Joseph C. Pires, Ph.D. - Publications

2000 University of Wisconsin, Madison, Madison, WI 
Phylogenetics, evolution, systematics, plants

88 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
2016 McKain MR, Tang H, McNeal JR, Ayyampalayam S, Davis JI, dePamphilis CW, Givnish TJ, Pires JC, Stevenson DW, Leebens-Mack JH. A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales. Genome Biology and Evolution. PMID 26988252 DOI: 10.1093/gbe/evw060  0.56
2015 Washburn JD, Schnable JC, Davidse G, Pires JC. Phylogeny and photosynthesis of the grass tribe Paniceae. American Journal of Botany. 102: 1493-505. PMID 26373976 DOI: 10.3732/ajb.1500222  0.92
2015 Mohammadin S, Edger PP, Pires JC, Schranz ME. Positionally-conserved but sequence-diverged: identification of long non-coding RNAs in the Brassicaceae and Cleomaceae. Bmc Plant Biology. 15: 217. PMID 26362138 DOI: 10.1186/s12870-015-0603-5  0.92
2015 Barrett CF, Baker WJ, Comer JR, Conran JG, Lahmeyer SC, Leebens-Mack JH, Li J, Lim GS, Mayfield-Jones DR, Perez L, Medina J, Pires JC, Santos C, Wm Stevenson D, Zomlefer WB, et al. Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots. The New Phytologist. PMID 26350789 DOI: 10.1111/nph.13617  0.92
2015 Kellar PR, Ahrendsen DL, Aust SK, Jones AR, Pires JC. Biodiversity comparison among phylogenetic diversity metrics and between three North American prairies. Applications in Plant Sciences. 3. PMID 26191461 DOI: 10.3732/apps.1400108  0.92
2015 Cotton JL, Wysocki WP, Clark LG, Kelchner SA, Pires JC, Edger PP, Mayfield-Jones D, Duvall MR. Resolving deep relationships of PACMAD grasses: a phylogenomic approach. Bmc Plant Biology. 15: 178. PMID 26160195 DOI: 10.1186/s12870-015-0563-9  0.92
2015 Edger PP, Heidel-Fischer HM, Bekaert M, Rota J, Glöckner G, Platts AE, Heckel DG, Der JP, Wafula EK, Tang M, Hofberger JA, Smithson A, Hall JC, Blanchette M, Bureau TE, ... ... Pires JC, et al. The butterfly plant arms-race escalated by gene and genome duplications. Proceedings of the National Academy of Sciences of the United States of America. PMID 26100883 DOI: 10.1073/pnas.1503926112  0.92
2015 Norup MF, Petersen G, Burrows S, Bouchenak-Khelladi Y, Leebens-Mack J, Pires JC, Linder HP, Seberg O. Evolution of Asparagus L. (Asparagaceae): Out-of-South-Africa and multiple origins of sexual dimorphism. Molecular Phylogenetics and Evolution. 92: 25-44. PMID 26079131 DOI: 10.1016/j.ympev.2015.06.002  0.92
2015 Saarela JM, Wysocki WP, Barrett CF, Soreng RJ, Davis JI, Clark LG, Kelchner SA, Pires JC, Edger PP, Mayfield DR, Duvall MR. Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes. Aob Plants. 7. PMID 25940204 DOI: 10.1093/aobpla/plv046  0.92
2015 Augustin MM, Ruzicka DR, Shukla AK, Augustin JM, Starks CM, O'Neil-Johnson M, McKain MR, Evans BS, Barrett MD, Smithson A, Wong GK, Deyholos MK, Edger PP, Pires JC, Leebens-Mack JH, et al. Elucidating steroid alkaloid biosynthesis in Veratrum californicum: production of verazine in Sf9 cells. The Plant Journal : For Cell and Molecular Biology. 82: 991-1003. PMID 25939370 DOI: 10.1111/tpj.12871  0.92
2015 Mason AS, Pires JC. Unreduced gametes: meiotic mishap or evolutionary mechanism? Trends in Genetics : Tig. 31: 5-10. PMID 25445549 DOI: 10.1016/j.tig.2014.09.011  0.92
2015 Hertweck KL, Kinney MS, Stuart SA, Maurin O, Mathews S, Chase MW, Gandolfo MA, Pires JC. Phylogenetics, divergence times and diversification from three genomic partitions in monocots Botanical Journal of the Linnean Society. 178: 375-393. DOI: 10.1111/boj.12260  0.92
2014 Yoo MJ, Liu X, Pires JC, Soltis PS, Soltis DE. Nonadditive gene expression in polyploids. Annual Review of Genetics. 48: 485-517. PMID 25421600 DOI: 10.1146/annurev-genet-120213-092159  0.92
2014 Floyd SK, Ryan JG, Conway SJ, Brenner E, Burris KP, Burris JN, Chen T, Edger PP, Graham SW, Leebens-Mack JH, Pires JC, Rothfels CJ, Sigel EM, Stevenson DW, Neal Stewart C, et al. Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor. Molecular Phylogenetics and Evolution. 81: 159-73. PMID 25263420 DOI: 10.1016/j.ympev.2014.06.017  0.92
2014 Barrett CF, Freudenstein JV, Li J, Mayfield-Jones DR, Perez L, Pires JC, Santos C. Investigating the path of plastid genome degradation in an early-transitional clade of heterotrophic orchids, and implications for heterotrophic angiosperms. Molecular Biology and Evolution. 31: 3095-112. PMID 25172958 DOI: 10.1093/molbev/msu252  0.92
2014 Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Da Silva C, Just J, Falentin C, Koh CS, ... ... Pires JC, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science (New York, N.Y.). 345: 950-3. PMID 25146293 DOI: 10.1126/science.1253435  0.92
2014 Delaux PM, Varala K, Edger PP, Coruzzi GM, Pires JC, Ané JM. Comparative phylogenomics uncovers the impact of symbiotic associations on host genome evolution. Plos Genetics. 10: e1004487. PMID 25032823 DOI: 10.1371/journal.pgen.1004487  0.92
2014 Edger PP, Tang M, Bird KA, Mayfield DR, Conant G, Mummenhoff K, Koch MA, Pires JC. Secondary structure analyses of the nuclear rRNA internal transcribed spacers and assessment of its phylogenetic utility across the Brassicaceae (mustards). Plos One. 9: e101341. PMID 24984034 DOI: 10.1371/journal.pone.0101341  0.92
2014 Conant GC, Birchler JA, Pires JC. Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time. Current Opinion in Plant Biology. 19: 91-8. PMID 24907529 DOI: 10.1016/j.pbi.2014.05.008  0.92
2014 Grewe F, Edger PP, Keren I, Sultan L, Pires JC, Ostersetzer-Biran O, Mower JP. Comparative analysis of 11 Brassicales mitochondrial genomes and the mitochondrial transcriptome of Brassica oleracea. Mitochondrion. 19: 135-43. PMID 24907441 DOI: 10.1016/j.mito.2014.05.008  0.92
2014 Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin IA, Zhao M, Ma J, Yu J, Huang S, Wang X, Wang J, Lu K, Fang Z, Bancroft I, ... ... Pires JC, et al. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nature Communications. 5: 3930. PMID 24852848 DOI: 10.1038/ncomms4930  0.92
2014 Larson G, Piperno DR, Allaby RG, Purugganan MD, Andersson L, Arroyo-Kalin M, Barton L, Climer Vigueira C, Denham T, Dobney K, Doust AN, Gepts P, Gilbert MT, Gremillion KJ, Lucas L, ... ... Pires JC, et al. Current perspectives and the future of domestication studies. Proceedings of the National Academy of Sciences of the United States of America. 111: 6139-46. PMID 24757054 DOI: 10.1073/pnas.1323964111  0.92
2014 Gerbault P, Allaby RG, Boivin N, Rudzinski A, Grimaldi IM, Pires JC, Climer Vigueira C, Dobney K, Gremillion KJ, Barton L, Arroyo-Kalin M, Purugganan MD, Rubio de Casas R, Bollongino R, Burger J, et al. Storytelling and story testing in domestication. Proceedings of the National Academy of Sciences of the United States of America. 111: 6159-64. PMID 24753572 DOI: 10.1073/pnas.1400425111  0.92
2014 Woodhouse MR, Cheng F, Pires JC, Lisch D, Freeling M, Wang X. Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids. Proceedings of the National Academy of Sciences of the United States of America. 111: 5283-8. PMID 24706847 DOI: 10.1073/pnas.1402475111  0.92
2014 Henriquez CL, Arias T, Pires JC, Croat TB, Schaal BA. Phylogenomics of the plant family Araceae. Molecular Phylogenetics and Evolution. 75: 91-102. PMID 24594061 DOI: 10.1016/j.ympev.2014.02.017  0.92
2014 Arias T, Beilstein MA, Tang M, McKain MR, Pires JC. Diversification times among Brassica (Brassicaceae) crops suggest hybrid formation after 20 million years of divergence. American Journal of Botany. 101: 86-91. PMID 24388963 DOI: 10.3732/ajb.1300312  0.92
2014 Hertweck KL, Pires JC. Systematics and evolution of inflorescence structure in the tradescantia alliance (commelinaceae) Systematic Botany. 39: 105-116. DOI: 10.1600/036364414X677991  0.92
2014 Wysocki WP, Clark LG, Kelchner SA, Burke SV, Pires JC, Edger PP, Mayfield DR, Triplett JK, Columbus JT, Ingram AL, Duvall MR. A multi-step comparison of short-read full plastome sequence assembly methods in grasses Taxon. 63: 899-910. DOI: 10.12705/634.5  0.92
2013 Haudry A, Platts AE, Vello E, Hoen DR, Leclercq M, Williamson RJ, Forczek E, Joly-Lopez Z, Steffen JG, Hazzouri KM, Dewar K, Stinchcombe JR, Schoen DJ, Wang X, Schmutz J, ... ... Pires JC, et al. An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nature Genetics. 45: 891-8. PMID 23817568 DOI: 10.1038/ng.2684  0.92
2013 Subramaniam S, Wang X, Freeling M, Pires JC. The fate of Arabidopsis thaliana homeologous CNSs and their motifs in the Paleohexaploid Brassica rapa. Genome Biology and Evolution. 5: 646-60. PMID 23493633 DOI: 10.1093/gbe/evt035  0.92
2013 Mayfield-Jones D, Washburn JD, Arias T, Edger PP, Pires JC, Conant GC. Watching the grin fade: tracing the effects of polyploidy on different evolutionary time scales. Seminars in Cell & Developmental Biology. 24: 320-31. PMID 23466286 DOI: 10.1016/j.semcdb.2013.02.002  0.92
2013 Witzig SB, Freyermuth SK, Siegel MA, Izci K, Pires JC. Is DNA Alive? A Study of Conceptual Change Through Targeted Instruction Research in Science Education. 43: 1361-1375. DOI: 10.1007/s11165-012-9311-4  0.92
2012 Johnson MT, Carpenter EJ, Tian Z, Bruskiewich R, Burris JN, Carrigan CT, Chase MW, Clarke ND, Covshoff S, Depamphilis CW, Edger PP, Goh F, Graham S, Greiner S, Hibberd JM, ... ... Pires JC, et al. Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. Plos One. 7: e50226. PMID 23185583 DOI: 10.1371/journal.pone.0050226  0.92
2012 Bekaert M, Edger PP, Hudson CM, Pires JC, Conant GC. Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinolate synthesis. The New Phytologist. 196: 596-605. PMID 22943527 DOI: 10.1111/j.1469-8137.2012.04302.x  0.92
2012 Schnable JC, Wang X, Pires JC, Freeling M. Escape from preferential retention following repeated whole genome duplications in plants. Frontiers in Plant Science. 3: 94. PMID 22639677 DOI: 10.3389/fpls.2012.00094  0.92
2012 Heneen WK, Geleta M, Brismar K, Xiong Z, Pires JC, Hasterok R, Stoute AI, Scott RJ, King GJ, Kurup S. Seed colour loci, homoeology and linkage groups of the C genome chromosomes revealed in Brassica rapa-B. oleracea monosomic alien addition lines. Annals of Botany. 109: 1227-42. PMID 22628364 DOI: 10.1093/aob/mcs052  0.92
2012 Seberg O, Petersen G, Davis JI, Pires JC, Stevenson DW, Chase MW, Fay MF, Devey DS, Jørgensen T, Sytsma KJ, Pillon Y. Phylogeny of the Asparagales based on three plastid and two mitochondrial genes. American Journal of Botany. 99: 875-89. PMID 22539521 DOI: 10.3732/ajb.1100468  0.92
2012 Reneker J, Lyons E, Conant GC, Pires JC, Freeling M, Shyu CR, Korkin D. Long identical multispecies elements in plant and animal genomes. Proceedings of the National Academy of Sciences of the United States of America. 109: E1183-91. PMID 22496592 DOI: 10.1073/pnas.1121356109  0.92
2012 Van de Peer Y, Pires JC. Getting up to speed. Current Opinion in Plant Biology. 15: 111-4. PMID 22483403 DOI: 10.1016/j.pbi.2012.03.012  0.92
2012 Matsushita SC, Tyagi AP, Thornton GM, Pires JC, Madlung A. Allopolyploidization lays the foundation for evolution of distinct populations: evidence from analysis of synthetic Arabidopsis allohexaploids. Genetics. 191: 535-47. PMID 22426881 DOI: 10.1534/genetics.112.139295  0.92
2012 Tang H, Woodhouse MR, Cheng F, Schnable JC, Pedersen BS, Conant G, Wang X, Freeling M, Pires JC. Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Genetics. 190: 1563-74. PMID 22308264 DOI: 10.1534/genetics.111.137349  0.92
2012 McKain MR, Wickett N, Zhang Y, Ayyampalayam S, McCombie WR, Chase MW, Pires JC, dePamphilis CW, Leebens-Mack J. Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae). American Journal of Botany. 99: 397-406. PMID 22301890 DOI: 10.3732/ajb.1100537  0.4
2012 Jiao Y, Leebens-Mack J, Ayyampalayam S, Bowers JE, McKain MR, McNeal J, Rolf M, Ruzicka DR, Wafula E, Wickett NJ, Wu X, Zhang Y, Wang J, Zhang Y, Carpenter EJ, ... ... Pires JC, et al. A genome triplication associated with early diversification of the core eudicots. Genome Biology. 13: R3. PMID 22280555 DOI: 10.1186/gb-2012-13-1-r3  0.92
2011 Hudson CM, Puckett EE, Bekaert M, Pires JC, Conant GC. Selection for higher gene copy number after different types of plant gene duplications. Genome Biology and Evolution. 3: 1369-80. PMID 22056313 DOI: 10.1093/gbe/evr115  0.92
2011 Bachtrog D, Kirkpatrick M, Mank JE, McDaniel SF, Pires JC, Rice W, Valenzuela N. Are all sex chromosomes created equal? Trends in Genetics : Tig. 27: 350-7. PMID 21962970 DOI: 10.1016/j.tig.2011.05.005  0.92
2011 Wang X, Torres MJ, Pierce G, Lemke C, Nelson LK, Yuksel B, Bowers JE, Marler B, Xiao Y, Lin L, Epps E, Sarazen H, Rogers C, Karunakaran S, Ingles J, ... ... Pires JC, et al. A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations. Bmc Genomics. 12: 470. PMID 21955929 DOI: 10.1186/1471-2164-12-470  0.92
2011 Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, ... ... Pires JC, et al. The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics. 43: 1035-9. PMID 21873998 DOI: 10.1038/ng.919  0.92
2011 Zou J, Fu D, Gong H, Qian W, Xia W, Pires JC, Li R, Long Y, Mason AS, Yang TJ, Lim YP, Park BS, Meng J. De novo genetic variation associated with retrotransposon activation, genomic rearrangements and trait variation in a recombinant inbred line population of Brassica napus derived from interspecific hybridization with Brassica rapa. The Plant Journal : For Cell and Molecular Biology. 68: 212-24. PMID 21689170 DOI: 10.1111/j.1365-313X.2011.04679.x  0.92
2011 Zuccolo A, Bowers JE, Estill JC, Xiong Z, Luo M, Sebastian A, Goicoechea JL, Collura K, Yu Y, Jiao Y, Duarte J, Tang H, Ayyampalayam S, Rounsley S, Kudrna D, ... ... Pires JC, et al. A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure. Genome Biology. 12: R48. PMID 21619600 DOI: 10.1186/gb-2011-12-5-r48  0.92
2011 Raven PH, Chase JM, Pires JC. Introduction to special issue on biodiversity. American Journal of Botany. 98: 333-5. PMID 21613129 DOI: 10.3732/ajb.1100055  0.44
2011 Xiong Z, Gaeta RT, Pires JC. Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus. Proceedings of the National Academy of Sciences of the United States of America. 108: 7908-13. PMID 21512129 DOI: 10.1073/pnas.1014138108  0.92
2011 Mayfield D, Chen ZJ, Pires JC. Epigenetic regulation of flowering time in polyploids. Current Opinion in Plant Biology. 14: 174-8. PMID 21470900 DOI: 10.1016/j.pbi.2011.03.008  0.92
2011 Navabi ZK, Stead KE, Pires JC, Xiong Z, Sharpe AG, Parkin IA, Rahman MH, Good AG. Analysis of B-genome chromosome introgression in interspecific hybrids of Brassica napus × B. carinata. Genetics. 187: 659-73. PMID 21196520 DOI: 10.1534/genetics.110.124925  0.92
2010 Navabi ZK, Parkin IA, Pires JC, Xiong Z, Thiagarajah MR, Good AG, Rahman MH. Introgression of B-genome chromosomes in a doubled haploid population of Brassica napus x B. carinata. Genome / National Research Council Canada = GéNome / Conseil National De Recherches Canada. 53: 619-29. PMID 20725149 DOI: 10.1139/g10-039  0.92
2010 Xiong Z, Kim JS, Pires JC. Integration of genetic, physical, and cytogenetic maps for Brassica rapa chromosome A7. Cytogenetic and Genome Research. 129: 190-8. PMID 20628251 DOI: 10.1159/000314640  0.92
2010 Birchler JA, Pires JC. Advances in plant cytogenetics. Preface. Cytogenetic and Genome Research. 129: 5. PMID 20628247 DOI: 10.1159/000308300  0.92
2010 Duarte JM, Wall PK, Edger PP, Landherr LL, Ma H, Pires JC, Leebens-Mack J, dePamphilis CW. Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. Bmc Evolutionary Biology. 10: 61. PMID 20181251 DOI: 10.1186/1471-2148-10-61  0.92
2010 Givnish TJ, Ames M, McNeal JR, McKain MR, Steele PR, Depamphilis CW, Graham SW, Pires JC, Stevenson DW, Zomlefer WB, Briggs BG, Duvall MR, Moore MJ, Heaney JM, Soltis DE, et al. Assembling the tree of the monocotyledons: Plastome sequence phylogeny and evolution of Poales Annals of the Missouri Botanical Garden. 97: 584-616. DOI: 10.3417/2010023  0.92
2009 Wright KM, Pires JC, Madlung A. Mitotic instability in resynthesized and natural polyploids of the genus Arabidopsis (Brassicaceae). American Journal of Botany. 96: 1656-64. PMID 21622352 DOI: 10.3732/ajb.0800270  0.92
2009 Trick M, Kwon SJ, Choi SR, Fraser F, Soumpourou E, Drou N, Wang Z, Lee SY, Yang TJ, Mun JH, Paterson AH, Town CD, Pires JC, Pyo Lim Y, Park BS, et al. Complexity of genome evolution by segmental rearrangement in Brassica rapa revealed by sequence-level analysis. Bmc Genomics. 10: 539. PMID 19922648 DOI: 10.1186/1471-2164-10-539  0.92
2009 Decker JE, Pires JC, Conant GC, McKay SD, Heaton MP, Chen K, Cooper A, Vilkki J, Seabury CM, Caetano AR, Johnson GS, Brenneman RA, Hanotte O, Eggert LS, Wiener P, et al. Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Proceedings of the National Academy of Sciences of the United States of America. 106: 18644-9. PMID 19846765 DOI: 10.1073/pnas.0904691106  0.92
2009 Edger PP, Pires JC. Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes. Chromosome Research : An International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology. 17: 699-717. PMID 19802709 DOI: 10.1007/s10577-009-9055-9  0.92
2009 Gaeta RT, Yoo SY, Pires JC, Doerge RW, Chen ZJ, Osborn TC. Analysis of gene expression in resynthesized Brassica napus Allopolyploids using arabidopsis 70mer oligo microarrays. Plos One. 4: e4760. PMID 19274085 DOI: 10.1371/journal.pone.0004760  0.92
2008 Lim KY, Soltis DE, Soltis PS, Tate J, Matyasek R, Srubarova H, Kovarik A, Pires JC, Xiong Z, Leitch AR. Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae). Plos One. 3: e3353. PMID 18843372 DOI: 10.1371/journal.pone.0003353  0.92
2008 Pires JC, Hertweck KL. A renaissance of cytogenetics: Studies in polyploidy and chromosomal evolution Annals of the Missouri Botanical Garden. 95: 275-281. DOI: 10.3417/2007176  0.92
2007 Gaeta RT, Pires JC, Iniguez-Luy F, Leon E, Osborn TC. Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. The Plant Cell. 19: 3403-17. PMID 18024568 DOI: 10.1105/tpc.107.054346  0.92
2007 Telgmann-Rauber A, Jamsari A, Kinney MS, Pires JC, Jung C. Genetic and physical maps around the sex-determining M-locus of the dioecious plant asparagus. Molecular Genetics and Genomics : Mgg. 278: 221-34. PMID 17609979 DOI: 10.1007/s00438-007-0235-z  0.92
2006 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, ... ... Pires JC, et al. Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). Omics : a Journal of Integrative Biology. 10: 231-7. PMID 16901231 DOI: 10.1089/omi.2006.10.231  0.92
2006 Lukens LN, Pires JC, Leon E, Vogelzang R, Oslach L, Osborn T. Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids. Plant Physiology. 140: 336-48. PMID 16377753 DOI: 10.1104/pp.105.066308  0.92
2006 Paterson AH, Bowers JE, Estill JC, Osborn TC, Pires JC, Amasino R, Quiros CF, Farnham M. Evolutionary history of the angiosperms and its relevance to Brassica Acta Horticulturae. 706: 49-53.  0.92
2005 Givnish TJ, Pires JC, Graham SW, McPherson MA, Prince LM, Patterson TB, Rai HS, Roalson EH, Evans TM, Hahn WJ, Millam KC, Meerow AW, Molvray M, Kores PJ, O'Brien HE, et al. Repeated evolution of net venation and fleshy fruits among monocots in shaded habitats confirms a priori predictions: evidence from an ndhF phylogeny. Proceedings. Biological Sciences / the Royal Society. 272: 1481-90. PMID 16011923 DOI: 10.1098/rspb.2005.3067  0.92
2005 Walling JG, Pires JC, Jackson SA. Preparation of samples for comparative studies of plant chromosomes using in situ hybridization methods. Methods in Enzymology. 395: 443-60. PMID 15865979 DOI: 10.1016/S0076-6879(05)95024-6  0.92
2005 Kovarik A, Pires JC, Leitch AR, Lim KY, Sherwood AM, Matyasek R, Rocca J, Soltis DE, Soltis PS. Rapid concerted evolution of nuclear ribosomal DNA in two Tragopogon allopolyploids of recent and recurrent origin. Genetics. 169: 931-44. PMID 15654116 DOI: 10.1534/genetics.104.032839  0.92
2004 Pires JC, Lim KY, Kovarík A, Matyásek R, Boyd A, Leitch AR, Leitch IJ, Bennett MD, Soltis PS, Soltis DE. Molecular cytogenetic analysis of recently evolved Tragopogon (Asteraceae) allopolyploids reveal a karyotype that is additive of the diploid progenitors. American Journal of Botany. 91: 1022-35. PMID 21653458 DOI: 10.3732/ajb.91.7.1022  0.92
2004 Jeffrey Chen Z, Wang J, Tian L, Lee HS, Wang JJ, Chen M, Lee JJ, Josefsson C, Madlung A, Watson B, Lippman Z, Vaughn M, Chris Pires J, Colot V, Doerge RW, et al. The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Biological Journal of the Linnean Society. Linnean Society of London. 82: 689-700. PMID 18079994 DOI: 10.1111/j.1095-8312.2004.00351.x  0.92
2004 Lee HS, Wang J, Tian L, Jiang H, Black MA, Madlung A, Watson B, Lukens L, Pires JC, Wang JJ, Comai L, Osborn TC, Doerge RW, Chen ZJ. Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species. Plant Biotechnology Journal. 2: 45-57. PMID 17166142 DOI: 10.1046/j.1467-7652.2003.00048.x  0.92
2004 Lukens LN, Quijada PA, Udall J, Pires JC, Schranz ME, Osborn TC. Genome redundancy and plasticity within ancient and recent Brassica crop species Biological Journal of the Linnean Society. 82: 665-674. DOI: 10.1111/j.1095-8312.2004.00352.x  0.92
2004 Pires JC, Zhao J, Schranz ME, Leon EJ, Quijada PA, Lukens LN, Osborn TC. Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae) Biological Journal of the Linnean Society. 82: 675-688. DOI: 10.1111/j.1095-8312.2004.00350.x  0.92
2004 Soltis DE, Soltis PS, Pires JC, Kovarik A, Tate JA, Mavrodiev E. Recent and recurrent polyploidy in Tragopogon (Asteraceae): Cytogenetic, genomic and genetic comparisons Biological Journal of the Linnean Society. 82: 485-501. DOI: 10.1111/j.1095-8312.2004.00335.x  0.92
2004 Sytsma KJ, Litt A, Zjhra ML, Pires JC, Nepokroeff M, Conti E, Walker J, Wilson PG. Clades, clocks, and continents: Historical and biogeographical analysis of Myrtaceae, Vochysiaceae, and relatives in the Southern Hemisphere International Journal of Plant Sciences. 165: S85-S105.  0.92
2004 Givnish TJ, Millam KC, Evans TM, Hall JC, Pires JC, Berry PE, Sytsma KJ. Ancient vicariance or recent long-distance dispersal? Inferences about phylogeny and South American-African disjunctions in rapateaceae and bromeliaceae based on ndhF sequence data International Journal of Plant Sciences. 165: S35-S54.  0.92
2003 Levin RA, Wagner WL, Hoch PC, Nepokroeff M, Pires JC, Zimmer EA, Sytsma KJ. Family-level relationships of Onagraceae based on chloroplast rbcL and ndhF data. American Journal of Botany. 90: 107-15. PMID 21659085 DOI: 10.3732/ajb.90.1.107  0.92
2003 Hass BL, Pires JC, Porter R, Phillips RL, Jackson SA. Comparative genetics at the gene and chromosome levels between rice ( Oryza sativa) and wildrice ( Zizania palustris). Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 107: 773-82. PMID 12904864 DOI: 10.1007/s00122-003-1273-5  0.92
2003 Bremer B, Bremer K, Chase MW, Reveal JL, Soltis DE, Soltis PS, Stevens PF, Anderberg AA, Fay MF, Goldblatt P, Judd WS, Källersjö M, Kårehed J, Kron KA, Lundberg J, ... ... Pires JC, et al. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II Botanical Journal of the Linnean Society. 141: 399-436. DOI: 10.1046/j.1095-8339.2003.t01-1-00158.x  0.92
2002 Sytsma KJ, Morawetz J, Pires JC, Nepokroeff M, Conti E, Zjhra M, Hall JC, Chase MW. Urticalean rosids: circumscription, rosid ancestry, and phylogenetics based on rbcL, trnL-F, and ndhF sequences. American Journal of Botany. 89: 1531-46. PMID 21665755 DOI: 10.3732/ajb.89.9.1531  0.92
2002 Pires JC, Sytsma KJ. A phylogenetic evaluation of a biosystematic framework: Brodiaea and related petaloid monocots (Themidaceae). American Journal of Botany. 89: 1342-59. PMID 21665737 DOI: 10.3732/ajb.89.8.1342  0.92
2001 Kiger RW, Case F.W. J, Pires JC. New infraspecific names in North American Liliales Taxon. 50: 201.  0.92
1999 Givnish TJ, Evans TM, Pires JC, Sytsma KJ. Polyphyly and convergent morphological evolution in Commelinales and Commelinidae: evidence from rbcL sequence data. Molecular Phylogenetics and Evolution. 12: 360-85. PMID 10413629 DOI: 10.1006/mpev.1999.0601  0.92
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