Computational tools for inferring transcription factor activity

D Hecker, M Lauber, F Behjati Ardakani… - …, 2023 - Wiley Online Library
Transcription factors (TFs) are essential players in orchestrating the regulatory landscape in
cells. Still, their exact modes of action and dependencies on other regulatory aspects remain …

Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology

JA Tangeman, SM Rebull, E Grajales-Esquivel… - …, 2024 - journals.biologists.com
Ocular lens development entails epithelial to fiber cell differentiation, defects in which cause
congenital cataracts. We report the first single-cell multiomic atlas of lens development …

A logic-incorporated gene regulatory network deciphers principles in cell fate decisions

G Xue, X Zhang, W Li, L Zhang, Z Zhang, X Zhou… - Elife, 2024 - elifesciences.org
Organisms utilize gene regulatory networks (GRN) to make fate decisions, but the regulatory
mechanisms of transcription factors (TF) in GRNs are exceedingly intricate. A longstanding …

Cell reprogramming design by transfer learning of functional transcriptional networks

TP Wytock, AE Motter - … of the National Academy of Sciences, 2024 - National Acad Sciences
Recent developments in synthetic biology, next-generation sequencing, and machine
learning provide an unprecedented opportunity to rationally design new disease treatments …

[HTML][HTML] Characterization and Optimization of Multiomic Single-Cell Epigenomic Profiling

L Sandoval, W Mohammed Ismail, A Mazzone… - Genes, 2023 - mdpi.com
The snATAC+ snRNA platform allows epigenomic profiling of open chromatin and gene
expression with single-cell resolution. The most critical assay step is to isolate high-quality …

The Clock:Cycle complex is a major transcriptional regulator of Drosophila photoreceptors that protects the eye from retinal degeneration and oxidative stress

J Jauregui-Lozano, H Hall, SC Stanhope… - PLoS …, 2022 - journals.plos.org
The aging eye experiences physiological changes that include decreased visual function
and increased risk of retinal degeneration. Although there are transcriptomic signatures in …

Transcriptomic signatures of progressive and regressive liver fibrosis and portal hypertension

O Petrenko, P Königshofer, K Brusilovskaya, BS Hofer… - Iscience, 2024 - cell.com
Persistent liver injury triggers a fibrogenic program that causes pathologic remodeling of the
hepatic microenvironment (ie, liver fibrosis) and portal hypertension. The dynamics of gene …

Denervation alters the secretome of myofibers and thereby affects muscle stem cell lineage progression and functionality

H Henze, SS Hüttner, P Koch, SC Schüler… - NPJ Regenerative …, 2024 - nature.com
Skeletal muscle function crucially depends on innervation while repair of skeletal muscle
relies on resident muscle stem cells (MuSCs). However, it is poorly understood how …

Algorithms for Autonomous Formation of Multicellular Shapes from Single Cells

E Appleton, N Mehdipour, T Daifuku, D Briers… - ACS Synthetic …, 2024 - ACS Publications
Multicellular organisms originate from a single cell, ultimately giving rise to mature
organisms of heterogeneous cell type composition in complex structures. Recent work in the …

Benchmarking of ATAC sequencing data from BGI's low-cost DNBSEQ-G400 instrument for identification of open and occupied chromatin regions

M Naval-Sanchez, N Deshpande, M Tran… - Frontiers in Molecular …, 2022 - frontiersin.org
Background: Chromatin falls into one of two major subtypes: closed heterochromatin and
euchromatin which is accessible, transcriptionally active, and occupied by transcription …