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Article
Open AccessSRTsim: spatial pattern preserving simulations for spatially resolved transcriptomics
Spatially resolved transcriptomics (SRT)-specific computational methods are often developed, tested, validated, and evaluated in silico using simulated data. Unfortunately, existing simulated SRT data are ofte...
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Chapter and Conference Paper
System of Systems Architecting with Knowledge Graph: A Case Study from Air Interdiction Operation
Knowledge graph is a promising technology for addressing military problems. It combines the priori knowledge of human with fast computing and large storage capability of machines, and plays an important role i...
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Article
Open AccessStructural and mechanistic basis for recognition of alternative tRNA precursor substrates by bacterial ribonuclease P
Binding of precursor tRNAs (ptRNAs) by bacterial ribonuclease P (RNase P) involves an encounter complex (ES) that isomerizes to a catalytic conformation (ES*). However, the structures of intermediates and the ...
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Article
Open AccessModeling zero inflation is not necessary for spatial transcriptomics
Spatial transcriptomics are a set of new technologies that profile gene expression on tissues with spatial localization information. With technological advances, recent spatial transcriptomics data are often i...
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Article
Open AccessA novel nonparametric computational strategy for identifying differential methylation regions
DNA methylation has long been known as an epigenetic gene silencing mechanism. For a motivating example, the methylomes of cancer and non-cancer cells show a number of methylation differences, indicating that ...
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Chapter and Conference Paper
A UAF Based Method for Next Generation Air Traffic Management System Development
Next generation air traffic management system (ATM) is a typical system of systems (SoS). With the significantly increasing complexity of next generation ATM and its development, an advanced and systematic met...
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Article
Open AccessSPARK-X: non-parametric modeling enables scalable and robust detection of spatial expression patterns for large spatial transcriptomic studies
Spatial transcriptomic studies are becoming increasingly common and large, posing important statistical and computational challenges for many analytic tasks. Here, we present SPARK-X, a non-parametric method f...
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Article
Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies
Identifying genes that display spatial expression patterns in spatially resolved transcriptomic studies is an important first step toward characterizing the spatial transcriptomic landscape of complex tissues....
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Article
Open AccessAccuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis
Dimensionality reduction is an indispensable analytic component for many areas of single-cell RNA sequencing (scRNA-seq) data analysis. Proper dimensionality reduction can allow for effective noise removal and...
