User:Lindsay V. Clark

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Software: new script)
(Handy scripts)
(2 intermediate revisions not shown.)
Line 37: Line 37:
===Handy scripts===
===Handy scripts===
-
Convert TASSEL's HapMap format to adegenet's genind format: [[Media:hapMap2genind.R.txt]]
+
*Convert TASSEL's HapMap format to adegenet's genlight format: [[Media:hapMap2genlight.R.txt]]
 +
*Convert TASSEL's HapMap format to adegenet's genind format: [[Media:hapMap2genind.R.txt]]
 +
*Convert adegenet's genind format to STRUCTURE format: [[Media:genind2structure.R.txt]]
==Presentations==
==Presentations==

Revision as of 16:36, 18 March 2013

Lindsay V. Clark
Lindsay V. Clark

Postdoctoral Research Associate, Plant Population Genetics

Energy Biosciences Institute

University of Illinois, Urbana-Champaign

Contents

Research and Personal Info

I am a postdoc studying the genetic diversity and population structure of Miscanthus, a perennial grass being developed as a bioenergy crop, under Dr. Erik Sacks at the University of Illinois, Urbana-Champaign.

I recently finished my Ph.D. (September 2011) in the Genetics Graduate Group at UC Davis as a member of the Jasieniuk lab in the Department of Plant Sciences. My dissertation research was on the evolution of invasiveness in blackberry (Rubus), particularly relating to hybridization and asexual reproduction. I have also written software in R for the analysis of polyploid data.

I graduated from Dartmouth College in 2004, having majored in Genetics, Cell & Developmental Biology and minored in Chemistry. From June 2002 to June 2004 I did my undergraduate thesis research in Thomas Jack's lab, where I worked on developing knockout mutants for a gene family putatively involved in floral development in Arabidopsis.

From November 2004 - July 2006 I worked at the Grape Genetics Research Unit in Geneva, NY. Under the direction of Amanda Garris, I worked on gene cloning and QTL mapping towards an understanding of light detection and winter dormancy in grapevine.

Contact: email

ResearcherID

Academia.edu profile

Curriculum Vitae

Publications

  • Lindsay V. Clark and Marie Jasieniuk (2011) "POLYSAT: an R package for polyploid microsatellite analysis." Molecular Ecology Resources 11(3):562-566. doi:10.1111/j.1755-0998.2011.02985.x
  • Lindsay V. Clark and Marie Jasieniuk (2012) "Spontaneous hybrids between native and exotic Rubus in the Western United States produce offspring both by apomixis and by sexual recombination." Heredity 109(5):320-328. doi:10.1038/hdy.2012.45
  • Lindsay V. Clark, Katherine J. Evans, and Marie Jasieniuk "Origins and distribution of invasive Rubus fruticosus L. agg. (Rosaceae) clones in the Western United States." Biological Invasions (in press). doi:10.1007/s10530-012-0369-8
  • Amanda Garris, Lindsay Clark, Chris Owens, Steven McKay, James Luby, Kathy Mathiason, and Anne Fennell (2009) "Mapping of Photoperiod-Induced Growth Cessation in the Wild Grape Vitis riparia Michx." Journal of the American Society for Horticultural Science 134:261-272.

Software

polysat: tools for polyploid microsatellite analysis

Handy scripts

Presentations

  • "Using molecular markers to investigate invasive Rubus and genetic diversity of Miscanthus". Invited seminar speaker, Western Kentucky University Biology Department, September 7, 2012.
  • "Genetic diversity and population structure of Miscanthus in Japan" at the 3rd Pan American Congress on Plants and Bioenergy, Champaign, Illinois, June 17, 2012.
  • "Polyploid data analysis, and how to gently transition from software user to software developer" for UC Davis Ecological Genetics grad course, February 28, 2011 PDF
  • “Hybridization of native and invasive blackberries in California” at UC Davis Weed Day, July 17, 2008.

Posters

Awards

  • Plant Sciences Departmental Research Assistantship
  • Jastro-Shields Research Grant
  • Department of Plant Sciences Graduate Student Travel Award
  • California Weed Science Society Scholarship

Teaching experience

  • Associate Instructor, Plant Genetics and Biotechnology Laboratory, UC Davis Department of Plant Sciences, Summer 2009
  • Guest lecturer, Ecological Genetics, UC Davis Ecology Graduate Group, Winter 2011
  • Teaching assistant, Principles of Genetics Laboratory, UC Davis Department of Molecular and Cellular Biology, Winter 2010
  • Teaching assistant, Genes and Gene Expression, UC Davis Department of Molecular and Cellular Biology, Fall 2009, Winter 2011
  • Teaching assistant, Human Heredity, UC Davis Department of Molecular and Cellular Biology, Spring 2007, Spring 2009
  • Teaching assistant, Plant Genetics and Biotechnology Laboratory, UC Davis Department of Plant Sciences, Winter 2009
  • Undergraduate teaching assistant, Molecular Biology Lab, Dartmouth College Department of Biological Sciences, Summer 2003

Protocols

Personal tools