Epernicus: James C Estill, B.S.

James C Estill, B.S.

(Ph.D. in progress)

Position:
Graduate Student - Ph.D.

Plant Biology

University of Georgia (Athens, GA)
Advisor:
Jeffrey L Bennetzen
Degrees:

Ph.D. (in progress), Plant Biology, University of Georgia (Athens, GA)

B.S., Biology, Western Kentucky University (Bowling Green, KY)
Past Advisors:

Andrew H. Paterson (as Technician)

Zack E. Murrell (as Undergraduate Student)

Thomas K. Green (as Undergraduate Student)
Research:
Evolution and demography of LTR retrotransposons in plant genomes

Generally I am interested in the application of the tools of bioinformatics and molecular biology to the study of plant evolutionary and ecophysiological genomics. Over the past decade, a large focus of descriptive genomics has been the construction and annotation of high resolution genome maps for a handful of model species. My dissertation research is focused on the next stage of genomics, which is the use of these high resolution genome maps to study fundamental patterns of genome architecture, and the expansion of knowledge gained from these model genomes to the study of other species. It is my hope that many of the tools that I develop can be applied to questions using non-model species in the emerging field of ecological genomics.
Other Experience:
2007 Google Summer of Code Student - Developed a command line interface to a BioSQL phylogenetic database
Honors:
1996 Young Botanist Award (Botanical Society of America)

Communities:

James Estill's Genealogy

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James Estill's Publications (15)

Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome.
Baucom RS, Estill JC, Chaparro C, Upshaw N, Jogi A, Deragon JM, Westerman RP, Sanmiguel PJ, Bennetzen JL

PLoS genetics. 2009 Nov;5(11):e1000732
The B73 maize genome: complexity, diversity, and dynamics.
Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK

Science (New York, N.Y.). 2009 Nov 20;326(5956):1112-5
The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes.
Estill JC, Bennetzen JL

Plant methods. 2009 Jun 19;5(1):8
Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains.
Nelson W, Luo M, Ma J, Estep M, Estill J, He R, Talag J, Sisneros N, Kudrna D, Kim H, Ammiraju JS, Collura K, Bharti AK, Messing J, Wing RA, Sanmiguel P, Bennetzen JL, Soderlund C

BMC genomics. 2008 Dec 19;9(1):621
Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome.
Baucom RS, Estill JC, Leebens-Mack JH, Bennetzen JL

Genome research. 2008 Nov 24
Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon.
Paterson AH, Chapman BA, Kissinger JC, Bowers JE, Feltus FA, Estill JC

Trends in genetics : TIG. 2006 Nov;22(11):597-602
A framework linkage map of bermudagrass (Cynodon dactylon x transvaalensis) based on single-dose restriction fragments.
Bethel CM, Sciara EB, Estill JC, Bowers JE, Hanna W, Paterson AH

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 2006 Feb;112(4):727-37
Organization and evolution of resistance gene analogs in peanut.
Yuksel B, Estill JC, Schulze SR, Paterson AH

Molecular genetics and genomics : MGG. 2005 Oct;274(3):248-63
Comparative genomics of Gossypium and Arabidopsis: unraveling the consequences of both ancient and recent polyploidy.
Rong J, Bowers JE, Schulze SR, Waghmare VN, Rogers CJ, Pierce GJ, Zhang H, Estill JC, Paterson AH

Genome research. 2005 Sep;15(9):1198-210
Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses.
Bowers JE, Arias MA, Asher R, Avise JA, Ball RT, Brewer GA, Buss RW, Chen AH, Edwards TM, Estill JC, Exum HE, Goff VH, Herrick KL, Steele CL, Karunakaran S, Lafayette GK, Lemke C, Marler BS, Masters SL, McMillan JM, Nelson LK, Newsome GA, Nwakanma CC, Odeh RN, Phelps CA, Rarick EA, Rogers CJ, Ryan SP, Slaughter KA, Soderlund CA, Tang H, Wing RA, Paterson AH

Proceedings of the National Academy of Sciences of the United States of America. 2005 Sep 13;102(37):13206-11
Exploratory integration of peanut genetic and physical maps and possible contributions from Arabidopsis.
Yüksel B, Bowers JE, Estill J, Goff L, Lemke C, Paterson AH

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 2005 Jun;111(1):87-94
The effect of deforestation on the genetic diversity and structure in Acer saccharum (Marsh): evidence for the loss and restructuring of genetic variation in a natural system
Regina S Baucom, James C Estill, Cruzan Mitch

Conservation Genetics. 2005;6:39-50
An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments.
Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH

Genome research. 2004 Sep;14(9):1812-9
Structure and evolution of cereal genomes.
Paterson AH, Bowers JE, Peterson DG, Estill JC, Chapman BA

Current opinion in genetics & development. 2003 Dec;13(6):644-50
Phytogeography of rare plant species endemic to the Southeastern United States
James C Estill, Mitch Cruzan

Castanea. 2001;66(1-2):3-23

James Estill's Posters and Presentations (4)

Distilling transposable element exemplars from host genomes builds a framework for understanding TE diversity in the grasses (presentation)
James C Estill, Regina S Baucom, Jeffrey L Bennetzen

51st Maize Genetics Conference ; 03/2009
The DAWG-PAWS wheat annotation pipeline (presentation)
James C Estill, Jeff L Bennetzen

Plant and Animal Genome XVII Conference; 01/2009
A RepMiner analysis of maize LTR Retrotransposons reveals a previously unrecognized split in the Huck family. (poster)
James C Estill, Regina S Baucom, Jeffrey L Bennetzen

50th Maize Genetics Conference; 03/2008
RepMiner: A Graph Theory Based Approach Applied to Classification and Assembly of the Repetitive Fraction of Sample Sequence Data (poster)
James C. Estill and Jeff Bennetzen

49th Maize Genetics Conference; 03/2007

One Figure

Insertions Dates of LTR Retrotransposons in Maize

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