Computational principles and challenges in single-cell data integration

R Argelaguet, ASE Cuomo, O Stegle… - Nature biotechnology, 2021 - nature.com
The development of single-cell multimodal assays provides a powerful tool for investigating
multiple dimensions of cellular heterogeneity, enabling new insights into development …

Enhancers in disease: molecular basis and emerging treatment strategies

A Claringbould, JB Zaugg - Trends in molecular medicine, 2021 - cell.com
Enhancers are genomic sequences that play a key role in regulating tissue-specific gene
expression levels. An increasing number of diseases are linked to impaired enhancer …

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

C Bravo González-Blas, S De Winter, G Hulselmans… - Nature …, 2023 - nature.com
Joint profiling of chromatin accessibility and gene expression in individual cells provides an
opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present …

Multi-omics single-cell data integration and regulatory inference with graph-linked embedding

ZJ Cao, G Gao - Nature Biotechnology, 2022 - nature.com
Despite the emergence of experimental methods for simultaneous measurement of multiple
omics modalities in single cells, most single-cell datasets include only one modality. A major …

[HTML][HTML] Spatial multiomics map of trophoblast development in early pregnancy

A Arutyunyan, K Roberts, K Troulé, FCK Wong… - Nature, 2023 - nature.com
The relationship between the human placenta—the extraembryonic organ made by the
fetus, and the decidua—the mucosal layer of the uterus, is essential to nurture and protect …

Single-cell roadmap of human gonadal development

L Garcia-Alonso, V Lorenzi, CI Mazzeo… - Nature, 2022 - nature.com
Gonadal development is a complex process that involves sex determination followed by
divergent maturation into either testes or ovaries. Historically, limited tissue accessibility, a …

The landscape of cell–cell communication through single-cell transcriptomics

AA Almet, Z Cang, S Jin, Q Nie - Current opinion in systems biology, 2021 - Elsevier
Cell–cell communication is a fundamental process that shapes biological tissue. Historically,
studies of cell–cell communication have been feasible for one or two cell types and a few …

Chromatin accessibility profiling methods

L Minnoye, GK Marinov, T Krausgruber, L Pan… - Nature Reviews …, 2021 - nature.com
Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied
characteristic of the eukaryotic genome. As active regulatory DNA elements are generally …

Hippo signaling instructs ectopic but not normal organ growth

W Kowalczyk, L Romanelli, M Atkins, H Hillen… - Science, 2022 - science.org
The Hippo signaling pathway is widely considered a master regulator of organ growth
because of the prominent overgrowth phenotypes caused by experimental manipulation of …

[HTML][HTML] Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation

C Bravo Gonzalez-Blas, I Matetovici, H Hillen… - Nature Cell …, 2024 - nature.com
In the mammalian liver, hepatocytes exhibit diverse metabolic and functional profiles based
on their location within the liver lobule. However, it is unclear whether this spatial variation …