• List of base-pair substitutions found in Mutation Accumulation lines of Escherichia coli K-12 PFM2 and its derivative strains (DNA repair) 

  Foster, Patricia L; Lee, Heewook; Popodi, Ellen M; Towns, Jesse P; Tang, Haixu

  List of base-pair substitutions found in mutation accumulation of the following E. coli strains: 1. K12 PFM2 (LB) 2. K12 PFM2 (minimal) 3. ED1a 4. IAI1 5. PFM101 6. PFM133 7. PFM35 8. PFM40 9. PFM88 10. PFM180 11. ...
• List of base-pair substitutions found in 21 mutation accumulation lines of Wild-type 6K (E. coli PFM2) 

  Lee, Heewook; Popodi, Ellen; Tang, Haixu; Foster, Patricia L (2012-09-19)

  List of base-pair substitutions found in 21 mutation accumulation lines of Wild-type 6K (E. coli PFM2)
• Assortative mating and self-fertilization differ in their contributions to reinforcement, cascade speciation, and diversification. 

  Castillo, DM; Gibson, AK; Moyle, LC (Current Zoology, )

  Cascade speciation and reinforcement can evolve rapidly when traits are pleiotropic and act as both signal/cue in non-random mating. Reproductive isolation due to these traits can be rapid, facilitating cascade speciation ...
• Conspecific plant-soil feedbacks of temperate tree species in the southern Appalachians, USA 

  Reinhart, K.O.; Johnson, D.; Clay, K. (PLOS ONE, 2012)

  Many tree species have seedling recruitment patterns suggesting that they are affected by non-competitive distance-dependent sources of mortality. We conducted an experiment, with landscape-level replication, to identify ...
• Global Patterns of Tissue-Specific Alternative Polyadenylation in Drosophila 

  Smibert, P.; Miura, P.; Westholm, J.O.; Shenker, S.; May, G.; Duff, M.O.; Zhang, D.; Eads, B.D.; Carlson, J.; Brown, J.B.; Eisman, R.C.; Andrews, J.; Kaufman, T.; Cherbas, P.; Celniker, S.E.; Graveley, B.R.; Lai, E.C. (Cell Reports, 2012)

  We analyzed the usage and consequences of alternative cleavage and polyadenylation (APA) in $\textit{Drosophila melanogaster}$ by using >1 billion reads of stranded mRNA-seq across a variety of dissected tissues. Beyond ...
• Tissue Damage Disrupts Developmental Progression and Ecdysteroid Biosynthesis in Drosophila 

  Hackney, J.F.; Zolali-Meybodi, O.; Cherbas, P. (PLOS ONE, 2012)

  In humans, chronic inflammation, severe injury, infection and disease can result in changes in steroid hormone titers and delayed onset of puberty; however the pathway by which this occurs remains largely unknown. Similarly, ...
• Cryptocephal, the Drosophila melanogaster ATF4, Is a Specific Coactivator for Ecdysone Receptor Isoform B2 

  Gauthier, S.A.; VanHaaften, E.; Cherbas, L.; Cherbas, P.; Hewes, R.S. (PLoS Genetics, 2012)

  The ecdysone receptor is a heterodimer of two nuclear receptors, the Ecdysone receptor (EcR) and Ultraspiracle (USP). In $\textit{Drosophila melanogaster}$, three EcR isoforms share common DNA and ligand-binding domains, ...
• Analysis of model replication origins in Drosophila reveals new aspects of the chromatin landscape and its relationship to origin activity and the prereplicative complex 

  Liu, J.; Mconnell, K.; Dixon, M.; Calvi, B.R. (The American Society for Cell Biology, 2012)

  Epigenetic regulation exerts a major influence on origins of DNA replication during development. The mechanisms for this regulation, however, are poorly defined. We showed previously that acetylation of nucleosomes regulates ...
• TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction 

  Doyle, E.L.; Booher, N.J.; Standage, D.S.; Voytas, D.F.; Brendel, V.P.; Vandyk, J.K.; Bogdanove, A.J. (Oxford University Press, 2012)

  Transcription activator-like (TAL) effectors are repeat-containing proteins used by plant pathogenic bacteria to manipulate host gene expression. Repeats are polymorphic and individually specify single nucleotides in the ...
• ParsEval: Parallel comparison and analysis of gene structure annotations 

  Standage, D.S.; Brendel, V.P. (BioMed Central Ltd., 2012)

  Background: Accurate gene structure annotation is a fundamental but somewhat elusive goal of genome projects, as witnessed by the fact that (model) genomes typically undergo several cycles of re-annotation. In many cases, ...
• Primary and Secondary siRNAs in Geminivirus-induced Gene Silencing 

  Aregger, M.; Borah, B.K.; Seguin, J.; Rajeswaran, R.; Gubaeva, E.G.; Zvereva, A.S.; Windels, D.; Vazquez, F.; Blevins, T.; Farinelli, L.; Pooggin, M.M. (Public Library of Science, 2012)

  In plants, RNA silencing-based antiviral defense is mediated by Dicer-like (DCL) proteins producing short interfering (si)RNAs. In $\textit{Arabidopsis}$ infected with the bipartite circular DNA geminivirus $\textit{Cabbage ...
• Functional Consequences of Subunit Diversity in RNA Polymerases II and V 

  Tan, E.H.; Blevins, T.; Ream, T.S.; Pikaard, C.S. (Elsevier (Cell Press), 2012)

  Multisubunit RNA polymerases IV and V (Pol IV and Pol V) evolved as specialized forms of Pol II that mediate RNA-directed DNA methylation (RdDM) and transcriptional silencing of transposons, viruses, and endogenous repeats ...
• Natal-host environmental effects on juvenile size, transmission success, and operational sex ratio in the entomopathogenic nematode Steinernema carpocapsae 

  Therese, M.O.; Bashey, F. (American Society of Parasitologists, 2012)

  Trans-host effects can alter the ecological and evolutionary dynamics of parasite and host populations. Here, we examine whether resource limitation within a parasite's natal host affects propagule size and influences ...
• Adaptation, Exaptation, and Constraint: A Hormonal Perspective 

  Ketterson, Ellen D.; Nolan, Val Jr (American Society of Naturalists, 1999-07)

  We approach conceptual issues in evolutionary biology from an endocrinological perspective, noting that single hormones typically act on several target tissues and thereby mediate suites of correlated phenotypic traits. ...
• Testosterone and Avian Life Histories: Effects of Experimentally Elevated Testosterone on Behavior and Correlates of Fitness in the Dark-Eyed Junco (Junco hyemalis) 

  Ketterson, Ellen D.; Nolan, Val Jr; Wolf, Licia; Ziegenfus, Charles (American Society of Naturalists, 1992-12)

  Hormones influence many aspects of organismal behavior, physiology, and morphol- ogy, and thus hormones may lie at the root of many life-history trade-offs. By manipulating hormones we can create novel phenotypes (i.e., ...
• Hormones and Life Histories: An Integrative Approach 

  Ketterson, Ellen D.; Nolan, Val Jr (American Society of Naturalists, 1992-11)

  Because of their role in mediating life‐history trade‐offs, hormones are expected to be strongly associated with components of fitness; however, few studies have examined how natural selection acts on hormonal variation ...
• Ordinary Extraordinary Junco 

  Ketterson, Ellen (Indiana University Department of Biology, 2013)

  The Ordinary Extraordinary Junco is a documentary film project designed to engage, entertain, and inspire student and adult audiences of all backgrounds. The feature-length film (88 min.) is comprised of eight shorter video ...
• 1996 Nestlogs WVS 

  Ketterson/Nolan Research Group (2013-10-31)

  Dark-eyed Junco (Junco hyemalis) nest data from Ketterson/Nolan Lab field work at Mountain Lake Biological Station, Pembroke, VA. Nestlogs include comments from observers for each nest visit as well as the following summary ...
• 1995 Nestlogs WP 

  Ketterson/Nolan Research Group (2013-10-31)

  Dark-eyed Junco (Junco hyemalis) nest data from Ketterson/Nolan Lab field work at Mountain Lake Biological Station, Pembroke, VA. Nestlogs include comments from observers for each nest visit as well as the following summary ...
• 1995 Nestlogs WVS 

  Ketterson/Nolan Research Group (2013-10-31)

  Dark-eyed Junco (Junco hyemalis) nest data from Ketterson/Nolan Lab field work at Mountain Lake Biological Station, Pembroke, VA. Nestlogs include comments from observers for each nest visit as well as the following summary ...

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