Rolling back human pluripotent stem cells to an eight-cell embryo-like stage

MA Mazid, C Ward, Z Luo, C Liu, Y Li, Y Lai, L Wu, J Li… - Nature, 2022 - nature.com
After fertilization, the quiescent zygote experiences a burst of genome activation that initiates
a short-lived totipotent state. Understanding the process of totipotency in human cells would …

hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data

S Morabito, F Reese, N Rahimzadeh, E Miyoshi… - Cell reports …, 2023 - cell.com
Biological systems are immensely complex, organized into a multi-scale hierarchy of
functional units based on tightly regulated interactions between distinct molecules, cells …

[HTML][HTML] Maladaptive innate immune training of myelopoiesis links inflammatory comorbidities

X Li, H Wang, X Yu, G Saha, L Kalafati, C Ioannidis… - Cell, 2022 - cell.com
Bone marrow (BM)-mediated trained innate immunity (TII) is a state of heightened immune
responsiveness of hematopoietic stem and progenitor cells (HSPC) and their myeloid …

Spatially resolved multiomics of human cardiac niches

K Kanemaru, J Cranley, D Muraro, AMA Miranda… - Nature, 2023 - nature.com
The function of a cell is defined by its intrinsic characteristics and its niche: the tissue
microenvironment in which it dwells. Here we combine single-cell and spatial …

Multiomic analysis reveals conservation of cancer-associated fibroblast phenotypes across species and tissue of origin

DS Foster, M Januszyk, D Delitto, KE Yost, M Griffin… - Cancer Cell, 2022 - cell.com
Cancer-associated fibroblasts (CAFs) are integral to the solid tumor microenvironment.
CAFs were once thought to be a relatively uniform population of matrix-producing cells, but …

Innate immune training of granulopoiesis promotes anti-tumor activity

L Kalafati, I Kourtzelis, J Schulte-Schrepping, X Li… - Cell, 2020 - cell.com
Trained innate immunity, induced via modulation of mature myeloid cells or their bone
marrow progenitors, mediates sustained increased responsiveness to secondary …

Single-cell biological network inference using a heterogeneous graph transformer

A Ma, X Wang, J Li, C Wang, T Xiao, Y Liu… - Nature …, 2023 - nature.com
Single-cell multi-omics (scMulti-omics) allows the quantification of multiple modalities
simultaneously to capture the intricacy of complex molecular mechanisms and cellular …

Divergent transcriptional regulation of astrocyte reactivity across disorders

JE Burda, TM O'Shea, Y Ao, KB Suresh, S Wang… - Nature, 2022 - nature.com
Astrocytes respond to injury and disease in the central nervous system with reactive
changes that influence the outcome of the disorder,,–. These changes include differentially …

Benchmarking atlas-level data integration in single-cell genomics

MD Luecken, M Büttner, K Chaichoompu, A Danese… - Nature …, 2022 - nature.com
Single-cell atlases often include samples that span locations, laboratories and conditions,
leading to complex, nested batch effects in data. Thus, joint analysis of atlas datasets …

[HTML][HTML] Spatial multi-omic map of human myocardial infarction

C Kuppe, RO Ramirez Flores, Z Li, S Hayat… - Nature, 2022 - nature.com
Myocardial infarction is a leading cause of death worldwide. Although advances have been
made in acute treatment, an incomplete understanding of remodelling processes has limited …