James Leebens-Mack

Summary

Affiliation: University of Georgia
Country: USA

Publications

  1. pmc Characterization of the basal angiosperm Aristolochia fimbriata: a potential experimental system for genetic studies
    Barbara J Bliss
    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
    BMC Plant Biol 13:13. 2013
  2. pmc A genome triplication associated with early diversification of the core eudicots
    Yuannian Jiao
    Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Genome Biol 13:R3. 2012
  3. pmc The phenylalanine ammonia lyase (PAL) gene family shows a gymnosperm-specific lineage
    Ujwal R Bagal
    Institute of Bioinformatics, The University of Georgia, Athens, GA 30602 7229, USA
    BMC Genomics 13:S1. 2012
  4. pmc Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)
    Jim Leebens-Mack
    Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
    OMICS 10:231-7. 2006
  5. pmc A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure
    Andrea Zuccolo
    Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, 1657 East Helen Street, Tucson, AZ 85721, USA
    Genome Biol 12:R48. 2011
  6. pmc Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies
    Laura M Zahn
    Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Genome Biol 11:R101. 2010
  7. pmc 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
    University of Bremen, Fachbereich 02 Biology Chemistry, Evolutionary Developmental Genetics Group Leobener Str, UFT, 28359 Bremen, Germany
    Evodevo 1:13. 2010
  8. pmc An expressed sequence tag (EST) library from developing fruits of an Hawaiian endemic mint (Stenogyne rugosa, Lamiaceae): characterization and microsatellite markers
    Charlotte Lindqvist
    Natural History Museum, University of Oslo, PO Box 1172 Blindern, 0318 Oslo, Norway
    BMC Plant Biol 6:16. 2006
  9. pmc Comparison of next generation sequencing technologies for transcriptome characterization
    P Kerr Wall
    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
    BMC Genomics 10:347. 2009
  10. pmc Insights into the Musa genome: syntenic relationships to rice and between Musa species
    Magali Lescot
    French Agricultural Research Center for International Development, UMR 1096, Avenue Agropolis, TA40 03, FR 34398, Montpellier, Cedex 5, France
    BMC Genomics 9:58. 2008

Collaborators

  • Kimmen Sjolander
  • Douglas E Soltis
  • Robert K Jansen
  • Jonathan A Eisen
  • Rod A Wing
  • Victor A Albert
  • Jeff J Doyle
  • Andrew H Paterson
  • Rob DeSalle
  • Hong Ma
  • HervĂ© Philippe
  • Xun Gu
  • Yin Long Qiu
  • Claude W dePamphilis
  • P Kerr Wall
  • Yuannian Jiao
  • Pamela S Soltis
  • Saravanaraj Ayyampalayam
  • J Chris Pires
  • John E Carlson
  • Barbara J Bliss
  • Ujwal R Bagal
  • John E Bowers
  • Andrea Zuccolo
  • Abdelali Barakat
  • Lena Landherr
  • Yi Hu
  • AndrĂ© S Chanderbali
  • Jill M Duarte
  • Aravinda L Yellina
  • Laura M Zahn
  • Magali Lescot
  • Charlotte Lindqvist
  • Zhengqiu Cai
  • Siela N Maximova
  • Sandra W Clifton
  • Paula E Ralph
  • Stefan Wanke
  • Christoph Neinhuis
  • Norman Wickett
  • Kathiravetpilla Arumuganathan
  • Jun Wang
  • Dennis W Stevenson
  • Norman J Wickett
  • W Walter Lorenz
  • Michael R McKain
  • Michael K Deyholos
  • Eric J Carpenter
  • Gane Ka Shu Wong
  • Joel McNeal
  • Richard McCombie
  • Megan Rolf
  • Daniel R Ruzicka
  • Toni M Kutchan
  • Xiaolei Wu
  • Eric Wafula
  • Yong Zhang
  • Yeting Zhang
  • Jeffrey F D Dean
  • Jose Luis Goicoechea
  • Jill Duarte
  • Kristi Collura
  • James C Estill
  • Andre Chanderbali
  • Aswathy Sebastian
  • Jeffrey Tomkins
  • Dina Mandoli
  • Brad Barbazuk
  • Yeisoo Yu
  • Dave Kudrna
  • Zhiyong Xiong
  • Steve Rounsley
  • Meizhong Luo
  • Haibao Tang
  • Jody Banks
  • Srikar Chamala
  • Naomi S Altman
  • Qing Zhang
  • Svetlana Orashakova
  • Raad Gharaibeh
  • Lena L Landherr
  • Xuan Ma
  • Donglan Tian
  • Annette Becker
  • Sabrina Lange
  • Cynthia J Gibas
  • Robert Erdmann
  • Patrick P Edger
  • Erik Wolcott
  • Stephan C Schuster

Detail Information

Publications12

  1. pmc Characterization of the basal angiosperm Aristolochia fimbriata: a potential experimental system for genetic studies
    Barbara J Bliss
    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
    BMC Plant Biol 13:13. 2013
    ..It would be desirable to identify a basal angiosperm experimental system that possesses many of the features found in existing plant model systems (e.g., Arabidopsis and Oryza)...
  2. pmc A genome triplication associated with early diversification of the core eudicots
    Yuannian Jiao
    Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Genome Biol 13:R3. 2012
    ..Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear...
  3. pmc The phenylalanine ammonia lyase (PAL) gene family shows a gymnosperm-specific lineage
    Ujwal R Bagal
    Institute of Bioinformatics, The University of Georgia, Athens, GA 30602 7229, USA
    BMC Genomics 13:S1. 2012
    ..Our objective was to re-evaluate this finding, assess the evolutionary history of PAL genes across major angiosperm and gymnosperm lineages, and characterize PAL gene expression patterns in Pinus taeda...
  4. pmc Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)
    Jim Leebens-Mack
    Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
    OMICS 10:231-7. 2006
    ..Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors...
  5. pmc A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure
    Andrea Zuccolo
    Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, 1657 East Helen Street, Tucson, AZ 85721, USA
    Genome Biol 12:R48. 2011
    ..A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome...
  6. pmc Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies
    Laura M Zahn
    Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Genome Biol 11:R101. 2010
    ..However, our understanding of floral developmental processes among the basal eudicots remains limited...
  7. pmc 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
    University of Bremen, Fachbereich 02 Biology Chemistry, Evolutionary Developmental Genetics Group Leobener Str, UFT, 28359 Bremen, Germany
    Evodevo 1:13. 2010
    ..At the same time gene phylogenies reveal a complex history of gene duplications and repeated subfunctionalization of paralogs...
  8. pmc An expressed sequence tag (EST) library from developing fruits of an Hawaiian endemic mint (Stenogyne rugosa, Lamiaceae): characterization and microsatellite markers
    Charlotte Lindqvist
    Natural History Museum, University of Oslo, PO Box 1172 Blindern, 0318 Oslo, Norway
    BMC Plant Biol 6:16. 2006
    ..We constructed an EST library from developing fleshy nutlets of Stenogyne rugosa principally to identify genetic markers for the Hawaiian endemic mints...
  9. pmc Comparison of next generation sequencing technologies for transcriptome characterization
    P Kerr Wall
    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
    BMC Genomics 10:347. 2009
    ..19). We also generated 454-GS20 sequences and de novo assemblies for the basal eudicot California poppy (Eschscholzia californica) and the magnoliid avocado (Persea americana) using a variety of methods for cDNA synthesis...
  10. pmc Insights into the Musa genome: syntenic relationships to rice and between Musa species
    Magali Lescot
    French Agricultural Research Center for International Development, UMR 1096, Avenue Agropolis, TA40 03, FR 34398, Montpellier, Cedex 5, France
    BMC Genomics 9:58. 2008
    ..Until now, however, no large-scale analyses of Musa genomic sequence have been conducted. This study compares genomic sequence in two Musa species with orthologous regions in the rice genome...
  11. pmc Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels
    Jill M Duarte
    Department of Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
    BMC Evol Biol 10:61. 2010
    ....
  12. pmc Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids
    Zhengqiu Cai
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, Patterson Laboratories 141, University of Texas, Austin, TX 78712, USA
    BMC Evol Biol 6:77. 2006
    ....