User:Lindsay V. Clark

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[[Image:LindsayClarkface2.jpg|thumb|left|Lindsay V. Clark]]
[[Image:LindsayClarkface2.jpg|thumb|left|Lindsay V. Clark]]
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'''Postdoctoral Research Associate, Plant Population Genetics'''
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'''Research Specialist, Plant Population Genetics'''
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'''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 ==
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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, 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.
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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.
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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''.
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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.
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[[Image:plantintube.JPG|200 px|right]]
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Contact: [[Special:Emailuser/Lindsay_V._Clark|email]]
Contact: [[Special:Emailuser/Lindsay_V._Clark|email]]
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[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/.
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[http://ucdavis.academia.edu/LindsayClark Academia.edu profile]
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[[Media:lvclark_CV_2011_December13.pdf|Curriculum Vitae]]
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== Publications ==
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* 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]]
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* 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]]
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* 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]]
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*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.
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== Software ==
== Software ==
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[[polysat]]: tools for polyploid microsatellite analysis
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'''[https://github.com/lvclark/polysat/wiki polysat]: tools for polyploid microsatellite analysis'''
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===Handy scripts===
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Convert TASSEL's HapMap format to adegenet's genind format: [[Media:hapMap2genind.R.txt]]
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Convert adegenet's genind format to STRUCTURE format: [[Media:genind2structure.R.txt]]
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==Presentations==
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*"Using molecular markers to investigate invasive ''Rubus'' and genetic diversity of ''Miscanthus''".  Invited seminar speaker, Western Kentucky University Biology Department, September 7, 2012.
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*[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.
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*"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]]
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*“Hybridization of native and invasive blackberries in California” at UC Davis Weed Day, July 17, 2008.
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==Posters==
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*[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]]
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*[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]]
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*[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.
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==Awards==
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*Plant Sciences Departmental Research Assistantship
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*Jastro-Shields Research Grant
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*Department of Plant Sciences Graduate Student Travel Award
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*California Weed Science Society Scholarship
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==Teaching experience==
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'''[https://github.com/lvclark/tagdigger tagdigger]: Search for tags in FASTQ files from GBS or RAD-seq
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*Associate Instructor, Plant Genetics and Biotechnology Laboratory, UC Davis Department of Plant Sciences, Summer 2009
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*Guest lecturer, Ecological Genetics, UC Davis Ecology Graduate Group, Winter 2011
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*Teaching assistant, Principles of Genetics Laboratory, UC Davis Department of Molecular and Cellular Biology, Winter 2010
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*Teaching assistant, Genes and Gene Expression,  UC Davis Department of Molecular and Cellular Biology, Fall 2009, Winter 2011
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*Teaching assistant, Human Heredity, UC Davis Department of Molecular and Cellular Biology, Spring 2007, Spring 2009
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*Teaching assistant, Plant Genetics and Biotechnology Laboratory, UC Davis Department of Plant Sciences, Winter 2009
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*Undergraduate teaching assistant, Molecular Biology Lab, Dartmouth College Department of Biological Sciences, Summer 2003
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==Protocols==
==Protocols==

Current revision

Lindsay V. Clark
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

Personal tools