People

The PMN staff members work at the Carnegie Institution for Science in the Department of Plant Biology, located on the Stanford University campus. The PMN curators are involved in curating pathways from Arabidopsis into AraCyc, plus they also curate pathways from diverse species that can be entered into the appropriate species-specific metabolic databases, or directly into PlantCyc. In addition, all of the pathways supported by experimental evidence are entered into MetaCyc.

PMN staff members will also be involved in the generation of new species-specific metabolic pathway databases, such as PoplarCyc.

To send a general message to the PMN, please use our Feedback Form, but we also welcome messages to individual PMN staff members.

PMN staff


Seung Yon (Sue) Rhee, Ph.D.
Principal Investigator
(650) 739-4251
srhee_at_carnegiescience.edu

Rhee lab website and photo

Flavia Bossi, Ph.D.
Post-doctoral Scholar

Jiun Yen, Ph.D.
Post-doctoral Scholar

Bo Xue, M.S.
Research Assistant (Software Developer)

Angela Xu, B.A.
Research Assistant (Curation database)

Kevin Radja, B.S.
Research Assistant (Bioinformatics)

Charles Hawkins, Ph.D.
PMN BioCurator
chawkins_at_carnegiescience.edu

Alumni


Peifen Zhang, Ph.D.
PMN Director

Taehyong Kim, Ph.D.
Post-doctoral Scholar

Chuan Wang, Ph.D.
Post-doctoral Scholar

Pascal Schlapfer, Ph.D.
Post-doctoral Scholar

Ricardo Nilo Poyanco, Ph.D.
Post-doctoral Scholar

Lee Chae, Ph.D.
Post-doctoral Scholar

Kate Dreher, Ph.D.
Scientific Curator

A. S. Karthikeyan, Ph.D.
Scientific Curator

Robert Muller, Ph.D.
Techteam Manager

Vanessa Kirkup
Web Master

Cynthia Lee
Software Developer

Anjo Chi
Software Developer

Larry Ploetz
System Administrator

Shanker Singh
Database Administrator

Michael Banf, Ph.D.
Post-doctoral Scholar

Interns


Ashley Joseph (2013-2014)

Varun Dwaraka (2012)

Caryn Johansen (2012-2014)

Tam Tran (2011-2012)

Damian Priamurskiy (2011-2012)

Purva Karia (2011)

Niek de Klein (2010-2011)

Kris Sankaran (2010-2011)

Ricardo Pinho (2008)

Michael Ahn (2008)

Galyna Vakulenko (2018)

Original PMN team


PMN staff - May 2008:

Anjo Chi, Bob Muller, Larry Ploetz, Sue Rhee, Vanessa Kirkup, Kate Dreher, A.S Karthikeyan, Peifen Zhang, and Cynthia Lee
Not shown: Eva Huala, Chris Wilks, Raymond Chetty, Shanker Singh, and Tom Meyer

 

 Peifen Zhang, director

Sue Rhee - PI; Peifen Zhang - Director

Collaborators curate pathways or provide support for individual species-specific databases that were created and/or maintained by them. There is data exchange between PlantCyc and the collaborators' databases. There is also coordination of curation to set consistent curation rules and eliminate redundant efforts.

The release notes associated with each new version of PlantCyc list the information from the collaborators' databases that has been entered into PlantCyc. Each additional pathway entered may help to improve the ability of the Pathologic program to predict more pathways as new single species databases are generated using PlantCyc as a reference standard.

MetaCyc (general contact information)
SRI International

Peter Karp
Bioinformatics Director
pkarp_at_ai.sri.com

Ron Caspi
Curator
caspi_at_ai.sri.com

Carol Fulcher
Curator
fulcher_at_ai.sri.com

MaizeGDB - co-curator of CornCyc (general contact information)
MaizeGDB

Carolyn Lawrence
MaizeGDB Director
USDA ARS Iowa State University
carolyn.lawrence_at_ars.usda.gov

Mary Schaeffer
MaizeGDB Curator
USDA ARS MWA
SchaefferM_at_missouri.edu

Jack Gardiner
MaizeGDB Curator
University of Arizona & Iowa State University
jack.m.gardiner_at_gmail.com

Lisa Harper
MaizeGDB Curator
USDA-ARS-PGEC
ligule_at_berkeley.edu

Taner Sen
MaizeGDB Computational Biologist
USDA ARS Iowa State University
taner.sen_at_ars.usda.gov

Carson Andorf
MaizeGDB Bioinformatics Engineer
USDA-ARS Iowa State University
carson.andorf_at_ars.usda.gov

Walther Group at GoFORSYS - co-curator of ChlamyCyc (general contact information)
Walther Group at GoFORSYS

Dirk Walther
Group Leader Bioinformatics
Max Planck Institute of Molecular Plant Physiology
walther_at_mpimp-golm.mpg.de

Patrick May
ChlamyCyc 1.0 curator

CapCyc, CoffeaCyc, LycoCyc, NicotianaCyc, PetuniaCyc, PotatoCyc, and SolaCyc (general contact information)
Sol Genomics Network (SGN)

Lukas Mueller
SGN Director
Boyce Thompson Institute
lam87_at_cornell.edu

Hartmut Foerster
MetaCyc Curator
Boyce Thompson Institute
hf263_at_cornell.edu

PMN contributors from around the world have added to or helped to improve the content of AraCyc, PlantCyc, and the other PlantCyc-derived databases that are part of the PMN.

In addition to the active contributions from the PMN editorial board and PMN collaborators, the following individuals have contributed significantly in improving the content of PlantCyc, AraCyc and the other PlantCyc-derived databases that are part of the PMN.

  • Some contributors have contacted us with suggestions and revisions.
  • Some have generously responded to appeals for help from the curators.
  • Some have attended curatorial jamborees.

Contributors for PMN release - June 2013

  • Danny Alexander - Metabolon, Inc., USA
  • Thomas Colquhoun - University of Florida, USA
  • Steve Gagne - National Research Council-Plant Biotechnology Institute / University of Saskatchewan, Canada
  • Guy Hanke - University of Osnabrück, Germany
  • Ko Hirano - BioScience Center, Nagoya University, Japan
  • Reinhard Jetter - The University of British Columbia, Canada
  • John Lunn - Max Planck Institute of Molecular Plant Physiology, Germany
  • John Ohlrogge - Michigan State University, USA
  • Burkhard Schulz - Purdue University, USA
  • Yuzo Shioi - Shizuoka University, Japan
  • David Twell - University of Leicester, UK
  • Zhe-Yong Xue - Key Laboratory of Plant Molecular Biology Institute of Botany, Chinese Academy of Sciences, China

    • Contributors for prior PMN releases

  • Imad Ajjawi - Michigan State University, USA
  • Jose Alonso - North Carolina State University, USA
  • Richard Amasino - University of Wisconsin, USA
  • Carlos Andreo - Centro de Estudios Fotosintéticos y Bioquímicos, Argentina
  • Anne Arnold - Max-Planck-Institute, Germany
  • Ian Baldwin - Max Planck Institute for Chemical Ecology, Germany
  • Bonnie Bartel - Rice University, USA
  • Dorothea Bartels - Universität Bonn, Germany
  • Jacqueline Bede - McGill University, Canada
  • Ludger Beerhues - Technische Universitat Braunschweig, Germany
  • Shannon Bell - Michigan State University, USA
  • EJ Blom - Keygene, The Natherlands
  • Steve Cannon - USDA-ARS and Iowa State University
  • Frédéric Carrière - Centre National de la Recherche Scientifique, France
  • Dring Crowel - Idaho State University, USA
  • Christophe D'Hulst - Unité de Glycobiologie Structurale et Fonctionnelle, France
  • Seth DeBolt - University of Kentucky, USA
  • David Dixon - Durham University, UK
  • Richard Dixon - The Samuel Roberts Noble Foundation, USA
  • Bradley Dotson - University of California, Berkeley, USA
  • Natalia Dudareva - Purdue University, USA
  • Timothy Durrett - University of Osnabrück, Germany
  • Martin Engqvist - Botanisches Institut, Universitat zu Koln, Germany
  • Ray Fall - University of Colorado, Boulder, USA
  • Alisdair Fernie - Max-Planck-Institute of Molecular Plant Physiology, Germany
  • Ben Field - John Innes Centre, UK
  • Oliver Fiehn - University of California, Davis, USA
  • Ulf-Ingo Fluegge - University of Cologne, Germany
  • Geoffrey Fucile - University of Toronto, Canada
  • Andrzej Guranowski - The University of Life Sciences, Poland
  • James Harrison - University of Queensland, Australia
  • Zuhua He - Chinese Academy of Sciences, China
  • Joshua Heazlewood - Lawrence Berkeley National Laboratory, USA
  • Peter Hedden - Rothamsted Research, UK
  • Julian Hibberd - University of Cambridge, UK
  • Ito Hisashi - Hokkaido University, Japan
  • Tomas Hluska - Palacky University Olomouc, Czech Republic
  • Alexis Hoffman - Iowa State University, USA
  • Gregg Howe - Michigan State University, USA
  • Jungim Hur - University of California, Los Angeles, USA
  • Rob Ingle - University of Cape Town, South Africa
  • John Jelesko - Virginia Tech, USA
  • Vijay Joshi - Cornell University, USA
  • Matthew Ryan Keogh - North Carolina State University, USA
  • Woo Taek Kim - Yonsei University, Korea
  • Daniel Kliebenstein - University of California, Davis, USA
  • Abe Koo - Michigan State University, USA
  • Juergen Kroymann - Université Paris-Sud, France **repeat contributor
  • J. Clark Lagarias - University of California, Davis, USA
  • Rob Last - Michigan State University, USA
  • David Liscombe - University of Calgary, Canada
  • Peter Lundquist - Cornell University, USA
  • Daniel Lynch - Williams College, USA
  • Hiroshi Maeda - Purdue University, USA
  • Frédéric Marsolais - Southern Crop Protection and Food Research Centre, Canada
  • Seiichi P. T. Matsuda - Rice University, USA
  • Carlos Menck - Universidade de São Paulo, Brazil
  • Hisashi Miyagawa - Kyoto University, Japan
  • Stephanie Moon - Iowa State University, USA
  • David Oliver - Iowa State University, USA
  • Jon Page - National Research Council-Plant Biotechnology Institute, Canada
  • Mark Poolman - Oxford Brookes University, UK
  • Alain Rahier - Institut de Biologie Moléculaire des Plantes, France
  • Stephane Ravanel - Institut de Recherches en Technologies et Sciences pour le Vivant, France
  • Bryan Reynaert - Universidad de Chile, Chile
  • Stan Roux - University of Texas at Austin, USA
  • Radin Sadre - RWTH Aachen University, Germany
  • Bernd Schneider - Max Planck Institute for Chemical Ecology Beutenberg Campus, Germany
  • Henrik Scheller - Lawrence Berkeley National Laboratory, USA
  • Jiho Seo - Yonsei University, Korea
  • Mitsunori Seo - RIKEN, Japan
  • Paul Staswick - University of Nebraska-Lincoln, USA
  • Iris Steinbrunner - Technical University of Dresden, Germany
  • Yi-Shin Su - Stanford University, USA
  • Lee Sweetlove - University of Oxford, UK
  • Yi Tao - Xiamen University, China
  • Raimund Tenhaken - Universitat Salzburg, Austria
  • Andrea Thum - Michigan State University, USA
  • Axel Tiessen - CINVESTAV Campus Guanajuato, Mexico
  • Chung-Jui Tsai - University of Georgia, USA
  • Claus Wasternack - Leibniz-Institute of Plant Biochemistry, Germany
  • Beata Wolucka - Scientific Institute of Public Health, Belgium
  • Eleanore Wurtzel - The City University of New York, USA
  • Zhiyong Xie - Shanghai University of Traditional Chinese Medicine, China
  • Yue Yang - Michigan State University, USA
  • Jeorg Ziegler - University of Calgary, Canada
  • Bethany Zolman - University of Missouri-St. Louis, USA

    • We are grateful to our contributors and welcome any additional feedback from the community.

    We look forward to adding your name to the contributor list!

    The Plant Metabolic Network editorial board is an international assemblage of some of the world-class experts and leaders in varied domains of plant primary and secondary metabolism.

    Our board provides overall vision and guidance to the PMN project and plays an active role in ensuring the high quality of the information present in the PMN.

    More specifically, editors may review curated pathways for their accuracy and coverage before they are published online, either directly or via solicitation to other experts. They may also identify missing pathways and enzymes and inform curators of literature references to be used for curating new pathways or updating existing pathways.

    Primary Metabolism

    Amines and Polyamines

    Markus Piotrowski - Ruhr University Bochum, Germany

    Amino Acids

    Thomas Leustek - Rutgers University, USA

    Carbohydrates

    Maor Bar-Peled - Complex Carbohydrate Research Center, University of Georgia, USA

    Cofactors, Prostethic Groups, and Electron Carriers

    Tadhg Begley - Texas A&M University, USA
    Dean Dellapenna - Michigan State University, USA
    Nick Smirnoff - University of Exeter, UK
    Alison Smith - University of Cambridge, UK
    Takashi Hashimoto - Nara Institute of Science and Technology, Japan
    Ed Cahoon - University of Nebraska-Lincoln, USA

    Fatty Acids and Lipids

    Jan Jaworski - Donald Danforth Plant Science Center, USA
    Basil Nikolau - Iowa State University, USA
    Ruth Welti - Kansas State University, USA

    Hormones and Regulators

    Sue Abrams - National Research Council-Plant Biotechnology Institute, Canada
    Jerry Cohen - University of Minnesota, USA
    Mary Wildermuth - University of California, Berkeley, USA

    Nucleosides and Nucleotides

    Rita Zrenner - Max Planck Institute of Molecular Plant Physiology, Germany

    Secondary Metabolism

    Alkaloids

    Peter Facchini - University of Calgary, Canada

    Flavonoids

    Erich Grotewold - Ohio State University, USA
    Lloyd Sumner - The Samuel Roberts Noble Foundation, USA
    Brenda Winkel - Virginia Tech, USA
    Oliver Yu - Donald Danforth Plant Science Center, USA

    Phenylpropanoids

    Clint Chapple - Purdue University, USA
    David Gang - University of Arizona, USA

    Plant Volatiles

    Eran Pichersky - University of Michigan, USA

    Terpenoids

    Jonathan Page - National Research Council-Plant Biotechnology Institute, Canada
    Mark Lange - Washington State University, USA

    Transporters

    Wolf Frommer - Carnegie Institution for Science, USA

    We are grateful to these distinguished individuals for their contributions! 

    Emeriti board members

    In Memoriam - Joachim Schroeder - University of Freiburg, Germany
    We thank Dr. Schroeder for his advice on polyketides. He passed away in March of 2011.

      

    The PMN is funded by the National Science Foundation (Grant #: 1546838, 1026003 and 0640769) and the Department of Energy (BER Grant #:  ER65472), governed by an Editorial Board composed of internationally renowned scientists, and executed at the Carnegie Institution for Science, Department of Plant Biology.