James Christopher Estill

Email: JamesEstill at gmail.com
Phone: 706-542-9729

Address:
Department of Plant Biology
The University of Georgia
Athens, GA 30602-7271

Education

University of Georgia. 2006-Present.
PhD in Progress, Department of Plant Biology
Dissertation: Evolution and Genome Cartology of LTR Retrotransposons

University of Tennessee, Knoxville. 1996-2000.
32 Hours Graduate Level Coursework.

Western Kentucky University. 1991-1996.
BS - Biology
Minor Environmental Studies
Graduate of the WKU Honors Program
Honors Thesis: Demographic and Molecular Genetic Analysis of Spiraea virginiana

Professional Skills

Laboratory: 10 Years Bench Experience
  • Molecular Biology: DNA Isolation, PCR, Restriction Digestion, Blotting, Southern Hybridization
  • Molecular Markers: AFLPs, PCR-RFLPs, Isozymes, ISSRs, Heteroduplex
  • Library Screening: High-throughput Combinatorial Experimental Design and Deconvolution
  • DNA Sequencing: Tracefile Analysis, Manual Sequencing, P33 Labeling 
  • Lab Automation: Packard Robot Programming
Field Biology: 6 Years Field Experience 
  • Southeastern US Vascular plant site identification and key identification to species
  • Site identification of freshwater algae genera
  • Classical Orienteering & GPS use
  • Pollination ecology and ecological sampling including permanent plots, line transect and others
  • Limnology and Forest Ecology Measurements
Computing: 12 Years Programming and Web Development Experience
  • Hardware: Skilled in general hardware installation and trouble shooting
  • Languages: ArcAvenue, Emacs Lisp, HTML, PERL, R/GnuS, SQL, Visual Basic
  • Version Control: CVS, SVN
  • Operating Systems: Windows, UNIX, LINUX, Mac OS, VMS
  • Bioinformatics: Apollo, BioPerl, CAP3, CLUSTAL, Cytoscape, DIALIGN, GFF2PS, InterProScan, Mesquite, NCBI-BLAST, PAUP, PHYLIP, RAXML, Sequencher, Sockeye, TGICL, Treeview
  • Cluster Computing: Open PBS, Platform LSF
  • GIS: ArcView, ArcInfo, 3DEM
  • Statistics and Mathematics: Crimestat II, SPSS, Matlab, Maple, R
  • Office Productivity: MS Office Suite, Open Office
  • Web: MS Frontpage, Adobe Acrobat
  • Imaging: FineReader OCR, Optimas, GIMP, Photoshop
  • Database: MS Access, MySQL, PostgreSQL

Professional Experience

UGA Plant Comparitive Genomics Lab. Graduate Research. 2006-Present.
  • Developed informatics resources for eukaryotic genome annotation and transposable element classification towards a unified study of the evolution and genome cartology of LTR retrotransposons in the grasses.
UGA Plant Genome Mapping Lab. Research Technician. 2000-2005.
  • Conducted wet lab work, developed informatic resources, and analyzed hybridization data related to physical mapping of various crop genomes including banana, brassica, cotton, maize, papaya, peanut, rice, sorghum, sugarcane.
UTK Plant Ecological Genetics Lab. Graduate Research. 1996-2000.
  • Developed a database of vascular plants endemic to the SE United States to study geographic and taxonomic patterns of endemism, Studied the phylogeography of two vascular plants endemic to the Southern Appalachians, Contributed to the study of the ecological genetics of Helianthus eggertii, Acer saccharum, and Pityopsis ruthii.
WKU Florisitics and Phylogeography Lab. Undergraduate Research. 1995-1996.
  • Contributed to a floristic inventory of the Raymond Athey Barrens, Conducted a status survey of the the federally threatened vascular plant Spiraea virginiana in Tennessee, Developed molecular markers contributing to the phylogeographic study of S. virginiana.
WKU Organic Chemistry Lab. Undergraduate Research. 1994-1995.
  • Synthesized and NMR characterized model dibenzyl sulfide compounds, Used novel 1H NMR technique to quantify sulfur bond cleavage products, Determined the efficacy of this method for describing the sulfur chemistry of petroleum products.

Publications

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

  2. RS Baucom*, JC Estill*, C Chapparro, N Upshaw, A Jogi, JM Deragon, RP Westerman, PJ SanMiguel, JL Bennetzen. 2009. "Exceptional diversity, non-random distribution and rapid evolution of retroelements in the B73 Maize genome." PLOS Genetics. Accepted.
    abstract | pdf    - *Authors contributed equally to this work

  3. JC Estill and JL Bennetzen. 2009. "The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes." Plant Methods. 5:8.
    abstract | software website | pdf

  4. RS Baucom, JC Estill, JC Leebans-Mack, and JL Bennetzen. 2009. “Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome.Genome Research. 19(2): 243-254.
    abstract | pub med | pdf

  5. WM Nelson, M Luo, J Ma, M Estep, J Estill, R He, J Talag, N Cisneros, D Kudrna, HR Kim, JSS Ammiraju, K Collura, AK Bharti, J Messing, RA Wing, P SanMiguel, JL Bennetzen and C Soderlund. 2008. “Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains.BMC Genomics. 9:621.
    abstract | pub med | pdf

  6. KM Devos, A Costa de Oliveira, X Xu, JC Estill, MC Estep, A Jogi, M Morales, J Pinheiro, P San Miguel, and JL Bennetzen. 2008. “Structure and organization of the wheat genome – the number of genes in the hexaploid wheat genome.” In R Appels, R Eastwood, E Lagudah, P Langridge, M Mackay, L McIntyre, and P Sharp. (Eds). Proceedings 11th International Wheat Genetics Symposium. Sydney, Sydney University Press.
    abstract | pdf

  7. AH Paterson, BA Chapman, JC Kissenger, JE Bowers, FA Feltus and JC Estill. 2006. "Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon." Trends in Genetics. 22(11): 597-602.
    abstract | pdf.

  8. AH Paterson, JE Bowers, JC Estill, TC Osborn, JC Pires, R Amasino, CF Quiros, and M Farnham. 2006. "Evolutionary history of the Angiosperms and its relevance to Brassica." Acta Hort. (ISHS). 706:49-54.
    abstract | pdf.

  9. CM Bethel, EB Sciara, JC Estill, JE Bowers, W Hanna, AH Paterson. 2006. "A framework linkage map of bermudagrass (Cynodon dactylon x transvaalensis) based on single-dose restriction fragments." Theoretical and Applied Genetics. 112(4): 727-737.
    abstract | pdf.

  10. B Yüksel, JC Estill, SR Schulze, and AH Paterson. 2005. "Organization and evolution of resistance gene analogs in peanut." Molecular Genetics and Genomics. 274(3): 248-263.
    abstract | pdf.

  11. JE Bowers, MA Arias, R Asher, JA Avise, RT Ball, GA Brewer,  RW Buss, AH Chen, TM Edwards, JC Estill, HE Exum, VH Goff, KL Herrick, CL James Steele, S Karunakaran, GK Lafayette, C Lemke, BS Marler, SL Masters, JM McMillan, LK Nelson, GA Newsome, CC Nwakanma, RN Odeh, CA Phelps, EA Rarick, CJ Rogers, SP Ryan, KA Slaughter, CA Soderlund, H Tang, RA Wing, AH Paterson. 2005. "Comparative physical mapping links retention of microsynteny to chromosome structure and recombination in grasses." PNAS. 102(37):13206-13211.
    abstract | pdf.

  12. J Rong, JE Bowers, SR Schulze, VN Waghmare, CJ Rogers, GJ Pierce, Hua Zhang, JC Estill, and Andrew H. Paterson. 2005. "Comparative genomics of Gossypium and Arabidopsis: unraveling the consequences of both ancient and recent polyploidy." Genome Research. 15(9): 1198-1210.
    abstract | pdf.

  13. B Yüksel, JE Bowers, JC Estill, C Lemke, and AH Paterson. 2005. "Exploratory integration of peanut genetic and physical maps and possible contributions from Arabidopsis." Theoretical and Applied Genetics. 111: 87-94.
    abstract | pdf.

  14. RS Baucom, JC Estill and M Cruzan. 2005. "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 ." Conservation Genetics. 6: 39-50.
    abstract | pdf.

  15. FA Feltus, J Wan, SR Schulze, JC Estill, N Jiang and A Paterson. 2004. "An SNP resource for rice genetics and breeding based on subspecies Indica and Japonica genome alignments". Genome Research. 14: 1812-1819.
    abstract | pdf.

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

  17. JC Estill and M Cruzan. 2001. "Phytogeography of rare plant species endemic to the Southeastern United States." Castanea. 66(1-2): 3-23.
    abstract | pdf.


Manuscripts Submitted and in Preparation

  • JC Estill, RS Baucom, and JL Bennetzen. "RepMiner and its use for LTR retrotransposon analysis in maize." Manuscript in preparation for submission to Genome Research.
  • JC Estill and JL Bennetzen. "Affinity propagation clustering efficiently and effectively defines representative exemplars from large molecular sequence databases of transposable elements." Manuscript in preparation.

Presentations


Other Professional Contributions


Software

DAWGPAWS: Genome Annotation Pipeline. 2006-Present.
http://dawgpaws.sourceforge.net/
SLOC: 24,400
RepMiner: Taxonomies for Transposable Elements. 2006–Present.
http://jestill.myweb.uga.edu/RepMiner.htm
SLOC: 22,600
PhyTools: Command Line Topological Query Application for BioSQL. 2007.
http://tinyurl.com/clnalt
SLOC: 2,300
DNA DABBLER: DNA Sequence Database and BLAST Builder. 2003-2007.
http://jestill.myweb.uga.edu/DNA_DABBLER.htm
SLOC: 3,700
MyGCAT: My Genome Collection with Assigned Taxonomy. 2005.
http://mygcat.sourceforge.org
SLOC: 2,700
BACMan: BAC Data Management. 2000-2005.
http://bacman.sourceforge.net/
SLOC: 8,900
OligoMan: Oligonucleotide Data Management. 2005.
http://jestill.myweb.uga.edu/OligoMan.htm
LabMan: Laboratory Management Database. 2000-2004.
http://jestill.myweb.uga.edu/labman.htm
BACEater: Automated BAC Library Scoring Processor. 2004.
http://plantgenome.agtec.uga.edu/bacman/program/BACEater.html
BACGrid: Digital BAC Library Scoring Software. 2001.
http://plantgenome.agtec.uga.edu/bacman/program/BACGrid.html

Teaching and Mentoring Experience

Wheat Annotation Workshop
2009 Summer 3 Day Course Annotation Trainer (UGA & U Maryland)
Assisted 12 graduate students and postdoctoral participants in developing manual genome annotation skills using annotation results from the JCVI annotation pipeline as well as the DAWGPAWS annotation pipeline, Presented lecture on the use of the DAWGPAWS pipeline to generate annotation results.
Computational Phyloinformatics Summer Course (NESCent)
2008 Summer 3 Day Course Teaching Assistant
Assisted 12 graduate student and postdoctoral participants in software installation, Assisted participants in completing computational phyloinformatics coding assignments in SQL and Perl
Bioinformatics and Modeling Lab (UGA - GENE 4220L)
2008 Spring Semester Teaching Assistant
Taught one lab section of 15 students that met bi-weekly, Independently developed and taught seven lectures, Led bi-weekly laboratory exercises, Managed course WebCT content, Graded lab reports, quizzes and exams
Undergraduate Training in Wheat Genome Annotation
2006 Fall Semester.
2007 Spring Semester.
Led genome annotation training for a group of 8 undergraduate students over the course of two semesters, Devloped lectures on the basics of genome annotation, Led students in hands on annotation curation of hexaploid wheat BACs
Ecological Basis of Environmental Issues Lab (UGA - ECOL 1000)
2004 Spring Semester Teaching Assistant
Taught one lab section of 14 students, Introduced weekly topics with short lectures, Led field measures and computer ecological modeling exercises
General Ecology Lab (UTK - BIO 250)
2000 Spring Semester Teaching Assistant
1998 Fall Semester Lead Teaching Assistant
1998 Spring Semester Teaching Assistant
Taught two lab sections of 12 students per semester, Introduced weekly topics with short lectures, Mentored students in developing independent research projects, Edited a lab manual and established a course web page
Fundamentals of Genetics Lab (UTK - BIO 240)
1999 Fall Semester Teaching Assistant
Taught 2 lab sections of 20 students each, Introduced topics with short lectures, Wrote weekly quizzes, Graded quizzes, exams, and lab reports.
Plant Ecology (UTK - BOT 431)
1997 Fall Semester Teaching Assistant
Taught one course section of 8 students meeting twice a week, Mentored students in developing, collecting data, and analyzing results from personal research projects
Prepared materials for laboratory and field lab exercises and established course web page
Fundamentals of Botany II Lab (UTK - BOT 120)
1997 Spring Semester Teaching Assistant
Taught two lab sections of 20 students each, wrote weekly quizzes, graded exams, quizzes and lab reports
Established a course web page
Fundamentals of Botany I Lab (UTK - BOT 110)
1996 Fall Semester Teaching Assistant
Taught two lab sections of 20 students each, wrote weekly quizzes, graded exams, quizzes and lab reports
Established a course web page

Academic Honors and Honorary Organizations


Professional Service


Grants and Financial Awards

2007. Google Summer of Code.
$4500 - A PERL based Command Line Interface to a Topological Query Application for BioSQL in Support of High Throughput Classification and Analysis of LTR Retrotransposons in Plant Genomes.
1998. H. R. DeSelm Award.
$250 - Phacelia fimbriata Field Research in the Great Smoky Mountains National Park.
1997. Botanical Society of the University of Tennessee Supplemental Grant.
$150 - Acer saccharum Field Research in the Great Smoky Mountains National Park.
1997. UTK Scholarly Activity and Research Incentive Fund.
$3000 - Historical Patterns of Natural Hybridization in the Florida Rock Rose (Piriqueta sp.).
1997. UTK Graduate Teaching Assistant Minigrant.
$250 - Travel Funds to Present an Electronic Poster at a Teaching Symposium Sponsored by the American Institute of Biological Sciences.


Author: James Estill
Last Updated: Ocotber 16, 2009

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