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== Lindsay V. Clark ==
[[Image:LindsayClarkface2.jpg|thumb|left|Lindsay V. Clark]]


[[Image:OWWEmblem.png|thumb|left|Lindsay V. Clark (an artistic interpretation)]]
'''Postdoctoral Research Associate, Plant Population Genetics'''


Hi, my name is Lindsay V. Clark, and I'm currently at University of California - Davis. I learned about [[OpenWetWare]] from Through a labmate., and I've joined because I am a grad student in Marie Jasieniuk's lab at UC Davis, and would like to be able to edit content on the lab web site..  You can [[Special:Emailuser/Lindsay V. Clark|email me through OpenWetWare]].
'''Department of Crop Sciences'''


== Welcome Lindsay V. Clark! ==
'''University of Illinois, Urbana-Champaign'''


We've automatically generated this User page to help you start contributing to OWW.  You can add information to this page about who you are and what you do so others can find out what you are doing, and maybe even collaborate with you!
== Research and Personal Info ==


The first step is to familiarize yourself with a wiki. See below for some tips to customize this User page. Don't be afraid to edit!  As with all pages on the wiki, all versions are saved so its easy to undo.
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.


When you feel comfortable, we encourage you to remove this introduction and add content about yourself.
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.


== Basic Wiki Instructions ==
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''.


# Start off by clicking the 'edit' button to the right of this section, or at the top of the page.
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.
# Now you should see the text of this section as text within an editor box.  There are several buttons in the editor box, but don't worry about those for now.  Just type something in the box, scroll down to the bottom, and hit the 'Preview' button.
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[[Image:plantintube.JPG|200 px|right]]


== Personal/Lab Info ==
Contact: [[Special:Emailuser/Lindsay_V._Clark|email]]
We have gone ahead and filled in some information you provided us in your membership application at the top of this page.  Please take a moment to embellish this and tell the community a little more about you.  Put links to your lab pages, your projects and your interests.  If you run out of ideas, take a look at some of the other User pages.  For example, check out [[User:Julius_B._Lucks]], [[User:Jason_R._Kelly]] and [[User:Reshma_P._Shetty]]. 


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[https://www.researchgate.net/profile/Lindsay_Clark/?ev=hdr_xprf ResearchGate]


Don't forget to remove these instructions from this page when you are done!
[http://scholar.google.com/citations?user=d2OkHU4AAAAJ&hl=en Google Scholar]
 
[http://www.researcherid.com/rid/B-3165-2008 ResearcherID]
 
[http://ucdavis.academia.edu/LindsayClark Academia.edu profile]
 
[[Media:lvclark_CV_2014_January.pdf|Curriculum Vitae]]
 
== Publications ==
* Lindsay V. Clark and Andrea Drauch Schreier (2015) "Resolving microsatellite genotype ambiguity in populations of allopolyploid and diploidized autopolyploid organisms using negative correlations between alleles." Preprint on bioRxiv.  [[doi:10.1101/020610]]
* Lindsay V. Clark, J. Ryan Stewart, Aya Nishiwaki, Yo Toma, Jens Bonderup Kjeldsen, Uffe Jørgensen, Hua Zhao, Junhua Peng, Ji Hye Yoo, Kweon Heo, Chang Yeon Yu, Toshihiko Yamada, and Erik J. Sacks (2015) "Genetic structure of ''Miscanthus sinensis'' and ''Miscanthus sacchariflorus'' in Japan indicates a gradient of bidirectional but asymmetric introgression."  Journal of Experimental Botany.  [[doi:10.1093/jxb/eru511]]  (Open access.)  [http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP048207 Sequence data]  [http://hdl.handle.net/2142/73212 Datasets and R scripts]
* Lindsay V. Clark, Joe E. Brummer, Katarzyna Głowacka, Megan Hall, Kweon Heo, Junhua Peng, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao, Stephen P. Long, and Erik J. Sacks (2014) "A footprint of past climate change on the diversity and population structure of ''Miscanthus sinensis''." Annals of Botany 114(1):97-107.  [[doi:10.1093/aob/mcu084]].  [http://aob.oxfordjournals.org/cgi/reprint/mcu084%3fijkey=okEMkNdchNlzIsv&keytype=ref Free offprint] [http://www.ncbi.nlm.nih.gov/Traces/sra/?study=SRP026347 Sequence data] [http://hdl.handle.net/2142/49963 Datasets and R scripts]
* Siyao Liu, Lindsay V. Clark, Kankshita Swaminathan, Justin M. Gifford, John A. Juvik, Erik J. Sacks (2015) "High density genetic map of ''Miscanthus sinensis'' reveals inheritance of zebra stripe." GCB Bioenergy. [[doi:10.1111/gcbb.12275]]
* Hironori Nagano, Lindsay V. Clark, Hua Zhao, Junhua Peng, Ji Hye Yoo, Kweon Heo, Chang Yeon Yu, Kossonsou Guillaume Anzoua, Tomoaki Matsuo, Erik J. Sacks, and Toshihiko Yamada (2015) "Contrasting allelic distribution of ''Co''/''Hd1'' homologues in ''Miscanthus sinensis'' from the East Asian mainland and the Japanese archipelago."  Journal of Experimental Botany. [[doi:10.1093/jxb/erv292]]
* Katarzyna Głowacka, Lindsay V. Clark, Shivani Adhikari, Junhua Peng, J. Ryan Stewart, Aya Nishiwaki, Toshihiko Yamada, Uffe Jørgensen, Trevor R. Hodkinson, Justin Gifford, John A. Juvik, Erik J. Sacks (2015) "Genetic variation in ''Miscanthus'' ×''giganteus'' and the importance of estimating genetic distance thresholds for differentiating clones." GCB Bioenergy 7(2):386-404.  [[doi:10.1111/gcbb.12166]]
* 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, Katherine J. Evans, and Marie Jasieniuk (2013) "Origins and distribution of invasive ''Rubus fruticosus'' L. agg. (Rosaceae) clones in the Western United States."  Biological Invasions 15(6):1331-1342. [[doi:10.1007/s10530-012-0369-8]]
* 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]]  (Open access.)  Datasets and R scripts: [[doi:10.5061/dryad.m466f]]
* 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 ==
'''[[polysat]]: tools for polyploid microsatellite analysis'''
 
===Handy R functions===
*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]] - updated version at https://github.com/lvclark/R_genetics_conv
*Convert adegenet's genind format to STRUCTURE format: [[Media:genind2structure.R.txt]] - updated version at https://github.com/lvclark/R_genetics_conv
*Draw an arc on a plot by clicking: [[Media: LVC_describeArc.R.txt]]
*Make a map of USDA plant hardiness zones for any region of the world: [[Media:plotHardinessZones.R.txt]]
 
==Presentations==
*"Diversifying the cultivars of ''Miscanthus'' and Miscane available for bioenergy feedstocks through breeding and genomics" at the 4th Pan-American Congress on Plants and Bioenergy, June 7, 2014.
*"Genetic Diversity and Population Structure of ''Miscanthus sinensis''" at Plant and Animal Genome XXII, January 11, 2014.
*"Genetic diversity of ''Miscanthus'' as a resource for breeding ''Miscanthus'', Miscanes, and Sugarcane" at the Energy Biosciences Institute retreat, July 15, 2013.
*"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==
*"Genome-wide association analysis of flowering time in ''Miscanthus sinensis''" at Plant and Animal Genome XXIII, January 10-14, 2015.
*"Genetic structure of ''Miscanthus sinensis'' from Asia and the United States" at Plant and Animal Genome XXI, January 12-16, 2013.
*"Microsatellites distinguish sexual vs. apomictic reproduction in spontaneous ''Rubus'' hybrids" at Plant and Animal Genome XIX, January 15-19, 2011. [[Media:LVCpag2011.pdf | PDF]]
*"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==
*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==
*[[Sacks:RAD-seq]]
*[[Jasieniuk:Converting_codominant_to_dominant_data]]
*[[Jasieniuk:Implementation_of_a_method_to_calculate_microsatellite_genotype_distance_in_polyploids]]

Revision as of 13:11, 26 July 2015

Lindsay V. Clark

Postdoctoral Research Associate, 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, 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

ResearchGate

Google Scholar

ResearcherID

Academia.edu profile

Curriculum Vitae

Publications

  • Lindsay V. Clark and Andrea Drauch Schreier (2015) "Resolving microsatellite genotype ambiguity in populations of allopolyploid and diploidized autopolyploid organisms using negative correlations between alleles." Preprint on bioRxiv. doi:10.1101/020610
  • Lindsay V. Clark, J. Ryan Stewart, Aya Nishiwaki, Yo Toma, Jens Bonderup Kjeldsen, Uffe Jørgensen, Hua Zhao, Junhua Peng, Ji Hye Yoo, Kweon Heo, Chang Yeon Yu, Toshihiko Yamada, and Erik J. Sacks (2015) "Genetic structure of Miscanthus sinensis and Miscanthus sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression." Journal of Experimental Botany. doi:10.1093/jxb/eru511 (Open access.) Sequence data Datasets and R scripts
  • Lindsay V. Clark, Joe E. Brummer, Katarzyna Głowacka, Megan Hall, Kweon Heo, Junhua Peng, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao, Stephen P. Long, and Erik J. Sacks (2014) "A footprint of past climate change on the diversity and population structure of Miscanthus sinensis." Annals of Botany 114(1):97-107. doi:10.1093/aob/mcu084. Free offprint Sequence data Datasets and R scripts
  • Siyao Liu, Lindsay V. Clark, Kankshita Swaminathan, Justin M. Gifford, John A. Juvik, Erik J. Sacks (2015) "High density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe." GCB Bioenergy. doi:10.1111/gcbb.12275
  • Hironori Nagano, Lindsay V. Clark, Hua Zhao, Junhua Peng, Ji Hye Yoo, Kweon Heo, Chang Yeon Yu, Kossonsou Guillaume Anzoua, Tomoaki Matsuo, Erik J. Sacks, and Toshihiko Yamada (2015) "Contrasting allelic distribution of Co/Hd1 homologues in Miscanthus sinensis from the East Asian mainland and the Japanese archipelago." Journal of Experimental Botany. doi:10.1093/jxb/erv292
  • Katarzyna Głowacka, Lindsay V. Clark, Shivani Adhikari, Junhua Peng, J. Ryan Stewart, Aya Nishiwaki, Toshihiko Yamada, Uffe Jørgensen, Trevor R. Hodkinson, Justin Gifford, John A. Juvik, Erik J. Sacks (2015) "Genetic variation in Miscanthus ×giganteus and the importance of estimating genetic distance thresholds for differentiating clones." GCB Bioenergy 7(2):386-404. doi:10.1111/gcbb.12166
  • 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, Katherine J. Evans, and Marie Jasieniuk (2013) "Origins and distribution of invasive Rubus fruticosus L. agg. (Rosaceae) clones in the Western United States." Biological Invasions 15(6):1331-1342. doi:10.1007/s10530-012-0369-8
  • 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 (Open access.) Datasets and R scripts: doi:10.5061/dryad.m466f
  • 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 R functions

Presentations

  • "Diversifying the cultivars of Miscanthus and Miscane available for bioenergy feedstocks through breeding and genomics" at the 4th Pan-American Congress on Plants and Bioenergy, June 7, 2014.
  • "Genetic Diversity and Population Structure of Miscanthus sinensis" at Plant and Animal Genome XXII, January 11, 2014.
  • "Genetic diversity of Miscanthus as a resource for breeding Miscanthus, Miscanes, and Sugarcane" at the Energy Biosciences Institute retreat, July 15, 2013.
  • "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

  • "Genome-wide association analysis of flowering time in Miscanthus sinensis" at Plant and Animal Genome XXIII, January 10-14, 2015.
  • "Genetic structure of Miscanthus sinensis from Asia and the United States" at Plant and Animal Genome XXI, January 12-16, 2013.
  • "Microsatellites distinguish sexual vs. apomictic reproduction in spontaneous Rubus hybrids" at Plant and Animal Genome XIX, January 15-19, 2011. PDF
  • "Hybridization Between Native And Introduced Rubus In California And The Pacific Northwest" at Plant and Animal Genome XVIII, January 9-13, 2010. 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

  • 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

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