Journal ArticleDOI
Computational principles and challenges in single-cell data integration.
Ricard Argelaguet,Ricard Argelaguet,Anna S E Cuomo,Anna S E Cuomo,Oliver Stegle,Oliver Stegle,John C. Marioni,John C. Marioni,John C. Marioni +8 more
TLDR
In this article, a broad collection of approaches ranging from batch correction of individual omics datasets to association of chromatin accessibility and genetic variation with transcription are reviewed, as the number of single-cell experiments with multiple data modalities increases.Abstract:
The development of single-cell multimodal assays provides a powerful tool for investigating multiple dimensions of cellular heterogeneity, enabling new insights into development, tissue homeostasis and disease. A key challenge in the analysis of single-cell multimodal data is to devise appropriate strategies for tying together data across different modalities. The term ‘data integration’ has been used to describe this task, encompassing a broad collection of approaches ranging from batch correction of individual omics datasets to association of chromatin accessibility and genetic variation with transcription. Although existing integration strategies exploit similar mathematical ideas, they typically have distinct goals and rely on different principles and assumptions. Consequently, new definitions and concepts are needed to contextualize existing methods and to enable development of new methods. As the number of single-cell experiments with multiple data modalities increases, Argelaguet and colleagues review the concepts and challenges of data integration.read more
Citations
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Journal ArticleDOI
Spatial components of molecular tissue biology
TL;DR: In this paper , the authors identify the key biological questions in spatial analysis of tissues and develop the requisite computational tools to address them, and group these biological problems and related computational algorithms into classes across length scales, thus characterizing common issues that need to be addressed.
Journal ArticleDOI
Multi-omics single-cell data integration and regulatory inference with graph-linked embedding
Zhi-Jie Cao,Ge Gao +1 more
TL;DR: GLUE as discussed by the authors is a graph-linked unified embedding (GLUE) framework for heterogeneous single-cell multi-omics data, which bridges the gap by modeling regulatory interactions across omics layers explicitly.
Journal ArticleDOI
A harmonized atlas of mouse spinal cord cell types and their spatial organization
Daniel E. Russ,Ryan B. Patterson Cross,Li Li,Stephanie C. Koch,Kaya J.E. Matson,Archana Yadav,Mor R. Alkaslasi,Mor R. Alkaslasi,Dylan I. Lee,Claire E. Le Pichon,Vilas Menon,Ariel J. Levine +11 more
TL;DR: In this article, a harmonized cell atlas of the mouse post-natal spinal cord is presented, which provides an integrated view of spinal cell types, their gene expression signatures, and their molecular organization.
Posted ContentDOI
An integrated cell atlas of the human lung in health and disease
Lisa Sikkema,D. Strobl,Luke Zappia,Elo Madissoon,NS Markov,Laure-Emmanuelle Zaragosi,Meshal Ansari,Marie-Jeanne Arguel,Leonie Apperloo,Christophe Bécavin,Marijn Berg,Evgeny Chichelnitskiy,Mei-I Chung,Anna Collin,Aca Gay,Baharak Hooshiar Kashani,Meena Jain,Theodoros Kapellos,TM Kole,Christoph Mayr,Micheal Von Papen,Lance M. Peter,Ciro Ramírez-Suástegui,Janine Schniering,Chase J. Taylor,Thomas Walzthoeni,C Xu,LT Bui,C. De Donno,Leander Dony,Minzhe Guo,AJ Gutierrez,Lukas Heumos,Ni Huang,Ignacio L. Ibarra,Nikki D. Jackson,Preetish Kadur Lakshminarasimha Murthy,Mohammad Lotfollahi,Tracy Tabib,Carlos Talavera-López,Kyle J. Travaglini,Anna Wilbrey-Clark,KB Worlock,Masafumi Yoshida,Tushar J. Desai,Oliver Eickelberg,Caroline Falk,Naftali Kaminski,Mark A. Krasnow,Robert Lafyatis,Marko Nikolic,Joseph E. Powell,Jayaraj Rajagopal,Orit Rozenblatt-Rosen,Max A. Seibold,Dean Sheppard,David Shepherd,Sarah A. Teichmann,Alexander M. Tsankov,Jeffrey A. Whitsett,Y Xu,NE Banovich,Pascal Barbry,Teressa A. Duong,K. Meyer,JA Kropski,Dana Pe'er,H. Schiller,Pramila Tata,JL Schultze,A Iu Misharin,M. Nawijn,Malte D Luecken,Fabian J. Theis +73 more
TL;DR: The integrated Human Lung Cell Atlas (HLCA) is presented, combining 46 datasets of the human respiratory system into a single atlas spanning over 2.2 million cells from 444 individuals across health and disease.
Journal ArticleDOI
Single-cell atlases: shared and tissue-specific cell types across human organs
TL;DR: Key biological insights obtained from cross-tissue studies into epithelial, fibroblast, vascular and immune cells based on single-cell gene expression data in humans are highlighted and compared with mechanisms reported in mice.
References
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limma powers differential expression analyses for RNA-sequencing and microarray studies
Matthew E. Ritchie,Belinda Phipson,Di Wu,Yifang Hu,Charity W. Law,Wei Shi,Gordon K. Smyth,Gordon K. Smyth +7 more
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