Publications
Chenevert, M., Miller, B., Karkoutli, A., Rusnak, A., Lott, S., and Atallah, J. (2022). The early embryonic transcriptome of a Hawaiian Drosophila picture-wing fly shows evidence of altered gene expression and novel gene evolution. Journal of Experimental Zoology Part B. {advance online publication} https://doi.org/10.1002/jez.b.23129
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Panta, M., Mishra, A., Hoque, M.D., and Atallah. J. (2021). ClassifyTE: a stacking-based prediction of hierarchical classification of transposable elements. Bioinformatics March 2 2021 {early view)}. https://doi.org/10.1093/bioinformatics/btab146
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LeBien, J., McCollam, G., and Atallah, J. (2020). An in silico model of LINE-1-mediated neoplastic evolution. Bioinformatics 36(14): 4144-4153. https://doi.org/10.1093/bioinformatics/btaa279
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Kalay, G., Atallah, J., Sierra, N., May, M., Tang, A.M., Crofton, A.E., Murugesan, M.K., Wykoff-Clary, S. and Lott, S.E. (2020). Evolution of larval segment position across 12 Drosophila species. Evolution 74(7): 1409-1422. https://doi.org/10.1111/evo.13911
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Atallah, J., and Lott, S.E. (2018). Evolution of maternal and zygotic mRNA complements in the early Drosophila embryo. PLoS Genetics 14 (12):e1007838. https://doi.org/10.1371/journal.pgen.1007838
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Jasper, W.C., Linksvayer, T.A., Atallah, J., Friedman, D., Chiu, J.C., and Johnson, B.R. (2015). Large scale coding sequence change underlies the evolution of post-developmental novelty in honey bees. Molecular Biology and Evolution 32:334-346. http://dx.doi.org/10.1093/molbev/msu292
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Shelomi, M., Jasper, W.C., Atallah, J., Kimsey, L.S., and Johnson, B.R. (2014). Differential expression of endogenous plant cell wall degrading enzyme genes in the stick insect (Phasmatodea) midgut. BMC Genomics 15:917. http://dx.doi.org/10.1186/1471-2164-15-917
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Malagón, J.N., Ahuja, A., Sivapatham, G., Hung, J., Lee, J., Muñoz-Gómez, S.A., Atallah, J., Singh, R.S., and Larsen, E. (2014). Evolution of Drosophila sex comb length illustrates the inextricable interplay between selection and variation. Proceedings of the National Academy of Sciences USA 111: E4103-E4109. http://dx.doi.org/10.1073/pnas.1322342111
See also the PNAS review of this paper by Abouheif and Rafiqi (2014): http://dx.doi.org/10.1073/pnas.1415189111
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Atallah, J., Teixeira, L., Salazar, R., Zaragoza, G., and Kopp, A. (2014). The making of a pest: the evolution of a fruit-penetrating ovipositor in Drosophila suzukii and related species. Proceedings of the Royal Society B 281:20132840. http://dx.doi.org/10.1098/rspb.2013.2840
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Chen, Z.*, Sturgill, D.*, Qu, J., Jiang, H., Park, S., Boley, N., Suzuki, A.M., Fletcher, A.R., Plachetzki, D.C., FitzGerald, P.C., Artieri, C.G., Atallah, J., Barmina, O., Brown, J.B., Blankenburg, K.P., Clough, E., Dasgupta, A., Gubbala, S., Han, Y., Jayaseelan, J.C., Kalra, D., Kim, Y., Kovar, C.L., Lee, S., Li, M., Malley, J.D., Malone, J.H., Mathew, T., Mattiuzzo, N.R., Munidasa, M., Muzny, D.M., Ongeri, F., Perales, L., Przytycka, T.M., Pu, L., Robinson, G., Thornton, R.L., Saada, N., Scherer, S.E., Smith, H.E., Vinson, C., Warner, C.B., Worley, K.C., Wu, Y., Zou, X., Cherbas, P., Kellis, M., Eisen, M.B., Piano, F., Kionte, K., Fitch, D.H., Sternberg, P.W., Cutter, A.D., Duff, M.O., Hoskins, R.A., Graveley, B.R., Gibbs, R.A., Bickel, P.J., Kopp, A., Carninci, P., Celniker, S.E., Oliver B., and Richards, S. (2014). Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Research 24:1209-1223. http://dx.doi.org/10.1101/gr.159384.113
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Atallah, J., Vurens, G., Mavong, S., Mutti, A., Hoang, D., and Kopp, A. (2014). Sex-specific repression of dachshund is required for Drosophila sex comb development. Developmental Biology 386:440-447. http://dx.doi.org/10.1016/j.ydbio.2013.12.017
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Atallah, J.*, Plachetzki, D.C., Jasper, W.C., Johsnon, B.R.* (2013). The utility of shallow RNA-Seq for documenting differential gene expression in genes with high and low levels of expression. PLOS ONE 8:e84160. http://dx.doi.org/10.1371/journal.pone.0084160
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Johnson, B.R., Borowiec, M.L., Chiu, J.C., Lee, E.K., Atallah, J., and Ward, P.S. (2013). Phylogenomics resolves evolutionary relationships among ants, bees, and wasps. Current Biology 23:2058-2062. http://dx.doi.org/10.1016/j.cub.2013.08.050
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Johnson, B.R., Atallah, J., and Plachetzki, D.C. (2013). The importance of tissue specificity for RNA-Seq: highlighting the errors of composite structure extractions. BMC Genomics 14:586. http://dx.doi.org/10.1186/1471-2164-14-586
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Atallah, J., Hideaki, W., and Kopp, A. (2012). Many ways to make a novel structure: a new mode of sex comb development in Drosophilidae. Evolution & Development 14:476-483. http://dx.doi.org/10.1111/ede.12001
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Larsen, E.W., and Atallah, J. (2011). Epigenesis, preformation and the Humpty Dumpty problem. In B. Hallgrímsson and B.K. Hall (eds.). Epigenetics: Linking Genotype and Phenotype in Development and Evolution, San Francisco: University of California Press, pp. 103-115.
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Atallah, J., and Larsen, E. (2009). Genotype-phenotype mapping: developmental biology confronts the toolkit paradox. International Review of Cell & Molecular Biology 278:119-148. http://dx.doi.org/10.1016/S1937-6448(09)78003-7
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Atallah, J., Liu, N.H., Dennis, P., Hon, A., and Larsen, E. (2009). Developmental constraints and convergent evolution in Drosophila sex comb formation. Evolution & Development 11:205-218. http://dx.doi.org/10.1111/j.1525-142X.2009.00320.x
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Atallah, J., Liu, N.H., Dennis, P., Hon, A., Godt, D., and Larsen, E. (2009). Cell dynamics and developmental bias in the ontogeny of a complex sexually dimorphic trait in Drosophila melanogaster. Evolution & Development 11:191-204. http://dx.doi.org/10.1111/j.1525-142X.2009.00319.x
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Atallah, J.*, Dworkin, I.*, Cheung, U.*, Greene, A., Ing, B., Leung, L., and Larsen, E.* (2004). The environmental and genetic regulation of obake expressivity: morphogenetic fields as evolvable systems. Evolution & Development 6:114-122. http://dx.doi.org/10.1111/j.1525-142X.2004.04017.x