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Functional enrichment analysis is an essential task for the interpretation of gene lists derived from large-scale genetic, transcriptomic and proteomic studies. WebGestalt (WEB-based GEne SeT AnaLysis Toolkit) has become one of the popular software tools in this field since its publication in 2005. For the last 7 years, WebGestalt data holdings have grown(More)
Increasing crop yield is a major challenge for modern agriculture. The development of new plant types, which is known as ideal plant architecture (IPA), has been proposed as a means to enhance rice yield potential over that of existing high-yield varieties. Here, we report the cloning and characterization of a semidominant quantitative trait locus, IPA1(More)
High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis and function of gene expression variation between seemingly identical cells. Here we sequence single-cell RNA-seq libraries prepared from over 1,700 primary mouse bone-marrow-derived dendritic cells spanning several experimental conditions. We find(More)
Lithium is commonly used to treat bipolar disorder, which is associated with altered circadian rhythm. Lithium is a potent inhibitor of glycogen synthase kinase 3 (GSK3), which regulates circadian rhythm in several organisms. In experiments with cultured cells, we show here that GSK3beta phosphorylates and stabilizes the orphan nuclear receptor(More)
Large-scale surveys of single-cell gene expression have the potential to reveal rare cell populations and lineage relationships but require efficient methods for cell capture and mRNA sequencing. Although cellular barcoding strategies allow parallel sequencing of single cells at ultra-low depths, the limitations of shallow sequencing have not been(More)
Since their arrival in the Tibetan Plateau during the Neolithic Age, Tibetans have been well-adapted to extreme environmental conditions and possess genetic variation that reflect their living environment and migratory history. To investigate the origin of Tibetans and the genetic basis of adaptation in a rigorous environment, we genotyped 30 Tibetan(More)
In hyperspectral image analysis, the principal components analysis (PCA) and the maximum noise fraction (MNF) are most commonly used techniques for dimensionality reduction (DR), referred to as PCA-DR and MNF-DR, respectively. The criteria used by the PCA-DR and the MNF-DR are data variance and signal-to-noise ratio (SNR) which are designed to measure data(More)
Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases. The two major subspecies of Asian cultivated rice (Oryza sativa L.), indica and japonica, have shown obvious differences in rice blast resistance, but the genomic basis that underlies the difference is not clear. We performed a genomewide comparison of the major class of(More)
Independent component analysis (ICA) has shown success in many applications. This paper investigates a new application of the ICA in endmember extraction and abundance quantification for hyperspectral imagery. An endmember is generally referred to as an idealized pure signature for a class whose presence is considered to be rare. When it occurs, it may not(More)
The semantic gap between low-level visual features and high-level semantics has been investigated for decades but still remains a big challenge in multimedia. When "search" became one of the most frequently used applications, "intent gap", the gap between query expressions and users' search intents, emerged. Researchers have been focusing on three(More)