A5033072328- Wheat and Barley Genetics and Pathology
- Genetic Associations and Epidemiology
- Crop Yield and Soil Fertility
- Bioenergy crop production and management
- Genetics and Plant Breeding
- Plant nutrient uptake and metabolism
- COVID-19 Clinical Research Studies
- Epigenetics and DNA Methylation
- Genomic variations and chromosomal abnormalities
- SARS-CoV-2 detection and testing
- Genomics and Phylogenetic Studies
- Genetic Mapping and Diversity in Plants and Animals
- Plant Disease Resistance and Genetics
- SARS-CoV-2 and COVID-19 Research
- Genetic and phenotypic traits in livestock
- Statistical Methods and Inference
- Cancer-related molecular mechanisms research
- Phytase and its Applications
- Health, Environment, Cognitive Aging
- Agriculture, Plant Science, Crop Management
- Genomics and Rare Diseases
- Agricultural Productivity and Crop Improvement
- COVID-19 and healthcare impacts
- Immune cells in cancer
- Skin and Cellular Biology Research
Northwest A&F University
2012-2024
University of Michigan
2017-2022
Zero to Three
2020
Michigan United
2018
Shandong Academy of Agricultural Sciences
2003
Abstract Several biobanks, including UK Biobank (UKBB), are generating large-scale sequencing data. An existing method, SAIGE-GENE, performs well when testing variants with minor allele frequency (MAF) ≤ 1%, but inflation is observed in variance component set-based tests restricting to MAF 0.1% or 0.01%. Here, we propose SAIGE-GENE+ greatly improved type I error control and computational efficiency facilitate rare variant We further show that incorporating multiple cutoffs functional...
There is growing concern of health effects exposure to pollutant mixtures. We initially proposed an Environmental Risk Score (ERS) as a summary measure examine the risk multi-pollutants in epidemiologic research considering only main effects. expand ERS by consideration pollutant-pollutant interactions using modern machine learning methods. illustrate multi-pollutant approaches predicting marker oxidative stress (gamma-glutamyl transferase (GGT)), common disease pathway linking environmental...
In wheat breeding, improved quality traits, including grain and dough rheological properties, have long been a critical goal. To understand the genetic basis of key traits wheat, two single-locus five multi-locus GWAS models were performed for six three properties based on 19, 254 SNPs in 267 bread accessions. As result, 299 quantitative trait nucleotides (QTNs) within 105 regions identified to be associated with these four environments. Of which, 40 core QTN stably detected at least...
As most existing genome-wide association studies (GWASs) were conducted in European-ancestry cohorts, and as the polygenic risk score (PRS) models have limited transferability across ancestry groups, PRS research on non-European-ancestry groups needs to make efficient use of available data until we attain large sample sizes all groups. Here propose a method using transfer learning techniques. Our approach, TL-PRS, uses gradient descent fine-tune baseline model from an group with GWASs...
Evasion of immunosurveillance is critical for cancer initiation and development. The expression “don’t eat me” signals protects cells from being phagocytosed by macrophages, the blockade such demonstrates therapeutic potential restoring susceptibility to macrophage-mediated phagocytosis. However, whether additional self-protective mechanisms play a role against macrophage surveillance remains unexplored. Here, we derived macrophage-resistant model deficient in CD47, major signal, via...
Abstract Background Amino acid transporters (AATs) plays an essential roles in growth and development of plants, including amino acids long-range transport, seed germination, quality formation, responsiveness to pathogenic bacteria abiotic stress by modulating the transmembrane transfer acids. In this study, we performed a genome-wide screening analyze AAT genes foxtail millet ( Setaria italica L.), especially those associated with formation stresses response. Results A total number 94 were...
Compared to C3 species, C4 plants showed higher photosynthetic capacity as well water and nitrogen use efficiency due the presence of pathway. Previous studies have shown that all genes required for pathway exist in genomes species are expressed. In this study, encoding six key enzymes (β-CA, PEPC, ME, MDH, RbcS, PPDK) five important gramineous crops (C4: maize, foxtail millet, sorghum; C3: rice wheat) were systematically identified compared. Based on sequence characteristics evolutionary...
Latent class models have become a popular means of summarizing survey questionnaires and other large sets categorical variables. Often these classes are primary interest to better understand complex patterns in data. Increasingly, latent reified into predictors outcomes interests, treating the most likely as true which an individual belongs even though there is uncertainty membership. This can be viewed form measurement error predictors, leading bias estimates regression parameters...
Abstract With very large sample sizes, population-based cohorts and biobanks provide an exciting opportunity to identify genetic components of complex traits. To analyze rare variants, gene or region-based multiple variant aggregate tests are commonly used increase association test power. However, due the substantial computation cost, existing cannot hundreds thousands samples while accounting for confounders, such as population stratification relatedness. Here we propose a scalable...
Whilst the COVID-19 diagnostic test has a high false-negative rate, not everyone initially negative is re-tested. Michigan Medicine, primary regional centre, provided an ideal setting for studying testing patterns during first wave of pandemic.
Abstract Importance The diagnostic tests for COVID-19 have a high false negative rate, but not everyone with an initial result is re-tested. Michigan Medicine, being one of the primary regional centers accepting cases, provided ideal setting studying repeated testing patterns during first wave pandemic. Objective To identify characteristics patients who underwent and determine if was associated patient downstream outcomes among positive cases. Design This cross-sectional study described...
Abstract As most existing genome-wide association studies (GWAS) were conducted in European ancestry cohorts and as the PRS models have limited transferability across groups, research on non-European groups is negatively impacted. Here we propose a novel method using transfer learning techniques. Our approach, TL-PRS, uses gradient descent to fine-tune baseline model from an group with large sample GWAS dataset of target ancestry. In our application constructing for six quantitative two...
During the breeding progress, screening excellent wheat varieties and lines takes lots of labor time. Moreover, different climatic conditions will bring more complex unpredictable situations. Therefore, selection efficiency needs to be improved by applying proper index. This study evaluates capability CTD as an index for evaluating germplasm in field proposes a strategy efficient application programs. In this study, 186 bread were grown evaluated three continuous years with varied...
Abstract UK Biobank has released the large-scale whole-exome sequencing (WES) data, but best practices remain unclear for rare variant tests, and an existing approach, SAIGE-GENE, can have inflated type I error rates with high computation costs. Here, we propose SAIGE-GENE+ greatly improved control computational efficiency compared to SAIGE-GENE. In analysis of UKBB WES data 30 quantitative 141 binary traits, identified 551 gene-phenotype associations. addition, showed that incorporating...
Abstract Rht14 , was considered as a GA‐responsive dwarf gene in durum wheat ( Triticum L.). The object of this paper is to understand the responsiveness after applying exogenous GA 3 on important morphological and agronomic traits, its potential application breeding. In study, F 2:3 lines, 3:4 lines 4:5 derived from reciprocal crosses between Castelporziano (CP), donor tall cultivar Langdon (L) were used evaluate effects with crucial traits. After plant height more significantly increased...
Testing for SARS-CoV-2 antibodies is commonly used to determine prior COVID-19 infections and gauge levels of infection- or vaccine-induced immunity. Michigan Medicine, a primary regional health center, provided an ideal setting understand serologic testing patterns over time. Between 27 April 2020 3 May 2021, characteristics 10,416 individuals presenting antibody tests (10,932 in total) were collected. Relative the vaccine roll-out date, 14 December 2020, data split into pre- (8026...
This study aims to assess the effectiveness of dwarfing genes Rht-B1a/B1b and Rht-D1a/D1b on phenotype yield spring soft wheat under drought conditions in Kazakhstan.From 2018 2022, laboratory experiments were conducted at S. Seifullin Kazakh Agrotechnical Research University, field trials performed two sites Kazakhstan.The involved phenotypic analysis plant height (PH) coleoptile length (CL), as well measurement.The RhtB1a RhtD1a alleles significantly influenced traits.Hybrids carrying...