Bioinformatics software and methodology
Lindsay V. Clark, Wittney Mays, Alexander E. Lipka, and Erik J. Sacks (2022) “A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing data from highly duplicated genomes.” BMC Bioinformatics 23: 101. doi:10.1186/s12859-022-04635-9
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 and Andrea Drauch Schreier (2017) “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 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 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
Joyce N. Njuguna, Lindsay V. Clark, Alexander E. Lipka, Kossonou G. Anzoua, Larisa Bagmet, Pavel Chebukin, Maria S. Dwiyanti, Elena Dzyubenko, Nicolay Dzyubenko, Bimal Kumar Ghimire, Xiaoli Jin, Douglas A. Johnson, Jens Bonderup Kjeldsen, Hironori Nagano, Ivone de Bem Oliveira, Junhua Peng, Karen Koefoed Petersen, Andrey Sabitov, Eun Soo Seong, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao, Patricio Munoz, Stephen P. Long, and Erik J. Sacks (2023) “Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids.” The Plant Genome 16(4): e20401. doi:10.1002/tpg2.20401
Jean-Tristan Brandenburg, Lindsay Clark, Gerrit Botha, Sumir Panji, Shakuntala Baichoo, Christopher Fields, Scott Hazelhurst (2022) “H3AGWAS: A portable workflow for genome-wide association studies.” BMC Bioinformatics 23: 498. doi:10.1186/s12859-022-05034-w
Lavanya Singh, James Emmanuel San, Houriiyah Tegally, Pius M. Brzoska, Ugochukwu J. Anyaneji, Eduan Wilkinson, Lindsay Clark, Jennifer Giandhari, Sureshne Pillay, Richard J. Lessels, Darren Patrick Martin, Manohar Furtado, Anmol M. Kiran, Tulio de Oliveira (2022) “Targeted Sanger sequencing to recover key mutations in SARS-CoV-2 variants genome assemblies produced by next generation sequencing.” Microbial Genomics 8(3). doi:10.1099/mgen.0.000774
Seattle Children’s Research Institute
Angela M. Bard, Lindsay V. Clark, Erdal Cosgun, Kimberly A. Aldinger, Andrew Timms, Lely A. Quina, Juan M. Lavista Ferres, David Jardine, Elisabeth A. Haas, Tatiana M Becker, Chelsea M Pagan, Avni Santani, Diego Martinez, Soumitra Barua, Zakkary McNutt, Addie Nesbitt, Ed Mitchell, Jan-Marino Ramirez (in press) “Known pathogenic gene variants and new candidates detected in Sudden Unexpected Infant Death (SUID) using Whole Genome Sequencing (WGS).” American Journal of Medical Genetics Part A.
Weston T. Powell, Lindsay V. Clark, Lucille M. Rich, Elizabeth R. Vanderwall, Camille Gates, Maria P. White, and Jason S. Debley (in press) “Altered circadian gene expression in primary human airway epithelial cells in asthma.” ERJ Open Research.
HPCBio projects, Roy J. Carver Biotechnology Center
Paterne A. Agre, Lindsay V. Clark, Ana Luisa Garcia-Oliveira, Rajaguru Bohar, Patrick Adebola, Robert Asiedu, Ryohei Terauchi, and Asrat Asfaw (2024) “Identification of diagnostic KASP-SNP markers for routine breeding activities in yam (Dioscorea spp.).” The Plant Genome. doi:10.1002/tpg2.20419
Sean T. Bresnahan, Ellen Lee, Lindsay V. Clark, Rong Ma, Juliana Rangel, Christina M. Grozinger, and Hongmei Li-Byarlay (2023) “Examining parent-of-origin effects on transcription and RNA methylation in mediating aggressive behavior in honey bees (Apis mellifera).” BMC Genomics 24: 315. doi:10.1186/s12864-023-09411-4
Jeremy M. Bingen, Lindsay V. Clark, Mark R. Band, Ilyas Munzier, and Michael Carrithers (2023) “Differential DNA methylation associated with multiple sclerosis and disease modifying treatments in an underrepresented minority population.” Frontiers in Genetics 13. doi:10.3389/fgene.2022.1058817
Elizabeth L. Geary, Patricia M. Oba, Catherine C. Applegate, Lindsay V. Clark, Christopher J. Fields, and Kelly S. Swanson (2022) “Effect of a mildly cooked human-grade dog diet on gene expression, skin and coat health measures, and fecal microbiota of healthy adult dogs.” Journal of Animal Science 100(10): 1-15. doi:10.1093/jas/skac265
Colin Lim, Tristan X. McCallister, Christian Saporito-Magriña, Garrett D. McPheron, Ramya Krishnan, M. Alejandra Zeballos C., Jackson E. Powell, Lindsay V. Clark, Pablo Perez-Pinera, and Thomas Gaj (2022) “CRISPR base editing of cis-regulatory elements enables the perturbation of neurodegeneration-linked genes.” Molecular Therapy (in press). doi:10.1016/j.ymthe.2022.08.008
Shannon E. Finnet, Fei He, Lindsay V. Clark, and Maria Regina Cattai de Godoy (2022) “Functional properties of miscanthus fiber and prebiotic blends in extruded canine diets.” Journal of Animal Science 100(4): skac078. doi:10.1093/jas/skac078
Karen Chiu, Shah Tauseef Bashir, Ahmed Abdel-Hamid, Lindsay Clark, Isaac Cann, Romana Nowak, Jodi Flaws (2022) “Isolation of DiNP-Degrading Microbes from the Mouse Colon and the Influence DiNP Exposure Has on the Microbiota, Intestinal Integrity, and Immune Status of the Colon.” Toxics 10(2): 75. doi:10.3390/toxics10020075
Lauren Marie Reilly, Fei He, Lindsay V. Clark, and Maria Regina Cattai de Godoy (2021) “Longitudinal assessment of taurine and amino acid concentrations in dogs fed a green lentil diet.” Journal of Animal Science 99(11): skab315. doi:10.1093/jas/skab315
Eleonora Gatta, Vikram Saudagar, Jenny Drnevich, Marc Forrest, James Auta, Lindsay Clark, Henry Sershen, Robert Smith, Dennis Grayson, John Davis, and Alessandro Guidotti (2021) “Concordance of immune-related markers in lymphocytes and prefrontal cortex in schizophrenia.” Schizophrenia Bulletin Open 2(1):sgab002. doi:10.1093/schizbullopen/sgab002.
Hongmei Li-Byarlay, Humberto Boncristiani, Gary Howell, Jake Herman, Lindsay Clark, Micheline K. Strand, David Tarpy and Olav Rueppell (2020) “Transcriptomic and Epigenomic Dynamics of Honey Bees in Response to Lethal Viral Infection.” Frontiers in Genetics 11:1056. doi:10.3389/fgene.2020.566320
Miscanthus
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) “Genome‐wide association and genomic prediction for biomass yield in a genetically diverse Miscanthus sinensis germplasm panel phenotyped at five locations in Asia and North America.” GCB Bioenergy 11(8): 988-1007. doi:10.1111/gcbb.12620 Datasets and R Scripts DNA Sequence Data
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 11(10): 1125-1145. doi:10.1111/gcbb.12606 Datasets and R Scripts
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 (2019) “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 124(4): 731-748. doi:10.1093/aob/mcy161. Datasets and R Scripts DNA Sequence data
Lindsay V. Clark, Elena Dzyubenko, Nikolay Dzyubenko, Larisa Bagmet, Andrey Sabitov, Pavel Chebukin, Douglas 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(5): 941-955. doi:10.1093/aob/mcw137 Datasets and R scripts DNA Sequence data
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 66:4213-4225. doi:10.1093/jxb/eru511 Datasets and R scripts DNA Sequence data
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 Datasets and R scripts DNA Sequence data
Sarah Widener, Joyce N. Njuguna, Lindsay V. Clark, Kossonou G. Anzoua, Larisa Bagmet, Pavel Chebukin, Maria S. Dwiyanti, Elena Dzyubenko, Nicolay Dzyubenko, Bimal Kumar Ghimire, Xiaoli Jin, Uffe Jørgensen, Jens Bonderup Kjeldsen, Hironori Nagano, Junhua Peng, Karen Koefoed Petersen, Andrey Sabitov, Eun Soo Seong, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao, Diego Jarquin, Erik Sacks, and Alexander E. Lipka (2024) “Genotype by environment model predictive ability in Miscanthus.” GCB Bioenergy 16(1):e13113. doi:10.1111/gcbb.13113
Joyce N. Njuguna, Lindsay V. Clark, Alexander E. Lipka, Kossonou G. Anzoua, Larisa Bagmet, Pavel Chebukin, Maria S. Dwiyanti, Elena Dzyubenko, Nicolay Dzyubenko, Bimal Kumar Ghimire, Xiaoli Jin, Douglas A. Johnson, Hironori Nagano, Junhua Peng, Karen Koefoed Petersen, Andrey Sabitov, Eun Soo Seong, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao, Stephen P. Long, and Erik J. Sacks (2023) “Genome-wide association and genomic prediction for yield and component traits of Miscanthus sacchariflorus.” GCB Bioenergy 15(11):1355-1372. doi:10.1111/gcbb.13097
Joyce N. Njuguna, Lindsay V. Clark, Kossonou G. Anzoua, Larisa Bagmet, Pavel Chebukin, Maria S. Dwiyanti, Elena Dzyubenko, Nicolay Dzyubenko, Bimal Kumar Ghimire, Xiaoli Jin, Douglas A. Johnson, Uffe Jørgensen, Jens Bonderup Kjeldsen, Hironori Nagano, Junhua Peng, Karen Koefoed Petersen, Andrey Sabitov, Eun Soo Seong, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao, Stephen P. Long, and Erik J. Sacks (2023) “Biomass yield in a genetically diverse Miscanthus sacchariflorus germplasm panel phenotyped at five locations in Asia, North America and Europe.” GCB Bioenergy 15(5):642-662. doi:10.1111/GCBB.13043
Zhihui Guo, Meilan Xu, Hironori Nagano, Lindsay V. Clark, Erik J. Sacks, and Toshihiko Yamada (2021) “Characterization of the Ghd8 Flowering Time Gene in a Mini-Core Collection of Miscanthus sinensis.” Genes 12(2):288. doi:10.3390/genes12020288
Hongxu Dong, Lindsay V Clark, Xiaoli Jin, Kossonou Anzoua, Larisa Bagmet, Pavel Chebukin, Elena Dzyubenko, Nicolay Dzyubenko, Bimal Kumar Ghimire, Kweon Heo, Douglas A Johnson, Hironori Nagano, Andrey Sabitov, Junhua Peng, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao, Stephen P Long, and Erik J Sacks (2021) “Managing flowering time in Miscanthus and sugarcane to facilitate intra- and intergeneric crosses.” PLoS ONE 16(1): e0240390. doi:10.1371/journal.pone.0240390
Therese Mitros, Adam M. Session, Brandon T. James, Guohong Albert Wu, Mohammad B. Belaffif, Lindsay V. Clark, Shengqiang Shu, Hongxu Dong, Adam Barling, Jessica R. Holmes, Jessica E. Mattick, Jessen V. Bredeson, Siyao Liu, Kerrie Farrar, Katarzyna Głowacka, Stanisław Jeżowski, Kerrie Barry, Won Byoung Chae, John A. Juvik, Justin Gifford, Adebosola Oladeinde, Toshihiko Yamada, Jane Grimwood, Nicholas H. Putnam, Jose De Vega, Susanne Barth, Manfred Klaas, Trevor Hodkinson, Laigeng Li, Xiaoli Jin, Junhua Peng, Chang Yeon Yu, Kweon Heo, Ji Hye Yoo, Bimal Kumar Ghimire, Iain S. Donnison, Jeremy Schmutz, Matthew E. Hudson, Erik J. Sacks, Stephen P. Moose, Kankshita Swaminathan, and Daniel S. Rokhsar (2020) Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nature Communications 11:5442. doi:10.1038/s41467-020-18923-6
Marcus O. Olatoye, Lindsay V. Clark, Nicholas R. Labonte, Hongxu Dong, Maria S. Dwiyanti, Kossonou G. Anzoua, Joe E. Brummer, Bimal K. Ghimire, Elena Dzyubenko, Nikolay Dzyubenko, Larisa Bagmet, Andrey Sabitov, Pavel Chebukin, Katarzyna Głowacka, Kweon Heo, Xiaoli Jin, Hironori Nagano, Junhua Peng, Chang Y. Yu, Ji H. Yoo, Hua Zhao, Stephen P. Long, Toshihiko Yamada, Erik J. Sacks and Alexander E. Lipka (2020) “Training Population Optimization for Genomic Selection in Miscanthus.” G3, 10(7):2465-2476. doi:10.1534/g3.120.401402
Marcus O. Olatoye, Lindsay V. Clark, Jianping Wang, Xiping Yang, Toshihiko Yamada, Erik J. Sacks, and Alexander E. Lipka (2019) “Evaluation of genomic selection and marker-assisted selection in Miscanthus and energycane.” Molecular Breeding, 39:171. doi:10.1007/s11032-019-1081-5
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, Lindsay V. Clark, Alexander E. Lipka, Joe E. Brummer, Katarzyna Głowacka, Megan C. Hall, Kweon Heo, Xiaoli Jin, Junhua Peng, Toshihiko Yamada, Bimal Kumar Ghimire, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao, Stephen P. Long, and Erik J. Sacks (2019) “Winter hardiness of Miscanthus (III): Genome‐wide association and genomic prediction for overwintering ability in Miscanthus sinensis.” GCB Bioenergy 11(8): 930-955. doi:10.1111/gcbb.12615
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 66:4227-4237. 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
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. doi:10.2135/cropsci2014.12.0808
Blackberry, Grape, Rice
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 Cited in the Flora of North America
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 Datasets and R scripts: doi:10.5061/dryad.m466f Cited in the Flora of North America
Marlee R. Labroo, Lindsay V. Clark, Shilai Zhang, Fengyi Hu, Dayun Tao, Ruaraidh Sackville Hamilton, and Erik J. Sacks (2023) “Solving the mystery of Obake rice in Africa: Population structure analyses of Oryza longistaminata reveal three genetic groups and evidence of both recent and ancient introgression with O. sativa.” Frontiers in Plant Science 14. fpls.2023.1278196
Sandeep A. Sakhale, Shailesh Yadav, Lindsay V. Clark, Alexander E. Lipka, Arvind Kumar, and Erik J. Sacks (2023) “Genome-wide association analysis for emergence pf deeply sown rice (Oryza sativa) reveals novel aus-specific phytohormone candidate genes for adaptation to dry-direct seeding in the field.” Frontiers in Plant Science 14. doi:10.3389/fpls.2023.1172816
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. doi:10.21273/JASHS.134.2.261