Exploring tissue architecture using spatial transcriptomics

A Rao, D Barkley, GS França, I Yanai - Nature, 2021 - nature.com
Deciphering the principles and mechanisms by which gene activity orchestrates complex
cellular arrangements in multicellular organisms has far-reaching implications for research …

Computational and analytical challenges in single-cell transcriptomics

O Stegle, SA Teichmann, JC Marioni - Nature Reviews Genetics, 2015 - nature.com
The development of high-throughput RNA sequencing (RNA-seq) at the single-cell level has
already led to profound new discoveries in biology, ranging from the identification of novel …

SpatialDE: identification of spatially variable genes

V Svensson, SA Teichmann, O Stegle - Nature methods, 2018 - nature.com
Technological advances have made it possible to measure spatially resolved gene
expression at high throughput. However, methods to analyze these data are not established …

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

K Achim, JB Pettit, LR Saraiva, D Gavriouchkina… - Nature …, 2015 - nature.com
Understanding cell type identity in a multicellular organism requires the integration of gene
expression profiles from individual cells with their spatial location in a particular tissue …

SINCERA: a pipeline for single-cell RNA-Seq profiling analysis

M Guo, H Wang, SS Potter, JA Whitsett… - PLoS computational …, 2015 - journals.plos.org
A major challenge in developmental biology is to understand the genetic and cellular
processes/programs driving organ formation and differentiation of the diverse cell types that …

Identification of cell types in multiplexed in situ images by combining protein expression and spatial information using CELESTA

W Zhang, I Li, NE Reticker-Flynn, Z Good, S Chang… - Nature …, 2022 - nature.com
Advances in multiplexed in situ imaging are revealing important insights in spatial biology.
However, cell type identification remains a major challenge in imaging analysis, with most …

Single-cell transcriptomics bioinformatics and computational challenges

OB Poirion, X Zhu, T Ching, L Garmire - Frontiers in genetics, 2016 - frontiersin.org
The emerging single-cell RNA-Seq (scRNA-Seq) technology holds the promise to
revolutionize our understanding of diseases and associated biological processes at an …

Statistical methods in integrative genomics

S Richardson, GC Tseng, W Sun - Annual review of statistics …, 2016 - annualreviews.org
Statistical methods in integrative genomics aim to answer important biology questions by
jointly analyzing multiple types of genomic data (vertical integration) or aggregating the …

Myofibroblasts are distinguished from activated skin fibroblasts by the expression of AOC3 and other associated markers

L Hsia, N Ashley, D Ouaret, LM Wang… - Proceedings of the …, 2016 - National Acad Sciences
Pericryptal myofibroblasts in the colon and rectum play an important role in regulating the
normal colorectal stem cell niche and facilitating tumor progression. Myofibroblasts …

Synaptic and peptidergic connectome of a neurosecretory center in the annelid brain

EA Williams, C Verasztó, S Jasek, M Conzelmann… - Elife, 2017 - elifesciences.org
Neurosecretory centers in animal brains use peptidergic signaling to influence physiology
and behavior. Understanding neurosecretory center function requires mapping cell types …