jansen RK

Journal of molecular evolution 67(6):696-704, 2008 Dec - Who cited this? | PubMed ID: 19018585 | Fulltext

Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions.

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Guisinger MM, Kuehl JV, Boore JL, and Jansen RK

Proceedings of the National Academy of Sciences of the United States of America 105(47):18424-9, 2008 Nov 25 - Who cited this? | PubMed ID: 19011103 | Fulltext

Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae).

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Jansen RK, Wojciechowski MF, Sanniyasi E, Lee SB, and Daniell H

Molecular phylogenetics and evolution 48(3):1204-17, 2008 Sep - Who cited this? | PubMed ID: 18638561 | Fulltext

Phylogenetic utility of 141 low-copy nuclear regions in taxa at different taxonomic levels in two distantly related families of rosids.

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Steele PR, Guisinger-Bellian M, Linder CR, and Jansen RK

Molecular phylogenetics and evolution, 2008 May 21 - Who cited this? | PubMed ID: 18620872 | Fulltext

Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes.

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Haberle RC, Fourcade HM, Boore JL, and Jansen RK

Journal of molecular evolution 66(4):350, 2008 Apr - Who cited this? | PubMed ID: 18330485 | Fulltext

The complete nucleotide sequence of the cassava (Manihot esculenta) chloroplast genome and the evolution of atpF in Malpighiales: RNA editing and multiple losses of a group II intron.

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Daniell H, Wurdack KJ, Kanagaraj A, Lee SB, Saski C, and Jansen RK

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 116(5):723-37, 2008 Mar - Who cited this? | PubMed ID: 18214421 | Fulltext

Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns.

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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, and Boore JL

Proceedings of the National Academy of Sciences of the United States of America 104(49):19369, 2007 Dec 4 - Who cited this? | PubMed ID: 18048330 | Fulltext

Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae).

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Hansen DR, Dastidar SG, Cai Z, PENAFLOR C, Kuehl JV, Boore JL, and Jansen RK

Molecular phylogenetics and evolution 45(2):547, 2007 Nov - Who cited this? | PubMed ID: 17644003 | Fulltext

Bridging the Rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms.

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Alverson AJ, Jansen RK, and Theriot EC

Molecular phylogenetics and evolution 45(1):193-210, 2007 Oct - Who cited this? | PubMed ID: 17553708 | Fulltext

Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes.

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Saski C, Lee SB, Fjellheim S, Guda C, Jansen RK, Luo H, Tomkins J, Rognli OA, Daniell H, and Clarke JL

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 115(4):571-90, 2007 Aug - Who cited this? | PubMed ID: 17534593 | Fulltext

Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions.

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Lee HL, Jansen RK, Chumley TW, and Kim KJ

Molecular biology and evolution 24(5):1161, 2007 May - Who cited this? | PubMed ID: 17329229 | Fulltext

The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms.

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Samson N, Bausher MG, Lee SB, Jansen RK, and Daniell H

Plant biotechnology journal 5(2):339-53, 2007 Mar - Who cited this? | PubMed ID: 17309688 | Fulltext

Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus.

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Raubeson LA, Peery R, Chumley TW, Dziubek C, Fourcade HM, Boore JL, and Jansen RK

BMC genomics 8:174, 2007 - Who cited this? | PubMed ID: 17573971 | Fulltext

The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants.

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Chumley TW, Palmer JD, Mower JP, Fourcade HM, Calie PJ, Boore JL, and Jansen RK

Molecular biology and evolution 23(11):2175, 2006 Nov - Who cited this? | PubMed ID: 16916942 | Fulltext

Distance-based genome rearrangement phylogeny.

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Wang LS, Warnow T, Moret BM, Jansen RK, and Raubeson LA

Journal of molecular evolution 63(4):473-83, 2006 Oct - Who cited this? | PubMed ID: 17021931 | Fulltext

Molecular evidence for the age, origin, and evolutionary history of the American desert plant genus Tiquilia (Boraginaceae).

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Moore MJ and Jansen RK

Molecular phylogenetics and evolution 39(3):668-87, 2006 Jun - Who cited this? | PubMed ID: 16495087 | Fulltext

Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes.

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Daniell H, Lee SB, Grevich J, Saski C, Quesada-Vargas T, Guda C, Tomkins J, and Jansen RK

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 112(8):1503-18, 2006 May - Who cited this? | PubMed ID: 16575560 | Fulltext

ChloroplastDB: the Chloroplast Genome Database.

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Cui L, Veeraraghavan N, Richter A, Wall K, Jansen RK, Leebens-Mack J, Makalowska I, and Depamphilis CW

Nucleic acids research 34(Database issue), 2006 Jan 1 - Who cited this? | PubMed ID: 16381961 | Fulltext

The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms.

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Lee SB, Kaittanis C, Jansen RK, Hostetler JB, Tallon LJ, Town CD, and Daniell H

BMC genomics 7:61, 2006 - Who cited this? | PubMed ID: 16553962 | Fulltext

Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids.

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Jansen RK, Kaittanis C, Saski C, Lee SB, Tomkins J, Alverson AJ, and Daniell H

BMC evolutionary biology 6:32, 2006 - Who cited this? | PubMed ID: 16603088 | Fulltext

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).

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Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, dePamphilis C, Desalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, Koonin EV,

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Omics : a journal of integrative biology 10(2):231, 2006 Summer - Who cited this? | PubMed ID: 16901231 | Fulltext

Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms.

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Ruhlman T, Lee SB, Jansen RK, Hostetler JB, Tallon LJ, Town CD, and Daniell H

BMC genomics 7:222, 2006 - Who cited this? | PubMed ID: 16945140 | Fulltext

The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms.

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Bausher MG, Singh ND, Lee SB, Jansen RK, and Daniell H

BMC plant biology 6:21, 2006 - Who cited this? | PubMed ID: 17010212 | Fulltext

Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids.

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Cai Z, PENAFLOR C, Kuehl JV, Leebens-Mack J, Carlson JE, Depamphilis CW, Boore JL, and Jansen RK

BMC evolutionary biology 6:77, 2006 - Who cited this? | PubMed ID: 17020608 | Fulltext

Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone.

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Leebens-Mack J, Raubeson LA, Cui L, Kuehl JV, Fourcade MH, Chumley TW, Boore JL, Jansen RK, and Depamphilis CW

Molecular biology and evolution 22(10):1948, 2005 Oct - Who cited this? | PubMed ID: 15944438 | Fulltext

Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae).

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Kim KJ, Choi KS, and Jansen RK

Molecular biology and evolution 22(9):1783-92, 2005 Sep - Who cited this? | PubMed ID: 15917497 | Fulltext

Complete chloroplast genome sequence of Gycine max and comparative analyses with other legume genomes.

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Saski C, Lee SB, Daniell H, Wood TC, Tomkins J, Kim HG, and Jansen RK

Plant molecular biology 59(2):309-22, 2005 Sep - Who cited this? | PubMed ID: 16247559 | Fulltext

Methods for obtaining and analyzing whole chloroplast genome sequences.

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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, and Cui L

Methods in enzymology 395:348-84, 2005 - Who cited this? | PubMed ID: 15865976 | Fulltext

Automatic annotation of organellar genomes with DOGMA.

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Wyman SK, Jansen RK, and Boore JL

Bioinformatics (Oxford, England) 20(17):3252, 2004 Nov 22 - Who cited this? | PubMed ID: 15180927 | Fulltext

Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes.

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Cosner ME, Raubeson LA, and Jansen RK

BMC evolutionary biology 4:27, 2004 Aug 23 - Who cited this? | PubMed ID: 15324459 | Fulltext

ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae.

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Goertzen LR, Cannone JJ, Gutell RR, and Jansen RK

Molecular phylogenetics and evolution 29(2):216-34, 2003 Nov - Who cited this? | PubMed ID: 13678678 | Fulltext

The influence of the Miocene Mediterranean desiccation on the geographical expansion and genetic variation of Androcymbium gramineum (Cav.) McBride (Colchicaceae).

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Caujapé-Castells J and Jansen RK

Molecular ecology 12(6):1515-25, 2003 Jun - Who cited this? | PubMed ID: 12755880 | Fulltext

Origin of Macaronesian Sideritis L. (Lamioideae: Lamiaceae) inferred from nuclear and chloroplast sequence datasets.

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Barber JC, Francisco-Ortega J, Santos-Guerra A, Turner KG, and Jansen RK

Molecular phylogenetics and evolution 23(3):293-306, 2002 Jun - Who cited this? | PubMed ID: 12099789 | Fulltext

Fast phylogenetic methods for the analysis of genome rearrangement data: an empirical study.

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Wang LS, Jansen RK, Moret BM, Raubeson LA, and Warnow T

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:524-35, 2002 - Who cited this? | PubMed ID: 11928504 | Fulltext

The phylogeny of the Asteridae sensu lato based on chloroplast ndhF gene sequences.

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Olmstead RG, Kim KJ, Jansen RK, and Wagstaff SJ

Molecular phylogenetics and evolution 16(1):96, 2000 Jul - Who cited this? | PubMed ID: 10877943 | Fulltext

The complete external transcribed spacer of 18S-26S rDNA: amplification and phylogenetic utility at low taxonomic levels in asteraceae and closely allied families.

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Linder CR, Goertzen LR, Heuvel BV, Francisco-Ortega J, and Jansen RK

Molecular phylogenetics and evolution 14(2):285-303, 2000 Feb - Who cited this? | PubMed ID: 10679161 | Fulltext

A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data.

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Cosner ME, Jansen RK, Moret BM, Raubeson LA, Wang LS, Warnow T, and Wyman S

Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 8:104-15, 2000 - Who cited this? | PubMed ID: 10977071 | Fulltext

Molecular evidence for multiple origins of woodiness and a new world biogeographic connection of the Macaronesian island endemic Pericallis (Asteraceae: senecioneae).

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Panero JL, Francisco-Ortega J, Jansen RK, and Santos-Guerra A

Proceedings of the National Academy of Sciences of the United States of America 96(24):13886-91, 1999 Nov 23 - Who cited this? | PubMed ID: 10570168 | Fulltext

More characters or more taxa for a robust phylogeny--case study from the coffee family (Rubiaceae).

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Bremer B, Jansen RK, Oxelman B, Backlund M, Lantz H, and Kim KJ

Systematic biology 48(3):413-35, 1999 Sep - Who cited this? | PubMed ID: 12066290 | Fulltext

Internal transcribed spacer sequence phylogeny of Crambe L. (Brassicaceae): molecular data reveal two Old World disjunctions.

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Francisco-Ortega J, Fuertes-Aguilar J, Gómez-Campo C, Santos-Guerra A, and Jansen RK

Molecular phylogenetics and evolution 11(3):361-80, 1999 Apr - Who cited this? | PubMed ID: 10196078 | Fulltext

Molecular evidence for an African origin of the Hawaiian endemic Hesperomannia (Asteraceae).

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Kim HG, Keeley SC, Vroom PS, and Jansen RK

Proceedings of the National Academy of Sciences of the United States of America 95(26):15440-5, 1998 Dec 22 - Who cited this? | PubMed ID: 9860987 | Fulltext

The highly rearranged chloroplast genome of Trachelium caeruleum (Campanulaceae): multiple inversions, inverted repeat expansion and contraction, transposition, insertions/deletions, and several repeat families.

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Cosner ME, Jansen RK, Palmer JD, and Downie SR

Current genetics 31(5):419-29, 1997 May - Who cited this? | PubMed ID: 9162114 | Fulltext

Chloroplast DNA evidence of colonization, adaptive radiation, and hybridization in the evolution of the Macaronesian flora.

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Francisco-Ortega J, Jansen RK, and Santos-Guerra A

Proceedings of the National Academy of Sciences of the United States of America 93(9):4085-90, 1996 Apr 30 - Who cited this? | PubMed ID: 11607675 | Fulltext

ndhF sequence evolution and the major clades in the sunflower family.

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Kim KJ and Jansen RK

Proceedings of the National Academy of Sciences of the United States of America 92(22):10379-83, 1995 Oct 24 - Who cited this? | PubMed ID: 7479788 | Fulltext

Phylogenetic analysis of restriction site data.

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Holsinger KE and Jansen RK

Methods in enzymology 224:439-55, 1993 - Who cited this? | PubMed ID: 8264404 | Fulltext

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