TY - JOUR AU - Barrett, C. H. AU - Harder, L. D. AU - Worley, A. C. PY - 1996 DA - 1996// TI - The comparative biology of pollination and mating in flowering plants JO - Philos T Roy Soc B VL - 351 UR - https://doi.org/10.1098/rstb.1996.0110 DO - 10.1098/rstb.1996.0110 ID - Barrett1996 ER - TY - JOUR AU - Regel, P. J. PY - 1977 DA - 1977// TI - Ecology and evolution of flowering plant dominance JO - Science VL - 196 UR - https://doi.org/10.1126/science.196.4290.622 DO - 10.1126/science.196.4290.622 ID - Regel1977 ER - TY - JOUR AU - Endress, P. K. AU - Matthews, M. L. PY - 2006 DA - 2006// TI - First steps toward a floral structural characterization of the major Rosid subclades JO - Plant Syst Evol VL - 260 ID - Endress2006 ER - TY - JOUR AU - Becker, A. AU - Thiessen, G. PY - 2003 DA - 2003// TI - The major clades of MADS-box genes and their role in the development and evolution of flowering plants JO - Mol Biol Evol VL - 29 ID - Becker2003 ER - TY - JOUR AU - Harrison, J. AU - Möller, M. AU - Cronk, Q. C. B. PY - 1999 DA - 1999// TI - Evolution and development of floral diversity in Streptocarpus and Saintpaulia JO - Ann Bot-London VL - 84 UR - https://doi.org/10.1006/anbo.1999.0887 DO - 10.1006/anbo.1999.0887 ID - Harrison1999 ER - TY - JOUR AU - Clark, J. L. AU - Roalson, E. H. AU - Pritchard, R. A. AU - Coleman, C. L. AU - Teoh, V. -. H. AU - Matos, J. PY - 2011 DA - 2011// TI - Independent origin of radial floral symmetry in the Gloxinieae (Gesnerioideae: Gesneriaceae) is supported by the rediscovery of Phinaea pulchella in Cuba JO - Syst Bot VL - 36 UR - https://doi.org/10.1600/036364411X583709 DO - 10.1600/036364411X583709 ID - Clark2011 ER - TY - JOUR AU - Roalson, E. H. AU - Roberts, W. R. PY - 2016 DA - 2016// TI - Distinct processes drive diversification in different clades of Gesneriaceae JO - Syst Biol VL - 65 UR - https://doi.org/10.1093/sysbio/syw012 DO - 10.1093/sysbio/syw012 ID - Roalson2016 ER - TY - JOUR AU - Wiehler, H. PY - 1976 DA - 1976// TI - A report on the classification of Achimenes, Eucodonia, Gloxinia, Goyazia, and Anetanthus (Gesneriaceae) JO - Selbyana VL - 1 ID - Wiehler1976 ER - TY - JOUR AU - Wiehler, H. PY - 1983 DA - 1983// TI - A synopsis of the neotropical Gesneriaceae JO - Selbyana VL - 6 ID - Wiehler1983 ER - TY - JOUR AU - Roalson, E. H. AU - Skog, L. E. AU - Zimmer, E. A. PY - 2003 DA - 2003// TI - Phylogenetic relationships and the diversification of floral form in Achimenes (Gesneriaceae) JO - Syst Bot VL - 28 ID - Roalson2003 ER - TY - JOUR AU - Perret, M. AU - Chautems, A. AU - Spichiger, R. AU - Barraclough, T. G. AU - Savolainen, V. PY - 2007 DA - 2007// TI - The geographical pattern of speciation and floral diversification in the Neotropics: the Tribe Sinningieae (Gesneriaceae) as a case study JO - Evolution VL - 61 UR - https://doi.org/10.1111/j.1558-5646.2007.00136.x DO - 10.1111/j.1558-5646.2007.00136.x ID - Perret2007 ER - TY - BOOK AU - Ramírez Roa, M. A. PY - 1987 DA - 1987// TI - Revision de Achimenes (Gesneriaceae) PB - Universidad Nacional Autonoma de Mexico D.F CY - Thesis ID - Ramírez Roa1987 ER - TY - JOUR AU - Martén-Rodríguez, S. AU - Quesada, M. AU - Castro, A. A. AU - Lopezaraiza-Mikel, M. AU - Fenster, C. B. PY - 2015 DA - 2015// TI - A comparison of reproductive strategies between island and mainland Caribbean Gesneriaceae JO - J Ecol VL - 103 UR - https://doi.org/10.1111/1365-2745.12457 DO - 10.1111/1365-2745.12457 ID - Martén-Rodríguez2015 ER - TY - JOUR AU - Marra, N. J. AU - Romero, A. AU - DeWoody, J. A. PY - 2014 DA - 2014// TI - Natural selection and the genetic basis of osmoregulation in heteromyid rodents as revealed by RNA-seq JO - Mol Ecol VL - 23 UR - https://doi.org/10.1111/mec.12764 DO - 10.1111/mec.12764 ID - Marra2014 ER - TY - JOUR AU - Davies, K. T. J. AU - Bennett, N. C. AU - Tsagkogeorga, G. AU - Rossiter, S. J. AU - Faulkes, C. G. PY - 2015 DA - 2015// TI - Family-wide molecular adaptations to underground life in African mole-rats revealed by phylogenomic analysis JO - Mol Biol Evol VL - 32 ID - Davies2015 ER - TY - JOUR AU - Davidson, R. M. AU - Gowda, M. AU - Moghe, G. AU - Lin, H. AU - Vaillancourt, B. AU - Shiu, S. H. AU - Jiang, N. AU - Robin, B. C. PY - 2012 DA - 2012// TI - Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution JO - Plant J VL - 71 ID - Davidson2012 ER - TY - JOUR AU - Li, Q. G. AU - Zhang, L. AU - Li, C. AU - Dunwell, J. M. AU - Zhang, Y. M. PY - 2013 DA - 2013// TI - Comparative genomics suggests that an ancestral polyploidy event leads to enhanced root nodule symbiosis in the Papilionoideae JO - Mol Biol Evol VL - 30 UR - https://doi.org/10.1093/molbev/mst152 DO - 10.1093/molbev/mst152 ID - Li2013 ER - TY - JOUR AU - Yang, Z. AU - Wafula, E. K. AU - Honaas, L. A. AU - Zhang, H. AU - Das, M. AU - Fernandez-Aparicio, M. AU - Huang, K. AU - Bandaranayake, P. C. G. AU - Wu, B. AU - Der, J. P. AU - Clarke, C. R. AU - Ralph, P. E. AU - Landherr, L. AU - Altman, N. S. AU - Timko, M. P. AU - Yoder, J. I. AU - Westwood, J. H. AU - Pamphilis, C. W. PY - 2015 DA - 2015// TI - Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty JO - Mol Biol Evol VL - 32 UR - https://doi.org/10.1093/molbev/msu343 DO - 10.1093/molbev/msu343 ID - Yang2015 ER - TY - JOUR AU - Rowland, L. J. AU - Alkharouf, N. AU - Darwish, O. AU - Ogden, E. L. AU - Polashock, J. J. AU - Bassil, N. V. AU - Main, D. PY - 2012 DA - 2012// TI - Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation JO - BMC Plant Biol VL - 12 UR - https://doi.org/10.1186/1471-2229-12-46 DO - 10.1186/1471-2229-12-46 ID - Rowland2012 ER - TY - JOUR AU - Zhang, X. M. AU - Zhao, L. AU - Larson-Rabin, Z. AU - Li, D. Z. AU - Guo, Z. H. PY - 2012 DA - 2012// TI - De novo sequencing and characterization of the floral transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae) JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0042082 DO - 10.1371/journal.pone.0042082 ID - Zhang2012 ER - TY - JOUR AU - Díaz-Riquelme, J. AU - Martínez-Zapater, J. M. AU - Carmona, M. J. PY - 2014 DA - 2014// TI - Transcriptional analysis of tendril and inflorescence development in grapevine (Vitis vinifera L.) JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0092339 DO - 10.1371/journal.pone.0092339 ID - Díaz-Riquelme2014 ER - TY - JOUR AU - Zahn, L. M. AU - Ma, X. AU - Altman, N. S. AU - Zhang, Q. AU - Wall, P. K. AU - Tian, D. AU - Gibas, C. J. AU - Gharaibeh, R. AU - Leebens-Mack, J. H. AU - Pamphilis, C. W. AU - Ma, H. PY - 2010 DA - 2010// TI - Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies JO - Genome Biol VL - 11 UR - https://doi.org/10.1186/gb-2010-11-10-r101 DO - 10.1186/gb-2010-11-10-r101 ID - Zahn2010 ER - TY - JOUR AU - Qiu, W. M. AU - Zhu, A. D. AU - Wang, Y. AU - Chai, L. J. AU - Ge, X. X. AU - Deng, X. X. AU - Guo, W. W. PY - 2012 DA - 2012// TI - Comparative transcript profiling of gene expression between seedless Ponkan mandarin and its seedy wild type during floral organ development by suppression subtractive hybridization and cDNA microarray JO - BMC Genomics VL - 13 UR - https://doi.org/10.1186/1471-2164-13-397 DO - 10.1186/1471-2164-13-397 ID - Qiu2012 ER - TY - JOUR AU - Logacheva, M. D. AU - Kasianov, A. S. AU - Vinogradov, D. V. AU - Samigullin, T. H. AU - Gelfand, M. S. AU - Makeev, V. J. AU - Penin, A. A. PY - 2011 DA - 2011// TI - De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum) JO - BMC Genomics VL - 12 UR - https://doi.org/10.1186/1471-2164-12-30 DO - 10.1186/1471-2164-12-30 ID - Logacheva2011 ER - TY - JOUR AU - Vining, K. J. AU - Romanel, E. AU - Jones, R. C. AU - Klocko, A. AU - Alves-Ferreira, M. AU - Hefer, C. A. AU - Aamarasinghe, V. AU - Dharmawardhana, P. AU - Naithani, S. AU - Ranik, M. AU - Wesley-Smith, J. AU - Solomon, J. AU - Jaiswai, P. AU - Myburg, A. A. AU - Straus, S. H. PY - 2014 DA - 2014// TI - The floral transcriptome of Eucalyptus grandis JO - New Phytol VL - 206 UR - https://doi.org/10.1111/nph.13077 DO - 10.1111/nph.13077 ID - Vining2014 ER - TY - JOUR AU - Wei, W. AU - Qi, X. AU - Wang, L. AU - Zhang, Y. AU - Hua, W. AU - Li, D. AU - Lv, H. AU - Zhang, X. PY - 2011 DA - 2011// TI - Characterization of the sesame (Sesamum indicum) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers JO - BMC Genomics VL - 12 UR - https://doi.org/10.1186/1471-2164-12-451 DO - 10.1186/1471-2164-12-451 ID - Wei2011 ER - TY - JOUR AU - Bhide, A. AU - Schliesky, S. AU - Reich, M. AU - Weber, A. P. M. AU - Becker, A. PY - 2014 DA - 2014// TI - Analysis of the floral transcriptome of Tarenaya hassleriana (Cleomaceae), a member of the sister group to the Brassicaceae: towards understanding the base of morphological diversity in Brassicales JO - BMC Genomics VL - 15 UR - https://doi.org/10.1186/1471-2164-15-140 DO - 10.1186/1471-2164-15-140 ID - Bhide2014 ER - TY - JOUR AU - Ness, R. W. AU - Siol, M. AU - Barrett, S. C. H. PY - 2011 DA - 2011// TI - De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants JO - BMC Genomics VL - 12 UR - https://doi.org/10.1186/1471-2164-12-298 DO - 10.1186/1471-2164-12-298 ID - Ness2011 ER - TY - JOUR AU - Kobayashi, M. J. AU - Takeuchi, Y. AU - Kenta, T. AU - Kume, T. AU - Diway, B. AU - Shimizu, K. K. PY - 2013 DA - 2013// TI - Mass flowering of the tropical tree Shorea beccariana was preceded by expression changes in flowering and drought-responsive genes JO - Mol Ecol VL - 22 UR - https://doi.org/10.1111/mec.12344 DO - 10.1111/mec.12344 ID - Kobayashi2013 ER - TY - JOUR PY - 2015 DA - 2015// TI - UniProt: a hub for protein information JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku989 DO - 10.1093/nar/gku989 ID - ref30 ER - TY - JOUR AU - Pruitt, K. D. AU - Tatusova, T. AU - Maglott, D. R. PY - 2005 DA - 2005// TI - NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki025 DO - 10.1093/nar/gki025 ID - Pruitt2005 ER - TY - JOUR AU - Yi, X. AU - Zhang, Z. AU - Ling, Y. AU - Xu, W. AU - Su, Z. PY - 2015 DA - 2015// TI - PNRD: a plant non-coding RNA database JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1162 DO - 10.1093/nar/gku1162 ID - Yi2015 ER - TY - JOUR AU - Ashburner, M. AU - Ball, C. A. AU - Blake, J. A. AU - Botstein, D. AU - Butler, H. AU - Cherry, J. M. AU - Davis, A. P. AU - Dolinski, K. AU - Dwight, S. S. AU - Eppig, J. T. AU - Harris, M. A. AU - Hill, D. P. AU - Issel-Tarver, L. AU - Kasarskis, A. AU - Lewis, S. AU - Matese, J. C. AU - Richardson, J. E. AU - Ringwald, M. AU - Rubin, G. M. AU - Sherlock, G. PY - 2000 DA - 2000// TI - Gene Ontology: tool for the unification of biology JO - Nat Genet VL - 25 UR - https://doi.org/10.1038/75556 DO - 10.1038/75556 ID - Ashburner2000 ER - TY - JOUR AU - Quevillon, E. AU - Silventoinen, V. AU - Pillai, S. AU - Harte, N. AU - Mulder, N. AU - Apweller, R. AU - Lopez, R. PY - 2005 DA - 2005// TI - InterProScan: protein domains identifier JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki442 DO - 10.1093/nar/gki442 ID - Quevillon2005 ER - TY - JOUR AU - Myhre, S. AU - Tveit, H. AU - Mollestad, T. AU - Lægreid, A. PY - 2006 DA - 2006// TI - Additional gene ontology structure for improved biological reasoning JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl334 DO - 10.1093/bioinformatics/btl334 ID - Myhre2006 ER - TY - JOUR AU - Eddy, S. R. PY - 1998 DA - 1998// TI - Profile Hidden Markov Models JO - Bioinformatics VL - 14 UR - https://doi.org/10.1093/bioinformatics/14.9.755 DO - 10.1093/bioinformatics/14.9.755 ID - Eddy1998 ER - TY - JOUR AU - Yant, L. AU - Collani, S. AU - Puzey, J. AU - Levy, C. AU - Kramer, E. M. PY - 2015 DA - 2015// TI - Molecular basis for three-dimensional elaboration of the Aquilegia petal spur JO - P Roy Soc B-Biol Sci VL - 282 UR - https://doi.org/10.1098/rspb.2014.2778 DO - 10.1098/rspb.2014.2778 ID - Yant2015 ER - TY - JOUR AU - Hay, A. AU - Tsiantis, M. PY - 2010 DA - 2010// TI - KNOX genes: versatile regulators of plant development and diversity JO - Development VL - 137 UR - https://doi.org/10.1242/dev.030049 DO - 10.1242/dev.030049 ID - Hay2010 ER - TY - JOUR AU - Eklund, D. M. AU - Ståldal, V. AU - Valsecchi, I. AU - Cierlik, I. AU - Eriksson, C. AU - Hiratsu, K. AU - Ohme-Takagi, M. AU - Sundström, J. F. AU - Thelander, M. AU - Ezcurra, I. AU - Sundberg, E. PY - 2010 DA - 2010// TI - The Arabidopsis thaliana STYLISH1 protein acts as a transcriptional activator regulating auxin biosynthesis JO - Plant Cell VL - 22 UR - https://doi.org/10.1105/tpc.108.064816 DO - 10.1105/tpc.108.064816 ID - Eklund2010 ER - TY - JOUR AU - Choe, S. PY - 2007 DA - 2007// TI - Signal-transduction pathways toward the regulation of brassinosteroid biosynthesis JO - J Plant Biol VL - 50 UR - https://doi.org/10.1007/BF03030649 DO - 10.1007/BF03030649 ID - Choe2007 ER - TY - JOUR AU - Yin, Y. AU - Vafeados, D. AU - Tao, Y. AU - Yoshida, S. AU - Asami, T. AU - Chory, J. PY - 2005 DA - 2005// TI - A new class of transcription factors mediates brassinosteroid-regulated gene expression in Arabidopsis JO - Cell VL - 120 UR - https://doi.org/10.1016/j.cell.2004.11.044 DO - 10.1016/j.cell.2004.11.044 ID - Yin2005 ER - TY - JOUR AU - Langmead, B. AU - Trapnell, C. AU - Pop, M. AU - Salzberg, S. L. PY - 2009 DA - 2009// TI - Ultrafast and memory-efficient alignment of short DNA sequences to the human genome JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-3-r25 DO - 10.1186/gb-2009-10-3-r25 ID - Langmead2009 ER - TY - JOUR AU - Li, B. AU - Dewey, C. N. PY - 2011 DA - 2011// TI - RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome JO - BMC Bioinformatics VL - 12 UR - https://doi.org/10.1186/1471-2105-12-323 DO - 10.1186/1471-2105-12-323 ID - Li2011 ER - TY - JOUR AU - Rau, A. AU - Maugis-Rabusseau, C. AU - Martin-Magniette, M. L. AU - Celeux, G. PY - 2015 DA - 2015// TI - Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btu845 DO - 10.1093/bioinformatics/btu845 ID - Rau2015 ER - TY - JOUR AU - Dempster, A. P. AU - Laird, N. M. AU - Rubin, D. B. PY - 1977 DA - 1977// TI - Maximum likelihood from incomplete data via the EM algorithm JO - J Roy Stat Soc B Met. VL - 39 ID - Dempster1977 ER - TY - JOUR AU - Baudry, J. P. AU - Maugis, C. AU - Bertrand, M. PY - 2012 DA - 2012// TI - Slope heuristics: overview and implementation JO - Stat Comput VL - 22 UR - https://doi.org/10.1007/s11222-011-9236-1 DO - 10.1007/s11222-011-9236-1 ID - Baudry2012 ER - TY - JOUR AU - Anisimova, M. AU - Bielawski, J. P. AU - Yang, Z. PY - 2001 DA - 2001// TI - Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution JO - Mol Biol Evol VL - 18 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003945 DO - 10.1093/oxfordjournals.molbev.a003945 ID - Anisimova2001 ER - TY - JOUR AU - Yang, Z. AU - Nielsen, R. AU - Goldman, N. AU - Pedersen, A. M. K. PY - 2000 DA - 2000// TI - Codon-substitution models for heterogeneous selection pressure at amino acid sites JO - Genetics VL - 155 ID - Yang2000 ER - TY - JOUR AU - Yang, Z. AU - Wong, W. S. W. AU - Nielsen, R. PY - 2005 DA - 2005// TI - Bayes empirical Bayes inference of amino acid sites under positive selection JO - Mol Biol Evol VL - 22 UR - https://doi.org/10.1093/molbev/msi097 DO - 10.1093/molbev/msi097 ID - Yang2005 ER - TY - JOUR AU - Alexandre, H. AU - Vrignaud, J. AU - Mangin, B. AU - Joly, S. PY - 2015 DA - 2015// TI - Genetic architecture of pollination syndrome transition between hummingbird-specialist and generalist species in the genus Rhytidophyllum (Gesneriaceae) JO - Peer J VL - 3 UR - https://doi.org/10.7717/peerj.1028 DO - 10.7717/peerj.1028 ID - Alexandre2015 ER - TY - JOUR AU - Tanase, K. AU - Nishitani, C. AU - Hirakawa, H. AU - Isobe, S. AU - Tabata, S. AU - Ohmiya, A. AU - Onozaki, T. PY - 2012 DA - 2012// TI - Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology JO - BMC Genomics VL - 13 UR - https://doi.org/10.1186/1471-2164-13-292 DO - 10.1186/1471-2164-13-292 ID - Tanase2012 ER - TY - JOUR AU - Bakel, H. AU - Stout, J. M. AU - Cote, A. G. AU - Tallon, C. M. AU - Sharpe, A. G. AU - Hughes, T. R. AU - Page, J. E. PY - 2011 DA - 2011// TI - The draft genome and transcriptome of Cannabis sativa JO - Genome Biol VL - 12 UR - https://doi.org/10.1186/gb-2011-12-10-r102 DO - 10.1186/gb-2011-12-10-r102 ID - Bakel2011 ER - TY - JOUR AU - Parchman, T. L. AU - Geise, K. S. AU - Grahnen, J. E. AU - Benkman, C. W. AU - Buerkle, C. A. PY - 2010 DA - 2010// TI - Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery JO - BMC Genomics VL - 11 UR - https://doi.org/10.1186/1471-2164-11-180 DO - 10.1186/1471-2164-11-180 ID - Parchman2010 ER - TY - JOUR AU - Zhang, J. AU - Wu, K. AU - Zeng, S. AU - Silva JA, T. AU - Zhao, X. AU - Tian, C. E. AU - Xia, H. AU - Duan, J. PY - 2013 DA - 2013// TI - Transcriptome analysis of Cymbidium sinense and its application to the identification of genes associated with floral development JO - BMC Genomics VL - 14 UR - https://doi.org/10.1186/1471-2164-14-279 DO - 10.1186/1471-2164-14-279 ID - Zhang2013 ER - TY - JOUR AU - Melicher, D. AU - Torson, A. S. AU - Dworkin, I. AU - Bowsher, J. H. PY - 2014 DA - 2014// TI - A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach JO - BMC Genomics VL - 15 UR - https://doi.org/10.1186/1471-2164-15-188 DO - 10.1186/1471-2164-15-188 ID - Melicher2014 ER - TY - JOUR AU - Nakasugi, K. AU - Crowhurst, R. AU - Bally, J. AU - Waterhouse, P. PY - 2014 DA - 2014// TI - Combining transcriptome assemblies from multiple de novo assemblers in the allo-tetraploid plant Nicotiana benthamiana JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0091776 DO - 10.1371/journal.pone.0091776 ID - Nakasugi2014 ER - TY - STD TI - Chen S, McElroy JS, Dane F, Peatman E. Optimizing transcriptome assemblies for Eleusine indica leaf and seedling by combining multiple assemblies from three de novo assemblers. Plant Genome. 2015;8. ID - ref57 ER - TY - JOUR AU - Zhao, Q. Y. AU - Wang, Y. AU - Kong, Y. M. AU - Luo, D. AU - Li, X. AU - Hao, P. PY - 2011 DA - 2011// TI - Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study JO - BMC Genomics VL - 12 ID - Zhao2011 ER - TY - JOUR AU - Eisen, M. B. AU - Spellman, P. T. AU - Brown, P. O. AU - Botstein, D. PY - 1998 DA - 1998// TI - Cluster analysis and display of genome-wide expression patterns JO - P Natl Acad Sci USA VL - 95 UR - https://doi.org/10.1073/pnas.95.25.14863 DO - 10.1073/pnas.95.25.14863 ID - Eisen1998 ER - TY - JOUR AU - Jiang, D. AU - Tang, C. AU - Zhang, A. PY - 2004 DA - 2004// TI - Cluster analysis for gene expression data: a survey JO - IEEE T Knowl Data En VL - 16 UR - https://doi.org/10.1109/TKDE.2004.68 DO - 10.1109/TKDE.2004.68 ID - Jiang2004 ER - TY - CHAP AU - MacQueen, J. B. ED - Cam, L. M. ED - Neyman, J. PY - 1967 DA - 1967// TI - Some methods for classification and analysis of multivariate observations BT - Proceedings of the 5th Berkeley Symposium on Mathematical Statistics and Probability, number 1 PB - Univ Calif Press CY - Berkeley ID - MacQueen1967 ER - TY - JOUR AU - Ward, J. H. PY - 1963 DA - 1963// TI - Hierarchical grouping to optimize and objective function JO - J Am Stat Assoc VL - 58 UR - https://doi.org/10.1080/01621459.1963.10500845 DO - 10.1080/01621459.1963.10500845 ID - Ward1963 ER - TY - CHAP AU - Guzzi, P. H. AU - Masciari, E. AU - Mazzeo, G. M. AU - Zaniolo, C. ED - Bursa, M. ED - Khuri, S. ED - Renda, M. E. PY - 2014 DA - 2014// TI - A discussion on the biological relevance of clustering results BT - International Conference on Information Technology in bio- and medical informatics PB - Springer Intl Pub CY - Gewerbestrasse ID - Guzzi2014 ER - TY - JOUR AU - Si, Y. AU - Liu, P. AU - Li, P. AU - Brutnell, T. P. PY - 2014 DA - 2014// TI - Model-based clustering for RNA-seq data JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btt632 DO - 10.1093/bioinformatics/btt632 ID - Si2014 ER - TY - JOUR AU - Marioni, J. C. AU - Mason, C. E. AU - Mane, S. M. AU - Stephens, M. AU - Gilad, Y. PY - 2008 DA - 2008// TI - RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.079558.108 DO - 10.1101/gr.079558.108 ID - Marioni2008 ER - TY - JOUR AU - Anders, S. AU - Huber, W. PY - 2010 DA - 2010// TI - Differential expression analysis for sequence count data JO - Genome Biol VL - 11 UR - https://doi.org/10.1186/gb-2010-11-10-r106 DO - 10.1186/gb-2010-11-10-r106 ID - Anders2010 ER - TY - JOUR AU - Fukushima, A. AU - Nishizawa, T. AU - Hayakumo, M. AU - Hikosaka, S. AU - Saito, K. AU - Goto, E. AU - Kusano, M. PY - 2012 DA - 2012// TI - Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches JO - Plant Physiol VL - 158 UR - https://doi.org/10.1104/pp.111.188367 DO - 10.1104/pp.111.188367 ID - Fukushima2012 ER - TY - JOUR AU - Coneva, V. AU - Simopoulos, C. AU - Casaretto, J. A. AU - El-Kereamy, A. AU - Guevara, D. R. AU - Cohn, J. AU - Zhu, T. AU - Guo, L. AU - Alexander, D. C. AU - Bi, Y. M. AU - McNicholas, P. D. AU - Rothstein, S. J. PY - 2014 DA - 2014// TI - Metabolic and co-expression network-based analyses associated with nitrate response in rice JO - BMC Genomics VL - 15 UR - https://doi.org/10.1186/1471-2164-15-1056 DO - 10.1186/1471-2164-15-1056 ID - Coneva2014 ER - TY - JOUR AU - Langfelder, P. AU - Horvath, S. PY - 2008 DA - 2008// TI - WGCNA: an R package for weighted correlated network analysis JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-559 DO - 10.1186/1471-2105-9-559 ID - Langfelder2008 ER - TY - JOUR AU - Hollender, C. A. AU - Kang, C. AU - Darwish, O. AU - Geretz, A. AU - Matthews, B. F. AU - Slovin, J. AU - Alkharouf, N. AU - Liu, Z. PY - 2014 DA - 2014// TI - Floral transcriptomes in woodland strawberry uncover developing receptacle and anther gene networks JO - Plant Physiol VL - 165 UR - https://doi.org/10.1104/pp.114.237529 DO - 10.1104/pp.114.237529 ID - Hollender2014 ER - TY - JOUR AU - Fan, Z. AU - Li, J. AU - Li, X. AU - Wu, B. AU - Wang, J. AU - Liu, Z. AU - Yin, H. PY - 2015 DA - 2015// TI - Genome-wide transcriptome profiling provides insights into floral bud development of summer-flowering Camellia azalea JO - Sci Reports VL - 2015 ID - Fan2015 ER - TY - JOUR AU - Huang, Y. J. AU - Liu, L. L. AU - Huang, J. Q. AU - Wang, Z. J. AU - Chen, F. F. AU - Zhang, Q. X. AU - Zheng, B. S. AU - Chen, M. PY - 2013 DA - 2013// TI - Use of transcriptome sequencing to understand the pistillate flowering in hickory (Carya cathayensis Sarg.) JO - BMC Genomics VL - 14 UR - https://doi.org/10.1186/1471-2164-14-691 DO - 10.1186/1471-2164-14-691 ID - Huang2013 ER - TY - JOUR AU - Yoo, M. J. AU - Chanderbali, A. S. AU - Altman, N. S. AU - Soltis, P. S. AU - Soltis, D. E. PY - 2010 DA - 2010// TI - Evolutionary trends in the floral transcriptome: insights from one of the basalmost angiosperms, the water lily Nuphar advena (Nymphaeaceae) JO - Plant J VL - 64 UR - https://doi.org/10.1111/j.1365-313X.2010.04357.x DO - 10.1111/j.1365-313X.2010.04357.x ID - Yoo2010 ER - TY - JOUR AU - Annick, D. AU - Remay, A. AU - Raymond, O. AU - Balzergue, S. AU - Chauvet, A. AU - Maene, M. AU - Pécrix, Y. AU - Yang, S. H. AU - Jeauffre, J. AU - Thouroude, T. AU - Boltz, V. AU - Martin-Magniette, M. L. AU - Janczarski, S. AU - Legeai, F. AU - Renou, J. P. AU - Vergne, P. AU - Bris, M. AU - Foucher, F. AU - Bendahmane, M. PY - 2011 DA - 2011// TI - Genomic approach to study floral development genes in Rosa sp JO - PLoS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0028455 DO - 10.1371/journal.pone.0028455 ID - Annick2011 ER - TY - JOUR AU - Kater, M. M. AU - Dreni, L. AU - Colombo, L. PY - 2006 DA - 2006// TI - Functional conservation of MADS-box factors controlling floral organ identity in rice and Arabidopsis JO - J Exp Bot VL - 57 UR - https://doi.org/10.1093/jxb/erl097 DO - 10.1093/jxb/erl097 ID - Kater2006 ER - TY - JOUR AU - Urbanus, S. L. AU - Dinh, Q. D. AU - Angenent, G. C. AU - Immink, R. G. PY - 2010 DA - 2010// TI - Investigation of MADS domain transcription factor dynamics in the floral meristem JO - Plant Signal Behav VL - 5 UR - https://doi.org/10.4161/psb.5.10.12949 DO - 10.4161/psb.5.10.12949 ID - Urbanus2010 ER - TY - STD TI - Ding B, Mou F, Sun W, Chen S, Peng F, Bradshaw HD, Yuan YW. A dominant-negative actin mutation alters corolla tube width and pollinator visitation in Mimulus lewisii. New Phytol. In press. ID - ref77 ER - TY - JOUR AU - Golz, J. F. AU - Keck, E. J. AU - Hudson, A. PY - 2002 DA - 2002// TI - Spontaneous mutations in KNOX genes give rise to a novel floral structure in Antirrhinum JO - Curr Biol VL - 12 UR - https://doi.org/10.1016/S0960-9822(02)00721-2 DO - 10.1016/S0960-9822(02)00721-2 ID - Golz2002 ER - TY - JOUR AU - Box, M. S. AU - Dodsworth, S. AU - Rudall, P. J. AU - Bateman, R. M. AU - Glover, B. PY - 2011 DA - 2011// TI - Characterization of Linaria KNOX genes suggest a role in petal-spur development JO - Plant J VL - 68 UR - https://doi.org/10.1111/j.1365-313X.2011.04721.x DO - 10.1111/j.1365-313X.2011.04721.x ID - Box2011 ER - TY - JOUR AU - Grotewald, E. PY - 2006 DA - 2006// TI - The genetics and biochemistry of floral pigments JO - Annu Rev Plant Biol VL - 57 UR - https://doi.org/10.1146/annurev.arplant.57.032905.105248 DO - 10.1146/annurev.arplant.57.032905.105248 ID - Grotewald2006 ER - TY - JOUR AU - Saito, K. AU - Yonekura-Sakakibara, K. AU - Nakabayashi, R. AU - Higashi, Y. AU - Yamazaki, M. AU - Tohge, T. AU - Fernie, A. R. PY - 2013 DA - 2013// TI - The flavonoid biosynthetic pathway in Arabidopsis: structural and genetic diversity JO - Plant Physiol Bioch VL - 72 UR - https://doi.org/10.1016/j.plaphy.2013.02.001 DO - 10.1016/j.plaphy.2013.02.001 ID - Saito2013 ER - TY - JOUR AU - Whittall, J. B. AU - Voelckel, C. AU - Kliebenstein, D. J. AU - Hodges, S. A. PY - 2006 DA - 2006// TI - Convergence, constraint and the role of gene expression during adaptive radiation: floral anthocyanins in Aquilegia JO - Mol Ecol VL - 15 UR - https://doi.org/10.1111/j.1365-294X.2006.03114.x DO - 10.1111/j.1365-294X.2006.03114.x ID - Whittall2006 ER - TY - JOUR AU - Streisfeld, M. A. AU - Rausher, M. D. PY - 2009 DA - 2009// TI - Altered trans-regulatory control of gene expression in multiple anthocyanin genes contributes to adaptive flower color evolution in Mimulus aurantiacus JO - Mol Biol Evol VL - 26 UR - https://doi.org/10.1093/molbev/msn268 DO - 10.1093/molbev/msn268 ID - Streisfeld2009 ER - TY - JOUR AU - Smith, S. D. AU - Rausher, M. D. PY - 2011 DA - 2011// TI - Gene loss and parallel evolution contribute to species differences in flower color JO - Mol Biol Evol VL - 28 UR - https://doi.org/10.1093/molbev/msr109 DO - 10.1093/molbev/msr109 ID - Smith2011 ER - TY - JOUR AU - Smith, S. D. AU - Rausher, M. D. PY - 2013 DA - 2013// TI - Functional evolution of an anthocyanin pathway enzyme during a flower color transition JO - Mol Biol Evol VL - 30 UR - https://doi.org/10.1093/molbev/mss255 DO - 10.1093/molbev/mss255 ID - Smith2013 ER - TY - JOUR AU - Yuan, Y. W. AU - Sagawa, J. M. AU - Frost, L. AU - Vela, J. P. AU - Bradshaw, H. D. PY - 2014 DA - 2014// TI - Transcriptional control of floral anthocyanin pigmentation in monkeyflowers (Mimulus) JO - New Phytol VL - 204 UR - https://doi.org/10.1111/nph.12968 DO - 10.1111/nph.12968 ID - Yuan2014 ER - TY - JOUR AU - Streisfeld, M. A. AU - Rausher, M. D. PY - 2009 DA - 2009// TI - Genetic changes contributing to the parallel evolution of red floral pigmentation among Ipomoea species JO - New Phytol VL - 183 UR - https://doi.org/10.1111/j.1469-8137.2009.02929.x DO - 10.1111/j.1469-8137.2009.02929.x ID - Streisfeld2009 ER - TY - JOUR AU - Des Marais, D. L. AU - Rausher, M. D. PY - 2010 DA - 2010// TI - Parallel evolution at multiple levels in the origin of hummingbird pollinated flowers in Ipomoea JO - Evolution VL - 64 ID - Des Marais2010 ER - TY - JOUR AU - Wessinger, C. A. AU - Hileman, L. C. AU - Rausher, M. D. PY - 2014 DA - 2014// TI - Identification of major quantitative trait loci underlying floral pollination syndrome divergence in Penstemon JO - Philos T Roy Soc B VL - 369 UR - https://doi.org/10.1098/rstb.2013.0349 DO - 10.1098/rstb.2013.0349 ID - Wessinger2014 ER - TY - JOUR AU - Wessinger, C. A. AU - Rausher, M. D. PY - 2015 DA - 2015// TI - Ecological transition predictably associated with gene degeneration JO - Mol Biol Evol VL - 32 UR - https://doi.org/10.1093/molbev/msu298 DO - 10.1093/molbev/msu298 ID - Wessinger2015 ER - TY - JOUR AU - Lowry, D. B. AU - Sheng, C. C. AU - Lasky, J. R. AU - Willis, J. H. PY - 2012 DA - 2012// TI - Five anthocyanin polymorphisms are associated with an R2R3-MYB cluster in Mimulus guttatus (Phrymaceae) JO - Am J Bot VL - 99 UR - https://doi.org/10.3732/ajb.1100285 DO - 10.3732/ajb.1100285 ID - Lowry2012 ER - TY - JOUR AU - Seitz, C. AU - Eder, C. AU - Deimi, B. AU - Kellner, S. AU - Martens, S. AU - Forkmann, G. PY - 2006 DA - 2006// TI - Cloning, functional identification and sequence analysis of flavonoid 3′-hydroxylase and flavonoid 3′,5′-hydroxylase cDNAs reveals independent evolution of flavonoid 3′,5′-hydroxylase in the Asteraceae family JO - Plant Mol Biol VL - 61 UR - https://doi.org/10.1007/s11103-006-0012-0 DO - 10.1007/s11103-006-0012-0 ID - Seitz2006 ER - TY - JOUR AU - Seitz, C. AU - Ameres, S. AU - Schlangen, K. AU - Forkmann, G. AU - Halbwirth, H. PY - 2015 DA - 2015// TI - Multiple evolution of flavonoid 3′,5′-hydoxylase JO - Planta VL - 242 UR - https://doi.org/10.1007/s00425-015-2293-5 DO - 10.1007/s00425-015-2293-5 ID - Seitz2015 ER - TY - JOUR AU - Stankowski, S. AU - Streisfeld, M. A. PY - 2015 DA - 2015// TI - Introgressive hybridization facilitates adaptive divergence in a recent radiation of monkeyflowers JO - P Roy Soc B-Biol Sci VL - 282 UR - https://doi.org/10.1098/rspb.2015.1666 DO - 10.1098/rspb.2015.1666 ID - Stankowski2015 ER - TY - JOUR AU - Sagawa, J. M. AU - Stanley, L. E. AU - LaFountain, A. M. AU - Frank, H. A. AU - Liu, C. AU - Yuan, Y. W. PY - 2015 DA - 2015// TI - An R2R3-MYB transcription factor regulates carotenoid pigmentation in Mimulus lewisii flowers JO - New Phytol VL - 209 UR - https://doi.org/10.1111/nph.13647 DO - 10.1111/nph.13647 ID - Sagawa2015 ER - TY - JOUR AU - Quattrocchio, F. AU - Wing, J. AU - Woude, K. AU - Souer, E. AU - Vetten, N. AU - Mol, J. AU - Koes, R. PY - 1999 DA - 1999// TI - Molecular analysis of the anthocyanin2 gene of Petunia and its role in the evolution of flower color JO - Plant Cell VL - 11 UR - https://doi.org/10.1105/tpc.11.8.1433 DO - 10.1105/tpc.11.8.1433 ID - Quattrocchio1999 ER - TY - JOUR AU - Schwinn, K. AU - Venail, J. AU - Shang, Y. AU - Mackay, S. AU - Alm, V. AU - Butelli, E. AU - Oyama, R. AU - Bailey, P. AU - Davies, K. AU - Martin, C. PY - 2006 DA - 2006// TI - A small family of MYB-regulatory genes controls floral pigmentation intensity and patterning in the genus Antirrhinum JO - Plant Cell VL - 18 UR - https://doi.org/10.1105/tpc.105.039255 DO - 10.1105/tpc.105.039255 ID - Schwinn2006 ER - TY - JOUR AU - Dall’Osto, L. AU - Fiore, A. AU - Cazzinga, S. AU - Giuliano, G. AU - Bassi, R. PY - 2007 DA - 2007// TI - Different roles of alpha- and beta-branch xanthophylls in photosystem assembly and photoreception JO - J Biol Chem VL - 282 UR - https://doi.org/10.1074/jbc.M704729200 DO - 10.1074/jbc.M704729200 ID - Dall’Osto2007 ER - TY - BOOK AU - Glover, B. J. PY - 2014 DA - 2014// TI - Understanding flowers and flowering: an integrated approach PB - Oxford University Press CY - Oxford, UK UR - https://doi.org/10.1093/acprof:oso/9780199661596.001.0001 DO - 10.1093/acprof:oso/9780199661596.001.0001 ID - Glover2014 ER - TY - JOUR AU - LaFountain, A. M. AU - Frank, H. A. AU - Yuan, Y. -. W. PY - 2015 DA - 2015// TI - Carotenoid composition of the flowers of Mimulus lewisii and related species: implications regarding the prevalence and origin of two unique, allenic pigments JO - Arch Biochem Biophys VL - 573 UR - https://doi.org/10.1016/j.abb.2015.03.006 DO - 10.1016/j.abb.2015.03.006 ID - LaFountain2015 ER - TY - JOUR AU - Bradshaw, H. D. AU - Wilbert, M. AU - Otto, K. G. PY - 1995 DA - 1995// TI - Genetic mapping of floral traits associated with reproductive isolation in monkeyflowers (Mimulus) JO - Nature VL - 375 ID - Bradshaw1995 ER - TY - JOUR AU - Owen, C. R. AU - Bradshaw, H. D. PY - 2011 DA - 2011// TI - Induced mutations affecting pollinator choice in Mimulus lewisii (Phrymaceae) JO - Arthropod-Plant Inte VL - 5 UR - https://doi.org/10.1007/s11829-011-9133-8 DO - 10.1007/s11829-011-9133-8 ID - Owen2011 ER - TY - JOUR AU - Cronk, Q. AU - Ojeda, I. PY - 2008 DA - 2008// TI - Bird-pollinated flowers in an evolutionary and molecular context JO - J Exp Bot VL - 59 UR - https://doi.org/10.1093/jxb/ern009 DO - 10.1093/jxb/ern009 ID - Cronk2008 ER - TY - JOUR AU - Lin, R. AU - Wang, H. PY - 2005 DA - 2005// TI - Two homologous ATP-binding cassette transporter proteins, AtMDR1 and AtPGP1, regulate Arabidopsis photomorphogenesis and root development by mediating polar auxin transport JO - Plant Physiol VL - 138 UR - https://doi.org/10.1104/pp.105.061572 DO - 10.1104/pp.105.061572 ID - Lin2005 ER - TY - JOUR AU - Suzuki, H. AU - Nakayama, T. AU - Yonekura-Sakakibara, K. AU - Fukui, Y. AU - Nakamura, N. AU - Nakao, M. AU - Tanaka, Y. AU - Yamaguchi, M. A. AU - Kusumi, T. AU - Nishino, T. PY - 2001 DA - 2001// TI - Malonyl-CoA:anthocyanin 5-O-glucoside-6”’-O-malonyltransferase from scarlet sage (Salvia splendens) flowers. Enzyme purification, gene cloning, expression, and characterization JO - J Biol Chem VL - 276 UR - https://doi.org/10.1074/jbc.M108444200 DO - 10.1074/jbc.M108444200 ID - Suzuki2001 ER - TY - JOUR AU - Ho, W. W. AU - Smith, S. D. PY - 2016 DA - 2016// TI - Molecular evolution of anthocyanin pigmentation genes following losses of flower color JO - BMC Evol Biol VL - 16 UR - https://doi.org/10.1186/s12862-016-0675-3 DO - 10.1186/s12862-016-0675-3 ID - Ho2016 ER - TY - JOUR AU - Krogan, N. T. AU - Hogan, K. AU - Long, J. A. PY - 2012 DA - 2012// TI - APETALA2 negatively regulates multiple floral organ identity genes in Arabidopsis by recruiting the co-repressor TOPLESS and the histone deacetylase HDA19 JO - Development VL - 139 UR - https://doi.org/10.1242/dev.085407 DO - 10.1242/dev.085407 ID - Krogan2012 ER - TY - JOUR AU - Johanson, U. AU - West, J. AU - Lister, C. AU - Michaels, S. AU - Amasino, R. AU - Dean, C. PY - 2000 DA - 2000// TI - Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time JO - Science VL - 290 UR - https://doi.org/10.1126/science.290.5490.344 DO - 10.1126/science.290.5490.344 ID - Johanson2000 ER - TY - JOUR AU - Chiara, M. AU - Horner, D. S. AU - Spada, A. PY - 2013 DA - 2013// TI - De novo assembly of the transcriptome of the non-model Streptocarpus rexii employing a novel heuristic to recover locus-specific transcript clusters JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0080961 DO - 10.1371/journal.pone.0080961 ID - Chiara2013 ER - TY - JOUR AU - Ai, B. AU - Gao, Y. AU - Zhang, X. AU - Tao, J. AU - Kang, M. AU - Huang, H. PY - 2014 DA - 2014// TI - Comparative transcriptome resources of eleven Primulina species, a group of ‘stone plants’ from a biodiversity hot spot JO - Mol Ecol Resour VL - 15 UR - https://doi.org/10.1111/1755-0998.12333 DO - 10.1111/1755-0998.12333 ID - Ai2014 ER - TY - JOUR AU - Xiao, L. AU - Yang, G. AU - Zhang, L. AU - Yang, X. AU - Zhao, S. AU - Ji, Z. AU - Zhou, Q. AU - Hu, M. AU - Wang, Y. AU - Chen, M. AU - Xu, Y. AU - Jin, H. AU - Xiao, X. AU - Hu, G. AU - Bao, F. AU - Hu, Y. AU - Wan, P. AU - Li, L. AU - Deng, X. AU - Kuang, T. AU - Xiang, C. AU - Zhu, J. K. AU - Oliver, M. J. AU - He, Y. PY - 2015 DA - 2015// TI - The resurrection genome of Boea hygrometrica: a blueprint for survival of dehydration JO - P Natl Acad Sci USA VL - 112 UR - https://doi.org/10.1073/pnas.1505811112 DO - 10.1073/pnas.1505811112 ID - Xiao2015 ER - TY - JOUR AU - Zhu, Y. AU - Wang, B. AU - Phillips, J. AU - Zhang, Z. N. AU - Du, H. AU - Xu, T. AU - Huang, L. C. AU - Zhang, X. F. AU - Xu, G. H. AU - Li, W. L. AU - Wang, Z. AU - Wang, L. AU - Liu, Y. X. AU - Deng, X. PY - 2015 DA - 2015// TI - Global transcriptome analysis reveals acclimation-primed processes involved in the acquisition of desiccation tolerance in Boea hygrometrica JO - Plant Cell Physiol VL - 56 UR - https://doi.org/10.1093/pcp/pcv059 DO - 10.1093/pcp/pcv059 ID - Zhu2015 ER - TY - STD TI - FastQC. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Accessed 24 June 2014. UR - http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ID - ref113 ER - TY - STD TI - Hannon Lab. FASTX Toolkit. 2011. http://hannonlab.cshl.edu/fastx_toolkit/. Accessed 24 June 2014. UR - http://hannonlab.cshl.edu/fastx_toolkit/ ID - ref114 ER - TY - JOUR AU - Zerbino, D. R. AU - Birney, E. PY - 2008 DA - 2008// TI - Velvet: algorithms for de novo short read assembly using de Bruijn graphs JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.074492.107 DO - 10.1101/gr.074492.107 ID - Zerbino2008 ER - TY - JOUR AU - Grabherr, M. G. AU - Haas, B. J. AU - Yassour, M. AU - Levin, J. Z. AU - Thompson, D. A. AU - Amit, I. AU - Adiconis, X. AU - Fan, L. AU - Raychowdhury, R. AU - Zeng, Q. AU - Chen, Z. AU - Mauceli, E. AU - Hacohen, N. AU - Gnirke, A. AU - Rhind, N. AU - Palma, F. AU - Birren, B. W. AU - Nusbaum, C. AU - Lindblad-Toh, K. AU - Friedman, N. AU - Regev, A. PY - 2011 DA - 2011// TI - Full-length transcriptome assembly from RNA-Seq data without a reference genome JO - Nat Biotech VL - 29 UR - https://doi.org/10.1038/nbt.1883 DO - 10.1038/nbt.1883 ID - Grabherr2011 ER - TY - JOUR AU - Schulz, M. H. AU - Zerbino, D. R. AU - Vingron, M. AU - Birney, E. PY - 2012 DA - 2012// TI - Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts094 DO - 10.1093/bioinformatics/bts094 ID - Schulz2012 ER - TY - STD TI - Gilbert D. EvidentialGene: tr2aacds, mRNA transcript assembly software. 2013. Accessed 30 June 2014http://arthropods.eugenes.org/EvidentialGene/. Accessed 30 June 2014. UR - http://arthropods.eugenes.org/EvidentialGene/ ID - ref118 ER - TY - JOUR AU - Slater, G. S. AU - Birney, E. PY - 2005 DA - 2005// TI - Automated generation of heuristics for biological sequence comparison JO - BMC Bioinformatics VL - 6 UR - https://doi.org/10.1186/1471-2105-6-31 DO - 10.1186/1471-2105-6-31 ID - Slater2005 ER - TY - JOUR AU - Li, W. AU - Godzik, A. PY - 2006 DA - 2006// TI - Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl158 DO - 10.1093/bioinformatics/btl158 ID - Li2006 ER - TY - JOUR AU - Conesa, A. AU - Götz, S. AU - García-Gómez, J. M. AU - Terol, J. AU - Talón, M. AU - Robles, M. PY - 2005 DA - 2005// TI - Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti610 DO - 10.1093/bioinformatics/bti610 ID - Conesa2005 ER - TY - JOUR PY - 2015 DA - 2015// TI - Gene Ontology Consortium: going forward JO - Nucl Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1179 DO - 10.1093/nar/gku1179 ID - ref122 ER - TY - JOUR AU - Lagesen, K. AU - Hailin, P. AU - Rødland, E. A. AU - Staerfeldt, H. H. AU - Rognes, T. AU - Ussery, D. W. PY - 2007 DA - 2007// TI - RNAmmer: consistent and rapid annotation of ribosomal RNA genes JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm160 DO - 10.1093/nar/gkm160 ID - Lagesen2007 ER - TY - JOUR AU - Lowe, T. M. AU - Eddy, S. R. PY - 1997 DA - 1997// TI - tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.5.0955 DO - 10.1093/nar/25.5.0955 ID - Lowe1997 ER - TY - STD TI - Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc B Met. 1995;57:289–300. ID - ref125 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: a multiple sequence alignment with high accuracy and high throughput JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh340 DO - 10.1093/nar/gkh340 ID - Edgar2004 ER - TY - JOUR AU - Kearse, M. AU - Moir, R. AU - Wilson, A. AU - Stones-Havas, S. AU - Cheung, M. AU - Sturrock, S. AU - Buxton, S. AU - Cooper, A. AU - Markowitz, S. AU - Duran, C. AU - Thierer, T. AU - Ashton, B. AU - Meintjes, P. AU - Drummond, A. PY - 2012 DA - 2012// TI - Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts199 DO - 10.1093/bioinformatics/bts199 ID - Kearse2012 ER - TY - JOUR AU - Larkin, M. A. AU - Blackshields, G. AU - Brown, N. P. AU - Chenna, R. AU - McGettigan, P. A. AU - McWilliam, H. AU - Valentin, F. AU - Wallace, I. M. AU - Wilm, A. AU - Lopez, R. AU - Thompson, J. D. AU - Gibson, T. J. AU - Higgins, D. G. PY - 2007 DA - 2007// TI - Clustal W and Clustal X version 2.0. JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm404 DO - 10.1093/bioinformatics/btm404 ID - Larkin2007 ER - TY - JOUR AU - Emms, D. M. AU - Kelly, S. PY - 2015 DA - 2015// TI - OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy JO - Genome Biol VL - 16 UR - https://doi.org/10.1186/s13059-015-0721-2 DO - 10.1186/s13059-015-0721-2 ID - Emms2015 ER - TY - JOUR AU - Haas, B. J. AU - Papanicolaou, A. AU - Yassour, M. AU - Grabherr, M. AU - Blood, P. D. AU - Bowden, J. AU - Couger, M. B. AU - Eccles, D. AU - Li, B. AU - Lieber, M. AU - MacManes, M. D. AU - Ott, M. AU - Orvis, J. AU - Pochet, N. AU - Strozzi, F. AU - Weeks, N. AU - Westerman, R. AU - William, T. AU - Dewey, C. N. AU - Henschel, R. AU - LeDuc, R. D. AU - Friedman, N. AU - Regev, A. PY - 2013 DA - 2013// TI - De novo transcript sequence reconstruction from RNA-Seq Reference Generation and Analysis with Trinity JO - Nature Protoc VL - 8 UR - https://doi.org/10.1038/nprot.2013.084 DO - 10.1038/nprot.2013.084 ID - Haas2013 ER - TY - JOUR AU - Robinson, M. D. AU - Oshlack, A. PY - 2010 DA - 2010// TI - A scaling normalization method for differential expression analysis of RNA-seq data JO - Genome Biol VL - 11 UR - https://doi.org/10.1186/gb-2010-11-3-r25 DO - 10.1186/gb-2010-11-3-r25 ID - Robinson2010 ER - TY - JOUR AU - Capella-Gutiérrez, S. AU - Silla-Martínez, J. M. AU - Gabaldón, T. PY - 2009 DA - 2009// TI - trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp348 DO - 10.1093/bioinformatics/btp348 ID - Capella-Gutiérrez2009 ER - TY - JOUR AU - Felsenstein, J. PY - 1989 DA - 1989// TI - PHYLIP – Phylogeny Inference Package (Version 3.2) JO - Cladistics VL - 5 ID - Felsenstein1989 ER - TY - JOUR AU - Yang, Z. PY - 2007 DA - 2007// TI - PAML 4: phylogenetic analysis by maximum likelihood JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm088 DO - 10.1093/molbev/msm088 ID - Yang2007 ER - TY - JOUR AU - Al-Shahrour, F. AU - Díaz-Uriarte, R. AU - Dopazo, J. PY - 2004 DA - 2004// TI - Fatigo: a web tool for finding significant associations of gene ontology terms with groups of genes JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/btg455 DO - 10.1093/bioinformatics/btg455 ID - Al-Shahrour2004 ER -