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Zhang, Shufan

Publications and source records attributed to Zhang, Shufan.

5 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

MINE: maximally informative next experiment—toward a new GWAS experimental design and methodology

Abstract The computational methodology of Genome Wide Association Studies (GWAS) currently has several limitations: (i) the number of observations (rows) on a quantitative trait tends to be smaller than the number of single nucleotide polymorphisms (SNPs) (columns) in the design matrix; (ii) each SNP is usually modeled separately, failing to acknowledge interaction between each other (ie epistasis); (iii) there is implicit linkage disequilibrium (LD) between neighboring SNPs due to their linkage. To overcome these issues, we developed a tool that uses ensemble methods to fit mixed linear models to GWAS data, and these ensemble methods include the development of a new experimental design approach in GWAS, which uses the resultant models and data to select the next informative experiment over time. This new adaptive and staged approach for GWAS experimental design was developed and tested in a 3 yr adaptive model-guided discovery experiment against a fixed classical design. In Sorghum bicolor a total of 79, 86, and 78 accessions were tested in years 1, 2, and 3, respectively out of 343 accessions available in the Bioenergy Association Panel (BAP) each identified for 232,303 SNPs, 1 every 2–3 kb in the genomes. We demonstrated the feasibility of MINE enacted with 8 people in the field per year over 3 yr vs in 1 large classical design enacted with 20 people in 1 yr. The MINE results for chromosomal regions identified controlling dry weight were confirmed against results from previous sorghum GWAS experiments and 1 large classical design for the BAP panel.

Genetics & Heredity↗
DOE OSTI2025

MINE: a new way to design genetics experiments for discovery

Abstract The Maximally Informative Next Experiment or MINE is a new experimental design approach for experiments, such as those in omics, in which the number of effects or parameters p greatly exceeds the number of samples n (p > n). Classical experimental design presumes n > p for inference about parameters and its application to p > n can lead to over-fitting. To overcome p > n, MINE is an ensemble method, which makes predictions about future experiments from an existing ensemble of models consistent with available data in order to select the most informative next experiment. Its advantages are in exploration of the data for new relationships with n < p and being able to integrate smaller and more tractable experiments to replace adaptively one large classic experiment as discoveries are made. Thus, using MINE is model-guided and adaptive over time in a large omics study. Here, MINE is illustrated in two distinct multiyear experiments, one involving genetic networks in Neurospora crassa and a second one involving a genome-wide association study in Sorghum bicolor as a comparison to classic experimental design in an agricultural setting.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Computer vision models enable mixed linear modeling to predict arbuscular mycorrhizal fungal colonization using fungal morphology

Abstract The presence of Arbuscular Mycorrhizal Fungi (AMF) in vascular land plant roots is one of the most ancient of symbioses supporting nitrogen and phosphorus exchange for photosynthetically derived carbon. Here we provide a multi-scale modeling approach to predict AMF colonization of a worldwide crop from a Recombinant Inbred Line (RIL) population derived from Sorghum bicolor and S. propinquum . The high-throughput phenotyping methods of fungal structures here rely on a Mask Region-based Convolutional Neural Network (Mask R-CNN) in computer vision for pixel-wise fungal structure segmentations and mixed linear models to explore the relations of AMF colonization, root niche, and fungal structure allocation. Models proposed capture over 95% of the variation in AMF colonization as a function of root niche and relative abundance of fungal structures in each plant. Arbuscule allocation is a significant predictor of AMF colonization among sibling plants. Arbuscules and extraradical hyphae implicated in nutrient exchange predict highest AMF colonization in the top root section. Our work demonstrates that deep learning can be used by the community for the high-throughput phenotyping of AMF in plant roots. Mixed linear modeling provides a framework for testing hypotheses about AMF colonization phenotypes as a function of root niche and fungal structure allocations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Pathway for decarbonizing residential building operations in the US and China beyond the mid-century

With global carbon budget targets looming, residential buildings in top economies must become carbon neutral as soon as possible to reserve more emission space for emerging carbon-emitting economies. This study is the first to compare the operational decarbonization process of China’s and the United States (US) residential buildings from 2000 to 2060 by combining the end-use emission model with the decomposing structural decomposition (DSD) method and Monte Carlo simulation. The results show that from 2001 to 2020 China decarbonized 1544 mega-tons of carbon dioxide (MtCO 2 ) and the US decarbonized 1848 MtCO 2 . In the business-as-usual scenario, China will hit its emission peak in 2031 (±3) with 934 (±61) MtCO 2 , while the US will maintain a lock-in level of 736 (±133) MtCO 2 since the 2030s. In the decarbonization scenario, operational carbon neutrality for residential buildings in 2060 is promoted by an increase in clean power generation proportion, building-integrated power generation level, building electrification level, and a reduction in end-use energy intensity, which will contribute 34.4 %, 21.4 %, 14.3 %, and 29.9 % in China and 32.9 %, 33.1 %, 8.2 %, and 25.8 % in the US, respectively. Especially, building-integrated power generation in China only costs about 40 % of what it costs in the US. Besides, high-decarbonization strategies for residential building operations are proposed as references for governments to formulate targeted climate policies. Overall, this study offers data benchmarks for buildings’ carbon neutrality of top economies to further promote synergistic carbon neutrality with the buildings of emerging economies in the age of Post COP27.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗