[HTML][HTML] A transcription factor atlas of directed differentiation

J Joung, S Ma, T Tay, KR Geiger-Schuller… - Cell, 2023 - cell.com
Transcription factors (TFs) regulate gene programs, thereby controlling diverse cellular
processes and cell states. To comprehensively understand TFs and the programs they …

[HTML][HTML] Molecular basis for the genome engagement by Sox proteins

L Hou, Y Srivastava, R Jauch - Seminars in cell & developmental biology, 2017 - Elsevier
The Sox transcription factor family consists of 20 members in the human genome. Many of
them are key determinants of cellular identities and possess the capacity to reprogram cell …

Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma

J Peng, BF Sun, CY Chen, JY Zhou, YS Chen, H Chen… - Cell research, 2019 - nature.com
Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer
featured with high intra-tumoral heterogeneity and poor prognosis. To comprehensively …

AnimalTFDB 4.0: a comprehensive animal transcription factor database updated with variation and expression annotations

WK Shen, SY Chen, ZQ Gan, YZ Zhang… - Nucleic acids …, 2023 - academic.oup.com
Transcription factors (TFs) are proteins that interact with specific DNA sequences to regulate
gene expression and play crucial roles in all kinds of biological processes. To keep up with …

Gene expression across mammalian organ development

M Cardoso-Moreira, J Halbert, D Valloton, B Velten… - Nature, 2019 - nature.com
The evolution of gene expression in mammalian organ development remains largely
uncharacterized. Here we report the transcriptomes of seven organs (cerebrum, cerebellum …

RNA-Seq signatures normalized by mRNA abundance allow absolute deconvolution of human immune cell types

G Monaco, B Lee, W Xu, S Mustafah, YY Hwang… - Cell reports, 2019 - cell.com
The molecular characterization of immune subsets is important for designing effective
strategies to understand and treat diseases. We characterized 29 immune cell types within …

A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte

LW Plasschaert, R Žilionis, R Choo-Wing, V Savova… - Nature, 2018 - nature.com
The functions of epithelial tissues are dictated by the types, abundance and distribution of
the differentiated cells they contain. Attempts to restore tissue function after damage require …

AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors

H Hu, YR Miao, LH Jia, QY Yu, Q Zhang… - Nucleic acids …, 2019 - academic.oup.com
Abstract The Animal Transcription Factor DataBase (AnimalTFDB) is a resource aimed to
provide the most comprehensive and accurate information for animal transcription factors …

Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors

MD Young, TJ Mitchell, FA Vieira Braga, MGB Tran… - science, 2018 - science.org
Messenger RNA encodes cellular function and phenotype. In the context of human cancer, it
defines the identities of malignant cells and the diversity of tumor tissue. We studied 72,501 …

Resolving the fibrotic niche of human liver cirrhosis at single-cell level

P Ramachandran, R Dobie, JR Wilson-Kanamori… - Nature, 2019 - nature.com
Liver cirrhosis is a major cause of death worldwide and is characterized by extensive
fibrosis. There are currently no effective antifibrotic therapies available. To obtain a better …