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Ecological Genomics Institute



Badillo-Vargas, I., Rotenberg, D., Schneweis, B.A., and Whitfield, A.E. 2015. RNA interference tools for Frankliniella occidentalisJournal of Insect Physiology 76:36-46.

Brown, SJ and D. Tagu. 2015. Editorial overview: Insect Genomics How to sequence 5,000 insect genomes? Current Opinions in Insect Science. Science 7: iv-v.

Brown, S.P., and Jumpponen, A. 2015. Phylogenetic diversity analyses reveal disparity between fungal and bacterial communities during microbial primary succession. Soil Biology and Biochemistry 89: 52-60.

Brown, S.P., Olson, BJSC, and Jumpponen, A. 2015. Fungi and Algae Co-Occur in Snow: An Issue of Shared Habitat and Algal Facilitation of Heterotrophs? Artic, Antarctic and Alpine Research 47: 729-749-60.

Brown, S.P., Veach, A.M, Grond, K., Lickteig, S.K., Lothamer, K., Oliver, A.K., Rigdon-Huss, A.R., Jumpponen, A. 2015. Scraping the bottom of the barrel: are rare high throughput sequences artifacts? Fungal Ecology 13: 221-225. DOI: 10.1016 / j.funeco.2014.08.006

Chiara, M., Fanelli, F., Mulé, G., Logrieco, A., Pesole, G., Leslie, J., Horner, D., Toomajian, C. 2015. Genome Sequencing of Multiple Isolates Highlights Subtelomeric Genomic Diversity within Fusarium fujikuroi. Genome Biology and Evolution 7(11):3062-3069.

Culumber, Z. W., M. Schumer, S. Monks & M. Tobler. 2015. Environmental heterogeneity generatesopposite gene by environment interactions for two fitness-related traits within a population. Evolution 69 (2): 541-550.

Egan SP, Ragland GJ, Assour L, Powell TH, Hood GR, Emrich S, Nosil P, Feder JL. 2015. Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow. Ecological Letters. 18(8):817-25.

Eifert, C., M. Farnworth, T. Schulz–Mirbach, R. Riesch, D. Bierbach, S. Klaus, A. Wurster, M. Tobler, B. Streit, J. R. Indy, L. Arias–Rodriguez & M. Plath. 2015. Brain size variation in extremophile fish: local adaptation vs. phenotypic plasticityJournal of Zoology (London) 295 (2): 143‑153.

Everman, E.R, R.A. Cloyd, C. Copland, and T.J. Morgan. 2015. Short Communication: First Report of Spotted Wing Drosophila, Drosophila suzukii Matsumura (Diptera: Drosophilidae) in Kansas. Kan Ento. Soc. 88(1):128-133.

D Gates, SR Stricker, LA Mueller, BJSC Olson, SD Smith. Diversification of the R2R3 MYB transcription factors in the tomato family SolanaceaeJournal of Molecular Evolution. 83(1): 26-37. 

Gerken, A.R.T.F.C. Mackay, and T.J. Morgan. 2015. Artificial Selection on Chill-Coma Recovery Time in Drosophila melanogaster: Direct and correlated responses to selection. Journal of Thermal Biology. 59: 77-85.

Gerken, A.R., O.C. Eller, D.A. Hahn, and T.J. Morgan. 2015. Constraints, independence, and evolution of thermal plasticity: probing genetic architecture of long and short-term thermal acclimationProceedings of the National Academy of Sciences, doi:10.1073/pnas.1503456112 

K. J. Goodman, S. M. Parker, J. W. Edmonds and L. H. Zeglin. 2015. Expanding the scale of aquatic sciences: The role of the National Ecological Observatory Network (NEON). Freshwater Science, 34(1): 377-385.

Gray, M.M., St. Amand, P., Akhunov, E.D., Knapp, M., Garrett, K.A., Morgan, T.J., Baer, S.G., Maricle, B.R., Johnson, L.C. 2015. Ecotypes of an ecologically dominant grass (Andropogon gerardii) exhibit genetic divergence across the U.S. Midwest environmental gradient. Molecular Ecology. 23(24): 6011-6028.

Herndon, N. and Caragea, D. 2015. Empirical Study of Domain Adaptation Algorithms on the Task of Splice Site Prediction. Invited paper. In: Lecture Notes in Communications in Computer and Information Science (CCIS), Springer-Verlag Berlin Heidelberg, Volume 511 of the series Communications in Computer and Information Science pp 195-211.

Hope AG, Waltari E, Malaney JL, Payer DC, Cook JA, Talbot SL. 2015. Arctic Biodiversity: increasing richness accompanies shrinking refugia for a cold-associated tundra faunaEcosphere. Volume 6, Issue 9 September 2015 Pages 1–67. 

Johnson, L., J. T. Olsen, H. Tetreault, R. K. Goad, M. M. Mendola, A. DeLaCruz, H. Bryant, T. Morgan, M. Knapp, N. M. Bello, S. Baer and B. Maricle. Intraspecific variation of a dominant grass and local adaptation in reciprocal garden communities along a US Great Plains’ precipitation gradient: Implications for grassland restoration with climate changeEvolutionary Applications. 2015 Aug; 8(7): 705–723.

Jordan, KW, S Wang, Y Lun, L-J Gardiner, R MacLachlan, P Hucl, K Wiebe, D Wong, KL Forrest, IWGSC, AG Sharpe, CHD Sidebottom, N Hall, C Toomajian, T Close, J Dubcovsky, A Akhunov, L Talbert, UK Bansal, HS Bariana, MJ Hayden, C Pozniak, JA Jeddeloh, A Hall & E AkhunovA haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biology 16:48 (2015) (doi: 10.1186/s13059-015-0606-4).

Jumpponen, A., Brown, S.P., Trappe, J.M., Cázares, E., Strömmer, R. 2015. Analyses of sporocarps, morphotyped ectomycorrhizae, environmental ITS and LSU sequences identify common genera that occur at a periglacial site. Journal of Fungi 1: 76-93. DOI: 10.3390/jof1010076

Kharel K., Arthur F. H., Zhu K. Y., Campbell J. F. & Subramanyam B.  2015.  Influence of temperature and artificially-created physical barriers on the efficacy of synergized pyrethrin aerosolStored Prod. Res. 60: 36-42.

Lasky JR, Upadhyaya HD, Ramu P, Deshpande S, Hash CT, Bonnette J, Juenger TE, Hyma K, Acharya C, Mitchell SE, Buckler ES, Brenton Z, Kresovich S, Morris GP. 2015. Genome environment associations in sorghum landraces predict adaptive traitsScience Advances. Vol. 1, no. 6, e1400218, DOI: 10.1126/sciadv.1400218.

Li G, Wang Y, Chen MS, Edae E, Poland J, Akhunov E, Chao S, Bai G, Carver BF, Yan L. Precisely mapping a major gene conferring resistance to Hessian fly in bread wheat using genotyping-by-sequencingBMC Genomics. 2015, 16:108.

Majetic, C. J., S. D. Wiggam, C. J. Ferguson and R. A. Raguso. 2015. Timing is everything: temporal variation in floral scent, and its connections to pollinator behavior and female reproductive success in Phlox divaricata. American Midland Naturalist 173: 191-207.

Mandyam, K.G. and Jumpponen, A. 2015. Mutualism-parasitism paradigm synthesized from results of root-endophyte models. Frontiers in Microbiology 5: e776. DOI: 10.3389/fmicb.2014.00776.

Mendola, M., Baer, S.G., Johnson, L.C., Maricle, B.R. Ecotypic variation in functional traits of a dominant grassland species: Implication for plant and ecosystem response to climate change. Ecology, 96(9), 2015, pp. 2433–2445.

Oliver, A.K., Callaham, M.A., and Jumpponen, A. 2015. Soil fungal communities respond compositionally to recurring frequent prescribed burning in a managed southeastern US forest ecosystem. Forest Ecology and ManagementVolume 345, 1 June 2015, Pages 1–9.

Oliver, A.K., Brown, S.P., Callaham, M.A., Jumpponen, A. 2015. Polymerase matters: non-proofreading enzymes inflate community richness estimates by up to 15%Fungal Ecology 15: 86-89. DOI: 10.1016/j.funeco.2015.03.003

K O’Neil, BJSC Olson, N Huang, D Unis and R Clemø. 2015. Rapid selection against arbovirus-induced apoptosis during infection of a mosquito vectorProceedings of the National Academy of Sciences (USA), 112 (10), E1152-E1161

Passow, C. N.R. Greenway, L. Arias-Rodriguez, P. D. Jeyasingh & M. Tobler. 2015. Reduction of energetic demands through modification of body size and routine metabolic rates in extremophile fishPhysiological and Biochemical Zoology: Ecological and Evolutionary Approaches. Vol. 88, No. 4 (July/August 2015), pp. 371-383

Peacock E, Sonsthagen SA, Obbard ME, Boltunov A, Regehr EV, Ovsyanikov N, Aars J, Atkinson SN, Sage GK, Hope AG, Zeyl E, Bachmann L, Ehrich D, Scribner KT, Amstrup SC, Belikov S, Born E, Derocher AE, Stirling I, Taylor MK, Wiig Ø, Paetkau D, Talbot SL. 2015. Implications of the circumpolar genetic structure of polar bears for their ecology, evolution and conservation in a rapidly warming Arctic. PLoS ONE, 10(1), e112021.

Ragland, G.J., Almskaar, K., Vertacnik, K.L., Gough, H.M., Feder, J.L., Hahn, D.A., Schwarz, D. 2015. Differences in performance and transcriptome-wide gene expression associated with Rhagoletis (Diptera: Tephritidae) larvae feeding in alternate host fruit environments. Molecular Ecology. 2015 Jun;24(11):2759-76. doi: 10.1111/mec.13191.

Saravesi, K., Aikio, S., Wäli, P.R., Ruotsalainen, A.L., Kaukonen, M., Huusko, K., Brown, S.P, Jumpponen, A., Tuomi, J., Markkola, A. 2015. Moth outbreaks alter root-associated fungal communities in subarctic mountain birch forestsMicrobial Ecology 69: 788-797. DOI: 10.1007/s00248-015-0577-8

Stanescu, A., and Caragea, D. (2015). An empirical study of ensemble-based semi-supervised learning approaches for imbalanced splice site datasets. Invited to be published in SI of BMC System Biology. 9 Suppl 5: S1. doi:10.1186/1752-0509-9-S5-S1.

Stanescu, A., Tangirala, K. and Caragea, D. (2015). Predicting Alternatively Spliced Exons Using Semi-supervised Learning. In: International Journal on Data Mining and Bioinformatics (IJDMB). DOI: http://dx.doi.org/10.1504/IJDMB.2016.073337.

Sun, H., Santalahti, M., Pumpanen, J., Köster, K., Berninger, F., Raffaello, T., Jumpponen, A., Asiegbu, F.O., and Heinonsalo, J. 2015. Fungal community shifts in structure and function across a boreal forest fire chronosequence. Applied and Environmental MicrobiologyNovember 2015 vol. 81 no. 227869-7880.

Tobler, M., K. Scharnweber, R. GreenwayC. N. Passow, L. Arias-Rodriguez & F. J. Garcia-De-Leon. 2015. Convergent changes in the trophic ecology of extremophile fish occurring along replicated environmental gradientsFreshwater Biology 60 (4): 768-780.

Veach, A., Dodds, W. and Jumpponen, A. 2015. Woody plant encroachment, and its removal, impact bacterial and fungal communities across stream and terrestrial habitats in a tallgrass prairie ecosystem. FEMS Microbiology Ecology. DOI: 10.1093/femsec/fiv109.

Whitfield, A.E., Falk, B.W, Rotenberg, D. 2015. Insect vector-mediated transmission of plant virusesVirology 479-480:278-289.

Whitfield, A.E., and Rotenberg, D. 2015. Disruption of insect transmission of plant viruses. Current Opinion in Insect Science 8:79-87.

Wilson, L.R., D.J. Gibson, S.G. Baer, & L. Johnson. Plant community response to regional sources of dominant grasses in grasslands restored across a longitudinal gradient. Ecosphere. DOI: 10.1002/esc2.1329.

L. H. Zeglin. 2015. Stream microbial diversity responds to environmental changes: Review and synthesis of existing researchFrontiers in Microbiology 6: 454.

Zhao, C., Navarro Escalante, L., Benatti, T., Qu, J., Chellapilla, S., Waterhouse, R. M., Caragea, D., Richards, S. 2015. A  Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest (Mayetiola destructor). Current Biology, 25(5): 613-620.