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Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

Vanburen, Robert ; Bryant, Doug ; Edger, Patrick P ; Tang, Haibao ; Burgess, Diane ; Challabathula, Dinakar ; Spittle, Kristi ; Hall, Richard ; Gu, Jenny ; Lyons, Eric ; Freeling, Michael ; Bartels, Dorothea ; Ten Hallers, Boudewijn ; Hastie, Alex ; Michael, Todd P ; Mockler, Todd C

Nature, 26 November 2015, Vol.527(7579), pp.508-11 [Peer Reviewed Journal]

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Secondary structure analyses of the nuclear rRNA internal transcribed spacers and assessment of its phylogenetic utility across the Brassicaceae (mustards)

Edger, Patrick P ; Tang, Michelle ; Bird, Kevin A ; Mayfield, Dustin R ; Conant, Gavin ; Mummenhoff, Klaus ; Koch, Marcus A ; Pires, J Chris

PloS one, 2014, Vol.9(7), pp.e101341 [Peer Reviewed Journal]

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Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model

Eric Schranz, M ; Mohammadin, Setareh ; Edger, Patrick P

Current Opinion in Plant Biology, April 2012, Vol.15(2), pp.147-153 [Peer Reviewed Journal]

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Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome

Honaas, Loren A ; Wafula, Eric K ; Wickett, Norman J ; Der, Joshua P ; Zhang, Yeting ; Edger, Patrick P ; Altman, Naomi S ; Pires, J Chris ; Leebens-Mack, James H ; Depamphilis, Claude W

PloS one, 2016, Vol.11(1), pp.e0146062 [Peer Reviewed Journal]

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Anatolian origins and diversification of Aethionema, the sister lineage of the core Brassicaceae

Mohammadin, Setareh ; Peterse, Kim ; Van De Kerke, Sara J. ; Chatrou, Lars W. ; Donmez, Ali A. ; Mummenhoff, Klaus ; Pires, J. Chris ; Edger, Patrick P. ; Al - Shehbaz, Ihsan A. ; Schranz, M. Eric

American Journal of Botany, 2017 [Peer Reviewed Journal]

2017

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PYK10 myrosinase reveals a functional coordination between endoplasmic reticulum bodies and glucosinolates in Arabidopsis thaliana

Nakano, Ryohei T. ; Piślewska‐Bednarek, Mariola ; Yamada, Kenji ; Edger, Patrick P. ; Miyahara, Mado ; Kondo, Maki ; Böttcher, Christoph ; Mori, Masashi ; Nishimura, Mikio ; Schulze‐Lefert, Paul ; Hara‐Nishimura, Ikuko ; Bednarek, Paweł

Plant Journal, January 2017, Vol.89(2), pp.204-220 [Peer Reviewed Journal]

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Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple

Wai, Ching M. ; Vanburen, Robert ; Zhang, Jisen ; Huang, Lixian ; Miao, Wenjing ; Edger, Patrick P. ; Yim, Won C. ; Priest, Henry D. ; Meyers, Blake C. ; Mockler, Todd ; Smith, J. Andrew C. ; Cushman, John C. ; Ming, Ray

Plant Journal, October 2017, Vol.92(1), pp.19-30 [Peer Reviewed Journal]

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Functional network analysis of genes differentially expressed during xylogenesis in soc1ful woody Arabidopsis plants

Davin, Nicolas ; Edger, Patrick P. ; Hefer, Charles A. ; Mizrachi, Eshchar ; Schuetz, Mathias ; Smets, Erik ; Myburg, Alexander A. ; Douglas, Carl J. ; Schranz, Michael E. ; Lens, Frederic

Plant Journal, June 2016, Vol.86(5), pp.376-390 [Peer Reviewed Journal]

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The causes and consequences of subgenome dominance in hybrids and recent polyploids

Bird, Kevin A. ; Vanburen, Robert ; Puzey, Joshua R. ; Edger, Patrick P.

New Phytologist, October 2018, Vol.220(1), pp.87-93 [Peer Reviewed Journal]

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Subgenome assignment in allopolyploids: challenges and future directions

Edger, Patrick P ; Mckain, Michael R ; Bird, Kevin A ; Vanburen, Robert

Current Opinion in Plant Biology, April 2018, Vol.42, pp.76-80 [Peer Reviewed Journal]

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Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinolate synthesis

Bekaert, Michaël ; Edger, Patrick P. ; Hudson, Corey M. ; Pires, J. Chris ; Conant, Gavin C.

New Phytologist, October 2012, Vol.196(2), pp.596-605 [Peer Reviewed Journal]

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12
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Two-phase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative and absolute dosage constraints

Bekaert, Michaël ; Edger, Patrick P ; Pires, J Chris ; Conant, Gavin C

The Plant cell, May 2011, Vol.23(5), pp.1719-28 [Peer Reviewed Journal]

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13
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Positionally-conserved but sequence-diverged: identification of long non-coding RNAs in the Brassicaceae and Cleomaceae

Mohammadin, Setareh ; Edger, Patrick P ; Pires, J Chris ; Schranz, Michael Eric

BMC plant biology, 11 September 2015, Vol.15, pp.217 [Peer Reviewed Journal]

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The genome of black raspberry (Rubus occidentalis

Vanburen, Robert ; Bryant, Doug ; Bushakra, Jill M. ; Vining, Kelly J. ; Edger, Patrick P. ; Rowley, Erik R. ; Priest, Henry D. ; Michael, Todd P. ; Lyons, Eric ; Filichkin, Sergei A. ; Dossett, Michael ; Finn, Chad E. ; Bassil, Nahla V. ; Mockler, Todd C.

Plant Journal, September 2016, Vol.87(6), pp.535-547 [Peer Reviewed Journal]

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Whole genome and tandem duplicate retention facilitated glucosinolate pathway diversification in the mustard family

Hofberger, Johannes A ; Lyons, Eric ; Edger, Patrick P ; Chris Pires, J ; Eric Schranz, M

Genome biology and evolution, 2013, Vol.5(11), pp.2155-73 [Peer Reviewed Journal]

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16
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Molecular Resources from Transcriptomes in the Brassicaceae Family

Lopez, Lua ; Wolf, Eva M ; Pires, J Chris ; Edger, Patrick P ; Koch, Marcus A

Frontiers in plant science, 2017, Vol.8, pp.1488 [Peer Reviewed Journal]

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17
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Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes (Plant RNA Isolation and Transcriptome Sequencing)

Johnson, Marc T. J ; Carpenter, Eric J ; Tian, Zhijian ; Bruskiewich, Richard ; Burris, Jason N ; Carrigan, Charlotte T ; Chase, Mark W ; Clarke, Neil D ; Covshoff, Sarah ; dePamphilis, Claude W ; Edger, Patrick P ; Goh, Falicia ; Graham, Sean ; Greiner, Stephan ; Hibberd, Julian M ; Jordon-Thaden, Ingrid ; Kutchan, Toni M ; Leebens-Mack, James ; Melkonian, Michael ; Miles, Nicholas ; Myburg, Henrietta ; Patterson, Jordan ; Pires, J. Chris ; Ralph, Paula ; Rolf, Megan ; Sage, Rowan F ; Soltis, Douglas ; Soltis, Pamela ; Stevenson, Dennis ; Stewart, C. Neal ; Surek, Barbara ; Thomsen, Christina J. M ; Villarreal, Juan Carlos ; Wu, Xiaolei ; Zhang, Yong ; Deyholos, Michael K ; Wong, Gane Ka-Shu Quince, Christopher (Editor)

2012, Vol.7(11), p.e50226 [Peer Reviewed Journal]

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18
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Elucidating steroid alkaloid biosynthesis in Veratrum californicum: production of verazine in Sf9 cells

Augustin, Megan M. ; Ruzicka, Dan R. ; Shukla, Ashutosh K. ; Augustin, Jörg M. ; Starks, Courtney M. ; O' Neil‐Johnson, Mark ; Mckain, Michael R. ; Evans, Bradley S. ; Barrett, Matt D. ; Smithson, Ann ; Wong, Gane Ka‐Shu ; Deyholos, Michael K. ; Edger, Patrick P. ; Pires, J. Chris ; Leebens‐Mack, James H. ; Mann, David A. ; Kutchan, Toni M.

Plant Journal, June 2015, Vol.82(6), pp.991-1003 [Peer Reviewed Journal]

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19
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Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor

Floyd, Sandra K ; Ryan, Joseph G ; Conway, Stephanie J ; Brenner, Eric ; Burris, Kellie P ; Burris, Jason N ; Chen, Tao ; Edger, Patrick P ; Graham, Sean W ; Leebens-Mack, James H ; Pires, J. Chris ; Rothfels, Carl J ; Sigel, Erin M ; Stevenson, Dennis W ; Neal Stewart, C ; Wong, Gane Ka-Shu ; Bowman, John L

Molecular Phylogenetics and Evolution, December 2014, Vol.81, pp.159-173 [Peer Reviewed Journal]

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20
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Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution (Microbial Symbionts Affect Host Genomes)

Delaux, Pierre-Marc ; Varala, Kranthi ; Edger, Patrick P ; Coruzzi, Gloria M ; Pires, J. Chris ; Ané, Jean-Michel Mcdowell, John M. (Editor)

2014, Vol.10(7), p.e1004487 [Peer Reviewed Journal]

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21
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Comparative analysis of 11 Brassicales mitochondrial genomes and the mitochondrial transcriptome of Brassica oleracea

Grewe, Felix ; Edger, Patrick P ; Keren, Ido ; Sultan, Laure ; Pires, J. Chris ; Ostersetzer-Biran, Oren ; Mower, Jeffrey P

Mitochondrion, November 2014, Vol.19, pp.135-143 [Peer Reviewed Journal]

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22
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Domestication of Temperate and Coastal Hybrids with Distinct Ancestral Gene Selection in Octoploid Strawberry

Hardigan, Michael A. ; Poorten, Thomas J. ; Acharya, Charlotte B. ; Cole, Glenn S. ; Hummer, Kim E. ; Bassil, Nahla ; Edger, Patrick P. ; Knapp, Steven J.

Plant Genome, November 2018, Vol.11(3), pp.1-11 [Peer Reviewed Journal]

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23
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Seed desiccation mechanisms co‐opted for vegetative desiccation in the resurrection grass Oropetium thomaeum

Vanburen, Robert ; Wai, Ching Man ; Zhang, Qingwei ; Song, Xiaomin ; Edger, Patrick P. ; Bryant, Doug ; Michael, Todd P. ; Mockler, Todd C. ; Bartels, Dorothea

Plant, Cell & Environment, October 2017, Vol.40(10), pp.2292-2306 [Peer Reviewed Journal]

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24
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Watching the grin fade: Tracing the effects of polyploidy on different evolutionary time scales

Mayfield-Jones, Dustin ; Washburn, Jacob D ; Arias, Tatiana ; Edger, Patrick P ; Pires, J. Chris ; Conant, Gavin C

Seminars in Cell and Developmental Biology, April 2013, Vol.24(4), pp.320-331 [Peer Reviewed Journal]

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25
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Patterns of Population Variation in Two Paleopolyploid Eudicot Lineages Suggest That Dosage-Based Selection on Homeologs Is Long-Lived

Hao, Yue ; Washburn, Jacob D ; Rosenthal, Jacob ; Nielsen, Brandon ; Lyons, Eric ; Edger, Patrick P ; Pires, J Chris ; Conant, Gavin C

Genome biology and evolution, 01 March 2018, Vol.10(3), pp.999-1011 [Peer Reviewed Journal]

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26
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A Whole-Transcriptome Approach to Evaluating Reference Genes for Quantitative Gene Expression Studies: A Case Study in

Stanton, Kimmy A ; Edger, Patrick P ; Puzey, Joshua R ; Kinser, Taliesin ; Cheng, Philip ; Vernon, Daniel M ; Forsthoefel, Nancy R ; Cooley, Arielle M

G3 (Bethesda, Md.), 03 April 2017, Vol.7(4), pp.1085-1095

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27
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Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

Ma Hong ; Landherr Lena L ; Edger Patrick P ; Wall P Kerr ; Duarte Jill M ; Pires J Chris ; Leebens-Mack Jim ; Depamphilis Claude W

BMC Evolutionary Biology, 01 February 2010, Vol.10(1), p.61 [Peer Reviewed Journal]

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28
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Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution

Huang, Chien - Hsun ; Sun, Renran ; Hu, Yi ; Zeng, Liping ; Zhang, Ning ; Cai, Liming ; Zhang, Qiang ; Koch, Marcus A ; Al - Shehbaz, Ihsan ; Edger, Patrick P ; Pires, J. Chris ; Tan, Dun - Yan ; Zhong, Yang ; Ma, Hong

Molecular Biology and Evolution, 2016, Vol. 33(2), pp.394-412 [Peer Reviewed Journal]

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29
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Chromosome-scale scaffolding of the black raspberry ( L.) genome based on chromatin interaction data

Jibran, Rubina ; Dzierzon, Helge ; Bassil, Nahla ; Bushakra, Jill M ; Edger, Patrick P ; Sullivan, Shawn ; Finn, Chad E ; Dossett, Michael ; Vining, Kelly J ; Vanburen, Robert ; Mockler, Todd C ; Liachko, Ivan ; Davies, Kevin M ; Foster, Toshi M ; Chagné, David

Horticulture research, 2018, Vol.5, pp.8 [Peer Reviewed Journal]

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30
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A multi–step comparison of short–read full plastome sequence assembly methods in grasses

Wysocki, William P. ; Clark, Lynn G. ; Kelchner, Scot A. ; Burke, Sean V. ; Pires, J. Chris ; Edger, Patrick P. ; Mayfield, Dustin R. ; Triplett, Jimmy K. ; Columbus, J. Travis ; Ingram, Amanda L. ; Duvall, Melvin R.

TAXON, August 2014, Vol.63(4), pp.899-910 [Peer Reviewed Journal]

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31
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Evolutionary relationships in Panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae)

Burke, Sean V ; Wysocki, William P ; Zuloaga, Fernando O ; Craine, Joseph M ; Pires, J Chris ; Edger, Patrick P ; Mayfield-Jones, Dustin ; Clark, Lynn G ; Kelchner, Scot A ; Duvall, Melvin R

BMC plant biology, 18 June 2016, Vol.16(1), pp.140 [Peer Reviewed Journal]

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32
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Resolving deep relationships of PACMAD grasses: a phylogenomic approach

Cotton, Joseph L ; Wysocki, William P ; Clark, Lynn G ; Kelchner, Scot A ; Pires, J Chris ; Edger, Patrick P ; Mayfield-Jones, Dustin ; Duvall, Melvin R

BMC plant biology, 11 July 2015, Vol.15, pp.178 [Peer Reviewed Journal]

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33
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Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes

Saarela, Jeffery M ; Wysocki, William P ; Barrett, Craig F ; Soreng, Robert J ; Davis, Jerrold I ; Clark, Lynn G ; Kelchner, Scot A ; Pires, J. Chris ; Edger, Patrick P ; Mayfield, Dustin R ; Duvall, Melvin R

AoB PLANTS, 2015, Vol. 7 [Peer Reviewed Journal]

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34
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Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization

Emery, Marianne ; Willis, M Madeline S ; Hao, Yue ; Barry, Kerrie ; Oakgrove, Khouanchy ; Peng, Yi ; Schmutz, Jeremy ; Lyons, Eric ; Pires, J Chris ; Edger, Patrick P ; Conant, Gavin C

PLoS genetics, March 2018, Vol.14(3), pp.e1007267 [Peer Reviewed Journal]

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35
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Polyploid evolution of the Brassicaceae during the Cenozoic era

Kagale, Sateesh ; Robinson, Stephen J ; Nixon, John ; Xiao, Rong ; Huebert, Terry ; Condie, Janet ; Kessler, Dallas ; Clarke, Wayne E ; Edger, Patrick P ; Links, Matthew G ; Sharpe, Andrew G ; Parkin, Isobel A P

The Plant cell, July 2014, Vol.26(7), pp.2777-91 [Peer Reviewed Journal]

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36
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Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes

Edger, Patrick ; Pires, J.

Chromosome Research, 2009, Vol.17(5), pp.699-717 [Peer Reviewed Journal]

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37
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The pineapple genome and the evolution of CAM photosynthesis

Ming, Ray ; Vanburen, Robert ; Wai, Ching Man ; Tang, Haibao ; Schatz, Michael C ; Bowers, John E ; Lyons, Eric ; Wang, Ming-Li ; Chen, Jung ; Biggers, Eric ; Zhang, Jisen ; Huang, Lixian ; Zhang, Lingmao ; Miao, Wenjing ; Zhang, Jian ; Ye, Zhangyao ; Miao, Chenyong ; Lin, Zhicong ; Wang, Hao ; Zhou, Hongye ; Yim, Won C ; Priest, Henry D ; Zheng, Chunfang ; Woodhouse, Margaret ; Edger, Patrick P ; Guyot, Romain ; Guo, Hao-Bo ; Guo, Hong ; Zheng, Guangyong ; Singh, Ratnesh ; Sharma, Anupma ; Min, Xiangjia ; Zheng, Yun ; Lee, Hayan ; Gurtowski, James ; Sedlazeck, Fritz J ; Harkess, Alex ; Mckain, Michael R ; Liao, Zhenyang ; Fang, Jingping ; Liu, Juan ; Zhang, Xiaodan ; Zhang, Qing ; Hu, Weichang ; Qin, Yuan ; Wang, Kai ; Chen, Li-Yu ; Shirley, Neil ; Lin, Yann-Rong ; Liu, Li-Yu ; Hernandez, Alvaro G ; Wright, Chris L ; Bulone, Vincent ; Tuskan, Gerald A ; Heath, Katy ; Zee, Francis ; Moore, Paul H ; Sunkar, Ramanjulu ; Leebens-Mack, James H ; Mockler, Todd ; Bennetzen, Jeffrey L ; Freeling, Michael ; Sankoff, David ; Paterson, Andrew H ; Zhu, Xinguang ; Yang, Xiaohan ; Smith, J Andrew C ; Cushman, John C ; Paull, Robert E ; Yu, Qingyi

Nature genetics, December 2015, Vol.47(12), pp.1435-42 [Peer Reviewed Journal]

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A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome

Vanburen, Robert ; Wai, Ching Man ; Colle, Marivi ; Wang, Jie ; Sullivan, Shawn ; Bushakra, Jill M ; Liachko, Ivan ; Vining, Kelly J ; Dossett, Michael ; Finn, Chad E ; Jibran, Rubina ; Chagné, David ; Childs, Kevin ; Edger, Patrick P ; Mockler, Todd C ; Bassil, Nahla V

GigaScience, 01 August 2018, Vol.7(8) [Peer Reviewed Journal]

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