L Stein

Summary

Affiliation: Cold Spring Harbor Laboratory
Country: USA

Publications

  1. pmc Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza
    Hyeran Kim
    Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
    Genome Biol 9:R45. 2008
  2. pmc The Sequence Ontology: a tool for the unification of genome annotations
    Karen Eilbeck
    Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94729 3200, USA
    Genome Biol 6:R44. 2005
  3. doi request reprint Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges
    Lincoln D Stein
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Nat Rev Genet 9:678-88. 2008
  4. pmc The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics
    Lincoln D Stein
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    PLoS Biol 1:E45. 2003
  5. ncbi request reprint Integrating biological databases
    Lincoln D Stein
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nat Rev Genet 4:337-45. 2003
  6. ncbi request reprint Genome annotation: from sequence to biology
    L Stein
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nat Rev Genet 2:493-503. 2001
  7. pmc WormBase: network access to the genome and biology of Caenorhabditis elegans
    L Stein
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 29:82-6. 2001
  8. pmc The generic genome browser: a building block for a model organism system database
    Lincoln D Stein
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11790, USA
    Genome Res 12:1599-610. 2002
  9. pmc Reactome: a knowledgebase of biological pathways
    G Joshi-Tope
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
    Nucleic Acids Res 33:D428-32. 2005
  10. ncbi request reprint The Genome Knowledgebase: a resource for biologists and bioinformaticists
    G Joshi-Tope
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11790, USA
    Cold Spring Harb Symp Quant Biol 68:237-43. 2003

Detail Information

Publications37

  1. pmc Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza
    Hyeran Kim
    Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
    Genome Biol 9:R45. 2008
    ..sativa ssp. japonica reference genome sequence. Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date...
  2. pmc The Sequence Ontology: a tool for the unification of genome annotations
    Karen Eilbeck
    Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94729 3200, USA
    Genome Biol 6:R44. 2005
    ....
  3. doi request reprint Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges
    Lincoln D Stein
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Nat Rev Genet 9:678-88. 2008
    ..This article reviews the components of a biological cyberinfrastructure, discusses current and pending implementations, and notes the many challenges that lie ahead...
  4. pmc The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics
    Lincoln D Stein
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    PLoS Biol 1:E45. 2003
    ..elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes...
  5. ncbi request reprint Integrating biological databases
    Lincoln D Stein
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nat Rev Genet 4:337-45. 2003
    ..Depending on the data that they contain, the databases fulfil different functions. But, although they are architecturally similar, so far their integration has proved problematic...
  6. ncbi request reprint Genome annotation: from sequence to biology
    L Stein
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nat Rev Genet 2:493-503. 2001
    ..The tools and resources for annotation are developing rapidly, and the scientific community is becoming increasingly reliant on this information for all aspects of biological research...
  7. pmc WormBase: network access to the genome and biology of Caenorhabditis elegans
    L Stein
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 29:82-6. 2001
    ..It builds upon the existing ACeDB database of the C.elegans genome by providing data curation services, a significantly expanded range of subject areas and a user-friendly front end...
  8. pmc The generic genome browser: a building block for a model organism system database
    Lincoln D Stein
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11790, USA
    Genome Res 12:1599-610. 2002
    ..GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org...
  9. pmc Reactome: a knowledgebase of biological pathways
    G Joshi-Tope
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
    Nucleic Acids Res 33:D428-32. 2005
    ..The database is publicly available under open source terms, which allows both its content and its software infrastructure to be freely used and redistributed...
  10. ncbi request reprint The Genome Knowledgebase: a resource for biologists and bioinformaticists
    G Joshi-Tope
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11790, USA
    Cold Spring Harb Symp Quant Biol 68:237-43. 2003
  11. pmc Scriptable access to the Caenorhabditis elegans genome sequence and other ACEDB databases
    L D Stein
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 8:1308-15. 1998
    ..Both packages can be downloaded from URL. A Microsoft Windows port of AcePerl is in the planning stages...
  12. pmc Comparative genomics between rice and Arabidopsis shows scant collinearity in gene order
    H Liu
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 11:2020-6. 2001
    ..Computer simulation showed that these microscale collinearities are above the expectation for a random process. On the other hand, the order of exons within homologous genes (<2.5 kb) was preserved, as expected...
  13. pmc WormBase: new content and better access
    Tamberlyn Bieri
    Genome Sequencing Center, Washington University School of Medicine, St Louis, MO 63108, USA
    Nucleic Acids Res 35:D506-10. 2007
    ..Access to and searching WormBase has become more dependable and flexible via multiple mirror sites and indexing through Google...
  14. pmc WormBook: the online review of Caenorhabditis elegans biology
    Lisa R Girard
    Division of Biology, 156 29, Pasadena, CA 91125, USA
    Nucleic Acids Res 35:D472-5. 2007
    ..elegans research and continues to grow. WormBook represents a generic publishing infrastructure that is easily adaptable to other research communities to facilitate the dissemination of knowledge in the field...
  15. pmc Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics
    Nansheng Chen
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Biol 7:R126. 2006
    ..Taking this approach, we have identified numerous novel ciliary genes in C. elegans, some of which may be orthologs of unidentified human ciliopathy genes...
  16. pmc Gallus GBrowse: a unified genomic database for the chicken
    Carl J Schmidt
    Department of Animal and Food Sciences, University of Delaware, Newark, DE 19706, USA
    Nucleic Acids Res 36:D719-23. 2008
    ..net/cgi-bin/webBlat) for matching user-provided sequences to the chicken genome. These tools make the Gallus GBrowse server a valuable resource for researchers seeking genomic information regarding the chicken and other avian species...
  17. pmc Genome-wide detection and characterization of positive selection in human populations
    Pardis C Sabeti
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
    Nature 449:913-8. 2007
    ....
  18. pmc WormBase 2007
    Anthony Rogers
    Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 36:D612-7. 2008
    ..Improved search and display tools, wider cross-species comparisons and extended ontologies are some of the features that will help scientists extend their research and take advantage of other nematode species genome sequences...
  19. doi request reprint Using the Reactome database
    Lincoln D Stein
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    Curr Protoc Bioinformatics . 2004
    ....
  20. ncbi request reprint Unix survival guide
    Lincoln D Stein
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    Curr Protoc Bioinformatics . 2007
    ..This appendix provides the novice with easy-to-understand information needed to survive in the Unix environment...
  21. ncbi request reprint WormBase: methods for data mining and comparative genomics
    Todd W Harris
    Cold Spring Harbor Laboratory, NY, USA
    Methods Mol Biol 351:31-50. 2006
    ..No knowledge of programming is necessary or assumed, although users with intermediate skills in the Perl scripting language will be able to utilize additional data-mining approaches...
  22. pmc Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans
    Nansheng Chen
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 16:606-17. 2006
    ....
  23. pmc WormBase: better software, richer content
    Erich M Schwarz
    Division of Biology, 156 29 California Institute of Technology, Pasadena, CA, 91125, USA
    Nucleic Acids Res 34:D475-8. 2006
    ....
  24. pmc Gramene, a tool for grass genomics
    Doreen H Ware
    Cold Spring Harbor Laboratory, New York 11724, USA
    Plant Physiol 130:1606-13. 2002
    ..In this paper, we present a brief overview of the search tools available to the plant research community in Gramene...
  25. pmc The SNP Consortium website: past, present and future
    Gudmundur A Thorisson
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 31:124-7. 2003
    ..SNP linkage maps are available for download and for browsing in a comparative map viewer. All software components of the data coordinating center (DCC) website (http://snp.cshl.org) are open source...
  26. pmc WormBase: a cross-species database for comparative genomics
    Todd W Harris
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 31:133-7. 2003
    ..elegans researchers, to include researchers wishing to explore problems in functional and comparative genomics within the context of a powerful genetic system...
  27. pmc WormBase: a multi-species resource for nematode biology and genomics
    Todd W Harris
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 32:D411-7. 2004
    ..These advances continue to increase the utility of WormBase for C.elegans researchers, as well as for those researchers exploring problems in functional and comparative genomics in the context of a powerful genetic system...
  28. pmc WormBase as an integrated platform for the C. elegans ORFeome
    Nansheng Chen
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 14:2155-61. 2004
    ....
  29. ncbi request reprint Human genome: end of the beginning
    Lincoln D Stein
    Nature 431:915-6. 2004
  30. pmc WormBase: a comprehensive data resource for Caenorhabditis biology and genomics
    Nansheng Chen
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 33:D383-9. 2005
    ..Internally, we have restructured the database models to rationalize the representation of genes and to prepare the system to accept the genome sequences of three additional Caenorhabditis species over the coming year...
  31. pmc Identification of a nematode chemosensory gene family
    Nansheng Chen
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Proc Natl Acad Sci U S A 102:146-51. 2005
    ..The expansion of both the srab and sra gene families in C. elegans relative to C. briggsae is due to multiple rounds of tandem duplication and translocation of individual genes...
  32. pmc The International HapMap Project Web site
    Gudmundur A Thorisson
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 15:1592-3. 2005
    ....
  33. pmc The Bioperl toolkit: Perl modules for the life sciences
    Jason E Stajich
    University Program in Genetics, Duke University, Durham, North Carolina 27710, USA
    Genome Res 12:1611-8. 2002
    ..We conclude with a discussion of how the open-source nature of the project has contributed to the development effort...
  34. pmc A second generation human haplotype map of over 3.1 million SNPs
    Kelly A Frazer
    The Scripps Research Institute, 10550 North Torrey Pines Road MEM275, La Jolla, California 92037, USA
    Nature 449:851-61. 2007
    ..Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations...
  35. pmc The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant
    Katica Ilic
    Department of Plant Biology, Carnegie Institution, Stanford, California 94305, USA
    Plant Physiol 143:587-99. 2007
    ..The PSO, as well as contributed gene associations, can be obtained at www.plantontology.org...
  36. ncbi request reprint X Window System survival guide
    Lincoln D Stein
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    Curr Protoc Bioinformatics . 2007
    ..This appendix describes the two main options for overcoming this obstacle: a Virtual Network Computer (VNC) and the X Window System...
  37. pmc GMODWeb: a web framework for the Generic Model Organism Database
    Brian D O'Connor
    Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
    Genome Biol 9:R102. 2008
    ..GMODWeb was built using the open source Turnkey web framework and is available from http://turnkey.sourceforge.net...