John K Colbourne

Summary

Affiliation: Indiana University
Country: USA

Publications

  1. pmc 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. pmc De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system
    Mark P Peterson
    Dept of Biology, Center for Integrated Study of Animal Behavior, Indiana University, Bloomington, IN, USA
    BMC Genomics 13:305. 2012
  3. pmc 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
  4. doi request reprint Potential for sexual conflict assessed via testosterone-mediated transcriptional changes in liver and muscle of a songbird
    Mark P Peterson
    Department of Biology, Center for Integrative Study of Animal Behavior, Indiana University, Bloomington, IN 47405, USA
    J Exp Biol 217:507-17. 2014
  5. pmc Why so many unknown genes? Partitioning orphans from a representative transcriptome of the lone star tick Amblyomma americanum
    Amanda K Gibson
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    BMC Genomics 14:135. 2013
  6. doi request reprint 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
  7. ncbi request reprint 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
  8. pmc 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
  9. pmc 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
  10. pmc 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

Detail Information

Publications14

  1. pmc 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. pmc De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system
    Mark P Peterson
    Dept of Biology, Center for Integrated Study of Animal Behavior, Indiana University, Bloomington, IN, USA
    BMC Genomics 13:305. 2012
    ....
  3. pmc 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...
  4. doi request reprint Potential for sexual conflict assessed via testosterone-mediated transcriptional changes in liver and muscle of a songbird
    Mark P Peterson
    Department of Biology, Center for Integrative Study of Animal Behavior, Indiana University, Bloomington, IN 47405, USA
    J Exp Biol 217:507-17. 2014
    ..Thus, it appears that testosterone acts through both unique and shared transcriptional pathways in males and females, suggesting multiple mechanisms by which sexual conflict can be mediated...
  5. pmc Why so many unknown genes? Partitioning orphans from a representative transcriptome of the lone star tick Amblyomma americanum
    Amanda K Gibson
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    BMC Genomics 14:135. 2013
    ..We apply a general framework for quantifying the origin and true representation of unannotated sequences in a dataset and for evaluating the biological significance of orphan genes...
  6. doi request reprint 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
    ..Knowing which parts of the draft assembly are likely free of errors is critical if researchers are to draw reliable conclusions from the assembled sequence data...
  7. ncbi request reprint 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...
  8. pmc 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...
  9. pmc 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...
  10. pmc 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...
  11. ncbi request reprint 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...
  12. pmc 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...
  13. pmc Identification of maternally-loaded RNA transcripts in unfertilized eggs of Tribolium castaneum
    Kevin M Preuss
    Department of Biology, Indiana University, Bloomington, IN, USA
    BMC Genomics 13:671. 2012
    ..By studying maternal transcriptomes within and between divergent species, a better understanding of the evolutionary forces acting on maternal RNA allocation is possible...
  14. pmc 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
    ....