Dr. Daniel Peterson

Associate Professor
Specialty: Plant Genomics and Molecular Biology
Research Organism(s): pine, cotton, sorghum, various other plants and animals
Department: Plant and Soil Sciences - Main Campus

Mailing Address
Box 9555
Mississippi State, MS 39762

Physical Address
424 Dorman Hall
Mississippi State, MS 39762

Telephone: (662) 325-2747
Fax: (662) 325-8742

Assignment

My appointment is 75% research and 25% teaching. I teach one formal course per year and am primary advisor/mentor to graduate students, postdoctoral associates, and other research personnel.

Courses Taught

I teach the 8000-level lecture course "Genomes and Genomics" in fall semesters of every even numbered year (e.g., 2008, 2010, 2012). In the fall semester of every odd-numbered year I teach the 8000-level discussion course "Topics in Genomics."

Web Site Title

Mississippi Genome Exploration Laboratory (MGEL)
http://www.mgel.msstate.edu

Education

1998: Doctor of Philosophy: Botany - Colorado State University
1993: Master of Science: Botany - Colorado State University
1991: Bachelor of Science: Biology (cum laude) - Colorado State University

Experience

May 1, 2009-present: Associate Director - Life Sciences & Biotechnology Institute (LSBI) - Mississippi State University
March 2008-present: Associate Professor - Department of Plant and Soil Sciences - Mississippi State University
August 2002-February 2008: Assistant Professor - Department of Plant and Soil Sciences - Mississippi State University
October 2001-July 2002: Postdoctoral Research Coordinator II - Center for Applied Genetic Technologies - University of Georgia
Feb. 1999-Sept. 2001: Postdoctoral Research Associate – Department of Botany – University of Georgia
1998: Research Associate – Department of Biology – Colorado State University
1993-1998: Cell & Molecular Biology Program – Colorado State University
1993-1998: Graduate Research Assistant - Biology Department – Colorado State University
1991-1992: Graduate Teaching Assistant - Biology Department – Colorado State University
1991: NSF Research Experience for Undergraduates – Colorado State University
1990-1991: Tutor for College of Natural Sciences – Colorado State University

Select Awards and Honors

2008: Distinguished Fellow, Life Sciences and Biotechnology Institute, Mississippi State University (one of four inaugural inductees)
2007: Grantsmanship Award (plaque and $1000) – Sustained Excellence in External Competitive Grantsmanship - Mississippi Agricultural and Forestry Experiment Station (MAFES), Mississippi State University
2007: Sigma Xi Scientific Research Society, Mississippi State University
2006: Fellow of the Institute for Digital Biology (IDB) at Mississippi State University
2004: Grantsmanship Award (plaque and $500) - Most Success in Extramural Funding - Mississippi Agricultural and Forestry Experiment Station (MAFES), Mississippi State University
1994: Phi Kappa Phi National Honor Society, Colorado State University
1993: College of Natural Sciences Outstanding Graduate Teaching Assistant Award, Colorado State University
1993: Colorado Fellowship - Cell & Molecular Biology Interdisciplinary Program, Colorado State University
1990: Golden Key National Honor Society, Colorado State University
1990: Phi Beta Kappa National Honor Society, Colorado State University

Society Membership

Genetics Society of America (GSA)
American Society of Plant Biologists (ASPB)

Refereed Publications

Shan X, Ray DA, Bunge JA, Peterson DG (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. 2): S9.

Bunge JA, Chouvarine P, Peterson DG (2009) CotQuest: Improved algorithm and software for nonlinear regression analysis of DNA reassociation kinetics data. Analytical Biochemistry 388: 322-330.

Morse AM, Peterson DG, Islam-Faridi MN, Smith KE, Magbanua ZV, Garcia SA, Kubisiak TL, Amerson HV, Carlson JE, Nelson CD, Davis JM (2009) Evolution of genome size and complexity in Pinus. PLoS ONE 4: e4332.

Paterson AH, Bowers JE, 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 AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer KFX, Messing J, Rokhsar DS (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556.

Saha S, Bridges S, Magbanua Z, Peterson DG (2008) Discovering relationships among dispersed repeats using spatial association rule mining. BMC Bioinformatics 9: O4.

Saha S, Bridges S, Magbanua ZV, Peterson DG (2008) Empirical comparison of ab initio repeat finding programs. Nucleic Acids Research 36: 2284-2294.

Saha S, Bridges S, Magbanua ZV, Peterson DG (2008) Computational approaches and tools used in identification of dispersed repetitive DNA sequences. Tropical Plant Biology 1: 85-96.

Chouvarine P, Saha S, Peterson DG (2008) An automated, high-throughput sequence read classification pipeline for preliminary genome characterization. Analytical Biochemistry 373: 78-87.

Dennis JH, Fan H-Y, Reynolds SM, Yuan G, Meldrim J, Richter DJ, Peterson DG, Rando OJ, Noble WS, Kingston RE (2007) Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Genome Research 17: 928-939.

Bunge J, Epstein SS, Peterson DG (2006) Comment on "Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil." Science 313: 918.

Lamoureux D, Peterson DG, Li W, Fellers JP, Gill BS (2005) The efficacy of Cot-based gene enrichment in wheat (Triticum aestivum L.). Genome 48: 1120-1126.

Wicker T, Robertson JS, Schulze SR, Feltus FA, Magrini V, Morrison JA, Mardis ER, Wilson RK, Peterson DG, Paterson AH, Ivarie R (2005) The repetitive landscape of the chicken genome. Genome Research 15: 126-136.

Paterson AH, Bowers JE, Chapman BA, Peterson DG, Rong J, Wicker TM (2004) Comparative genome analysis of monocots and dicots, toward characterization of angiosperm diversity. Current Opinion in Biotechnology 15: 120-124.

Paterson AH, Bowers JE, Peterson DG, Estill JC, Chapman BA (2003) Structure and evolution of cereal genomes. Current Opinion in Genetics and Development 13: 644-650.

Peterson DG, Wessler SR, Paterson AH (2002) Efficient capture of unique sequences from eukaryotic genomes. Trends In Genetics 18: 547-550.

Peterson DG, Schulze SR, Sciara EB, Lee SA, Nagel A, Jiang N, Tibbitts DC, Wessler SR, Paterson AH (2002) Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Research 12: 795-807.

Tomkins JP, Peterson DG, Yang TJ, Main D, Ablett EF, Henry RJ, Lee LS, Holton TA, Waters D, Wing RA (2001) Grape (Vitis vinifera L.) BAC library construction, preliminary STC analysis, and identification of clones associated with flavonoid and stilbene biosynthesis. American Journal of Enology and Viticulture 52: 287-291.

Tomkins JP, Peterson DG, Yang T, Main D, Wilkins TA, Paterson AH, Wing RA (2001) Development of genomic resources for cotton (Gossypium hirsutum): BAC library construction, preliminary STC analysis, and identification of clones associated with fiber development. Molecular Breeding 8: 255-261.

Draye X, Lin Y-R, Qian X-y, Bowers JE, Burow GB, Morrell PL, Peterson DG, Presting GG, Ren S-x, Wing RA, Paterson AH (2001) Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses, using the Sorghum genome as a foundation. Plant Physiology 125: 1325-1341.

Peterson DG, Tomkins JP, Frisch DA, Wing RA, Paterson AH (2000) Construction of plant bacterial artificial chromosome libraries: An illustrated guide. Journal of Agricultural Genomics 5: http://wheat.pw.usda.gov/jag/.

Peterson DG, Lapitan NLV, Stack SM (1999) Localization of single- and low-copy sequences on tomato synaptonemal complex spreads using fluorescence in situ hybridization (FISH). Genetics 152: 427-439.

Peterson DG, Pearson WR, Stack SM (1998) Characterization of the tomato (Lycopersicon esculentum) genome using in vitro and in situ DNA reassociation. Genome 41: 346-356.

Peterson DG, Boehm KS, Stack SM (1997) Isolation of milligram quantities of nuclear DNA from tomato (Lycopersicon esculentum), a species containing high levels of polyphenolic compounds.Plant Molecular Biology Reporter 15: 148-153.

Peterson DG, Price HJ, Johnston JS, Stack SM (1996) DNA of content of heterochromatin and euchromatin in tomato (Lycopersicon esculentum) pachytene chromosomes. Genome 39: 77-82.

Peterson DG, Stack SM, Healy JL, Donohoe BS, Anderson LK (1994) The relationship between synaptonemal complex length and genome size in four vertebrate classes (Osteicthyes, Reptilia, Aves, Mammalia). Chromosome Research 2: 153-162.

Book Chapters

Plomion C, Chagné D, Pot D, Kumar S, Wilcox P, Burdon R, Prat D, Peterson DG, Paiva J, Chaumeil P, Vendramin G, Sebastiani F, Nelson CD, Echt C, Savolainen O, Kubisiak T, Cervera MT, Islam-Faridi MN (2007) The Pines. In: Genome Mapping and Molecular Breeding in Plants, Vol. 7, Forest Trees. Edited by: Kole CR. Springer - Heidelberg, Berlin, New York, Tokyo; pp. 29-78 (ISBN: 978-3-540-34540-4).

Peterson DG (2005) Reduced representation strategies and their application to plant genomes. In:The Handbook of Plant Genome Mapping: Genetic and Physical Mapping. Edited by: Meksem K, Kahl G. John Wiley & Sons, Inc. - Hoboken, NJ, pp. 307-335.