Model-free prediction test with application to genomics data

Article Statistics & Probability

Asymptotic Distribution-Free Independence Test for High Dimension Data

Zhanrui Cai et al.

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION (2023)

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Editorial Material Biochemical Research Methods

Method of the Year: spatially resolved transcriptomics

Vivien Marx

Summary: Nature Methods has named spatially resolved transcriptomics as Method of the Year 2020.

NATURE METHODS (2021)

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Article Biochemical Research Methods

SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network

Jian Hu et al.

Summary: SpaGCN is a spatially resolved transcriptomics data analysis tool that uses graph convolutional networks to identify spatial domains and spatially variable genes. By integrating gene expression, spatial location, and histology, SpaGCN can detect genes with enriched spatial expression patterns and transferable to other datasets for studying spatial gene expression variation. SpaGCN is computationally fast, platform independent, and ideal for diverse SRT studies.

NATURE METHODS (2021)

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Article Biochemical Research Methods

Joint probabilistic modeling of single-cell multi-omic data with totalVI

Adam Gayoso et al.

Summary: totalVI is a framework for end-to-end joint analysis of CITE-seq data which probabilistically represents data as a composite of biological and technical factors, providing a cohesive solution for common analysis tasks. It demonstrates strong performance in tasks such as dimensionality reduction, dataset integration, correlation estimation, and differential expression testing.

NATURE METHODS (2021)

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Article Biochemistry & Molecular Biology

Integrated analysis of multimodal single-cell data

Yuhan Hao et al.

Summary: The study introduces a weighted-nearest neighbor analysis framework to learn the relative utility of each data type in each cell, enabling integrative analysis of multiple modalities. Applied to a CITE-seq dataset, the method constructs a multimodal reference atlas of the circulating immune system and successfully identifies and validates previously unreported lymphoid subpopulations.

CELL (2021)

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Article Genetics & Heredity

Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer's disease

Samuel Morabito et al.

Summary: An integrative analysis of single-nucleus assay for transposase-accessible chromatin with sequencing and RNA sequencing in normal and Alzheimer's disease brain tissue reveals cell-type-specific cis-regulatory elements and candidate target genes. The study highlights the dynamic gene-regulatory landscape of the brain, identifying disease-related regulatory modules and transcription factors in specific cell types, demonstrating the utility of a multi-omic single-nucleus approach.

NATURE GENETICS (2021)

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Article Biotechnology & Applied Microbiology

SPARK-X: non-parametric modeling enables scalable and robust detection of spatial expression patterns for large spatial transcriptomic studies

Jiaqiang Zhu et al.

Summary: SPARK-X is a non-parametric method for rapid and effective detection of spatially expressed genes in large spatial transcriptomic studies, providing effective type I error control, high power, and significant computational savings. It has been successfully applied to analyze large datasets and identify spatially expressed genes within the same cell type, revealing new biological insights.

GENOME BIOLOGY (2021)

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Article Statistics & Probability