[HTML][HTML] A guidebook of spatial transcriptomic technologies, data resources and analysis approaches

L Yue, F Liu, J Hu, P Yang, Y Wang, J Dong… - Computational and …, 2023 - Elsevier
Advances in transcriptomic technologies have deepened our understanding of the cellular
gene expression programs of multicellular organisms and provided a theoretical basis for …

Joint dimension reduction and clustering analysis of single-cell RNA-seq and spatial transcriptomics data

W Liu, X Liao, Y Yang, H Lin, J Yeong… - Nucleic acids …, 2022 - academic.oup.com
Dimension reduction and (spatial) clustering is usually performed sequentially; however, the
low-dimensional embeddings estimated in the dimension-reduction step may not be …

Heteroskedastic PCA: Algorithm, optimality, and applications

AR Zhang, TT Cai, Y Wu - The Annals of Statistics, 2022 - projecteuclid.org
Heteroskedastic PCA: Algorithm, optimality, and applications Page 1 The Annals of Statistics
2022, Vol. 50, No. 1, 53–80 https://doi.org/10.1214/21-AOS2074 © Institute of Mathematical …

Distributed linear regression by averaging

E Dobriban, Y Sheng - 2021 - projecteuclid.org
Distributed linear regression by averaging Page 1 The Annals of Statistics 2021, Vol. 49, No. 2,
918–943 https://doi.org/10.1214/20-AOS1984 © Institute of Mathematical Statistics, 2021 …

Personalized pca: Decoupling shared and unique features

N Shi, R Al Kontar - Journal of machine learning research, 2024 - jmlr.org
In this paper, we tackle a significant challenge in PCA: heterogeneity. When data are
collected from different sources with heterogeneous trends while still sharing some …

Stochastic gradients for large-scale tensor decomposition

TG Kolda, D Hong - SIAM Journal on Mathematics of Data Science, 2020 - SIAM
Tensor decomposition is a well-known tool for multiway data analysis. This work proposes
using stochastic gradients for efficient generalized canonical polyadic (GCP) tensor …

[HTML][HTML] Spatial Transcriptomics in Human Cardiac Tissue

Q Nguyen, LW Tung, B Lin, R Sivakumar, F Sar… - International Journal of …, 2025 - mdpi.com
Spatial transcriptomics has transformed our understanding of gene expression by
preserving the spatial context within tissues. This review focuses on the application of spatial …

Biwhitening reveals the rank of a count matrix

B Landa, TTCK Zhang, Y Kluger - SIAM journal on mathematics of data …, 2022 - SIAM
Estimating the rank of a corrupted data matrix is an important task in data analysis, most
notably for choosing the number of components in principal component analysis. Significant …

Matrix denoising with partial noise statistics: optimal singular value shrinkage of spiked F-matrices

M Gavish, W Leeb, E Romanov - … and Inference: A Journal of the …, 2023 - academic.oup.com
We study the problem of estimating a large, low-rank matrix corrupted by additive noise of
unknown covariance, assuming one has access to additional side information in the form of …

Selecting the number of components in PCA via random signflips

D Hong, Y Sheng, E Dobriban - arxiv preprint arxiv:2012.02985, 2020 - arxiv.org
Dimensionality reduction via PCA and factor analysis is an important tool of data analysis. A
critical step is selecting the number of components. However, existing methods (such as the …