John K Colbourne
Affiliation: Indiana University
- The ecoresponsive genome of Daphnia pulexJohn 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...
- De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model systemMark P Peterson
Dept of Biology, Center for Integrated Study of Animal Behavior, Indiana University, Bloomington, IN, USA
BMC Genomics 13:305. 2012....
- ESTPiper--a web-based analysis pipeline for expressed sequence tagsZuojian 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...
- Potential for sexual conflict assessed via testosterone-mediated transcriptional changes in liver and muscle of a songbirdMark 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...
- Why so many unknown genes? Partitioning orphans from a representative transcriptome of the lone star tick Amblyomma americanumAmanda 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...
- A machine-learning approach to combined evidence validation of genome assembliesJeong 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...
- A microsatellite-based genetic linkage map of the waterflea, Daphnia pulex: On the prospect of crustacean genomicsMelania 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...
- Profiling sex-biased gene expression during parthenogenetic reproduction in Daphnia pulexBrian 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...
- Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveals novel crustacean metallothioneinsJoseph 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...
- Testosterone affects neural gene expression differently in male and female juncos: a role for hormones in mediating sexual dimorphism and conflictMark 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...
- Evolutionary history of contagious asexuality in Daphnia pulexSusanne 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...
- wFleaBase: the Daphnia genome databaseJohn 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...
- Identification of maternally-loaded RNA transcripts in unfertilized eggs of Tribolium castaneumKevin 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...
- Sampling Daphnia's expressed genes: preservation, expansion and invention of crustacean genes with reference to insect genomesJohn K Colbourne
The Center for Genomics and Bioinformatics, and Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
BMC Genomics 8:217. 2007....