Search Results - "Lipka, Alexander"

Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol by Lu, Fei, Lipka, Alexander E, Glaubitz, Jeff, Elshire, Rob, Cherney, Jerome H, Casler, Michael D, Buckler, Edward S, Costich, Denise E

“…Switchgrass (Panicum virgatum L.) is a perennial grass that has been designated as an herbaceous model biofuel crop for the United States of America. To…”
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GAPIT: genome association and prediction integrated tool by LIPKA, Alexander E, FENG TIAN, WANG, Oishan, PEIFFER, Jason, MENG LI, BRADBURY, Peter J, GORE, Michael A, BUCKLER, Edward S, ZHIWU ZHANG

“…Software programs that conduct genome-wide association studies and genomic prediction and selection need to use methodologies that maximize statistical power,…”
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Exploring the relationship between pattern-triggered immunity and quantitative resistance to Xanthomonas vasicola pv. vasculorum in maize by Mullens, Alexander, Lipka, Alexander, Balint-Kurti, Peter, Jamann, Tiffany M

“…Bacterial leaf streak (BLS) of maize is an emerging foliar disease of maize in the Americas. It is caused by the gram-negative non-vascular bacterium…”
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Evaluation of RR‐BLUP Genomic Selection Models that Incorporate Peak Genome‐Wide Association Study Signals in Maize and Sorghum by Rice, Brian, Lipka, Alexander E.

“…Core Ideas Augmenting RR‐BLUP models with peak GWAS markers can hypothetically boost prediction accuracy We conducted a simulation study in maize and sorghum…”
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simplePHENOTYPES: SIMulation of pleiotropic, linked and epistatic phenotypes by Fernandes, Samuel B, Lipka, Alexander E

“…Advances in genotyping and phenotyping techniques have enabled the acquisition of a great amount of data. Consequently, there is an interest in multivariate…”
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Lessons from Dwarf8 on the strengths and weaknesses of structured association mapping by Larsson, Sara J, Lipka, Alexander E, Buckler, Edward S

“…The strengths of association mapping lie in its resolution and allelic richness, but spurious associations arising from historical relationships and selection…”
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Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery by Xu, Xiaosa, Crow, Megan, Rice, Brian R., Li, Forrest, Harris, Benjamin, Liu, Lei, Demesa-Arevalo, Edgar, Lu, Zefu, Wang, Liya, Fox, Nathan, Wang, Xiaofei, Drenkow, Jorg, Luo, Anding, Char, Si Nian, Yang, Bing, Sylvester, Anne W., Gingeras, Thomas R., Schmitz, Robert J., Ware, Doreen, Lipka, Alexander E., Gillis, Jesse, Jackson, David

“…Crop productivity depends on activity of meristems that produce optimized plant architectures, including that of the maize ear. A comprehensive understanding…”
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Multi-Trait Genome-Wide Association Studies Reveal Loci Associated with Maize Inflorescence and Leaf Architecture by Rice, Brian R, Fernandes, Samuel B, Lipka, Alexander E

“…Maize inflorescence is a complex phenotype that involves the physical and developmental interplay of multiple traits. Given the evidence that genes could…”
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polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids by Clark, Lindsay V, Lipka, Alexander E, Sacks, Erik J

“…Low or uneven read depth is a common limitation of genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), resulting in high…”
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GAPIT Version 2: An Enhanced Integrated Tool for Genomic Association and Prediction by Tang, You, Liu, Xiaolei, Wang, Jiabo, Li, Meng, Wang, Qishan, Tian, Feng, Su, Zhongbin, Pan, Yuchun, Liu, Di, Lipka, Alexander E., Buckler, Edward S., Zhang, Zhiwu

“…Core Ideas Genome‐wide association study Genomic prediction Simulation and experimental design Most human diseases and agriculturally important traits are…”
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Accelerating the switchgrass (Panicum virgatum L.) breeding cycle using genomic selection approaches by Lipka, Alexander E, Lu, Fei, Cherney, Jerome H, Buckler, Edward S, Casler, Michael D, Costich, Denise E

“…Switchgrass (Panicum virgatum L.) is a perennial grass undergoing development as a biofuel feedstock. One of the most important factors hindering breeding…”
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Diversifying maize genomic selection models by Rice, Brian R., Lipka, Alexander E.

“…Genomic selection (GS) is one of the most powerful tools available for maize breeding. Its use of genome-wide marker data to estimate breeding values…”
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Interpretation of Manhattan Plots and Other Outputs of Genome-Wide Association Studies by Wang, Jiabo, Yu, Jianming, Lipka, Alexander E, Zhang, Zhiwu

“…With increasing marker density, estimation of recombination rate between a marker and a causal mutation using linkage analysis becomes less important. Instead,…”
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From association to prediction: statistical methods for the dissection and selection of complex traits in plants by Lipka, Alexander E, Kandianis, Catherine B, Hudson, Matthew E, Yu, Jianming, Drnevich, Jenny, Bradbury, Peter J, Gore, Michael A

“…•Controlling for spurious associations in statistical models is essential.•Computationally efficient approaches are critical for large data sets.•Statistical…”
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Optical topometry and machine learning to rapidly phenotype stomatal patterning traits for maize QTL mapping by Xie, Jiayang, Fernandes, Samuel B, Mayfield-Jones, Dustin, Erice, Gorka, Choi, Min, E Lipka, Alexander, Leakey, Andrew D B

“…Stomata are adjustable pores on leaf surfaces that regulate the tradeoff of CO2 uptake with water vapor loss, thus having critical roles in controlling…”
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Regularized multi-trait multi-locus linear mixed models for genome-wide association studies and genomic selection in crops by Lozano, Aurélie C., Ding, Hantian, Abe, Naoki, Lipka, Alexander E.

“…BackgroundWe consider two key problems in genomics involving multiple traits: multi-trait genome wide association studies (GWAS), where the goal is to detect…”
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Genomic prediction of cereal crop architectural traits using models informed by gene regulatory circuitries from maize by Bertolini, Edoardo, Manjunath, Mohith, Ge, Weihao, Murphy, Matthew D, Inaoka, Mirai, Fliege, Christina, Eveland, Andrea L, Lipka, Alexander E

“…Plant architecture is a major determinant of planting density, which enhances productivity potential for crops per unit area. Genomic prediction is well…”
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A foundation for provitamin A biofortification of maize: genome-wide association and genomic prediction models of carotenoid levels by Owens, Brenda F, Lipka, Alexander E, Magallanes-Lundback, Maria, Tiede, Tyler, Diepenbrock, Christine H, Kandianis, Catherine B, Kim, Eunha, Cepela, Jason, Mateos-Hernandez, Maria, Buell, C Robin, Buckler, Edward S, DellaPenna, Dean, Gore, Michael A, Rocheford, Torbert

“…Efforts are underway for development of crops with improved levels of provitamin A carotenoids to help combat dietary vitamin A deficiency. As a global staple…”
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Genome-Wide Analysis of Branched-Chain Amino Acid Levels in Arabidopsis Seeds by Angelovici, Ruthie, Lipka, Alexander E., Deason, Nicholas, Gonzalez-Jorge, Sabrina, Lin, Haining, Cepela, Jason, Buell, Robin, Gore, Michael A., DellaPenna, Dean

“…Branched-chain amino acids (BCAAs) are three of the nine essential amino acids in human and animal diets and are important for numerous processes in…”
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Characterization of Disease Resistance Loci in the USDA Soybean Germplasm Collection Using Genome-Wide Association Studies by Chang, Hao-Xun, Lipka, Alexander E, Domier, Leslie L, Hartman, Glen L

“…Genetic resistance is a key strategy for disease management in soybean. Over the last 50 years, soybean germplasm has been phenotyped for resistance to many…”
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