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Article
Open AccessLabel-aware distance mitigates temporal and spatial variability for clustering and visualization of single-cell gene expression data
Clustering and visualization are essential parts of single-cell gene expression data analysis. The Euclidean distance used in most distance-based methods is not optimal. The batch effect, i.e., the variability...
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Article
Open AccessIntegrated multi-omics analyses identify anti-viral host factors and pathways controlling SARS-CoV-2 infection
Host anti-viral factors are essential for controlling SARS-CoV-2 infection but remain largely unknown due to the biases of previous large-scale studies toward pro-viral host factors. To fill in this knowledge ...
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Article
Open AccessSingle-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance
Acute myeloid leukemia (AML) is a heterogeneous disease characterized by high rate of therapy resistance. Since the cell of origin can impact response to therapy, it is crucial to understand the lineage compos...
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Article
Open AccessEnabling long-cycling aqueous sodium-ion batteries via Mn dissolution inhibition using sodium ferrocyanide electrolyte additive
Aqueous sodium-ion batteries (AIBs) are promising candidates for large-scale energy storage due to their safe operational properties and low cost. However, AIBs have low specific energy (i.e., <80 Wh kg−1) and li...
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Article
Review of do** SrTiO3 for photocatalytic applications
As a representative composite metal oxide belonging to a perovskite, strontium titanate (SrTiO3) possesses the merits of chemical stability, low toxicity and low cost, endowing it with significant application pot...
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Article
Open AccessOccult polyclonality of preclinical pancreatic cancer models drives in vitro evolution
Heterogeneity is a hallmark of cancer. The advent of single-cell technologies has helped uncover heterogeneity in a high-throughput manner in different cancers across varied contexts. Here we apply single-cell...
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Article
Open AccessBi-order multimodal integration of single-cell data
Integration of single-cell multiomics profiles generated by different single-cell technologies from the same biological sample is still challenging. Previous approaches based on shared features have only provi...
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Article
Open AccessSensei: how many samples to tell a change in cell type abundance?
Cellular heterogeneity underlies cancer evolution and metastasis. Advances in single-cell technologies such as single-cell RNA sequencing and mass cytometry have enabled interrogation of cell type-specific exp...
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Chapter and Conference Paper
Quality Assurance and Verification of GFDM Satellite Imagery
As China's first civilian medium-sized agile satellite, the Gao Fen Duo Mo Satellite (GFDM) has realized a variety of agile imaging modes for the first time, and particularly, the active push-scan imaging mode...
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Article
Open AccessExtended live-cell barcoding approach for multiplexed mass cytometry
Sample barcoding is essential in mass cytometry analysis, since it can eliminate potential procedural variations, enhance throughput, and allow simultaneous sample processing and acquisition. Sample pooling af...
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Article
Publisher Correction: Single-cell manifold-preserving feature selection for detecting rare cell populations
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Article
Single-cell manifold-preserving feature selection for detecting rare cell populations
A key challenge in studying organisms and diseases is to detect rare molecular programs and rare cell populations that drive development, differentiation and transformation. Molecular features, such as genes a...
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Article
Open AccessMEDALT: single-cell copy number lineage tracing enabling gene discovery
We present a Minimal Event Distance Aneuploidy Lineage Tree (MEDALT) algorithm that infers the evolution history of a cell population based on single-cell copy number (SCCN) profiles, and a statistical routine...
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Article
Open AccessLatent periodic process inference from single-cell RNA-seq data
The development of a phenotype in a multicellular organism often involves multiple, simultaneously occurring biological processes. Advances in single-cell RNA-sequencing make it possible to infer latent develo...
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Chapter and Conference Paper
Stratified Test Alleviates Batch Effects in Single-Cell Data
Analyzing single-cell sequencing data across batches is challenging. We find that the Van Elteren test, a stratified version of Wilcoxon rank-sum test, elegantly mitigates the problem. We also modified the com...
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Article
Open AccessSingle-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling
Single-cell RNA-seq is a powerful tool in decoding the heterogeneity in complex tissues by generating transcriptomic profiles of the individual cell. Here, we report a single-nuclei RNA-seq (snRNA-seq) transcr...
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Chapter and Conference Paper
An Adaptive Comprehensive Learning Bacterial Foraging Optimization for Function Optimization
This paper proposes a variant of the bacterial foraging optimization (BFO) algorithm with time-varying chemotaxis step length and comprehensive learning strategy, namely Adaptive Comprehensive Learning Bacteri...
