Jim Leebens-Mack

Jim Leebens-Mack

UNVERIFIED PROFILE

Are you Jim Leebens-Mack?   Register this Author

Register author
Jim Leebens-Mack

Jim Leebens-Mack

Publications by authors named "Jim Leebens-Mack"

Are you Jim Leebens-Mack?   Register this Author

57Publications

1337Reads

48Profile Views

Distributed phenomics with the unPAK project reveals the effects of mutations.

Authors:
Matthew T Rutter Courtney J Murren Hilary S Callahan April M Bisner Jim Leebens-Mack Michael J Wolyniak Allan E Strand

Plant J 2019 Oct 9;100(1):199-211. Epub 2019 Jul 9.

Department of Biology, College of Charleston, 66 George Street, Charleston, SC, 29424, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1111/tpj.14427DOI Listing
October 2019

Shared expression of Crassulacean acid metabolism (CAM) genes predates the origin of CAM in the genus Yucca.

Authors:
Karolina Heyduk Jeremy N Ray Saaravanaraj Ayyampalayam Nida Moledina Anne Borland Scott A Harding Chung-Jui Tsai Jim Leebens-Mack

J Exp Bot 2019 Mar 14. Epub 2019 Mar 14.

Department of Plant Biology, University of Georgia, Athens, Georgia, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1093/jxb/erz105DOI Listing
March 2019

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

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

Front Plant Sci 2018 28;9:2000. Epub 2019 Jan 28.

Department of Plant Biology, University of Georgia, Athens, GA, United States.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.3389/fpls.2018.02000DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360190PMC
January 2019

Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement.

Authors:
Shan Wu Kin H Lau Qinghe Cao John P Hamilton Honghe Sun Chenxi Zhou Lauren Eserman Dorcus C Gemenet Bode A Olukolu Haiyan Wang Emily Crisovan Grant T Godden Chen Jiao Xin Wang Mercy Kitavi Norma Manrique-Carpintero Brieanne Vaillancourt Krystle Wiegert-Rininger Xinsun Yang Kan Bao Jennifer Schaff Jan Kreuze Wolfgang Gruneberg Awais Khan Marc Ghislain Daifu Ma Jiming Jiang Robert O M Mwanga Jim Leebens-Mack Lachlan J M Coin G Craig Yencho C Robin Buell Zhangjun Fei

Nat Commun 2018 11 2;9(1):4580. Epub 2018 Nov 2.

Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.

View Article

Download full-text PDF

 Source
http://www.nature.com/articles/s41467-018-06983-8
Publisher Site
http://dx.doi.org/10.1038/s41467-018-06983-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6214957PMC
November 2018

The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants.

Authors:
Adam J Bewick Chad E Niederhuth Lexiang Ji Nicholas A Rohr Patrick T Griffin Jim Leebens-Mack Robert J Schmitz

Genome Biol 2017 05 1;18(1):65. Epub 2017 May 1.

Department of Genetics, University of Georgia, Athens, GA, 30602, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1186/s13059-017-1195-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5410703PMC
May 2017

A Century of Sex Determination in Flowering Plants.

Authors:
Alex Harkess Jim Leebens-Mack

J Hered 2017 01 14;108(1):69-77. Epub 2016 Nov 14.

From the Department of Plant Biology, University of Georgia, Athens, GA 30602 (Harkess and Leebens-Mack), Alex Harkess is now at the Donald Danforth Plant Science Center, St. Louis MO 63132.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1093/jhered/esw060DOI Listing
January 2017

Timing of rapid diversification and convergent origins of active pollination within Agavoideae (Asparagaceae).

Authors:
Michael R McKain Joel R McNeal P Roxanne Kellar Luis E Eguiarte J Chris Pires Jim Leebens-Mack

Am J Bot 2016 Oct 20;103(10):1717-1729. Epub 2016 Oct 20.

Department of Plant Biology, University of Georgia, 120 Carlton Street, Athens, Georgia 30602 USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.3732/ajb.1600198DOI Listing
October 2016

Retrotransposon Proliferation Coincident with the Evolution of Dioecy in Asparagus.

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

G3 (Bethesda) 2016 09 8;6(9):2679-85. Epub 2016 Sep 8.

Department of Plant Biology, University of Georgia, Athens, Georgia 30602.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1534/g3.116.030239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015926PMC
September 2016

Gas exchange and leaf anatomy of a C3-CAM hybrid, Yucca gloriosa (Asparagaceae).

Authors:
Karolina Heyduk Nia Burrell Falak Lalani Jim Leebens-Mack

J Exp Bot 2016 Mar 29;67(5):1369-79. Epub 2015 Dec 29.

2502 Miller Plant Sciences, Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1093/jxb/erv536DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4762382PMC
March 2016

Plant Comparative and Functional Genomics.

Authors:
Xiaohan Yang Jim Leebens-Mack Feng Chen Yanbin Yin

Int J Genomics 2015 31;2015:924369. Epub 2015 Dec 31.

Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1155/2015/924369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4736190PMC
February 2016

Gene families as soft cliques with backbones: Amborella contrasted with other flowering plants.

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

BMC Genomics 2014 17;15 Suppl 6:S8. Epub 2014 Oct 17.

View Article

Download full-text PDF

 Source
http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
Publisher Site
http://dx.doi.org/10.1186/1471-2164-15-S6-S8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4240082PMC
December 2015

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

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

Mol Phylogenet Evol 2015 Nov 14;92:25-44. Epub 2015 Jun 14.

Natural History Museum of Denmark, Sølvgade 83, Opg. S, K-1307 Copenhagen K, Denmark. Electronic address:

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1016/j.ympev.2015.06.002DOI Listing
November 2015

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

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

New Phytol 2015 Aug 27;207(3):883-92. Epub 2015 Mar 27.

Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1111/nph.13389DOI Listing
August 2015

Multiple polyploidy events in the early radiation of nodulating and nonnodulating legumes.

Authors:
Steven B Cannon Michael R McKain Alex Harkess Matthew N Nelson Sudhansu Dash Michael K Deyholos Yanhui Peng Blake Joyce Charles N Stewart Megan Rolf Toni Kutchan Xuemei Tan Cui Chen Yong Zhang Eric Carpenter Gane Ka-Shu Wong Jeff J Doyle Jim Leebens-Mack

Mol Biol Evol 2015 Jan 27;32(1):193-210. Epub 2014 Oct 27.

Department of Plant Biology, University of Georgia.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1093/molbev/msu296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271530PMC
January 2015

Data access for the 1,000 Plants (1KP) project.

Authors:
Naim Matasci Ling-Hong Hung Zhixiang Yan Eric J Carpenter Norman J Wickett Siavash Mirarab Nam Nguyen Tandy Warnow Saravanaraj Ayyampalayam Michael Barker J Gordon Burleigh Matthew A Gitzendanner Eric Wafula Joshua P Der Claude W dePamphilis Béatrice Roure Hervé Philippe Brad R Ruhfel Nicholas W Miles Sean W Graham Sarah Mathews Barbara Surek Michael Melkonian Douglas E Soltis Pamela S Soltis Carl Rothfels Lisa Pokorny Jonathan A Shaw Lisa DeGironimo Dennis W Stevenson Juan Carlos Villarreal Tao Chen Toni M Kutchan Megan Rolf Regina S Baucom Michael K Deyholos Ram Samudrala Zhijian Tian Xiaolei Wu Xiao Sun Yong Zhang Jun Wang Jim Leebens-Mack Gane Ka-Shu Wong

Gigascience 2014 27;3:17. Epub 2014 Oct 27.

BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China ; Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada ; Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1186/2047-217X-3-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4306014PMC
January 2015

Yucca aloifolia (Asparagaceae) opts out of an obligate pollination mutualism.

Authors:
Jeremy D Rentsch Jim Leebens-Mack

Am J Bot 2014 Dec 26;101(12):2062-7. Epub 2014 Nov 26.

Department of Plant Biology, University of Georgia, Athens, Georgia 30602 USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.3732/ajb.1400351DOI Listing
December 2014

Advancing data reuse in phyloinformatics using an ontology-driven Semantic Web approach.

Authors:
Maryam Panahiazar Amit P Sheth Ajith Ranabahu Rutger A Vos Jim Leebens-Mack

BMC Med Genomics 2013 11;6 Suppl 3:S5. Epub 2013 Nov 11.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1186/1755-8794-6-S3-S5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3980757PMC
October 2014

Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?

Authors:
Craig F Barrett Chelsea D Specht Jim Leebens-Mack Dennis Wm Stevenson Wendy B Zomlefer Jerrold I Davis

Ann Bot 2014 Jan 25;113(1):119-33. Epub 2013 Nov 25.

Department of Biological Sciences, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032, USA.

View Article

Download full-text PDF

 Source
https://academic.oup.com/aob/article-lookup/doi/10.1093/aob/
Publisher Site
http://dx.doi.org/10.1093/aob/mct264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3864734PMC
January 2014

Phylogenetics and diversification of morning glories (tribe Ipomoeeae, Convolvulaceae) based on whole plastome sequences.

Authors:
Lauren A Eserman George P Tiley Robert L Jarret Jim H Leebens-Mack Richard E Miller

Am J Bot 2014 Jan 26;101(1):92-103. Epub 2013 Dec 26.

Plant Biology Department, University of Georgia, Athens, Georgia 30602 USA.

View Article

Download full-text PDF

 Source
http://doi.wiley.com/10.3732/ajb.1300207
Publisher Site
http://dx.doi.org/10.3732/ajb.1300207DOI Listing
January 2014

Assembly and validation of the genome of the nonmodel basal angiosperm Amborella.

Authors:
Srikar Chamala Andre S Chanderbali Joshua P Der Tianying Lan Brandon Walts Victor A Albert Claude W dePamphilis Jim Leebens-Mack Steve Rounsley Stephan C Schuster Rod A Wing Nianqing Xiao Richard Moore Pamela S Soltis Douglas E Soltis W Brad Barbazuk

Science 2013 Dec;342(6165):1516-7

Department of Biology, University of Florida, Gainesville, FL 32611, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1126/science.1241130DOI Listing
December 2013

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

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

Plant Sci 2013 Apr 16;203-204:115-23. Epub 2013 Jan 16.

Dipartimento di AGRARIA, Università Mediterranea di Reggio Calabria, Salita Melissari, 89124 Reggio Calabria (RC), Italy.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1016/j.plantsci.2013.01.002DOI Listing
April 2013

Characterization of the basal angiosperm Aristolochia fimbriata: a potential experimental system for genetic studies.

Authors:
Barbara J Bliss Stefan Wanke Abdelali Barakat Saravanaraj Ayyampalayam Norman Wickett P Kerr Wall Yuannian Jiao Lena Landherr Paula E Ralph Yi Hu Christoph Neinhuis Jim Leebens-Mack Kathiravetpilla Arumuganathan Sandra W Clifton Siela N Maximova Hong Ma Claude W dePamphilis

BMC Plant Biol 2013 Jan 24;13:13. Epub 2013 Jan 24.

Department of Biology, Institute of Molecular Evolutionary Genetics, and the Huck Institutes of the Life Sciences, 201 Life Sciences Building, Pennsylvania State University, University Park, PA 16802, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1186/1471-2229-13-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3621149PMC
January 2013

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

Authors:
Jeremy D Rentsch Jim Leebens-Mack

Ecol Evol 2012 Sep 1;2(9):2213-22. Epub 2012 Aug 1.

Department of Plant Biology, University of Georgia Athens, Georgia, 30602.

View Article

Download full-text PDF

 Source
http://doi.wiley.com/10.1002/ece3.328
Publisher Site
http://dx.doi.org/10.1002/ece3.328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488672PMC
September 2012

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.

Authors:
Angélique D'Hont France Denoeud Jean-Marc Aury Franc-Christophe Baurens Françoise Carreel Olivier Garsmeur Benjamin Noel Stéphanie Bocs Gaëtan Droc Mathieu Rouard Corinne Da Silva Kamel Jabbari Céline Cardi Julie Poulain Marlène Souquet Karine Labadie Cyril Jourda Juliette Lengellé Marguerite Rodier-Goud Adriana Alberti Maria Bernard Margot Correa Saravanaraj Ayyampalayam Michael R Mckain Jim Leebens-Mack Diane Burgess Mike Freeling Didier Mbéguié-A-Mbéguié Matthieu Chabannes Thomas Wicker Olivier Panaud Jose Barbosa Eva Hribova Pat Heslop-Harrison Rémy Habas Ronan Rivallan Philippe Francois Claire Poiron Andrzej Kilian Dheema Burthia Christophe Jenny Frédéric Bakry Spencer Brown Valentin Guignon Gert Kema Miguel Dita Cees Waalwijk Steeve Joseph Anne Dievart Olivier Jaillon Julie Leclercq Xavier Argout Eric Lyons Ana Almeida Mouna Jeridi Jaroslav Dolezel Nicolas Roux Ange-Marie Risterucci Jean Weissenbach Manuel Ruiz Jean-Christophe Glaszmann Francis Quétier Nabila Yahiaoui Patrick Wincker

Nature 2012 Aug;488(7410):213-7

Centre de coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAP, F-34398 Montpellier, France.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/nature11241DOI Listing
August 2012

A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure.

Authors:
Andrea Zuccolo John E Bowers James C Estill Zhiyong Xiong Meizhong Luo Aswathy Sebastian José Luis Goicoechea Kristi Collura Yeisoo Yu Yuannian Jiao Jill Duarte Haibao Tang Saravanaraj Ayyampalayam Steve Rounsley Dave Kudrna Andrew H Paterson J Chris Pires Andre Chanderbali Douglas E Soltis Srikar Chamala Brad Barbazuk Pamela S Soltis Victor A Albert Hong Ma Dina Mandoli Jody Banks John E Carlson Jeffrey Tomkins Claude W dePamphilis Rod A Wing Jim Leebens-Mack

Genome Biol 2011 27;12(5):R48. Epub 2011 May 27.

Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, 1657 East Helen Street, Tucson, AZ 85721, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1186/gb-2011-12-5-r48DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3219971PMC
February 2012

Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae).

Authors:
Michael R McKain Norman Wickett Yeting Zhang Saravanaraj Ayyampalayam W Richard McCombie Mark W Chase J Chris Pires Claude W dePamphilis Jim Leebens-Mack

Am J Bot 2012 Feb 1;99(2):397-406. Epub 2012 Feb 1.

Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA.

View Article

Download full-text PDF

 Source
http://doi.wiley.com/10.3732/ajb.1100537
Publisher Site
http://dx.doi.org/10.3732/ajb.1100537DOI Listing
February 2012

A genome triplication associated with early diversification of the core eudicots.

Authors:
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 Yeting Zhang Eric J Carpenter Michael K Deyholos Toni M Kutchan Andre S Chanderbali Pamela S Soltis Dennis W Stevenson Richard McCombie J Chris Pires Gane Ka-Shu Wong Douglas E Soltis Claude W Depamphilis

Genome Biol 2012 Jan 26;13(1):R3. Epub 2012 Jan 26.

Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1186/gb-2012-13-1-r3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334584PMC
January 2012

The impact of multiple protein sequence alignment on phylogenetic estimation.

Authors:
Li-San Wang Jim Leebens-Mack P Kerr Wall Kevin Beckmann Claude W dePamphilis Tandy Warnow

IEEE/ACM Trans Comput Biol Bioinform 2011 Jul-Aug;8(4):1108-19

Department of Pathology and Laboratory Medicine and Penn Center for Bioinformatics, 1424 Blockley Hall, 423 Guardian Drive, University of Pennsylvania, Philadelphia, PA 19104, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1109/TCBB.2009.68DOI Listing
September 2011

Ancestral polyploidy in seed plants and angiosperms.

Authors:
Yuannian Jiao Norman J Wickett Saravanaraj Ayyampalayam André S Chanderbali Lena Landherr Paula E Ralph Lynn P Tomsho Yi Hu Haiying Liang Pamela S Soltis Douglas E Soltis Sandra W Clifton Scott E Schlarbaum Stephan C Schuster Hong Ma Jim Leebens-Mack Claude W dePamphilis

Nature 2011 May 10;473(7345):97-100. Epub 2011 Apr 10.

Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/nature09916DOI Listing
May 2011

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

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

Evodevo 2010 Dec 1;1:13. Epub 2010 Dec 1.

University of Bremen, Fachbereich 02 Biology/Chemistry, Evolutionary Developmental Genetics Group Leobener Str,, UFT, 28359 Bremen, Germany.

View Article

Download full-text PDF

 Source
http://evodevojournal.biomedcentral.com/articles/10.1186/204
Publisher Site
http://dx.doi.org/10.1186/2041-9139-1-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3012024PMC
December 2010

Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop.

Authors:
Carsten Kettner Dawn Field Susanna-Assunta Sansone Chris Taylor Jan Aerts Nigel Binns Andrew Blake Cedrik M Britten Ario de Marco Jennifer Fostel Pascale Gaudet Alejandra González-Beltrán Nigel Hardy Jan Hellemans Henning Hermjakob Nick Juty Jim Leebens-Mack Eamonn Maguire Steffen Neumann Sandra Orchard Helen Parkinson William Piel Shoba Ranganathan Philippe Rocca-Serra Annapaola Santarsiero David Shotton Peter Sterk Andreas Untergasser Patricia L Whetzel

Stand Genomic Sci 2010 Dec 25;3(3):259-66. Epub 2010 Dec 25.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.4056/sigs.147362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035314PMC
December 2010

Plant reproductive genomics at the Plant and Animal Genome Conference.

Authors:
Jim Leebens-Mack Douglas E Soltis Pamela S Soltis

Comp Funct Genomics 2005 ;6(3):159-69

Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.

View Article

Download full-text PDF

 Source
http://www.hindawi.com/journals/ijg/2005/592439/abs/
Publisher Site
http://dx.doi.org/10.1002/cfg.469DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447523PMC
June 2010

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

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

BMC Evol Biol 2010 Feb 24;10:61. Epub 2010 Feb 24.

Department of Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.

View Article

Download full-text PDF

 Source
http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2
Publisher Site
http://dx.doi.org/10.1186/1471-2148-10-61DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848037PMC
February 2010

Evolution of plant MADS box transcription factors: evidence for shifts in selection associated with early angiosperm diversification and concerted gene duplications.

Authors:
Hongyan Shan Laura Zahn Stephane Guindon P Kerr Wall Hongzhi Kong Hong Ma Claude W DePamphilis Jim Leebens-Mack

Mol Biol Evol 2009 Oct 3;26(10):2229-44. Epub 2009 Jul 3.

State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Xiangshan, Beijing, People's Republic of China.

View Article

Download full-text PDF

 Source
https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
Publisher Site
http://dx.doi.org/10.1093/molbev/msp129DOI Listing
October 2009

Towards improved reconstruction of ancestral gene order in angiosperm phylogeny.

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

J Comput Biol 2009 Oct;16(10):1353-67

Department of Mathematics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario, Canada.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1089/cmb.2009.0103DOI Listing
October 2009

The effect of massive gene loss following whole genome duplication on the algorithmic reconstruction of the ancestral populus diploid.

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

Comput Syst Bioinformatics Conf 2008 ;7:261-71

Department of Biology, University of Ottawa, Ottawa, Ontario KIN 6N5, Canada.

View Article

Download full-text PDF

 Source
August 2009

Comparison of next generation sequencing technologies for transcriptome characterization.

Authors:
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 Pamela S Soltis Naomi Altman Claude W dePamphilis

BMC Genomics 2009 Aug 1;10:347. Epub 2009 Aug 1.

Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1186/1471-2164-10-347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2907694PMC
August 2009

Transcriptional signatures of ancient floral developmental genetics in avocado (Persea americana; Lauraceae).

Authors:
André S Chanderbali Victor A Albert Jim Leebens-Mack Naomi S Altman Douglas E Soltis Pamela S Soltis

Proc Natl Acad Sci U S A 2009 Jun 18;106(22):8929-34. Epub 2009 May 18.

Department of Biology and Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.

View Article

Download full-text PDF

 Source
http://www.pnas.org/cgi/doi/10.1073/pnas.0811476106
Publisher Site
http://dx.doi.org/10.1073/pnas.0811476106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683881PMC
June 2009

Parallel loss of plastid introns and their maturase in the genus Cuscuta.

Authors:
Joel R McNeal Jennifer V Kuehl Jeffrey L Boore Jim Leebens-Mack Claude W dePamphilis

PLoS One 2009 Jun 19;4(6):e5982. Epub 2009 Jun 19.

Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America.

View Article

Download full-text PDF

 Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0005982PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694360PMC
June 2009

Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome.

Authors:
Regina S Baucom James C Estill Jim Leebens-Mack Jeffrey L Bennetzen

Genome Res 2009 Feb 24;19(2):243-54. Epub 2008 Nov 24.

Department of Genetics, University of Georgia, Athens, Georgia 30602-7223, USA.

View Article

Download full-text PDF

 Source
http://genome.cshlp.org/cgi/doi/10.1101/gr.083360.108
Publisher Site
http://dx.doi.org/10.1101/gr.083360.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652206PMC
February 2009

Polyploidy and angiosperm diversification.

Authors:
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 Pamela S Soltis

Am J Bot 2009 Jan;96(1):336-48

Department of Botany, University of Florida, Gainesville, Florida 32611 USA.

View Article

Download full-text PDF

 Source
http://www.amjbot.org/content/96/1/336.full.pdf+html
Web Search
http://www.amjbot.org/cgi/doi/10.3732/ajb.0800079
Publisher Site
http://dx.doi.org/10.3732/ajb.0800079DOI Listing
January 2009

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.

Authors:
Chris F Taylor Dawn Field Susanna-Assunta Sansone Jan Aerts Rolf Apweiler Michael Ashburner Catherine A Ball Pierre-Alain Binz Molly Bogue Tim Booth Alvis Brazma Ryan R Brinkman Adam Michael Clark Eric W Deutsch Oliver Fiehn Jennifer Fostel Peter Ghazal Frank Gibson Tanya Gray Graeme Grimes John M Hancock Nigel W Hardy Henning Hermjakob Randall K Julian Matthew Kane Carsten Kettner Christopher Kinsinger Eugene Kolker Martin Kuiper Nicolas Le Novère Jim Leebens-Mack Suzanna E Lewis Phillip Lord Ann-Marie Mallon Nishanth Marthandan Hiroshi Masuya Ruth McNally Alexander Mehrle Norman Morrison Sandra Orchard John Quackenbush James M Reecy Donald G Robertson Philippe Rocca-Serra Henry Rodriguez Heiko Rosenfelder Javier Santoyo-Lopez Richard H Scheuermann Daniel Schober Barry Smith Jason Snape Christian J Stoeckert Keith Tipton Peter Sterk Andreas Untergasser Jo Vandesompele Stefan Wiemann

Nat Biotechnol 2008 Aug;26(8):889-96

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/nbt.1411DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771753PMC
August 2008

The Amborella genome: an evolutionary reference for plant biology.

Authors:
Douglas E Soltis Victor A Albert Jim Leebens-Mack Jeffrey D Palmer Rod A Wing Claude W dePamphilis Hong Ma John E Carlson Naomi Altman Sangtae Kim P Kerr Wall Andrea Zuccolo Pamela S Soltis

Genome Biol 2008 10;9(3):402. Epub 2008 Mar 10.

Department of Botany and the Genetics Institute, University of Florida, Gainesville, FL 32611, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1186/gb-2008-9-3-402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2397498PMC
June 2008

The minimum information about a genome sequence (MIGS) specification.

Authors:
Dawn Field George Garrity Tanya Gray Norman Morrison Jeremy Selengut Peter Sterk Tatiana Tatusova Nicholas Thomson Michael J Allen Samuel V Angiuoli Michael Ashburner Nelson Axelrod Sandra Baldauf Stuart Ballard Jeffrey Boore Guy Cochrane James Cole Peter Dawyndt Paul De Vos Claude DePamphilis Robert Edwards Nadeem Faruque Robert Feldman Jack Gilbert Paul Gilna Frank Oliver Glöckner Philip Goldstein Robert Guralnick Dan Haft David Hancock Henning Hermjakob Christiane Hertz-Fowler Phil Hugenholtz Ian Joint Leonid Kagan Matthew Kane Jessie Kennedy George Kowalchuk Renzo Kottmann Eugene Kolker Saul Kravitz Nikos Kyrpides Jim Leebens-Mack Suzanna E Lewis Kelvin Li Allyson L Lister Phillip Lord Natalia Maltsev Victor Markowitz Jennifer Martiny Barbara Methe Ilene Mizrachi Richard Moxon Karen Nelson Julian Parkhill Lita Proctor Owen White Susanna-Assunta Sansone Andrew Spiers Robert Stevens Paul Swift Chris Taylor Yoshio Tateno Adrian Tett Sarah Turner David Ussery Bob Vaughan Naomi Ward Trish Whetzel Ingio San Gil Gareth Wilson Anil Wipat

Nat Biotechnol 2008 May;26(5):541-7

Natural Environmental Research Council Centre for Ecology and Hydrology, Oxford OX1 3SR, UK.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1038/nbt1360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2409278PMC
May 2008

PlantTribes: a gene and gene family resource for comparative genomics in plants.

Authors:
P Kerr Wall Jim Leebens-Mack Kai F Müller Dawn Field Naomi S Altman Claude W dePamphilis

Nucleic Acids Res 2008 Jan 10;36(Database issue):D970-6. Epub 2007 Dec 10.

Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1093/nar/gkm972DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238917PMC
January 2008

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

Authors:
Magali Lescot Pietro Piffanelli Ana Y Ciampi Manuel Ruiz Guillaume Blanc Jim Leebens-Mack Felipe R da Silva Candice M R Santos Angélique D'Hont Olivier Garsmeur Alberto D Vilarinhos Hiroyuki Kanamori Takashi Matsumoto Catherine M Ronning Foo Cheung Brian J Haas Ryan Althoff Tammy Arbogast Erin Hine Georgios J Pappas Takuji Sasaki Manoel T Souza Robert N G Miller Jean-Christophe Glaszmann Christopher D Town

BMC Genomics 2008 Jan 30;9:58. Epub 2008 Jan 30.

French Agricultural Research Center for International Development, UMR 1096, Avenue Agropolis, TA40/03, FR-34398, Montpellier, Cedex 5, France.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1186/1471-2164-9-58DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2270835PMC
January 2008

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).

Authors:
Jim Leebens-Mack Todd Vision Eric Brenner John E Bowers Steven Cannon Mark J Clement Clifford W Cunningham Claude dePamphilis Rob deSalle Jeff J Doyle Jonathan A Eisen Xun Gu John Harshman Robert K Jansen Elizabeth A Kellogg Eugene V Koonin Brent D Mishler Hervé Philippe J Chris Pires Yin-Long Qiu Seung Y Rhee Kimmen Sjölander Douglas E Soltis Pamela S Soltis Dennis W Stevenson Kerr Wall Tandy Warnow Christian Zmasek

OMICS 2006 ;10(2):231-7

Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1089/omi.2006.10.231DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3167193PMC
November 2007

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

Authors:
Abdelali Barakat Kerr Wall Jim Leebens-Mack Yunjiao J Wang John E Carlson Claude W Depamphilis

Plant J 2007 Sep 17;51(6):991-1003. Epub 2007 Jul 17.

Department of Biology, Institute of Molecular Evolutionary Genetics, 403 Life Sciences Building, The Pennsylvania State University, University Park, PA 16802, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1111/j.1365-313X.2007.03197.xDOI Listing
September 2007

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

Authors:
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

Trends Plant Sci 2007 Aug 19;12(8):358-67. Epub 2007 Jul 19.

Department of Botany and the Genetics Institute, University of Florida, Gainesville, FL 32611, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1016/j.tplants.2007.06.012DOI Listing
August 2007

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

Authors:
Hongzhi Kong Lena L Landherr Michael W Frohlich Jim Leebens-Mack Hong Ma Claude W dePamphilis

Plant J 2007 Jun 23;50(5):873-85. Epub 2007 Apr 23.

State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China.

View Article

Download full-text PDF

 Source
http://doi.wiley.com/10.1111/j.1365-313X.2007.03097.x
Publisher Site
http://dx.doi.org/10.1111/j.1365-313X.2007.03097.xDOI Listing
June 2007

Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.

Authors:
Jill M Duarte Liying Cui P Kerr Wall Qing Zhang Xiaohong Zhang Jim Leebens-Mack Hong Ma Naomi Altman Claude W dePamphilis

Mol Biol Evol 2006 Feb 9;23(2):469-78. Epub 2005 Nov 9.

Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of the Life Sciences, The Pennsylvania State University, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1093/molbev/msj051DOI Listing
February 2006

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

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

BMC Evol Biol 2006 Feb 9;6:13. Epub 2006 Feb 9.

Department of Biology, Institute of Molecular Evolutionary Genetics, Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.

View Article

Download full-text PDF

 Source
http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2
Publisher Site
http://dx.doi.org/10.1186/1471-2148-6-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1421436PMC
February 2006

ChloroplastDB: the Chloroplast Genome Database.

Authors:
Liying Cui Narayanan Veeraraghavan Alexander Richter Kerr Wall Robert K Jansen Jim Leebens-Mack Izabela Makalowska Claude W dePamphilis

Nucleic Acids Res 2006 Jan;34(Database issue):D692-6

Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, PA 16802, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1093/nar/gkj055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347418PMC
January 2006

Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone.

Authors:
Jim Leebens-Mack Linda A Raubeson Liying Cui Jennifer V Kuehl Matthew H Fourcade Timothy W Chumley Jeffrey L Boore Robert K Jansen Claude W depamphilis

Mol Biol Evol 2005 Oct 8;22(10):1948-63. Epub 2005 Jun 8.

Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of Life Sciences, The Pennsylvania State University, PA, USA.

View Article

Download full-text PDF

 Source
http://dx.doi.org/10.1093/molbev/msi191DOI Listing
October 2005

Highly heterogeneous rates of evolution in the SKP1 gene family in plants and animals: functional and evolutionary implications.

Authors:
Hongzhi Kong Jim Leebens-Mack Weimin Ni Claude W dePamphilis Hong Ma

Mol Biol Evol 2004 Jan 31;21(1):117-28. Epub 2003 Oct 31.

Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China.

View Article

Download full-text PDF

 Source
https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
Publisher Site
http://dx.doi.org/10.1093/molbev/msh001DOI Listing
January 2004

Power analysis of tests for loss of selective constraint in cave crayfish and nonphotosynthetic plant lineages.

Authors:
Jim Leebens-Mack Claude DePamphilis

Mol Biol Evol 2002 Aug;19(8):1292-302

Department of Biology, Colgate University, New York , USA.

View Article

Download full-text PDF

 Source
http://academic.oup.com/mbe/article/19/8/1292/997604
Publisher Site
http://dx.doi.org/10.1093/oxfordjournals.molbev.a004190DOI Listing
August 2002

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

Authors:
Jim Leebens-Mack Olle Pellmyr Marcus Brock

Evolution 1998 Oct;52(5):1376-1382

Department of Biology, Vanderbilt University, Box 1812-B, Nashville, Tennessee, 37235.

View Article

Download full-text PDF

 Source
http://doi.wiley.com/10.1111/j.1558-5646.1998.tb02019.x
Publisher Site
http://dx.doi.org/10.1111/j.1558-5646.1998.tb02019.xDOI Listing
October 1998