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1

Sequencing and Analyzing the Transcriptomes of a Thousand Species Across the Tree of Life for Green Plants

Wong, Gane Ka-Shu, Soltis, Douglas E., Leebens-Mack, Jim, Wickett, Norman J., Barker, Michael S., de Peer, Yves Van, Graham, Sean W., Melkonian, Michael

Journal:

Annual Review of Plant Biology

Year:

2020

File:

PDF, 1.33 MB

2020

2

The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression

Douglas E. Soltis, Hong Ma, Michael W. Frohlich, Pamela S. Soltis, Victor A. Albert, David G. Oppenheimer, Naomi S. Altman, Claude dePamphilis, Jim Leebens-Mack

Journal:

Trends in Plant Science

Year:

2007

Language:

english

File:

PDF, 1.07 MB

english, 2007

3

Gene families as soft cliques with backbones:Amborellacontrasted with other flowering plants

Zheng, Chunfang, Kononenko, Alexey, Leebens-Mack, Jim, Lyons, Eric, Sankoff, David

Journal:

Year:

2014

Language:

english

File:

PDF, 1.84 MB

english, 2014

4

Phylogenomic analyses of species relationships in the genus Sabal (Arecaceae) using targeted sequence capture

Heyduk, Karolina, Trapnell, Dorset W., Barrett, Craig F., Leebens-Mack, Jim

Journal:

Biological Journal of the Linnean Society

Year:

2016

Language:

english

File:

PDF, 771 KB

english, 2016

5

Single nucleotide polymorphism isolated from a novel EST dataset in garden asparagus (Asparagus officinalis L.)

Mercati, Francesco, Riccardi, Paolo, Leebens-Mack, Jim, Abenavoli, Maria Rosa, Falavigna, Agostino, Sunseri, Francesco

Journal:

Year:

2013

Language:

english

File:

PDF, 955 KB

english, 2013

6

Large-scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants

Abdelali Barakat, Kerr Wall, Jim Leebens-Mack, Yunjiao J. Wang, John E. Carlson, Claude W. DePamphilis

Journal:

The Plant Journal

Year:

2007

Language:

english

File:

PDF, 946 KB

english, 2007

7

A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales

McKain, Michael R., Tang, Haibao, McNeal, Joel R., Ayyampalayam, Saravanaraj, Davis, Jerrold I., dePamphilis, Claude W., Givnish, Thomas J., Pires, J. Chris, Stevenson, Dennis Wm., Leebens-Mack, Jim H

Journal:

Genome Biology and Evolution

Year:

2016

Language:

english

File:

PDF, 621 KB

english, 2016

8

Evolution of Asparagus L. (Asparagaceae): Out-of-South-Africa and multiple origins of sexual dimorphism

Norup, Maria F., Petersen, Gitte, Burrows, Sandie, Bouchenak-Khelladi, Yanis, Leebens-Mack, Jim, Pires, J. Chris, Linder, H. Peter, Seberg, Ole

Journal:

Molecular Phylogenetics and Evolution

Year:

2015

Language:

english

File:

PDF, 3.21 MB

english, 2015

9

Plastid genomes and deep relationships among the commelinid monocot angiosperms

Craig F. Barrett, Jerrold I. Davis, Jim Leebens-Mack, John G. Conran, Dennis W. Stevenson

Journal:

Year:

2012

Language:

english

File:

PDF, 651 KB

english, 2012

10

Insights into the Musa genome: Syntenic relationships to rice and between Musa species

Magali Lescot, Pietro Piffanelli, Ana Y Ciampi, Manuel Ruiz, Guillaume Blanc, Jim Leebens-Mack, Felipe R da Silva, Candice MR Santos, Angélique D'Hont, Olivier Garsmeur, Alberto D Vilarinhos, Hiroyuki

Journal:

Year:

2008

Language:

english

File:

PDF, 904 KB

english, 2008

11

Floral homeotic C function genes repress specific B function genes in the carpel whorl of the basal eudicot California poppy (Eschscholzia californica)

Aravinda L Yellina, Svetlana Orashakova, Sabrina Lange, Robert Erdmann, Jim Leebens-Mack, Annette Becker

Journal:

Year:

2010

Language:

english

File:

PDF, 2.94 MB

english, 2010

12

Single nucleotide polymorphism-based parentage analysis and population structure in garden asparagus, a worldwide genetic stock classification

Mercati, Francesco, Riccardi, Paolo, Harkess, Alex, Sala, Tea, Abenavoli, Maria Rosa, Leebens-Mack, Jim, Falavigna, Agostino, Sunseri, Francesco

Journal:

Molecular Breeding

Year:

2015

Language:

english

File:

PDF, 1.21 MB

english, 2015

13

Leaf anatomy is not correlated to CAM function in a C3+CAM hybrid species, Yucca gloriosa

Heyduk, Karolina, Ray, Jeremy N, Leebens-Mack, Jim

Journal:

Annals of Botany

Year:

2020

Language:

english

File:

PDF, 1.02 MB

english, 2020

14

Towards Improved Reconstruction of Ancestral Gene Order in Angiosperm Phylogeny

Sankoff, David, Zheng, Chunfang, Wall, P. Kerr, dePamphilis, Claude, Leebens-Mack, Jim, Albert, Victor A.

Journal:

Journal of Computational Biology

Year:

2009

Language:

english

File:

PDF, 450 KB

english, 2009

15

Gas exchange and leaf anatomy of a C 3 –CAM hybrid, Yucca gloriosa (Asparagaceae)

Heyduk, Karolina, Burrell, Nia, Lalani, Falak, Leebens-Mack, Jim

Journal:

Journal of Experimental Botany

Year:

2016

Language:

english

File:

PDF, 2.72 MB

english, 2016

16

Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth

Hongzhi Kong, Lena L. Landherr, Michael W. Frohlich, Jim Leebens-Mack, Hong Ma, Claude W. DePamphilis

Journal:

The Plant Journal

Year:

2007

Language:

english

File:

PDF, 858 KB

english, 2007

17

Sex-biased gene expression in dioecious garden asparagus ( Asparagus officinalis )

Harkess, Alex, Mercati, Francesco, Shan, Hong-Yan, Sunseri, Francesco, Falavigna, Agostino, Leebens-Mack, Jim

Journal:

New Phytologist

Year:

2015

Language:

english

File:

PDF, 707 KB

english, 2015

18

Pollen Dispersal in Yucca filamentosa (Agavaceae): The Paradox of Self-Pollination Behavior by Tegeticula yuccasella (Prodoxidae)

Deborah L. Marr, Jim Leebens-Mack, Lindsey Elms and Olle Pellmyr

Journal:

American Journal of Botany

Year:

2000

Language:

english

File:

PDF, 1.27 MB

english, 2000

19

Utility of Amborella trichopoda and Nuphar advena Expressed Sequence Tags for Comparative Sequence Analysis

Jill M. Duarte, P. Kerr Wall, Laura M. Zahn, Pamela S. Soltis, Douglas E. Soltis, Jim Leebens-Mack, John E. Carlson, Hong Ma and Claude W. dePamphilis

Journal:

Year:

2008

Language:

english

File:

PDF, 2.02 MB

english, 2008

20

Pollination Biology in Hybridizing Baptisia (Fabaceae) Populations

Jim Leebens-Mack and Brook G. Milligan

Journal:

American Journal of Botany

Year:

1998

Language:

english

File:

PDF, 1.90 MB

english, 1998

21

Utility of Amborella trichopoda and Nuphar advena expressed sequence tags for comparative sequence analysis

Duarte, Jill M., Wall, Kerr P., Zahn, Laura M., Soltis, Pamela S., Soltis, Douglas E., Leebens-Mack, Jim, Carlson, John E., Ma, Hong W., dePamphilis, Claude W.

Journal:

Year:

2008

Language:

english

File:

PDF, 1.46 MB

english, 2008

22

Behind the Scenes: Planning a Multispecies Microarray Experiment

Altman, Naomi, Leebens-Mack, Jim, Zahn, Laura, Chanderbali, André, Tian, Donglan, Werner, Lillian, Ma, Hong, dePamphilis, Claude

Journal:

Year:

2006

Language:

english

File:

PDF, 8.39 MB

english, 2006

23

Identification of shared single copy nuclear genes inArabidopsis, Populus, VitisandOryzaand their phylogenetic utility across various taxonomic levels

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

Journal:

BMC Evolutionary Biology

Year:

2010

Language:

english

File:

PDF, 865 KB

english, 2010

24

TheAmborellagenome: an evolutionary reference for plant biology

Douglas E Soltis, Victor A Albert, Jim Leebens-Mack, Jeffrey D Palmer…

Journal:

Year:

2008

Language:

english

File:

PDF, 334 KB

english, 2008

25

Homoploid hybrid origin of Yucca gloriosa: intersectional hybrid speciation in Yucca (Agavoideae, Asparagaceae)

Jeremy D. Rentsch, Jim Leebens-Mack

Journal:

Ecology and Evolution

Year:

2012

Language:

english

File:

PDF, 4.15 MB

english, 2012

26

Genomes and evolution

Jim Leebens-Mack, Susan R Wessler, R Kelly Dawe

Journal:

Current Opinion in Genetics & Development

Year:

2007

Language:

english

File:

PDF, 79 KB

english, 2007

27

Plant reproductive genomics at the Plant and Animal Genome Conference

Jim Leebens-Mack, Douglas E. Soltis, Pamela S. Soltis

Journal:

Comparative and Functional Genomics

Year:

2005

Language:

english

File:

PDF, 165 KB

english, 2005

28

A genome triplication associated with early diversification of the core eudicots

Yuannian Jiao, Jim Leebens-Mack, Saravanaraj Ayyampalayam, John E Bowers, Michael R McKain, Joel McNeal, Megan Rolf, Daniel R Ruzicka, Eric Wafula, Norman J Wickett, Xiaolei Wu, Yong Zhang, Jun Wang,

Journal:

Year:

2012

Language:

english

File:

PDF, 319 KB

english, 2012

29

Host Specificity and the Genetic Structure of Two Yucca Moth Species in a Yucca Hybrid Zone

Jim Leebens-Mack, Olle Pellmyr and Marcus Brock

Journal:

Year:

1998

Language:

english

File:

PDF, 1.14 MB

english, 1998

30

Distributed phenomics with the un PAK project reveals the effects of mutations

Rutter, Matthew T., Murren, Courtney J., Callahan, Hilary S., Bisner, April, Leebens‐Mack, Jim, Wolyniak, Michael J., Strand, Allan E.

Journal:

The Plant Journal

Year:

2019

Language:

english

File:

PDF, 1.08 MB

english, 2019

31

Comparison of next generation sequencing technologies for transcriptome characterization

P Kerr Wall, Jim Leebens-Mack, André S Chanderbali, Abdelali Barakat, Erik Wolcott, Haiying Liang, Lena Landherr, Lynn P Tomsho, Yi Hu, John E Carlson, Hong Ma, Stephan C Schuster, Douglas E Soltis, P

Journal:

Year:

2009

Language:

english

File:

PDF, 1.52 MB

english, 2009

32

A Century of Sex Determination in Flowering Plants

Harkess, Alex, Leebens-Mack, Jim

Journal:

Journal of Heredity

Year:

2016

Language:

english

File:

PDF, 212 KB

english, 2016

33

Retrotransposon Proliferation Coincident with the Evolution of Dioecy in Asparagus

Harkess, Alex, Mercati, Francesco, Abbate, Loredana, McKain, Michael, Pires, J. Chris, Sala, Tea, Sunseri, Francesco, Falavigna, Agostino, Leebens-Mack, Jim

Journal:

G3 Genes|Genome|Genetics

Year:

2016

Language:

english

File:

PDF, 1.01 MB

english, 2016

34

Altered Gene Regulatory Networks Are Associated With the Transition From C3 to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae)

Heyduk, Karolina, Hwang, Michelle, Albert, Victor, Silvera, Katia, Lan, Tianying, Farr, Kimberly, Chang, Tien-Hao, Chan, Ming-Tsair, Winter, Klaus, Leebens-Mack, Jim

Journal:

Frontiers in Plant Science

Year:

2019

Language:

english

File:

PDF, 4.74 MB

english, 2019

35

[IEEE 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Philadelphia, PA, USA (2012.10.4-2012.10.7)] 2012 IEEE International Conference on Bioinformatics and Biomedicine - PhylOnt: A domain-specific ontology for phylogeny analysis

Panahiazar, Maryam, Ranabahu, Ajith, Taslimi, Vahid, Yalamanchili, Hima, Stoltzfus, Arlin, Leebens-Mack, Jim, Sheth, Amit P.

Year:

2012

Language:

english

File:

PDF, 1.60 MB

english, 2012

36

DARWIN BICENTENNIAL: THE "ABOMINABLE MYSTERY" || Polyploidy and angiosperm diversification

Douglas E. Soltis, Victor A. Albert, Jim Leebens-Mack, Charles D. Bell, Andrew H. Paterson, Chunfang Zheng, David Sankoff, Claude W. dePamphilis, P. Kerr Wall and Pamela S. Soltis

Journal:

American Journal of Botany

Year:

2009

Language:

english

File:

PDF, 2.76 MB

english, 2009

37

HOST SPECIFICITY AND THE GENETIC STRUCTURE OF TWO YUCCA MOTH SPECIES IN A YUCCA HYBRID ZONE

Leebens-Mack, Jim, Pellmyr, Olle, Brock, Marcus

Journal:

Year:

1998

Language:

english

File:

PDF, 1.19 MB

english, 1998

38

Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach

Liying Cui, Jim Leebens-Mack, Li-San Wang, Jijun Tang, Linda Rymarquis, David B Stern, Claude W dePamphilis

Journal:

BMC Evolutionary Biology

Year:

2006

Language:

english

File:

PDF, 438 KB

english, 2006

39

Plant Comparative and Functional Genomics

Yang, Xiaohan, Leebens-Mack, Jim, Chen, Feng, Yin, Yanbin

Journal:

International Journal of Genomics

Year:

2015

Language:

english

File:

PDF, 1.06 MB

english, 2015

40

Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)

Leebens-Mack, Jim, Vision, Todd, Brenner, Eric, Bowers, John E., Cannon, Steven, Clement, Mark J., Cunningham, Clifford W., DePamphilis, Claude, DeSalle, Rob, Doyle, Jeff J., Eisen, Jonathan A., Gu, X

Journal:

Omics A Journal of Integrative Biology

Year:

2006

Language:

english

File:

PDF, 83 KB

english, 2006

41

Parallel Loss of Plastid Introns and Their Maturase in the Genus Cuscuta

McNeal, Joel R., Kuehl, Jennifer V., Boore, Jeffrey L., Leebens-Mack, Jim, dePamphilis, Claude W., Kroymann, Juergen

Journal:

Year:

2009

Language:

english

File:

PDF, 274 KB

english, 2009

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