9 Works

A semi-parametric Bayesian approach for detection of gene expression heterosis with RNA-seq data

Ran Bi & Peng Liu
Heterosis refers to the superior performance of a hybrid offspring over its two inbred parents. Although heterosis has been widely observed in agriculture, its molecular mechanism is not well studied. Recent advances in high-throughput genomic technologies such as RNA sequencing (RNA-seq) facilitate the investigation of heterosis at the gene expression level. However, it is challenging to identify genes exhibiting heterosis using RNA-seq data because high-dimension of hypotheses tests are conducted with limited sample size. Furthermore,...

A semi-parametric Bayesian approach for detection of gene expression heterosis with RNA-seq data

Ran Bi & Peng Liu
Heterosis refers to the superior performance of a hybrid offspring over its two inbred parents. Although heterosis has been widely observed in agriculture, its molecular mechanism is not well studied. Recent advances in high-throughput genomic technologies such as RNA sequencing (RNA-seq) facilitate the investigation of heterosis at the gene expression level. However, it is challenging to identify genes exhibiting heterosis using RNA-seq data because high-dimension of hypotheses tests are conducted with limited sample size. Furthermore,...

Raw genotyped total called structural variant (SV)

Kittikun Songsomboon, Zachary Brenton, James Heuser, Stephen Kresovich, Nadia Shakoor & Elizabeth Cooper
Genomic structural mutations especially deletion are an important source of variation in many species and can play key roles in phenotypic diversification and evolution. Previous work in many plant species, including some crops, has identified multiple instances of structural variations (SVs) occurring in or near genes related to stress response and disease resistance, suggesting a possible role for SVs in local adaptation. Sorghum (Sorghum bicolor (L.) Moench) is one of the most widely grown cereal...

Improving cassava bacterial blight resistance by editing the epigenome

Kira Veley, kiona elliott, Greg Jensen, Zhenhui Zhong, Suhua Feng, Marisa Yoder, Kerrigan Gilbert, Jeffrey C. Berry, Basudev Ghoshal, Javier Gallego-Bartolomé, James Carrington, Steven E. Jacobsen & Rebecca Bart
The zipped folder contains all of the data used in figures for Veley et al. organized by figure number.

Value Function Guided Subgroup Identification via Gradient Tree Boosting: A Framework to Handle Multiple Outcomes for Optimal Treatment Recommendation

Pingye Zhang, Peng Liu, Junshui Ma & Yue Shentu
In randomized clinical trials, there has been an increasing interest in identifying subgroups with heterogeneous responses to study treatment based on baseline patient characteristics. Even though the benefit risk assessment of any patient population or subgroups is almost always a multi-facet consideration, the statistical literature of subgroup identification has largely been limited to a single clinical outcome. In the article, we propose a nonparametric method that searches for subgroup membership scores by maximizing a value...

Molecular systematics of the tribe Physarieae (Brassicaceae) based on the nuclear ITS, Luminidependens, and chloroplast ndhF: Sequence alignments, trees, and supplemental figures

Sara Fuentes-Soriano & Elizabeth Kellogg
Physarieae is a small tribe of herbaceous annual and woody perennial mustards that are mostly endemic to North America, with its members including a large amount of variation in floral, fruit and chromosomal variation. Building on a previous study of Physarieae based on morphology and ndhF plastid DNA, we reconstructed the evolutionary history of the tribe using new sequence data from two nuclear markers, and compared the new topologies against previously published cpDNA-based phylogenetic hypotheses....

Correlation and co-localization of QTLs for stomatal density, canopy temperature, and productivity with and without drought stress in Setaria

Parthiban Thathapalli Prakash, Darshi Banan, Rachel Paul, Maximilian Feldman, Dan Xie, Luke Freyfogle, Ivan Baxter & Andrew Leakey
Mechanistic modeling indicates that stomatal conductance could be reduced to improve water use efficiency (WUE) in C4 crops. Genetic variation in stomatal density and canopy temperature was evaluated in the model C4 genus, Setaria. Recombinant inbred lines (RILs) derived from a Setaria italica × Setaria viridis cross were grown with ample or limiting water supply under field conditions in Illinois. An optical profilometer was used to rapidly assess stomatal patterning, and canopy temperature was measured...

Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus

Kevin Bird, Chad Niederhuth, Shujun Ou, Malia Gehan, J. Chris Pires, Zhiyong Xiong, Robert VanBuren & Patrick Edger
Interspecific hybridization and allopolyploidization merge evolutionarily distinct parental genomes (subgenomes) into a single nucleus. A frequent observation is that one subgenome is "dominant” over the other subgenome, having a greater number of retained genes and being more highly expressed. Which subgenome becomes dominantly expressed in allopolyploids remains poorly understood. Here we “replayed the evolutionary tape” with six isogenic resynthesized Brassica napus (rapeseed) allopolyploid lines and investigated subgenome dominance patterns over the first ten generations post...

Value Function Guided Subgroup Identification via Gradient Tree Boosting: a Framework to Handle Multiple Outcomes for Optimal Treatment Recommendation

Pingye Zhang, Peng Liu, Junshui Ma & Yue Shentu
In randomized clinical trials, there has been an increasing interest in identifying subgroups with heterogeneous responses to study treatment based on baseline patient characteristics. Even though the benefit risk assessment of any patient population or subgroups is almost always a multi-facet consideration, the statistical literature of subgroup identification has largely been limited to a single clinical outcome. In the paper, we propose a nonparametric method that searches for subgroup membership scores by maximizing a value...

Registration Year

  • 2021
    9

Resource Types

  • Dataset
    5
  • Text
    4

Affiliations

  • Donald Danforth Plant Science Center
    9
  • Iowa State University
    5
  • Central South University
    4
  • Jiangsu University of Science and Technology
    4
  • Southern Medical University
    4
  • Shenzhen University
    4
  • University of Wisconsin–Madison
    4
  • Sheng Jing Hospital
    4
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    4
  • Kyoto University
    4