College of Agricultural Sciences

C. G. Jones, érrez, J. L., Byers, J. E., Crooks, J. A., Lambrinos, J. G., and Talley, T. S., “A framework for understanding physical ecosystem engineering by organisms”, Oikos, vol. 11970212756219717817397618556101106978124232863812171749206342175610594, no. 12, pp. 1862 - 1869, 2010.

J. H. Y. Edwards and Langpap, C., “Fuel Choice, Indoor Air pollution, and Children’s Health”, Environment and Development Economics, vol. 17, no. 04, pp. 379 - 406, 2012.

S. L. Stephens, Boerner, R. E. J., Moghaddas, J. J., Moghaddas, E. E. Y., Collins, B. M., Dow, C. B., Edminster, C., Fiedler, C. E., Fry, D. L., Hartsough, B. R., Keeley, J. E., Knapp, E. E., McIver, J., Skinner, C. N., and Youngblood, A., “Fuel treatment impacts on estimated wildfire carbon loss from forests in Montana, Oregon, California, and Arizona”, Ecosphere, vol. 3, no. 5, p. art38, 2012.

P. Piantoni, Bionaz, M., Graugnard, D. E., Daniels, K. M., Everts, R. E., Rodriguez-Zas, S. L., Lewin, H. A., Hurley, H. L., Akers, M., and Loor, J. J., “Functional and gene network analyses of transcriptional signatures characterizing pre-weaned bovine mammary parenchyma or fat pad uncovered novel inter-tissue signaling networks during development.”, BMC Genomics, vol. 11, p. 331, 2010.

M. L. Evans, Shry, S. J., Jacobson, D. P., Sard, N. M., and Malley, K. G. ’, “Functional gene diversity and migration timing in reintroduced Chinook salmon”, Conservation Genetics, vol. 16, no. 6, pp. 1455 - 1464, 2015.

K. M. Moyes, Drackley, J. K., Morin, D. E., Bionaz, M., Rodriguez-Zas, S. L., Everts, R. E., Lewin, H. A., and Loor, J. J., “Gene network and pathway analysis of bovine mammary tissue challenged with Streptococcus uberis reveals induction of cell proliferation and inhibition of PPARgamma signaling..”, BMC Genomics, vol. 10, p. 542, 2009.

J. F. Hancock, Edger, P. P., Callow, P. W., Herlache, T., and Finn, C. E., “Generating a Unique Germplasm Base for the Breeding of Day-neutral Strawberry Cultivars”, HortScience, vol. 53, no. 7, pp. 1069 - 1071, 2018.

R. Bruskiewich, Senger, M., Davenport, G., Ruiz, M., Rouard, M., Hazekamp, T., Takeya, M., Doi, K., Satoh, K., Costa, M., Simon, R., Balaji, J., Akintunde, A., Mauleon, R., Wanchana, S., Shah, T., Anacleto, M., Portugal, A., Ulat, V. Jun, Thongjuea, S., Braak, K., Ritter, S., Dereeper, A., Skofic, M., Rojas, E., Martins, N., Pappas, G., Alamban, R., Almodiel, R., Barboza, L. Hendrix, Detras, J., Manansala, K., Mendoza, M. Jonathan, Morales, J., Peralta, B., Valerio, R., Zhang, Y., Gregorio, S., Hermocilla, J., Echavez, M., Yap, J. Michael, Farmer, A., Schiltz, G., Lee, J., Casstevens, T., Jaiswal, P., Meintjes, A., Wilkinson, M., Good, B., Wagner, J., Morris, J., Marshall, D., Collins, A., Kikuchi, S., Metz, T., McLaren, G., and van Hintum, T., “The generation challenge programme platform: semantic standards and workbench for crop science.”, International journal of plant genomics, vol. 2008, p. 369601, 2008.

K. Gürcan, Mehlenbacher, S. A., and Erdogan, V., “Genetic diversity in hazelnut cultivars from Black Sea countries assessed using SSR markers”, Plant Breeding , vol. 129, pp. 422-434, 2010.

R. VanBuren, Bryant, D., Bushakra, J. M., Vining, K. J., Edger, P. P., Rowley, E. R., Priest, H. D., Michael, T. P., Lyons, E., Filichkin, S. A., Dossett, M., Finn, C. E., Bassil, N. V., and Mockler, T. C., “The genome of black raspberry (Rubus occidentalis).”, Plant J, vol. 87, no. 6, pp. 535-47, 2016.

A. A. Myburg, Grattapaglia, D., Tuskan, G. A., Hellsten, U., Hayes, R. D., Grimwood, J., Jenkins, J., Lindquist, E., Tice, H., Bauer, D., Goodstein, D. M., Dubchak, I., Poliakov, A., Mizrachi, E., Kullan, A. R. K., Hussey, S. G., Pinard, D., van der Merwe, K., Singh, P., van Jaarsveld, I., Silva-Junior, O. B., Togawa, R. C., Pappas, M. R., Faria, D. A., Sansaloni, C. P., Petroli, C. D., Yang, X., Ranjan, P., Tschaplinski, T. J., Ye, C. - Y., Li, T., Sterck, L., Vanneste, K., Murat, F., Soler, çal, San Clemente, élène, Saidi, N., Cassan-Wang, H., Dunand, C., Hefer, C. A., Bornberg-Bauer, E., Kersting, A. R., Vining, K. J., Amarasinghe, V., Ranik, M., Naithani, S., Elser, J., Boyd, A. E., Liston, A., Spatafora, J. W., Dharmwardhana, P., Raja, R., Sullivan, C., Romanel, E., Alves-Ferreira, M., ülheim, C., Foley, W., Carocha, V., Paiva, J., Kudrna, D., Brommonschenkel, S. H., Pasquali, G., Byrne, M., Rigault, P., Tibbits, J., Spokevicius, A., Jones, R. C., Steane, D. A., Vaillancourt, éE., Potts, B. M., Joubert, F., Barry, K., Pappas, G. J., Strauss, S. H., Jaiswal, P., Grima-Pettenati, J., Salse, érôme, Van de Peer, Y., Rokhsar, D. S., and Schmutz, J., “The genome of Eucalyptus grandis”, Nature, vol. 51, no. 75, pp. 356 - 362, 2014.

A. A. Myburg, Grattapaglia, D., Tuskan, G. A., Hellsten, U., Hayes, R. D., Grimwood, J., Jenkins, J., Lindquist, E., Tice, H., Bauer, D., Goodstein, D. M., Dubchak, I., Poliakov, A., Mizrachi, E., Kullan, A. R. K., Hussey, S. G., Pinard, D., van der Merwe, K., Singh, P., van Jaarsveld, I., Silva-Junior, O. B., Togawa, R. C., Pappas, M. R., Faria, D. A., Sansaloni, C. P., Petroli, C. D., Yang, X., Ranjan, P., Tschaplinski, T. J., Ye, C. - Y., Li, T., Sterck, L., Vanneste, K., Murat, F., Soler, M., San Clemente, H., Saidi, N., Cassan-Wang, H., Dunand, C., Hefer, C. A., Bornberg-Bauer, E., Kersting, A. R., Vining, K., Amarasinghe, V., Ranik, M., Naithani, S., Elser, J., Boyd, A. E., Liston, A., Spatafora, J. W., Dharmwardhana, P., Raja, R., Sullivan, C., Romanel, E., Alves-Ferreira, M., Külheim, C., Foley, W., Carocha, V., Paiva, J., Kudrna, D., Brommonschenkel, S. H., Pasquali, G., Byrne, M., Rigault, P., Tibbits, J., Spokevicius, A., Jones, R. C., Steane, D. A., Vaillancourt, R. E., Potts, B. M., Joubert, F., Barry, K., Pappas, G. J., Strauss, S. H., Jaiswal, P., Grima-Pettenati, J., Salse, J., Van de Peer, Y., Rokhsar, D. S., and Schmutz, J., “The genome of Eucalyptus grandis.”, Nature, vol. 510, pp. 356-62, 2014.

K. E. Bushley, Raja, R., Jaiswal, P., Cumbie, J. S., Nonogaki, M., Boyd, A. E., C Owensby, A., Knaus, B. J., Elser, J., Miller, D., Di, Y., McPhail, K. L., and Spatafora, J. W., “The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster”, PLOS Genetics, vol. 9, 2013.

V. Shulaev, Sargent, D. J., Crowhurst, R. N., Mockler, T. C., Folkerts, O., Delcher, A. L., Jaiswal, P., Mockaitis, K., Liston, A., Mane, S. P., Burns, P., Davis, T. M., Slovin, J. P., Bassil, N., Hellens, R. P., Evans, C., Harkins, T., Kodira, C., Desany, B., Crasta, O. R., Jensen, R. V., Allan, A. C., Michael, T. P., Setubal, J. Carlos, Celton, J. - M., D Rees, J. G., Williams, K. P., Holt, S. H., Rojas, J. Jairo Ruiz, Chatterjee, M., Liu, B., Silva, H., Meisel, L., Adato, A., Filichkin, S. A., Troggio, M., Viola, R., Ashman, T. - L., Wang, H., Dharmawardhana, P., Elser, J., Raja, R., Priest, H. D., Bryant, D. W., Fox, S. E., Givan, S. A., Wilhelm, L. J., Naithani, S., Christoffels, A., Salama, D. Y., Carter, J., Girona, E. Lopez, Zdepski, A., Wang, W., Kerstetter, R. A., Schwab, W., Korban, S. S., Davik, J., Monfort, A., Denoyes-Rothan, B., Arus, P., Mittler, R., Flinn, B., Aharoni, A., Bennetzen, J. L., Salzberg, S. L., Dickerman, A. W., Velasco, R., Borodovsky, M., Veilleux, R. E., and Folta, K. M., “The genome of woodland strawberry(Fragaria vesca).”, Nature genetics, vol. 43, pp. 109-16, 2011.

V. Shulaev, Sargent, D. J., Crowhurst, R. N., Mockler, T. C., Folkerts, O., Delcher, A. L., Jaiswal, P., Mockaitis, K., Liston, A., Mane, S. P., Burns, P., Davis, T. M., Slovin, J. P., Bassil, N., Hellens, R. P., Evans, C., Harkins, T., Kodira, C., Desany, B., Crasta, O. R., Jensen, R. V., Allan, A. C., Michael, T. P., Setubal, J. Carlos, Celton, J. - M., D Rees, J. G., Williams, K. P., Holt, S. H., Rojas, J. Jairo Ruiz, Chatterjee, M., Liu, B., Silva, H., Meisel, L., Adato, A., Filichkin, S. A., Troggio, M., Viola, R., Ashman, T. - L., Wang, H., Dharmawardhana, P., Elser, J., Raja, R., Priest, H. D., Bryant, D. W., Fox, S. E., Givan, S. A., Wilhelm, L. J., Naithani, S., Christoffels, A., Salama, D. Y., Carter, J., Girona, E. Lopez, Zdepski, A., Wang, W., Kerstetter, R. A., Schwab, W., Korban, S. S., Davik, J., Monfort, A., Denoyes-Rothan, B., Arus, P., Mittler, R., Flinn, B., Aharoni, A., Bennetzen, J. L., Salzberg, S. L., Dickerman, A. W., Velasco, R., Borodovsky, M., Veilleux, R. E., and Folta, K. M., “The genome of woodland strawberry(Fragaria vesca).”, Nature genetics, vol. 43, pp. 109-16, 2011.

G. T. Slavov, DiFazio, S. P., Martin, J., Schackwitz, W., Muchero, W., Rodgers-Melnick, E., Lipphardt, M. F., Pennacchio, C. P., Hellsten, U., Pennacchio, L. A., Gunter, L. E., Ranjan, P., Vining, K. J., Pomraning, K. R., Wilhelm, L. J., Pellegrini, M., Mockler, T. C., Freitag, M., Geraldes, A., El-Kassaby, Y. A., Mansfield, S. D., Cronk, Q. C. B., Douglas, C. J., Strauss, S. H., Rokhsar, D., and Tuskan, G. A., “Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa”, New Phytologist, vol. 19, no. 3, pp. 713 - 725, 2012.

Yping Chen, Pettis, J. S., Zhao, Y., Liu, X., Tallon, L. J., Sadzewicz, L. D., Li, R., Zheng, H., Huang, S., Zhang, X., Hamilton, M. C., Pernal, S. F., Melathopoulos, A. P., Yan, X., and Evans, J. D., “Genome sequencing and comparative genomics of honey bee microsporidia, Nosema apis reveal novel insights into host-parasite interactions”, BMC Genomics, vol. 14, no. 1, p. 451, 2013.

Y. P. Chen, Pettis, J. S., Zhao, Y., Liu, X., Tallon, L. J., Sadzewicz, L. D., Li, R., Zheng, H., Huang, S., Zhang, X., Hamilton, M. C., Pernal, S. F., Melathopoulos, A. P., Yan, X., and Evans, J. D., “Genome sequencing and comparative genomics of honey bee microsporidia, Nosema apis reveal novel insights into host-parasite interactions”, BMC Genomics, vol. 14, p. 451, 2013.

D. Bachelet, Hooper, R. P., Cushing, J. B., van Puijenbroek, P., Eckman, B., and Worrest, R. C., “Global climate change implications for digital government research: keynote panel”, in Proceedings of the 8th annual international conference on Digital government research: bridging disciplines & domains, 2007.

M. Shrivastava, Lou, S., Zelenyuk, A., Easter, R. C., Corley, R. A., Thrall, B. D., Rasch, P. J., Fast, J. D., Simonich, S. L. Massey, Shen, H., and Tao, S., “Global long-range transport and lung cancer risk from polycyclic aromatic hydrocarbons shielded by coatings of organic aerosol.”, Proc Natl Acad Sci U S A, vol. 114, no. 6, pp. 1246-1251, 2017.

Y. L. Ong, Ross, A. S., and Engle, D. A., “Glutenin Macropolymer in Salted and Alkaline Noodle Doughs”, Cereal Chemistry Journal, vol. 87, no. 1, pp. 79 - 85, 2010.

M. K. Tello-Ruiz, Stein, J., Wei, S., Preece, J., Olson, A., Naithani, S., Amarasinghe, V., Dharmawardhana, P., Jiao, Y., Mulvaney, J., Kumari, S., Chougule, K., Elser, J., Wang, B., Thomason, J., Bolser, D. M., Kerhornou, A., Walts, B., Fonseca, N. A., Huerta, L., Keays, M., Y Tang, A., Parkinson, H., Fabregat, A., McKay, S., Weiser, J., D’Eustachio, P., Stein, L., Petryszak, R., Kersey, P. J., Jaiswal, P., and Ware, D., “Gramene 2016: comparative plant genomics and pathway resources.”, Nucleic acids research, vol. 44, pp. D1133-40, 2016.

M. K. Tello-Ruiz, Naithani, S., Stein, J. C., Gupta, P., Campbell, M., Olson, A., Wei, S., Preece, J., Geniza, M. J., Jiao, Y., Lee, Y. Koung, Wang, B., Mulvaney, J., Chougule, K., Elser, J., Al-Bader, N., Kumari, S., Thomason, J., Kumar, V., Bolser, D. M., Naamati, G., Tapanari, E., Fonseca, N., Huerta, L., Iqbal, H., Keays, M., Fuentes, A. Munoz- Pome, Tang, A., Fabregat, A., D’Eustachio, P., Weiser, J., Stein, L. D., Petryszak, R., Papatheodorou, I., Kersey, P. J., Lockhart, P., Taylor, C., Jaiswal, P., and Ware, D., “Gramene 2018: unifying comparative genomics and pathway resources for plant research.”, Nucleic acids research, vol. 46, pp. D1181-D1189, 2018.

B. A. Endress, Parks, C. G., Naylor, B. J., Radosevich, S. R., and Porter, M., “Grassland response to herbicides and seeding of native grasses 6 years posttreatment”, Invasive Plant Science and Management, vol. 5, pp. 311–316, 2012.

B. A. Endress, Parks, C. G., Naylor, B. J., Radosevich, S. R., and Porter, M., “Grassland Response to Herbicides and Seeding of Native Grasses 6 Years PosttreatmentAbstract”, Invasive Plant Science and Management, vol. 52432, no. 03, pp. 311 - 316, 2012.