RESEARCH ARTICLES IN REVIEW
Wesleyan undergraduate authors are starred* for easy identification.
(1) Drum, ,A. Lanno, S.M., *Gregory, S.M., *Shimshak, *Barr, W., 1Gatesman. A, 1Schadt, M., Sanford, J., *Arkin, A., *Assignon, B., *Colorado, S., *Dalgarno, C., *Devanny, T., *Ghandour, T., *Griffin, R., *Hogan, M., *Horowitz, E., *McGhie, E., *Multer, J., *O’Halloran, H., *Ofori-Darko, K.,*Pokushalov, D., *Richards, N., Sagarin, K., *Taylor, N., *Thielking, A., *Towle, P., and J. D. Coolon. Genomics analysis of M. citrifolia fruit diet in Drosophila sechellia. (In Review at G3: Genes | Genomes | Genetics) 1=High school students (21 undergraduate coauthors from BIOL310!).
Preprint available on bioRxiv: 2021.06.21.449329
doi: https://doi.org/10.1101/2021.06.21.449329
(2) Drum, ,Z.A. Lanno, S.M., *Gregory, S.M., *Shimshak, S.J., *Ahamed, M., *Barr, W., *Bekele, B., *Biester, A., *Castro, C., *Connolly, L., *DelGaudio, N., *Humphrey, W., *Karimi, H., *Karolczak, S., *Lawrence, T., *McCracken, A., *Miller-Medzon, N., *Murphy, L., *Park, C., *Park, S., *Qiu, C., Serra, K., *Snyder, G., *Strauss, A., *Tang, S., *Vyzas, C., and J. D. Coolon. Genomics analysis of hexanoic acid exposure in Drosophila sechellia. (In Review at G3: Genes | Genomes | Genetics) (23 undergraduate coauthors from BIOL310!).
Preprint available on bioRxiv: bioRxiv 2021.06.08.447576;
doi: https://doi.org/10.1101/2021.06.08.447576
(3) Lanno, S. M., *Lam, I. *Sanchez, G., Drum, Z. and J.D. Coolon. Knockdown of Osiris Gene Expression Alters Sensitivity to Natural and Synthetic Insecticides (In Review at PLOS ONE).
PEER REVIEWED RESEARCH ARTICLES
At Wesleyan: Wesleyan undergraduate authors are starred* for easy identification.
(1) DeAngelis, M.W., Coolon, J.D., and R.I. Johnson. (2020) Comparative transcriptome analyses of the Drosophila pupal eye. G3: Genes | Genomes | Genetics. 11 (1), 1-15.
https://doi.org/10.1093/g3journal/jkaa003
(2) *Sanchez, G., *Linde, S.C., and J. D. Coolon. (2020) Genome Wide Effect of Tetracycline, Doxycycline and 4-epidoxycycline on gene expression in Saccharomyces cerevisiae. Yeast. 37 (7-8), 389-396.
https://doi.org/10.1002/yea.3515
(3) DeAngelis, M.W., *McGhie, E.W., Coolon, J.D., and R.I. Johnson. (2020) The Hippo Pathway component Mask is required for morphogenesis of the Drosophila pupal retina. Developmental Biology 464 (1), 53-70
https://doi.org/10.1016/j.ydbio.2020.05.002
(4) Lanno,S. M., *Lam, I., *Gregory, S.M., *Linde, S.C., *Shimshak, S.J., *Becker, M.V., *Brew, K.E., *Budhiraja, A., *Carter, E. A., Chigweshe, L., *Collins, K.P., Earley, T., *Einstein, H.L., *Fan, A.A., *Goss, S.S., *Hagen, E.A., *Hutcheon, S.B., *Kim, T.T., *Mitchell, M.A., *Neri, N.R., *Patterson, S.E., *Ransom, G., *Sanchez, L.J., *Weiner, B.M., *Zhao, D., and J. D. Coolon. (2019) Drosophila sechellia genomic response to L-DOPA exposure. G3: Genes | Genomes |
Genetics 9(12):3973-3980. (22 undergraduate coauthors from BIOL310!).
https://doi.org/10.1534/g3.119.400552
(5) Coolon, J. D. Drum, Z., Lanno, S. M., and C. R. Smith. (2019) Osiris genes and their role in insect adaptive evolution. In eLS, John Wiley & Sons, Ltd (Ed.).
https://doi.org/10.1002/9780470015902.a0028763
(6) Lanno, S. M. and J.D. Coolon. (2019) Derived esterase activity in Drosophila sechellia contributes to evolved octanoic acid resistance. Insect Molecular Biology. 28(6):798-806.
https://doi.org/10.1111/imb.12587
(7) Lanno, S. M., *Shimshak, S. J., *Peyser, R. D. and J.D. Coolon. (2019) Investigating the role of Osiris genes in Drosophila sechellia larval resistance to a host plant toxin. Ecology and Evolution. 9: 1922 – 1933.
https://doi.org/10.1002/ece3.4885
(8) Lanno, S. M., *Gregory, S., *Shimshak, S. J., *Alverson, M. K., *Chiu, K., *Feil, A. L., *Findley, G., *Forman, T. E., *Gordon, J. T., *Ho, J., *Krupp, J. L., *Lam, I., *Lane, J., *Linde,S. C., *Morse,A. E., *Rusk,S., *Ryan, R., *Saniee, A., *Sheth, R. B., *Siranosian, J. J., *Sirichantaropart, P., *Sternlieb,S. R., *Zaccardi, C. M., and J. D. Coolon. (2017) Drosophila sechellia genomic response to octanoic acid exposure. G3: Genes | Genomes | Genetics. 7(12) 3867-3873 (22 undergraduate coauthors from BIOL310!).
https://doi.org/10.1534/g3.117.300297
(9) *Peyser, R., Lanno, S. M., *Shimshak, S. J. and J. D. Coolon. (2017) Analysis of cytochrome P450 contribution to evolved plant toxin resistance in Drosophila sechellia. Insect Molecular Biology 26(6) 715-720. (Undergraduate first author!).
https://doi.org/10.1111/imb.12329
(10) Metzger, B. P. H., Wittkopp, P. J. and J. D. Coolon1. (2017) General properties of regulatory divergence over short and long evolutionary timescales. Genome Biology and Evolution 9 (4) 843-854. 1=Corresponding author (All Coolon parts done at Wesleyan, Wesleyan Affiliated).
https://doi.org/10.1093/gbe/evx035
(11) Andrade López, J. M., Lanno, S. M., *Auerbach, J., *Moskowitz, E., Sligar, L. A., Wittkopp, P. J., and J. D. Coolon1. (2017) Genetic basis of octanoic acid resistance in Drosophila sechellia: functional analysis of a fine-mapped region. Molecular Ecology 26 (4) 1148-1160. 1=Corresponding author (1/2 Experiments done at U. Michigan, 1/2 Experiments done at Wesleyan and written at Wesleyan, has two Wesleyan Undergraduate and 1 Wesleyan Graduate student author, Wesleyan Affiliated)
https://doi.org/10.1111/mec.14001
Prior to Wesleyan:
(12) Coolon, J. D.*, Stevenson, K. R.,McManus, C. J., Graveley, B. R., and P.J. Wittkopp. (2015) cis-and trans-regulation contribute to accelerated divergence of gene expression on the Drosophila X chromosome. Molecular Biology and Evolution, 32(10): 2605-2615.
*Corresponding author, Selected by Faculty of 1000.
https://doi.org/10.1093/molbev/msv135
(13) Coolon, J. D., McManus, C. J., Stevenson, K. R., Graveley, B. R., and P.J. Wittkopp. (2014) Tempo and mode of regulatory evolution in Drosophila. Genome Research, 24:797-808.
https://doi.org/10.1101/gr.163014.113
(14) McManus, C. J., Coolon, J. D., Duff, M., Eiper-Mains, J., Wittkopp P.J., and B. R. Graveley. (2014) Evolution of splicing regulatory networks in Drosophila. Genome Research, 24:786-796.
https://dx.doi.org/10.1101%2Fgr.161521.113
(15) Meiklejohn, C. D., Coolon, J. D., Hartl, D. L., and P. J. Wittkopp. (2014) The roles of cis- and trans regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression. Genome Research, 24:84-95.
https://dx.doi.org/10.1101%2Fgr.156414.113
(16) Coolon, J. D.,* Webb, W., and P. J. Wittkopp. (2013) Sex-specific effects of cis-regulatory variants in Drosophila melanogaster. Genetics. 195(4): 1419-1422.
* Corresponding author, Chosen by editors as issue highlight
https://doi.org/10.1534/genetics.113.156331
(17) Stevenson, K. R., Coolon, J. D., and P. J. Wittkopp. (2013) Reliable estimates of allele-specific expression derived from RNA-seq data aligned to a single reference genome. BMC Genomics, 14:536. Given “Highly Accessed” designation from journal, Selected by Faculty of 1000
https://dx.doi.org/10.1186%2F1471-2164-14-536
(18) Coolon, J. D.*, Jones, K. L., T. C. Todd, J. L., J. M. Blair, and M. A. Herman. (2013) Long-term nitrogen amendment alters soil bacterial diversity and assemblage in tallgrass prairie. PLoS ONE 8(6): e67884. * Corresponding author
https://doi.org/10.1371/journal.pone.0067884
(19) Coolon, J. D.*, Stevenson, K. R., McManus, C. J., Graveley, B. R., and P.J. Wittkopp. (2012) Genomic imprinting absent in Drosophila melanogaster adult females. 2012. Cell Reports, 2(1):69-75. * Corresponding author
https://doi.org/10.1016/j.celrep.2012.06.013
(20) McManus, C. J., Coolon, J. D., Duff, M., Eiper-Mains, J., Graveley, B. R., and P.J. Wittkopp. (2010) Regulatory divergence in Drosophila revealed by mRNA-seq. Genome Research, 20:816-825. Selected by Faculty of 1000
https://doi.org/10.1101/gr.102491.109
(21) Coolon, J. D., Jones, K. L., Narayanan, S., and S. M. Wisely. (2010) Microbial Ecological Response of the Intestinal Flora of Peromyscus maniculatus and P. leucopus to Heavy Metal Contamination. Molecular Ecology, 19 (supp1): 67-80. Next Generation Molecular Ecology special issue
https://doi.org/10.1111/j.1365-294X.2009.04485.x
(22) Coolon, J. D., Jones, K. L., *Carr, B. C., Todd, T. C., and M. A. Herman. (2009) Caenorhabditis elegans genomic response to soil bacteria predicts environment-specific genetic effects on life history traits. PLoS Genetics. 5(6): e1000503. Selected by Faculty of 1000, * Undergraduate author
https://doi.org/10.1371/journal.pgen.1000503
(23) Jones, K. L., Todd, T. C., *Wall-Beam, J. L. , Coolon, J. D., Blair, J. M., and M. A. Herman. (2006) Molecular approach for assessing responses of microbial-feeding nematodes to burning and chronic nitrogen enrichment in a native grassland. Molecular Ecology, 15, 2601-2609. * Undergraduate author
https://doi.org/10.1111/j.1365-294x.2006.02971.x
BOOK CHAPTERS
(1) Coolon, J. D., and P. J. Wittkopp. (2012) cis and trans-regulation in Drosophila interspecific hybrids.Hybrid and Polyploid Genomics. Editors: Z. Jeffrey Chen and Jim Birchler, Wiley-Blackwell
Publishing. Invited Book Chapter
https://doi.org/10.1002/9781118552872.ch3
(2) Herman, M. H., Coolon, J. D., Jones, K. L. and T. C. Todd. (2009) Ecological Genomics of Nematode Community Interactions: Model and Non-model Approaches. Evolutionary Biology Concept, Modeling, and Application II. ed. Axelle Pontarotti. Springer Tiergartenstr. 17 69121 Heidelberg Germany. Invited Book Chapter