Difference between revisions of "User:Lindsay V. Clark"

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[[Image:LindsayClarkface2.jpg|thumb|left|Lindsay V. Clark]]
 
[[Image:LindsayClarkface2.jpg|thumb|left|Lindsay V. Clark]]
  
'''Postdoctoral Research Associate, Plant Population Genetics'''
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'''Research Specialist, Plant Population Genetics'''
  
'''Energy Biosciences Institute'''
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'''Department of Crop Sciences'''
  
 
'''University of Illinois, Urbana-Champaign'''
 
'''University of Illinois, Urbana-Champaign'''
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== Research and Personal Info ==
 
== 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 [http://cropsci.illinois.edu/directory/esacks Dr. Erik Sacks] at the University of Illinois, Urbana-Champaign.
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I am a postdoc studying the genetic diversity and population structure of ''Miscanthus'', a perennial grass being developed as a bioenergy crop, in the lab of [http://cropsci.illinois.edu/directory/esacks Dr. Erik Sacks] at the University of Illinois, Urbana-Champaign.
 
 
I recently finished my Ph.D. (September 2011) in the [[UC Davis Genetics Graduate Group|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 [http://www.dartmouth.edu/~tjack/ 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 [http://www.ars.usda.gov/Main/site_main.htm?modecode=19-10-10-00 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.
 
 
 
[[Image:plantintube.JPG|200 px|right]]
 
  
 
Contact: [[Special:Emailuser/Lindsay_V._Clark|email]]
 
Contact: [[Special:Emailuser/Lindsay_V._Clark|email]]
  
[http://www.researcherid.com/rid/B-3165-2008 ResearcherID]
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This wiki page used to be my personal homepagePlease visit my new website at https://sites.google.com/site/lindsayvclarkgenetics/.
 
 
[http://ucdavis.academia.edu/LindsayClark Academia.edu profile]
 
 
 
[[Media:lvclark_CV_2011_December13.pdf|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) [http://journal.ashspublications.org/cgi/content/abstract/134/2/261 "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 ==
 
== Software ==
[[polysat]]: tools for polyploid microsatellite analysis
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'''[https://github.com/lvclark/polysat/wiki polysat]: tools for polyploid microsatellite analysis'''
 
 
===Handy scripts===
 
*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==
 
*"Using molecular markers to investigate invasive ''Rubus'' and genetic diversity of ''Miscanthus''".  Invited seminar speaker, Western Kentucky University Biology Department, September 7, 2012.
 
*[http://conferences.igb.illinois.edu/panamerican/sites/conferences.igb.illinois.edu.panamerican/files/u4/Clark_%20Bioenergy%20Congress%20presentation%202012.pdf "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 [[Media:LVC_PHR242_110228.pdf | PDF]]
 
*“Hybridization of native and invasive blackberries in California” at UC Davis Weed Day, July 17, 2008.
 
 
 
==Posters==
 
*[http://www.intl-pag.org/19/abstracts/P03b_PAGXIX_149.html "Microsatellites distinguish sexual vs. apomictic reproduction in spontaneous ''Rubus'' hybrids"] at Plant and Animal Genome XIX, January 15-19, 2011. [[Media:LVCpag2011.pdf | PDF]]
 
*[http://www.intl-pag.org/18/abstracts/P03a_PAGXVIII_125.html "Hybridization Between Native And Introduced ''Rubus'' In California And The Pacific Northwest"] at Plant and Animal Genome XVIII, January 9-13, 2010. [[Media:LVCpag2010.pdf | PDF]]
 
*[http://www.cal-ipc.org/symposia/archive/pdf/2008/posterClark.pdf “Hybridization between invasive and native blackberries (''Rubus'') in California”] at California Invasive Plant Council Symposium, October 2-4, 2008.
 
 
 
==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==
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'''[https://github.com/lvclark/tagdigger tagdigger]: Search for tags in FASTQ files from GBS or RAD-seq
*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==
 
==Protocols==

Latest revision as of 16:05, 1 November 2015

Lindsay V. Clark

Research Specialist, Plant Population Genetics

Department of Crop Sciences

University of Illinois, Urbana-Champaign

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, in the lab of Dr. Erik Sacks at the University of Illinois, Urbana-Champaign.

Contact: email

This wiki page used to be my personal homepage. Please visit my new website at https://sites.google.com/site/lindsayvclarkgenetics/.

Software

polysat: tools for polyploid microsatellite analysis

tagdigger: Search for tags in FASTQ files from GBS or RAD-seq

Protocols