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Genomics / Proteomics

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IDTitleSection/TopicAuthorsKeywords
1116Comparative plastid genomics of the Campanuloideae (Wahlenbergia and Platycodon) and close relative Pseudonemacladus: implications for phylogeny and genome evolution
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Genomics / ProteomicsHaberle, Rosemarie; Downie, Stephen; Kuehl, Jennifer; Cai, Zhengqiu; Boore, Jeffrey ; Jansen, Robert.Campanulaceae
chloroplast DNA
plastome
375Expanding our understanding of the evolution of the Carica papaya X and Y chromosomes
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Genomics / ProteomicsBrown, Jennifer; Lappin, Fiona; Weingartner, Laura; Hawkins, Kevin; McDermott, Ross; Harkess, Alex; Moore, Richard.Sex chromosome
Molecular evolution
Genome evolution
501Identification and evolution of putative trichome genes in milkweeds (Asclepias, Apocynaceae).
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Genomics / ProteomicsFathepure, Shakuntala; Straub, Shannon; Liston, Aaron; Cronn, Richard; Fishbein, Mark.
251Identification of Mitogen Activated Protein Kinase Family Members in Soybean
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Genomics / ProteomicsNeupane, Achal; Piya, Sarbottam; Reese, Neil; Rohila, Jai; Subramanian, Senthil; Nepal, Madhav.Mitogen Activated Protein Kinase
MAPK Identification
MAPK nomenclature
Soybean MAPK
968Large-scale transcriptome sequencing and phylogenetic hypotheses for monocots based on analyses 970 (and up to 1888) low copy nuclear genes
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Genomics / ProteomicsdePamphilis, Claude; Wickett, Norman; Duarte, JIll; Der, Joshua; McCain, Michael; Leebens-Mack, Jim; Edger, Patrick; Pires, Joseph; Wafula, Eric; Zhang, Yeting; Ayyampalayam, Saravanaraj; Barrett, Craig; Davis, Jerrold; Graham, Sean; McCombie, Richard; Zomlefer, Wendy; Stevenson, Dennis; Givnish, Thomas.monocotyledons
phylogenomics
Single/low copy nuclear genes
893Mixture models versus a priori partitioning schemes in analyses of plastome data sets: alarge angiosperm matrix revisited
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Genomics / ProteomicsClements, Mark; Moore, Michael; Mathews, Sarah.angiosperm
phylogeny
data partitioning
mixture models
Plastid genome
1006
Canceled
Molecular dissection of male germ lineage-specific promoters reveals multiple regulatory motifs
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Genomics / ProteomicsGou, Xiaoping; Yuan, Tong; Wei, Xiaoping; Zhang, Jinghua; Li, Jia; Russell, Scott.gene expression
sperm cell
male germ lineage
promoter
PzIPT
1043Rapid Reconstruction and Annotation of Vaccinium macrocarpon Organellar Genomes
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Genomics / ProteomicsFajardo, Diego; Senalik, Douglas; Steffan, Shawn; Harbut, Rebecca; Polashock, James; Vorsa, Nicholi ; Zalapa, Juan.Genomics
next generation sequencing
American cranberry
Mitochondria
587Retrotransposon amplification and sex chromosome evolution in Asparagus
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Genomics / ProteomicsHarkess, Alex; Leebens-Mack, Jim.sex chromosomes
retrotransposons
Genome evolution
974Scaling phylogenomics to over one thousand species: Relationships of Viridiplantae inferred from the 1KP (One Thousand Plants) project pilot data set
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Genomics / ProteomicsWickett, Norman; Leebens-Mack, Jim; Carpenter, Eric; Mirarab, Siavash; Ayyampalayam, Saravanaraj; Barker, Mike; Burleigh, J. Gordon; Gitzendanner, Matthew; Gonzales, Michael; Matasci, Naim; dePamphilis, Claude; Ruhfel, Brad; Wafula, Eric; Warnow, Tandy; Chen, Tao; Deyholos, Michael; Graham, Sean; Mathews, Sarah; Melkonian, Michael; Soltis, Douglas; Soltis, Pamela; Shaw, Jonathan; Stevenson, Dennis; Surek, Barbara; Villarreal, Juan; Zhang, Yong; Tian, Zhijian; Wong, Gane Ka-Shu.Genomics
transcriptomes
phylogenomics
green plants
Viridiplantae
land plants
Embryophytes
single/low copy nuclear genes
species tree reconciliation
supertrees
329The challenge of assembling highly heterozygous genomes from short read sequences
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Genomics / ProteomicsWeitemier, Kevin; Straub, Shannon; Parks, Matt; Cronn, Richard; Fishbein, Mark; Liston, Aaron.Apocynaceae
Asclepias
Genome Assembly
Heterozygosity
SNP detection
Sequence capture
952The draft genome sequence of Amborella trichopoda sheds light on the ancestral angiosperm genome
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Genomics / ProteomicsDer, Joshua; Ayyampalayam, Saravanaraj; Burnett, James; Chamala, Srikar; Chanderbali, Andre; Estill, James; Jiao, Yuannian; Liu, Kun; Ralph, Paula; Lan, Tianying; Lyons, Eric; Tang, Haibao; Tomsho, Lynn P.; Wafula, Eric; Walts, Brandon; Albert, Victor; Barbazuk, Brad; Ma, Hong; Leebens-Mack, Jim; Palmer, Jeffrey; Rounsley, Steve; Sankoff, David; Schuster, Stephan C.; Soltis, Douglas; Soltis, Pamela; Wessler, Susan; Wing, Rod; dePamphilis, Claude.Amborella
Amborella trichopoda
Whole Genome Shotgun
Genome Assembly
Genome evolution
Ancestral Genome
Nuclear Genome
FISH
Optical Map
angiosperm
Basal Angiosperm
905The effect of paleopolyploidy on genome evolution in Agavoideae
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Genomics / ProteomicsMcKain, Michael R.; Wickett, Norman; Zhang, Yeting; Ayyampalayam, Saravanaraj; McCombie, Richard; Chase, Mark; Pires, Joseph; dePamphilis, Claude; Leebens-Mack, Jim.paleopolyploidy
Agavoideae
bimodal karyotype
Sequence capture
455The investigation of selective sweeps within the Carica papaya X chromosome.
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Genomics / ProteomicsLappin, Fiona; Brown, Jennifer; Weingartner, Laura; Hawkins, Kevin; McDermott, Ross; Harkess, Alex; Moore, Richard.Carica papaya
Selective sweep
Sex chromosome
1008The Parasitic Plant Genome Project
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Genomics / ProteomicsHonaas, Loren; Wafula, Eric; Wickett, Norman; Zhang, Yeting; Zhang , Zhenzhen; Der, Joshua; Ralph, Paula; Landherr, Lena; Bao, Yongde; Wu, Biao; Gunathilake, Pradeepa; Fernandez-Aparicio, Monica; Das, Malay; Huang, Kan; Tomsho, Lynn P.; Schuster, Stephan C.; Taylor, Chris G. ; Altman, Naomi S. ; Yoder, John I. ; Timko, Michael P.; Westwood, James; dePamphilis, Claude.parasitic plant
Genomics
Orobanchaceae
EST
de novo transcriptome
243The relationship between recombination and genomic diversity in Carica papaya
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Genomics / ProteomicsBrown, Jennifer; Hawkins, Kevin; McDermott, Ross; Moore, Richard.
439The Role of Selection in Carica papaya Genomic Evolution
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Genomics / ProteomicsHawkins, Kevin; Brown, Jennifer; McDermott, Ross; Moore, Richard.Carica papaya
selection
recombination
864Transcriptome dynamics in the dormancy-spring growth transition of Douglas-fir needles.
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Genomics / ProteomicsKnaus, Brian J.; Dolan, Peter; Denver, Dee; Cronn, Richard.Bud burst
Dormancy
Douglas-fir
Pseudotsuga menzeisii
RNA-seq
Transcriptomics
904Using transcriptomic data to develop sequence-capture probes for diverse lineages.
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Genomics / ProteomicsDouglas, Norman; Moore, Michael.Transcriptomics
marker development
Sequence capture
Phylogenetics
population genetics

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