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Articles 1 - 5 of 5
Full-Text Articles in Genetics and Genomics
Root Hair Single Cell Type Specific Profiles Of Gene Expression And Alternative Polyadenylation Under Cadmium Stress, Jingyi Cao, Congting Ye, Guijie Hao, Carole Dabney-Smith, Arthur G. Hunt, Qingshun Q. Li
Root Hair Single Cell Type Specific Profiles Of Gene Expression And Alternative Polyadenylation Under Cadmium Stress, Jingyi Cao, Congting Ye, Guijie Hao, Carole Dabney-Smith, Arthur G. Hunt, Qingshun Q. Li
Plant and Soil Sciences Faculty Publications
Transcriptional networks are tightly controlled in plant development and stress responses. Alternative polyadenylation (APA) has been found to regulate gene expression under abiotic stress by increasing the heterogeneity at mRNA 3′-ends. Heavy metals like cadmium pollute water and soil due to mining and industry applications. Understanding how plants cope with heavy metal stress remains an interesting question. The Arabidopsis root hair was chosen as a single cell model to investigate the functional role of APA in cadmium stress response. Primary root growth inhibition and defective root hair morphotypes were observed. Poly(A) tag (PAT) libraries from single cell types, i.e., root …
Incorporating Pathway Information Into Feature Selection Towards Better Performed Gene Signatures, Suyan Tian, Chi Wang, Bing Wang
Incorporating Pathway Information Into Feature Selection Towards Better Performed Gene Signatures, Suyan Tian, Chi Wang, Bing Wang
Biostatistics Faculty Publications
To analyze gene expression data with sophisticated grouping structures and to extract hidden patterns from such data, feature selection is of critical importance. It is well known that genes do not function in isolation but rather work together within various metabolic, regulatory, and signaling pathways. If the biological knowledge contained within these pathways is taken into account, the resulting method is a pathway-based algorithm. Studies have demonstrated that a pathway-based method usually outperforms its gene-based counterpart in which no biological knowledge is considered. In this article, a pathway-based feature selection is firstly divided into three major categories, namely, pathway-level selection, …
Feature Selection For Longitudinal Data By Using Sign Averages To Summarize Gene Expression Values Over Time, Suyan Tian, Chi Wang
Feature Selection For Longitudinal Data By Using Sign Averages To Summarize Gene Expression Values Over Time, Suyan Tian, Chi Wang
Biostatistics Faculty Publications
With the rapid evolution of high-throughput technologies, time series/longitudinal high-throughput experiments have become possible and affordable. However, the development of statistical methods dealing with gene expression profiles across time points has not kept up with the explosion of such data. The feature selection process is of critical importance for longitudinal microarray data. In this study, we proposed aggregating a gene’s expression values across time into a single value using the sign average method, thereby degrading a longitudinal feature selection process into a classic one. Regularized logistic regression models with pseudogenes (i.e., the sign average of genes across time as predictors) …
Substantial Red Wolf Genetic Ancestry Persists In Wild Canids Of Southwestern Louisiana, Jennifer R. Adams, John J. Cox, Lisette P. Waits
Substantial Red Wolf Genetic Ancestry Persists In Wild Canids Of Southwestern Louisiana, Jennifer R. Adams, John J. Cox, Lisette P. Waits
Forestry and Natural Resources Faculty Publications
Concerns over red wolf (Canis rufus) extinction caused by hybridization with coyotes (C. latrans) led to the capture and removal of remnant wild wolves from southwestern Louisiana and southeastern Texas, United States, during the 1970s. Here we show that despite decades of unmitigated hybridization, and declaration of endangered red wolves as functionally extinct in the wild, red wolf mitochondrial or nuclear DNA ancestry persists in ∼55% of contemporary wild canids sampled in southwestern Louisiana. Surprisingly, one individual had 78–100% red wolf ancestry, which is within the range for 75% red wolf, red wolf backcross, or putative …
Genome-Wide Association Studies For Yield-Related Traits In Soft Red Winter Wheat Grown In Virginia, Brian P. Ward, Gina Brown-Guedira, Frederic L. Kolb, David A. Van Sanford, Priyanka Tyagi, Clay H. Sneller, Carl A. Griffey
Genome-Wide Association Studies For Yield-Related Traits In Soft Red Winter Wheat Grown In Virginia, Brian P. Ward, Gina Brown-Guedira, Frederic L. Kolb, David A. Van Sanford, Priyanka Tyagi, Clay H. Sneller, Carl A. Griffey
Plant and Soil Sciences Faculty Publications
Grain yield is a trait of paramount importance in the breeding of all cereals. In wheat (Triticum aestivum L.), yield has steadily increased since the Green Revolution, though the current rate of increase is not forecasted to keep pace with demand due to growing world population and increasing affluence. While several genome-wide association studies (GWAS) on yield and related component traits have been performed in wheat, the previous lack of a reference genome has made comparisons between studies difficult. In this study, a GWAS for yield and yield-related traits was carried out on a population of 322 soft red …