John K Colbourne

Summary

Affiliation: Indiana University
Country: USA

Publications

  1. ncbi The ecoresponsive genome of Daphnia pulex
    John K Colbourne
    Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA
    Science 331:555-61. 2011
  2. ncbi ESTPiper--a web-based analysis pipeline for expressed sequence tags
    Zuojian Tang
    The Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, USA
    BMC Genomics 10:174. 2009
  3. ncbi A microsatellite-based genetic linkage map of the waterflea, Daphnia pulex: On the prospect of crustacean genomics
    Melania E A Cristescu
    Department of Biology, Indiana University at Bloomington, Bloomington, IN 47405, USA
    Genomics 88:415-30. 2006
  4. ncbi A machine-learning approach to combined evidence validation of genome assemblies
    Jeong Hyeon Choi
    The Center for Genomics and Bioinformatics, School of Informatics and Department of Biology, Indiana University, IN 47405, USA
    Bioinformatics 24:744-50. 2008
  5. ncbi Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveals novel crustacean metallothioneins
    Joseph R Shaw
    Department of Biology, Dartmouth College, Hanover, New Hampshire 03755, USA
    BMC Genomics 8:477. 2007
  6. ncbi Profiling sex-biased gene expression during parthenogenetic reproduction in Daphnia pulex
    Brian D Eads
    The Center for Genomics and Bioinformatics and Department of Biology, Indiana University Bloomington, Indiana 47405, USA
    BMC Genomics 8:464. 2007
  7. ncbi wFleaBase: the Daphnia genome database
    John K Colbourne
    Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, USA
    BMC Bioinformatics 6:45. 2005
  8. ncbi Evolutionary history of contagious asexuality in Daphnia pulex
    Susanne Paland
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Evolution 59:800-13. 2005
  9. ncbi Testosterone affects neural gene expression differently in male and female juncos: a role for hormones in mediating sexual dimorphism and conflict
    Mark P Peterson
    Department of Biology, Center for Integrative Study of Animal Behavior, Indiana University, Bloomington, Indiana, United States of America
    PLoS ONE 8:e61784. 2013
  10. ncbi Sampling Daphnia's expressed genes: preservation, expansion and invention of crustacean genes with reference to insect genomes
    John K Colbourne
    The Center for Genomics and Bioinformatics, and Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    BMC Genomics 8:217. 2007

Detail Information

Publications10

  1. ncbi The ecoresponsive genome of Daphnia pulex
    John K Colbourne
    Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA
    Science 331:555-61. 2011
    ..Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges...
  2. ncbi ESTPiper--a web-based analysis pipeline for expressed sequence tags
    Zuojian Tang
    The Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, USA
    BMC Genomics 10:174. 2009
    ..We have developed a web-based EST analysis pipeline called ESTPiper, which streamlines typical large-scale EST analysis components...
  3. ncbi A microsatellite-based genetic linkage map of the waterflea, Daphnia pulex: On the prospect of crustacean genomics
    Melania E A Cristescu
    Department of Biology, Indiana University at Bloomington, Bloomington, IN 47405, USA
    Genomics 88:415-30. 2006
    ..By mapping 342 tentative orthologous gene pairs (Daphnia/Drosophila) into the Daphnia linkage map, we facilitate future comparative projects...
  4. ncbi A machine-learning approach to combined evidence validation of genome assemblies
    Jeong Hyeon Choi
    The Center for Genomics and Bioinformatics, School of Informatics and Department of Biology, Indiana University, IN 47405, USA
    Bioinformatics 24:744-50. 2008
    ..e. greater than 90%). Our combined evidence approach avoids the difficult and often ad hoc selection of many parameters the individual measures require, and significantly improves the overall precisions on the benchmarking data sets...
  5. ncbi Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveals novel crustacean metallothioneins
    Joseph R Shaw
    Department of Biology, Dartmouth College, Hanover, New Hampshire 03755, USA
    BMC Genomics 8:477. 2007
    ..Our experiments revealed interesting changes in gene transcription that suggest their biological roles and their potentially toxicological features in responding to this important environmental contaminant...
  6. ncbi Profiling sex-biased gene expression during parthenogenetic reproduction in Daphnia pulex
    Brian D Eads
    The Center for Genomics and Bioinformatics and Department of Biology, Indiana University Bloomington, Indiana 47405, USA
    BMC Genomics 8:464. 2007
    ..Both sex determination and the switch in their mode of reproduction is environmentally induced, making Daphnia an interesting comparative system for the study of sex-biased and reproductive genes...
  7. ncbi wFleaBase: the Daphnia genome database
    John K Colbourne
    Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, USA
    BMC Bioinformatics 6:45. 2005
    ..By consequence, the Daphnia Genomics Consortium (DGC) has launched an interdisciplinary research program to create the resources needed to study genes that affect ecological and evolutionary success in natural environments...
  8. ncbi Evolutionary history of contagious asexuality in Daphnia pulex
    Susanne Paland
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Evolution 59:800-13. 2005
    ..If environment-mediated selective asymmetries play no significant role in determining the outcome of competitive interactions between sexuals and asexuals, regions of contact may be setting the stage for continued asexual conquests...
  9. ncbi Testosterone affects neural gene expression differently in male and female juncos: a role for hormones in mediating sexual dimorphism and conflict
    Mark P Peterson
    Department of Biology, Center for Integrative Study of Animal Behavior, Indiana University, Bloomington, Indiana, United States of America
    PLoS ONE 8:e61784. 2013
    ..Hormonally regulated gene expression is a key mechanism underlying sexual dimorphism, and our study identifies specific genes that may mediate some of these processes...
  10. ncbi Sampling Daphnia's expressed genes: preservation, expansion and invention of crustacean genes with reference to insect genomes
    John K Colbourne
    The Center for Genomics and Bioinformatics, and Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    BMC Genomics 8:217. 2007
    ....