A5046944569- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- Plant Disease Resistance and Genetics
- Plant Virus Research Studies
- Agriculture, Soil, Plant Science
- Wheat and Barley Genetics and Pathology
- Embedded Systems Design Techniques
- Gut microbiota and health
- Software Testing and Debugging Techniques
- Formal Methods in Verification
- Genetic Mapping and Diversity in Plants and Animals
- RNA modifications and cancer
- Advances in Cucurbitaceae Research
- Plant tissue culture and regeneration
- Chromosomal and Genetic Variations
- Complexity and Algorithms in Graphs
- Hydraulic flow and structures
- Plant Disease Management Techniques
- Berry genetics and cultivation research
- Nitrogen and Sulfur Effects on Brassica
- Structural Integrity and Reliability Analysis
- Food Quality and Safety Studies
- Safety and Risk Management
- Peanut Plant Research Studies
- Powdery Mildew Fungal Diseases
Shanghai Institute for Science of Science
2020-2024
Fudan University
2020-2024
Shanghai Center for Brain Science and Brain-Inspired Technology
2020-2024
Zhongshan Hospital
2024
National University of Defense Technology
2023-2024
Xinjiang Academy of Agricultural Sciences
2022
Gansu Academy of Agricultural Sciences
2022
Tianjin Normal University
2019
Changchun University
2013
Abstract Current metagenome assembled human gut phage catalogs contained mostly fragmented genomes. Here, comprehensive virome detection procedure is developed involving virus‐like particle (VLP) enrichment from ≈500 g feces and combined sequencing of short‐ long‐read. Applied to 135 samples, a Chinese Gut Virome Catalog (CHGV) consisting 21,499 non‐redundant viral operational taxonomic units (vOTUs) that are significantly longer than those obtained by short‐read ≈35% (7675) complete...
DNA methylation plays a crucial role in the survival of bacteriophages (phages), yet understanding their genome remains limited. In this study, patterns are analyzed 8848 metagenome-assembled high-quality phages from 104 fecal samples using single-molecule real-time sequencing. The results demonstrate that 97.60% gut exhibit methylation, with certain factors correlating densities. Phages higher densities appear to have potential viability advantages. Strikingly, more than one-third possess...
Identifying viruses from metagenomes is a common step to explore the virus composition in human gut. Here, we introduce VirRep, hybrid language representation learning framework, for identifying gut metagenomes. VirRep combines context-aware encoder and an evolution-aware improve sequence by incorporating k-mer patterns homologies. Benchmarking on both simulated real datasets with varying viral proportions demonstrates that outperforms state-of-the-art methods. When applied fecal colorectal...
Extrachromosomal mobile genetic elements (eMGEs), including phages and plasmids, that can move across different microbes, play important roles in genome evolution shaping the structure of microbial communities. However, we still know very little about eMGEs, especially their abundances, distributions putative functions microbiomes. Thus, a comprehensive description eMGEs is great utility. Here present mMGE, catalog 517 251 non-redundant 92 492 plasmids 424 759 phages, derived from diverse...
Heat stress caused by global warming requires the development of thermotolerant crops to sustain yield. It is necessary understand molecular mechanisms that underlie heat tolerance in plants. Strigolactones (SLs) are a class carotenoid-derived phytohormones regulate plant and responses abiotic or biotic stresses. Although SL biosynthesis signaling processes well established, genes directly have rarely been reported. Here, we report MYB-like transcription factor AtMYBS1/AtMYBL, whose gene...
Abstract Recovering high-quality metagenome-assembled genomes (HQ-MAGs) is critical for exploring microbial compositions and microbe–phenotype associations. However, multiple sequencing platforms computational tools this purpose may confuse researchers thus call extensive evaluation. Here, we systematically evaluated a total of 40 combinations popular (i.e. strategies), involving eight assemblers, metagenomic binners four technologies, including short-, long-read metaHiC sequencing. We...
Abstract Current metagenome-assembled human phage catalogs contained mostly fragmented genomes. Here, we developed a vigorous detection method involving enrichment and long-read sequencing applied to 135 fecal samples. With ~10 times more efficient in obtaining complete genomes (~34%) than the Gut Virome Database, identified first megabasephage (~1.03Mb), revealed hidden diversity of gut phageome including dozens phages prevalent crAssphages Gubaphages.
Irrigation regimes should be chosen to maximize crop yield and water use efficiency. To realize high efficient with the appropriate furrow irrigation regime, effects of two (alternate conventional irrigation) three lower soil moisture limits (60, 70, 80%) were studied on winter wheat consumption using a multi-level fuzzy comprehensive evaluation method. The results show that under regimes, alternate irrigation, when limit is 70%, harvest index (0.45 0.39, respectively) productivity (1.86...
Abstract High quality is an important goal of wheat breeding. Several super-strong gluten varieties, e.g. ‘Xinmai 26’ and 45’, have been bred to meet the needs consumer market. However, genetic composition, transmission frequency contribution these varieties their progeny are not clear, which is. To analyze composition high-quality strong rates male female parents were determined using 6056 SNP markers detected by a widely used high-throughput array (15K chip). Additionally, chromosome...
Developing control programs for autonomous vehicles is a challenging task, mainly due to factors such as complex and dynamic environments, intricacy of tasks, uncertain sensor information. To tackle the challenge, this paper harnesses potential formal methods deep reinforcement learning (DRL) more comprehensive solution that integrates Generalized Reactivity(1) (GR(1)) synthesis with DRL. The GR(1) module takes care high-level task planning, ensuring vehicle follows correct-by-construction...
Synthesizing a reactive system fulfilling given requirements is an interesting and challenging problem in the field of formal method. By using temporal logic as specifications, related results have been well applied synthesis unmanned autonomous (UAS) controllers. But practice, static monolithic specifications are usually accompanied with being unsynthesizable dynamic complex environments. To improve flexibility controller synthesis, we propose based on different safety corresponding methods...
Abstract Accurate identification of viral genomes from metagenomic data provides a broad avenue for studying viruses in the human gut. Here, we introduce VirRep, novel virus method based on hybrid language representation learning framework. VirRep employs context-aware encoder and composition-focused to incorporate learned knowledge known biological insights better describe source DNA sequence. We benchmarked multiple gut virome datasets under different conditions demonstrated significant...