Plomion, C., Chagne, D., Pot, D., Kumar, S., Wilcox, P., Burdon, R., Prat, D., Peterson, D. G., Paiva, J., Chaumeil, P., Vendramin, G., Sebastiani, F., Nelson, C. D., Echt, C., Savolainen, O., Kubisiak, T., Cervera, M. T., & Islam-Faridi, M. N. (2007). The Pines. In C. R. Cole (Ed.), Genome Mapping and Molecular Breeding in Plants, Vol. 7, Forest Trees. Springer - Heidelberg, Berlin, New York, Tokyo. 29-78. [Document]

Peterson, D. G. (2005). Reduced Representation Strategies and Their Application to Plant Genomes. In K. Meksem K and G. Kahl (Eds.), The Handbook of Plant Genome Mapping: Genetic and Physical Mapping. Weinheim, Germany: WILEY-VCH Verlag GmbH & Co. KGaA. 307-335. [Document]

Buza, T., Jack, S., Halid, K., Khaitsa, M. L., Lawrence, M. L., Pruett, S., & Peterson, D. G. (2015). ERAIZDA: A Model for Holistic Annotation of Animal Infectious and Zoonotic Diseases. Database - The Journal of Biological Databases and Biocuration. Oxford University Press. 2015, 10. DOI:10.1093/database/bav110. [Abstract]

Green, R. E., Braun, E. L., Armstrong, J., Earl, D., Nguyen, N., Hickey, G., Vandewege, M. W., StJohn, J. A., Capella-Gutierrez, S., Castoe, T. A., Kern, C., Fujita, M. K., Opazo, J. C., Jurka, J., Kojima, K. K., Caballero, J., Hubley, R. M., Smit, A. F., Platt, R. N., Lavoie, C. A., Ramakodi, M. P., Finger, J. W., Jr., Suh, A., Isberg, S. R., Miles, L., Chong, A. Y., Jaratlerdsiri, W., Gongora, J., Moran, C., Iriarte, A., McCormack, J., Burgess, S. C., Edwards, S. V., Lyons, E., Williams, C., Breen, M., Howard, J. T., Gresham, C. R., Peterson, D. G., Schmitz, J., Pollock, D. D., Haussler, D., Triplett, E. W., Zhang, G., Irie, N., Jarvis, E. D., Brochu, C. A., Schmidt, C. J., McCarthy, F. M., Faircloth, B. C., Hoffman, F., Glenn, T. C., Gabaldon, T., Paten, B., & Ray, D. A. (2014). Three Crocodilian Genomes Reveal Ancestral Patterns of Evolution among Archosaurs. Science. 346(6215), 1254449. DOI:10.1126/science.1254449. [Document]

Jaratlerdsiri, W., Deakin, J., Godinez, R. M., Shan, X., Peterson, D. G., Marthey, S., Lyons, E., McCarthy, F. M., Isberg, S. R., Higgins, D. P., Chong, A. Y., John, J. S., Glenn, T. C., Ray, D. A., & Gongora, J. (2014). Comparative Genome Analyses Reveal Distinct Structure in the Saltwater Crocodile MHC. PLoS ONE. 9(12), e114631. DOI:10.1371/journal.pone.0114631. [Document]

Wang, X. Q., Showmaker, K. C., Yu, X. Q., Bi, T., Hsu, C. Y., Baird, S. M., Peterson, D. G., Li, X. D., & Lu, S. E. (2014). Draft genome sequence of Burkholderia pyrrocinia Lyc2, a biological control strain that can suppress multiple plant microbial pathogens. Genome Announcements. 2(5), pii: e00991-14. DOI:10.1128/genomeA.00991-14. [Document]

Magbanua, Z. V., Arick, M., II, Buza, T., Hsu, C. Y., Showmaker, K. C., Chouvarine, P., Deng, P., Peterson, D. G., & Lu, S. (2014). Transcriptomic Dissection of the Rice - Burkholderia glumae Interaction. BMC Genomics. 15, 755. DOI:10.1186/1471-2164-15-755. [Abstract]

Buza, T., Arick, M., II, Wang, H, & Peterson, D. G. (2014). Computational Prediction of Disease MicroRNAs in Domestic Animals. BMC Research Notes. 7, 403. DOI:10.1186/1756-0500-7-403. [Abstract] [Document Site]

Guo, H., Wang, X., Gundlach, H., Mayer, K. F., Peterson, D. G., Scheffler, B. E., Chee, P. W., & Paterson, A. H. (2014). Extensive and Biased Intergenomic Non-reciprocal DNA Exchanges Shaped a Nascent Polyploid Genome, Gossypium (Cotton). Genetics. 197(4), 1153-1163. DOI:10.1534/genetics.114.166124. [Abstract] [Document Site]

Kanizay, L. B., Pyhajarvi, T., Lowry, E. G., Hufford, M. B., Peterson, D. G., Ross-Ibarra, J., & Dawe, R. K. (2013). Diversity and Abundance of the Abnormal Chromosome 10 Meiotic Drive Complex in Zea Mays. Heredity. 110(6), 570-577. DOI:10.1038/hdy.2013.2. [Abstract] [Document Site]

Paterson, A. H., Wendel, J. F., Gundlach, H., Guo, H., Jenkins, J., Jin, D., Llewellyn, D., Showmaker, K. C., Shu, S., Udall, J., Yoo, M. J., Byers, R., Chen, W., Doron-Faigenboim, A., Duke, M. V., Gong, L., Grimwood, J., Grover, C., Grupp, K., Hu, G., Lee, T. H., Li, J., Lin, L., Liu, T., Marler, B. S., Page, J. T., Roberts, A. W., Romanel, E., Sanders, W. S., Szadkowski, E., Tan, X., Tang, H., Xu, C., Wang, J., Wang, Z., Zhang, D., Zhang, L., Ashrafi, H., Bedon, F., Bowers, J. E., Brubaker, C. L., Chee, P. W., Das, S., Gingle, A. R., Haigler, C. H., Harker, D., Hoffmann, L. V., Hovav, R., Jones, D. C., Lemke, C., Mansoor, S., Ur-Rahman, R., Rainville, L. N., Rambani, A., Reddy, U. K., Rong, J. K., Saranga, Y., Scheffler, B. E., Scheffler, J. A., Stelly, D. M., Triplett, B. A., Van, D. A., Vaslin, M. F., Waghmare, V. N., Walford, S. A., Wright, R. J., Zaki, E. A., Zhang, T., Dennis, E. S., Mayer, K. F., Peterson, D. G., Rokhsar, D. S., Wang, X., & Schmutz, J. (2012). Repeated Polyploidization of Gossypium Genomes and the Evolution of Spinnable Cotton Fibres. Nature. 492, 423-427. DOI:10.1038/nature11798. [Document Site]

Mackay, J., Dean, J. F., Plomion, C., Peterson, D. G., Canovas, F. M., Pavy, N., Ingvarsson, P. K., Savolainen, O., Guevara, M. A., Fluch, S., Vinceti, B., Abarca, D., Diaz-Sala, C., & Cervera, M. T. (2012). Towards Decoding the Conifer Giga-genome. Plant Molecular Biology. 80, 555-569. DOI:10.1007/s11103-012-9961-7. [Abstract] [Document] [Document Site]

Bellgard, M. I., Moolhuijzen, P. M., Guerrero, F. D., Schibeci, D., Rodriguez-Valle, M., Peterson, D. G., Dowd, S. E., Barrero, R., Hunter, A., Miller, R. J., & Lew-Tabor, A. E. (2012). CattleTickBase: An Integrated Internet-based Bioinformatics Resource for Rhipicephalus (Boophilus) Microplus. International Journal for Parasitology. 42(2), 161-169. DOI:10.1016/j.ijpara.2011.11.006. [Abstract] [Document] [Document Site]

StJohn, J. A., John, J. A., Braun, E. L., Isberg, S. R., Miles, L. G., Chong, A. Y., Gongora, J., Dalzell, P., Moran, C., BedHom, B., Abzhanov, A., Burgess, S. C., Cooksey, A. M., Castoe, T. A., Crawford, N. G., Densmore, L. D., Drew, J. C., Edwards, S. V., Faircloth, B. C., Fujita, M. K., Greenwold, M. J., Hoffmann, F. G., Howard, J. M., Iguchi, T., Janes, D. E., Khan, S. Y., Kohno, S., DeKoning, A. P. J., Lance, S. L., McCarthy, F. M., McCormack, J. E., Merchant, M. E., Peterson, D. G., Pollock, D. D., Pourmand, N., Raney, B. J., Roessler, K. A., Sanford, J. R., Sawyer, R. H., Schmidt, C. J., Triplett, E. W., Tuberville, T. D., Venegas-Anaya, M., Howard, J. T., Jarvis, E. D., Guillette, L. J., Glenn, T. C., Green, R. E., & Ray, D. A. (2012). Sequencing Three Crocodilian Genomes to Illuminate the Evolution of Archosaurs and Amniotes. Genome Biology. 13(1), 415. DOI:10.1186/gb-2012-13-1-415. [Document Site]

Chouvarine, P., Cooksey, A. M., McCarthy, F.M., Ray, D., Baldwin, B. S., Burgess, S. C., & Peterson, D. G. (2012). Transcriptome-based Differentiation of Closely-related Miscanthus Lines. PLoS ONE. 7(1), e29850. DOI:10.1371/journal.pone.0029850. [Abstract] [Document] [Document Site]

Liu, W., Thummasuwan, S., Sehgal, S. K., Chouvarine, P., & Peterson, D. G. (2011). Characterization of the Genome of Bald Cypress. BMC Genomics. 12(1), 553. [Abstract] [Document] [Document Site]

Moolhuijzen, P. M., Lew-Tabor, A. E., Morgan, J. A. T., Rodriguez-Valle, M., Peterson, D. G., Dowd, S. E., Guerrero, F. D., Bellgard, M. I., & Appels, R. (2011). The Complexity of Rhipicephalus (Boophilus) Microplus Genome Characterised Through Detailed Analysis of Two BAC Clones. BMC Research Notes. 4, 254. [Abstract] [Document]

Magbanua, Z. V., Ozkan, S., Bartlett, B. D., Chouvarine, P., Saski, C. A., Liston, A. I., Cronn, R. C., Nelson, C. D., & Peterson, D. G. (2011). Adventures in the Enormous: A 1.8 Million Clone BAC Library for the 21.7 Gb Genome of Loblolly Pine. PLoS ONE. 6, e16214. [Abstract] [Document]

Lin, L., Pierce, G. J., Bowers, J. E., Estill, J. C., Compton, R. O., Rainville, L. K., Kim, C., Lemke, C., Rong, J., Tang, H., Wang, X., Braidotti, M., Chen, A. H., Chicola, K., Collura, K., Epps, E., Golser, W., Grover, C., Ingles, J., Karunakaran, S., Kudrna, D., Olive, J., Tabassum, N., Um, E., Wissotski, M., Yu, Y., Zuccolo, A., Rahman, M. U., Peterson, D. G., Wing, R. A., Wendel, J. F., & Paterson, A. H. (2010). A Draft Physical Map of a D-Genome Cotton Species (Gossypium Raimondii). BMC Genomics. 11, 395. [Abstract] [Document]

Guerrero, F. D., Moolhuijzen, P., Peterson, D. G., Bidwell, S., Caler, E., Bellgard, M., Nene, V. M., & Djikeng, A. (2010). Reassociation Kinetics-Based Approach for Partial Genome Sequencing of the Cattle Tick, Rhipicephalus (Boophilus) Microplus. BMC Genomics. 11, 374. [Abstract] [Document]

Paterson, A. H., Rong, J. K., Gingle, A. R., Chee, P. W., Dennis, E. S., Llewellyn, D., Dure, L. S., Haigler, C., Myers, G. O., Peterson, D. G., Rahman, M. U., Zafar, Y., Reddy, U., Saranga, Y., Stewart, J. M., Udall, J. A., Waghmare, V. N., Wendel, J. F., Wilkins, T. A., Wright, R. J., Zaki, E., Hafez, E. E., & Zhu, J. (2010). Sequencing and Utilization of the Gossypium Genomes. Tropical Plant Biology. 3(2), 71-74. [Abstract] [Document]

Shan, X., Ray, D., Bunge, J. A., & Peterson, D. G. (2009). A Bacterial Artificial Chromosome Library for the Australian Saltwater Crocodile (Crocodylus Porosus) and Its Utilization in Gene Isolation and Genome Characterization. BMC Genomics. 10(Suppl), S9. [Abstract] [Document]

Bunge, J. A., Chouvarine, P., & Peterson, D. G. (2009). CotQuest: Improved Algorithm and Software for Nonlinear Regression Analysis of DNA Reassociation Kinetics Data. Analytical Biochemistry. 388, 322-330. [Abstract] [Document]

Morse, A. M., Peterson, D. G., Islam-Faridi, M. N., Smith, K. E., Magbanua, Z. V., Garcia, S. A., Kubisiak, T. L., Amerson, H. V., Carlson, J. E., & Nelson, C. D. (2009). Evolution of Genome Size and Complexity in Pinus. PLoS ONE. 4(2), e4332. [Abstract] [Document]

Paterson, A. H., Bowers, J. E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H., Haberer, G., Hellsten, U., Mitros, T., Poliakov, A., Schmutz, J., Spannagl, M., Tang, H., Wang, X., Wicker, T., Bharti, A. K., Chapman, J., Feltus, F. A., Gowik, U., Grigoriev, I. V., Lyons, E., Maher, C. A., Martis, M., Narechania, A., Otillar, R. P., Penning, B. W., Salamov, A. A., Wang, Y., Zhang, L., Carpita, N. C., Freeling, M., Gingle, A. R., Hash, C. T., Keller, B., Klein, P., Kresovich, S., McCann, M. C., Ming, R., Peterson, D. G., Rahman, M. U., Ware, D., Westhoff, P., Mayer, K. F. X., Messing, J., & Rokhsar, D. S. (2009). The Sorghum Bicolor Genome and the Diversification of Grasses. Nature. 457, 551-556. [Abstract] [Document]

Saha, S., Bridges, S., Magbanua, Z. V., & Peterson, D. G. (2008). Discovering Relationships Among Dispersed Repeats Using Spatial Association Rule Mining. BMC Bioinformatics. 9(Suppl 10), O4. [Document]

Saha, S., Bridges, S., Magbanua, Z. V., & Peterson, D. G. (2008). Empirical Comparison of Ab Initio Repeat Finding Programs. Nucleic Acids Research. 36(7), 2284-2294. DOI:10.1093/nar/gkn064. [Abstract] [Document] [Document Site]

Saha, S., Bridges, S., Magbanua, Z. V., & Peterson, D. G. (2008). Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences. Tropical Plant Biology. Springer New York. 1(1), 85-96. [Abstract] [Document]

Chouvarine, P., Saha, S., & Peterson, D. G. (2008). An Automated, High-throughput Sequence Read Classification Pipeline for Preliminary Genome Characterization. Analytical Biochemistry. 373, 78-87. [Abstract] [Document]

Dennis, J. H., Fan, H. Y., Reynolds, S. M., Yuan, G., Meldrim, J. C., Richter, D. J., Peterson, D. G., Rando, O. J., Noble, W. S., & Kingston, R. E. (2007). Independent and Complementary Methods for Large-scale Structural Analysis of Mammalian Chromatin. Genome Research. 17(6), 928-939. [Abstract] [Document]

Bunge, J., Epstein, S. S., & Peterson, D. G. (2006). Comment on "Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil". Science. 313, 918. [Abstract] [Document]

Lamoureux, D., Peterson, D. G., Li, W., Fellers, J. P., & Gill, B. S. (2005). The Efficacy of Cot-based Gene Enrichment in Wheat (Triticum Aestivum L.). Genome. 48, 1120-1126. [Abstract] [Document]

Wicker, T., Robertson, J. S., Schulze, S. R., Feltus, F. A., Magrini, V., Morrison, J. A., Mardis, E. R., Wilson, R. K., Peterson, D. G., Paterson, A. H., & Ivarie, R. (2005). The Repetitive Landscape of the Chicken Genome. Genome Research. 15, 126-136. [Abstract] [Document]

Paterson, A. H., Bowers, J. E., Chapman, B. A., Peterson, D. G., Rong, J., & Wicker, T. M. (2004). Comparative Genome Analysis of Monocots and Dicots, Toward Characterization of Angiosperm Diversity. Current Opinion in Biotechnology. 15(2), 120-124. [Abstract] [Document]

Paterson, A. H., Bowers, J. E., Peterson, D. G., Estill, J. C., & Chapman, B. A. (2003). Structure and Evolution of Cereal Genomes. Current Opinion in Genetics and Development. 13(6), 644-650. [Abstract] [Document]

Peterson, D. G., Wessler, S. R., & Paterson, A. H. (2002). Efficient Capture of Unique Sequences from Eukaryotic Genomes. Trends in Genetics. 18(11), 547-550. [Abstract] [Document]

Peterson, D. G., Schulze, S. R., Sciara, E. B., Lee, S. A., Bowers, J. E., Nagel, A., Jiang, N., Tibbitts, D. C., Wessler, S. R., & Paterson, A. H. (2002). Integration of Cot Analysis, DNA Cloning, and High-throughput Sequencing Facilitates Genome Characterization and Gene Discovery. Genome Research. 12, 795-807. [Abstract] [Document]

Saha, S., Bridges, S., Magbanua, Z. V., & Peterson, D. G. (2009). Discovering Spatially Related Repeats in Assembled Genomes Using Association Rule Mining. Midsouth Computational Biology and Bioinformatics Society (MCBIOS) Annual Meeting. Mississippi State University, Starkville, MS.

Saha, S., Bridges, S., Magbanua, Z. V., & Peterson, D. G. (2008). Data Mining of Spatial Relationships Among Dispersed Repetitive Regions. 6th Annual Graduate Student Association Research Symposium. Mississippi State University.

Thrash, A., Sanders, W. S., Arick, M., II, Nanduri, B., Perkins, A., Peterson, D. G., & Rhoads, D. (2016). An Update on the Collaborative MCBIOS Rattlesnake Genome Assembly Project. MidSouth Computational Biology and Bioinformatics Society. Memphis, TN.

Buza, T., Arick, M., II, Wang, H, & Peterson, D. G. (2014). Human Disease MicroRNAs and their Counterparts in Domestic Animals. Mississippi-INBRE Annual Research Symposium. The University of Southern Mississippi, Hattiesburg, MS: MS-INBRE. [Abstract] [Document Site]

Saha, S., Peterson, D. G., & Bridges, S. (2007). Targeted Data Mining of Spatial Proximity Relationships of Repetitive Regions in Genomes. 2007 Meeting on Genome Informatics at Cold Spring Harbor Laboratory. Cold Spring Harbor, New York.

Saha, S., Bridges, S., Magbanua, Z. V., & Peterson, D. G. (2007). Empirical Evaluation of Ab Initio Repeat Finders. MCBIOS (MidSouth Computational Biology and Bioinformatics Society). New Orleans, LA.

Grover, C., Paterson, A. H., Peterson, D. G., Sanders, W. S., Schmutz, J., Renny-Byfield, S., & Wendell, J. F. (2013). Genome Size Evolution In Gossypium (Cotton): Progress and Prospects. Plant and Animal Genome XXI. San Diego, CA. [Abstract] [Document Site]

Steele, R. D., Arick, M., II, Perkins, A., Nanduri, B., Peterson, D. G., Rhoads, D. D., & Sanders, W. S. (2016). A Mitochondrial Genome of the Timber Rattlesnake (Crotalus Horridus) and a Reptilian Mitochondrial Phylogeny. MidSouth Computational Biology and Bioinformatics Society. Memphis, TN.

Sanders, W. S., Ganji, S., Arnold, J. P., Arick, M., II, Showmaker, K. C., Bartlett, B. D., Cooksey, A., Watts, J., Knudstrup, S., Magbanua, Z. V., Peterson, D. G., & Wubben, M. J. (2014). Assembly, Annotation, and Proteogenomic Mapping of Rotylenchulus reniformis. Plant and Animal Genome XXII. San Diego, CA. [Abstract] [Document] [Document Site]

Ganji, S., Sanders, W. S., Stokes, J. V., Showmaker, K. C., Bartlett, B., Wang, H, Wubben, M., McCarthy, F.M., Magbanua, Z. V., & Peterson, D. G. (2013). The Genome of Reniform Nematode, Rotylenchulus reniformis. MCBIOS 2013. University of Missouri, Columbia, MO. [Abstract] [Document] [Document Site]

Showmaker, K. C., Ganji, S., Arick, M., II, Sanders, W. S., Magbanua, Z. V., Wubben, M. J., & Peterson, D. G. (2013). De Novo Transcriptome Assembly of the Plant-Parasitic Nematode Rotylenchulus reniformis. MCBIOS 2013. University of Missouri, Columbia, MO. [Abstract] [Document Site]

Sanders, W. S., Ganji, S., Arnold, J. P., Arick, M., II, Showmaker, K. C., Wubben, M. J., & Peterson, D. G. (2013). Identification of Protein Coding Genes in the Plant-parasitic Nematode Rotylenchulus reniformis through Comparative Proteogenomic Mapping with Caenorhabditis elegans. MCBIOS 2013. University of Missouri, Columbia, MO. [Abstract] [Document] [Document Site]

Sanders, W. S., Showmaker, K. C., Bartlett, B. D., Wang, H, Ganji, S., Wubben, M., McCarthy, F.M., Magbanua, Z. V., & Peterson, D. G. (2012). Assembling and Annotating the Genome of a Plant Parasitic Nematode, Rotylenchulus reniformis, with Sequences Obtained Using 2Nd Generation Sequencing Technologies. MCBIOS 2012. University of Mississippi. [Abstract]

Showmaker, K. C., Sanders, W. S., Bartlett, B., Wang, H, Ganji, S., Wubben, M. J., McCarthy, F.M., Magbanua, Z. V., & Peterson, D. G. (2012). Sequencing and Analysis of the Rotylenchulus reniformis Transcriptome. Plant and Animal Genome XX. San Diego, CA. [Abstract] [Document Site]

Sanders, W. S., Showmaker, K. C., Bartlett, B. D., Wang, H, Ganji, S., Wubben, M., McCarthy, F.M., Magbanua, Z. V., & Peterson, D. G. (2012). The Rotylenchulus reniformis Genome: Sequencing, Assembly, and Annotation. Plant and Animal Genomes XX. San Diego, CA. [Abstract] [Document]

Kumar, P. K. R., Li, P., Wimalanathan, K., Liu, L., Ji, G., Magbanua, Z. V., Lorenz, W. W., Nairn, C. J., Dean, J. F. D., Peterson, D. G., & Liang, C. (2011). The Pinus Taeda BAC Browser. Plant & Animal Genomes XIX Conference. San Diego, CA. [Abstract] [Document]

Islam-Faridi, N., Magbanua, Z. V., Majid, M. A., Butnor, J. R., Peterson, D. G., & Nelson, C. D. (2010). Chromosomal Distribution Of Pine Repetitive DNA Sequences. Plant & Animal Genomes XVIII Conference. San Diego, CA. [Abstract] [Document]

Peterson, D. G., & Abbott, C. F. (2014). Institute for Genomics, Biocomputing and Biotechnology - 2014.