Lukas A Mueller

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc AraCyc: a biochemical pathway database for Arabidopsis
    Lukas A Mueller
    The Arabidopsis Information Resource, Department of Plant Biology, Carnegie Institution of Washington, 260 Panama Street, Stanford 94305, USA
    Plant Physiol 132:453-60. 2003
  2. pmc Functional annotation of the Arabidopsis genome using controlled vocabularies
    Tanya Z Berardini
    Carnegie Institution, Department of Plant Biology, Stanford, California 94305, USA
    Plant Physiol 135:745-55. 2004
  3. pmc The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
    Ron Caspi
    SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA, Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA and Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853 USA
    Nucleic Acids Res 42:D459-71. 2014
  4. pmc The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community
    Seung Yon Rhee
    Carnegie Institution of Washington, 260 Panama Street, Stanford, CA 94305, USA
    Nucleic Acids Res 31:224-8. 2003
  5. pmc The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    Ron Caspi
    SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA, USA
    Nucleic Acids Res 40:D742-53. 2012
  6. pmc PatMatch: a program for finding patterns in peptide and nucleotide sequences
    Thomas Yan
    Department of Plant Biology, Carnegie Institution of Washington, 260 Panama Street, Stanford, CA 94305, USA
    Nucleic Acids Res 33:W262-6. 2005
  7. pmc Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts
    Chenwei Lin
    Department of Plant Breeding and Genetics, Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
    Theor Appl Genet 112:114-30. 2005
  8. pmc A sequence-based map of Arabidopsis genes with mutant phenotypes
    David W Meinke
    Department of Plant Biology, Carnegie Institution, 260 Panama Street, Stanford, California 94305, USA
    Plant Physiol 131:409-18. 2003
  9. ncbi request reprint Surviving in a sea of data: a survey of plant genome data resources and issues in building data management systems
    Leonore Reiser
    Carnegie Institution, Department of Plant Biology, Stanford, CA 94305, USA
    Plant Mol Biol 48:59-74. 2002
  10. pmc Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants
    Peifen Zhang
    Department of Plant Biology, Carnegie Institution, Stanford, California 94305, USA
    Plant Physiol 153:1479-91. 2010

Collaborators

Detail Information

Publications21

  1. pmc AraCyc: a biochemical pathway database for Arabidopsis
    Lukas A Mueller
    The Arabidopsis Information Resource, Department of Plant Biology, Carnegie Institution of Washington, 260 Panama Street, Stanford 94305, USA
    Plant Physiol 132:453-60. 2003
    ..AraCyc is available at the tools section of The Arabidopsis Information Resource Web site (http://www.arabidopsis.org/tools/aracyc)...
  2. pmc Functional annotation of the Arabidopsis genome using controlled vocabularies
    Tanya Z Berardini
    Carnegie Institution, Department of Plant Biology, Stanford, California 94305, USA
    Plant Physiol 135:745-55. 2004
    ....
  3. pmc The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
    Ron Caspi
    SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA, Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA and Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853 USA
    Nucleic Acids Res 42:D459-71. 2014
    ....
  4. pmc The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community
    Seung Yon Rhee
    Carnegie Institution of Washington, 260 Panama Street, Stanford, CA 94305, USA
    Nucleic Acids Res 31:224-8. 2003
    ..Finally, we have recently incorporated seed and DNA stock information from the Arabidopsis Biological Resource Center (ABRC) and implemented a shopping-cart style on-line ordering system...
  5. pmc The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    Ron Caspi
    SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA, USA
    Nucleic Acids Res 40:D742-53. 2012
    ..New developments include a zoomable web interface for diagrams; flux-balance analysis model generation from PGDBs; web services; and a new tool called Web Groups...
  6. pmc PatMatch: a program for finding patterns in peptide and nucleotide sequences
    Thomas Yan
    Department of Plant Biology, Carnegie Institution of Washington, 260 Panama Street, Stanford, CA 94305, USA
    Nucleic Acids Res 33:W262-6. 2005
    ..arabidopsis.org/home/tair/Software/Patmatch/. The PatMatch server is available on the web at http://www.arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl for searching Arabidopsis thaliana sequences...
  7. pmc Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts
    Chenwei Lin
    Department of Plant Breeding and Genetics, Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
    Theor Appl Genet 112:114-30. 2005
    ..Moreover, both belong to the Asterid I clade of dicot plant families. Thus, the biology of coffee (family Rubiacaeae) and tomato (family Solanaceae) may be united into one common network of shared discoveries, resources and information...
  8. pmc A sequence-based map of Arabidopsis genes with mutant phenotypes
    David W Meinke
    Department of Plant Biology, Carnegie Institution, 260 Panama Street, Stanford, California 94305, USA
    Plant Physiol 131:409-18. 2003
    ....
  9. ncbi request reprint Surviving in a sea of data: a survey of plant genome data resources and issues in building data management systems
    Leonore Reiser
    Carnegie Institution, Department of Plant Biology, Stanford, CA 94305, USA
    Plant Mol Biol 48:59-74. 2002
    ..These concepts include data descriptions, exchange format, curation, attribution, and database implementation...
  10. pmc Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants
    Peifen Zhang
    Department of Plant Biology, Carnegie Institution, Stanford, California 94305, USA
    Plant Physiol 153:1479-91. 2010
    ..These resources can be searched by text or BLAST, browsed, and downloaded from our project Web site (http://plantcyc.org)...
  11. pmc The Genome Database for Rosaceae (GDR): year 10 update
    Sook Jung
    Department of Horticulture, Washington State University, Pullman, WA 99164 6414, USA, Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA, Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853, USA, Department of Computer Science, Saginaw Valley State University, University Center, MI 48710, USA and Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
    Nucleic Acids Res 42:D1237-44. 2014
    ..Improved search pages are available for marker, trait locus, genetic diversity and publication data. New search tools for breeders enable selection comparison and assistance with breeding decision making. ..
  12. ncbi request reprint TAIR: a resource for integrated Arabidopsis data
    Margarita Garcia-Hernandez
    TAIR, Carnegie Institution of Washington, 260 Panama Street, Stanford, CA 94305, USA
    Funct Integr Genomics 2:239-53. 2002
    ..A significant new feature is the integration of the ABRC database functions and stock ordering system, which allows users to place orders for seed and DNA stocks directly from the TAIR site...
  13. doi request reprint Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case
    Gloria Lopez-Casado
    Department of Plant Biology, Cornell University, Ithaca, NY, USA
    Proteomics 12:761-74. 2012
    ..We conclude that RNA-Seq provides a cost-effective and robust platform for protein identification and will be increasingly valuable to the field of proteomics...
  14. pmc MetaCyc: a multiorganism database of metabolic pathways and enzymes
    Cynthia J Krieger
    SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA
    Nucleic Acids Res 32:D438-42. 2004
    ..In the past 2 years the data content and the Pathway Tools software used to query, visualize and edit MetaCyc have been expanded significantly. These enhancements are described in this paper...
  15. pmc The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond
    Lukas A Mueller
    Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
    Plant Physiol 138:1310-7. 2005
    ....
  16. pmc Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato
    Erwin Datema
    Applied Bioinformatics, Plant Research International, PO Box 16, 6700 AA, Wageningen, The Netherlands
    BMC Plant Biol 8:34. 2008
    ..This study presents a first genome-wide analysis of these two species, based on two large collections of BAC end sequences representing approximately 19% of the tomato genome and 10% of the potato genome...
  17. pmc Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade
    Feinan Wu
    Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, USA
    Genetics 174:1407-20. 2006
    ..2) No whole-genome duplication event (i.e., polyploidization) occurred immediately prior to or after the radiation of either Solanaceae or Rubiaceae as has been recently suggested...
  18. pmc Floral gene resources from basal angiosperms for comparative genomics research
    Victor A Albert
    Natural History Museum, University of Oslo, NO 0318 Oslo, Norway
    BMC Plant Biol 5:5. 2005
    ....
  19. doi request reprint The SGN comparative map viewer
    Lukas A Mueller
    Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, USA
    Bioinformatics 24:422-3. 2008
    ..The viewer is implemented in object oriented Perl, with a simple extensible interface to write data adapters for other relational database schemas and flat file formats...
  20. ncbi request reprint EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6,000 genes from a basal eudicot
    John E Carlson
    The School of Forest Resources and Huck Institutes for Life Sciences, Pennsylvania State University, 323 Forest Resources Building, University Park, 16802, USA
    Plant Mol Biol 62:351-69. 2006
    ....
  21. pmc A community-based annotation framework for linking solanaceae genomes with phenomes
    Naama Menda
    Department of Plant Breeding and Genetics, and Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853, USA
    Plant Physiol 147:1788-99. 2008
    ..All data, tools, and code developed at SGN are freely available to download and adapt...