Lindsay V. Clark

Research Specialist

Education

  • Bachelor of Arts, Genetics, Cell & Developmental Biology, Dartmouth College, 2004
  • Doctor of Philosophy, Genetics, University of California - Davis, 2011

Selected Articles in Journals

  • Lindsay V. Clark, Alexander E. Lipka, and Erik J. Sacks (2019) "polyRAD: Genotype calling with uncertainty from sequencing data in polyploids and diploids." G3 9(3) 663-673. doi:10.1534/g3.118.200913
  • Lindsay V. Clark, Maria S. Dwiyanti, Kossonou G. Anzoua, Joe E. Brummer, Bimal Kumar Ghimire, Katarzyna Głowacka, Megan Hall, Kweon Heo, Xiaoli Jin, Alexander E. Lipka, Junhua Peng, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao, Stephen P. Long, and Erik J. Sacks (2019) "Biomass yield in a genetically diverse Miscanthus sinensis germplasm panel evaluated at five locations revealed individuals with exceptional potential." GCB Bioenergy. doi:10.1111/gcbb.12606
  • Lindsay V. Clark, Xiaoli Jin, Karen K. Petersen, Kossanou G. Anzoua, Larissa Bagmet, Pavel Chebukin, Martin Deuter, Elena Dzyubenko, Nicolay Dzyubenko, Kweon Heo, Douglas A. Johnson, Uffe Jorgensen, Jens B. Kjeldsen, Hironori Nagano, Junhua Peng, Andrey Sabitov, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Stephen P. Long, and Erik J. Sacks (2018) "Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid M. sinensis, and diversity centered around the Yellow Sea." Annals of Botany. doi:10.1093/aob/mcy161.
  • Lindsay V. Clark and Erik J. Sacks (2016) TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data. Source Code for Biology and Medicine 11:11. DOI: 10.1186/s13029-016-0057-7
  • Lindsay V. Clark and Andrea Drauch Schreier (2016) Resolving microsatellite genotype ambiguity in populations of allopolyploid and diploidized autopolyploid organisms using negative correlations between allelic variables. Molecular Ecology Resources 17(5): 1090-1103. DOI: 10.1111/1755-0998.12639
  • Lindsay V. Clark, Elena Dzyubenko, Nikolay Dzyubenko, Larisa Bagmet, Andrey Sabitov, Pavel Chebukin, Doug A. Johnson, Jens Bonderup Kjeldsen, Karen Koefoed Petersen, Uffe Jørgensen, Ji Hye Yoo, Kweon Heo, Chang Yeon Yu, Hua Zhao, Xiaoli Jin, Junhua Peng, Toshihiko Yamada and Erik J. Sacks (2016) Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia. Annals of Botany 118:941-955. DOI: 10.1093/aob/mcw137
  • 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 66(14):4213-4225.
  • 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.
  • 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.
  • Lindsay V. Clark and Marie Jasieniuk (2011) "POLYSAT: an R package for polyploid microsatellite analysis." Molecular Ecology Resources 11(3):562-566.
  • 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.
  • 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.
  • Clifton-Brown, J. C., Harfouche, A., Casler, M. D., Jones, H. D., Macalpine, W. J., Murphy-Bokern, D., … Lewandowski, I. (2019). "Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow, and poplar." GCB Bioenergy, 11(1):118–151. doi:10.1111/gcbb.12566
  • Hongxu Dong, Siyao Liu, Lindsay V. Clark, Shailendra Sharma, Justin M. Gifford, John A. Juvik, Alexander E. Lipka, and Erik J. Sacks (2019) "Winter hardiness of Miscanthus (II): Genetic mapping for overwintering ability and adaptation traits in three interconnected Miscanthus populations." GCB Bioenergy. doi:10.1111/gcbb.12587
  • Hongxu Dong, Siyao Liu, Lindsay V. Clark, Shailendra Sharma, Justin M. Gifford, John A. Juvik, Alex E. Lipka, and Erik J. Sacks (2018) "Genetic mapping of biomass yield in three interconnected Miscanthus populations." GCB Bioenergy 10(3): 165-185. doi:10.1111/gcbb.12472.
  • Ji Hye Yoo, Eun Soo Seong, Bimal Kumar Ghimere, Kweon Heo, Xiaoli Jin, Toshihiko Yamada, Lindsay V. Clark, Erik J. Sacks, and Chang Yeon Yu (2018) "Establishment of Miscanthus sinensis with decreased lignin biosynthesis by Agrobacterium-mediated transformation using antisense COMT gene." Plant Cell, Tissue and Organ Culture 133(3):359-369. doi:10.1007/s11240-018-1389-6
  • Siyao Liu, Lindsay V. Clark, Kankshita Swaminathan, Justin M. Gifford, John A. Juvik, Erik J. Sacks (2016) "High density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe." GCB Bioenergy 8(3):616-630. 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 66(14):4227-4237.
  • Christopher M. Kaiser, Lindsay V. Clark, John A. Juvik, Thomas B. Voigt and Erik J. Sacks (2015) "Characterizing a Miscanthus Germplasm Collection for Yield, Yield Components, and Genotype × Environment Interactions" Crop Science 55(5):1978-1994.
  • 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.