A5073035070- Advanced Fiber Laser Technologies
- Plant Molecular Biology Research
- Photonic and Optical Devices
- Semiconductor Lasers and Optical Devices
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Single-cell and spatial transcriptomics
- Chromosomal and Genetic Variations
- Quantum optics and atomic interactions
- Spectroscopy and Laser Applications
- Wheat and Barley Genetics and Pathology
- Atomic and Subatomic Physics Research
- Advanced Fiber Optic Sensors
- Plant Gene Expression Analysis
- Genomics and Chromatin Dynamics
- Photonic Crystal and Fiber Optics
- Cancer-related molecular mechanisms research
- Plant Reproductive Biology
- RNA modifications and cancer
- Advanced Frequency and Time Standards
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- RNA Research and Splicing
- Genetics and Plant Breeding
- Smart Agriculture and AI
Shanghai Institute of Optics and Fine Mechanics
2016-2025
Huazhong Agricultural University
2011-2025
Nanjing University
2019-2025
Nanjing University of Chinese Medicine
2025
Jiangsu Province Hospital
2025
Shanghai Ocean University
2025
Zhejiang University
2005-2024
Chinese Academy of Sciences
2015-2024
University of Chinese Academy of Sciences
2020-2024
Nanjing Drum Tower Hospital
2023-2024
Yijun Ruan and colleagues report the draft genome of sweet orange, Citrus sinensis. Their data suggests orange originated from a cross between pummelo mandarin. Oranges are an important nutritional source for human health have immense economic value. Here we present comprehensive analysis (Citrus sinensis). The assembled sequence covers 87.3% estimated genome, which is relatively compact, as 20% composed repetitive elements. We predicted 29,445 protein-coding genes, half in heterozygous...
Abstract Significantly improved crop varieties are urgently needed to feed the rapidly growing human population under changing climates. While genome sequence information and excellent genomic tools in place for major species, systematic quantification of phenotypic traits or components thereof a high-throughput fashion remains an enormous challenge. In order help bridge genotype phenotype gap, we developed comprehensive framework data analysis plants, which enables extraction extensive list...
High-throughput phenotyping is emerging as an important technology to dissect phenotypic components in plants. Efficient image processing and feature extraction are prerequisites quantify plant growth performance based on traits. Issues include data management, analysis, result visualization of large-scale sets. Here, we present Integrated Analysis Platform (IAP), open-source framework for high-throughput phenotyping. IAP provides user-friendly interfaces, its core functions highly...
Abstract Floral homeotic transcription factors (TFs) act in a combinatorial manner to specify the organ identities flower. However, architecture and function of gene regulatory network (GRN) controlling floral specification is still poorly understood. In particular, interconnections TFs, microRNAs (miRNAs) other initiation growth have not been studied systematically so far. Here, using combination genome-wide TF binding, mRNA miRNA expression data, we reconstruct dynamic GRN meristem...
Pancreatic ductal adenocarcinoma (PDAC) is a highly metastatic disease refractory to all targeted and immune therapies. However, our understanding of PDAC microenvironment especially the very limited partly due inaccessibility tumor tissues. Here, we present single-cell transcriptomic landscape synchronously resected primary tumors matched liver metastases. We perform comparative analysis on both cellular composition functional phenotype between tumors. Tumor cells exhibit distinct profile...
Homoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative contribution of homoeologs transcriptome, critical for determining traits that influence wheat growth and development. Asymmetric transcription has been so far investigated in a tissue or organ-specific manner, which could be misleading due mixture cell types.
Recent methodological developments in plant phenotyping, as well the growing importance of its applications science and breeding, are resulting a fast accumulation multidimensional data. There is great potential for expediting both discovery application if these data made publicly available analysis. However, collection storage phenotypic observations not yet sufficiently governed by standards that would ensure interoperability among providers precisely link specific phenotypes associated...
Increasing grain yield is still the main target of wheat breeding; yet today's plants utilize less than half their potential. Owing to difficulty determining potential in a large population, few genetic factors regulating floret fertility (i.e. difference between and number) have been reported date. In this study, we conducted genome-wide association study (GWAS) by quantifying 54 traits (16 38 for assimilate partitioning spike morphology) 210 European winter accessions. The results GWAS...
A laser phase and frequency noise measurement method by an unbalanced Michelson interferometer composed of a 3 × optical fiber coupler is proposed. The relations differences the power spectral density (PSD) differential fluctuation, PSD instantaneous linewidth are derived strictly discussed carefully. obtains features narrow conveniently without any specific assumptions or models. technique also used to characterize external-cavity semiconductor laser, which confirms correction robustness method.
Plant phenotypic data shrouds a wealth of information which, when accurately analysed and linked to other types, brings light the knowledge about mechanisms life. As phenotyping is field research comprising manifold, diverse time-consuming experiments, findings can be fostered by reusing combining existing datasets. Their correct interpretation, thus replicability, comparability interoperability, possible provided that collected observations are equipped with an adequate set metadata. So far...
We propose a scheme for obtaining an electromagnetically induced grating in asymmetric semiconductor quantum well (QW) structure via Fano interference. In our structure, owing to interference, the diffraction intensity of grating, especially first-order diffraction, can be significantly enhanced. The efficiency controlled efficiently by tuning control field intensity, interaction length, coupling strength tunneling, etc. This investigation may used develop novel photonic devices QW systems.
Abstract Enhancers are critical for developmental stage-specific gene expression, but their dynamic regulation in plants remains poorly understood. Here we compare genome-wide localization of H3K27ac, chromatin accessibility and transcriptomic changes during flower development Arabidopsis . H3K27ac prevalently marks promoter-proximal regions, suggesting that is not a hallmark enhancers We provide computational experimental evidence to confirm distal DNase І hypersensitive sites predictive...
Non-human primates are attractive laboratory animal models that accurately reflect both developmental and pathological features of humans. Here we present a compendium cell types across multiple organs in cynomolgus monkeys (Macaca fascicularis) using single-cell chromatin accessibility RNA sequencing data. The integrated map enables in-depth dissection comparison molecular dynamics, cell-type compositions cellular heterogeneity tissues organs. Using transcriptomic data, infer pseudotime...
Genomic studies have demonstrated a high frequency of genetic alterations in components the SWI/SNF complex including core subunit SMARCA4. However, mechanisms tumorigenesis driven by SMARCA4 mutations, particularly colorectal cancer (CRC), remain largely unknown. In this study, we identified specific, hotspot mutation (c. 3721C>T) which results conversion from arginine to tryptophan at residue 1157 (R1157W) human CRC tissues associated with higher-grade tumors and controls progression....
Abstract Recent advancements in single-cell RNA sequencing (scRNA-seq) technology have enabled the comprehensive profiling of gene expression patterns at level, offering unprecedented insights into cellular diversity and heterogeneity within plant tissues. In this study, we present a systematic approach to construct database, scPlantDB, which is publicly available https://biobigdata.nju.edu.cn/scplantdb. We integrated transcriptomic profiles from 67 high-quality datasets across 17 species,...
Natural antisense transcripts (NATs), as one type of regulatory RNAs, occur prevalently in plant genomes and play significant roles physiological pathological processes. Although their important biological functions have been reported widely, a comprehensive database is lacking up to now. Consequently, we constructed NAT (PlantNATsDB) involving approximately 2 million pairs 69 species. GO annotation high-throughput small RNA sequencing data currently available were integrated investigate the...
Abstract Transcriptome analysis of early-developing maize (Zea mays) seed was conducted using Illumina sequencing. We mapped 11,074,508 and 11,495,788 paired-end reads from endosperm embryo, respectively, at 9 d after pollination to define gene structure alternative splicing events as well transcriptional regulators expression quantify transcript abundance in both embryo endosperm. identified a large number novel transcribed regions that did not fall within annotated regions, many the were...
In plants, microRNAs (miRNAs) regulate gene expression mainly at the post-transcriptional level. Previous studies have demonstrated that miRNA-mediated silencing pathways play vital roles in plant development. Here, we used a high-throughput sequencing approach to characterize miRNAs and their targeted transcripts leaf, flower fruit of sweet orange. A total 183 known 38 novel were identified. An in-house script was identify all potential secondary siRNAs derived from miRNA-targeted using...
A simple and low-cost 1550 nm semiconductor laser with subkilohertz intrinsic linewidth is experimentally demonstrated. commercial distributed feedback diode self-injection locked to the resonance transmission peaks of a fiber Bragg grating Fabry-Perot cavity through polarization-maintaining ring optical path length 4 m, frequency noise suppressed by over 70 dB in Fourier band from 5 Hz 1 kHz. The features an Lorentzian 125 as well relative intensity <-142 dBc/Hz above 2 MHz, provides 0.8...