Deciphering cell–cell interactions and communication from gene expression

E Armingol, A Officer, O Harismendy… - Nature Reviews …, 2021 - nature.com
Cell–cell interactions orchestrate organismal development, homeostasis and single-cell
functions. When cells do not properly interact or improperly decode molecular messages …

Generation, functional analysis and applications of isogenic three-dimensional self-aggregating cardiac microtissues from human pluripotent stem cells

G Campostrini, V Meraviglia, E Giacomelli… - Nature protocols, 2021 - nature.com
Tissue-like structures from human pluripotent stem cells containing multiple cell types are
transforming our ability to model and understand human development and disease. Here we …

Identification of kidney injury–released circulating osteopontin as causal agent of respiratory failure

FZ Khamissi, L Ning, E Kefaloyianni, H Dun… - Science …, 2022 - science.org
Tissue injury can drive secondary organ injury; however, mechanisms and mediators are not
well understood. To identify interorgan cross-talk mediators, we used acute kidney injury …

Grounding cognition: heterarchical control mechanisms in biology

W Bechtel, L Bich - … Transactions of the Royal Society B, 2021 - royalsocietypublishing.org
We advance an account that grounds cognition, specifically decision-making, in an activity
all organisms as autonomous systems must perform to keep themselves viable—controlling …

Junctional epithelium and hemidesmosomes: Tape and rivets for solving the “percutaneous device dilemma” in dental and other permanent implants

NG Fischer, C Aparicio - Bioactive materials, 2022 - Elsevier
The percutaneous device dilemma describes etiological factors, centered around the
disrupted epithelial tissue surrounding non-remodelable devices, that contribute to rampant …

[HTML][HTML] Chronic lung diseases: entangled in extracellular matrix

JK Burgess, MC Harmsen - European Respiratory Review, 2022 - Eur Respiratory Soc
The extracellular matrix (ECM) is the scaffold that provides structure and support to all
organs, including the lung; however, it is also much more than this. The ECM provides …

De novo reconstruction of cell interaction landscapes from single-cell spatial transcriptome data with DeepLinc

R Li, X Yang - Genome Biology, 2022 - Springer
Based on a deep generative model of variational graph autoencoder (VGAE), we develop a
new method, DeepLinc (deep learning framework for Landscapes of Interacting Cells), for …

Single-cell adaptations shape evolutionary transitions to multicellularity in green algae

CK Cornwallis, M Svensson-Coelho, M Lindh… - Nature Ecology & …, 2023 - nature.com
The evolution of multicellular life has played a pivotal role in sha** biological diversity.
However, we know surprisingly little about the natural environmental conditions that favour …

Glycemia regulation: from feedback loops to organizational closure

L Bich, M Mossio, AM Soto - Frontiers in Physiology, 2020 - frontiersin.org
Endocrinologists apply the idea of feedback loops to explain how hormones regulate certain
bodily functions such as glucose metabolism. In particular, feedback loops focus on the …

Reuniting philosophy and science to advance cancer research

T Pradeu, B Daignan‐Fornier, A Ewald… - Biological …, 2023 - Wiley Online Library
Cancers rely on multiple, heterogeneous processes at different scales, pertaining to many
biomedical fields. Therefore, understanding cancer is necessarily an interdisciplinary task …