Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges

H Nguyen, H Nguyen, D Tran, S Draghici… - Nucleic Acids …, 2024 - academic.oup.com
Single-cell RNA sequencing (scRNA-Seq) is a recent technology that allows for the
measurement of the expression of all genes in each individual cell contained in a sample …

Establishing a conceptual framework for holistic cell states and state transitions

SM Rafelski, JA Theriot - Cell, 2024 - cell.com
Cell states were traditionally defined by how they looked, where they were located, and what
functions they performed. In this post-genomic era, the field is largely focused on a …

[HTML][HTML] Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex

LA Huuki-Myers, KD Montgomery, SH Kwon… - BioRxiv, 2024 - ncbi.nlm.nih.gov
Background: Cellular deconvolution of bulk RNA-sequencing (RNA-seq) data using single
cell or nuclei RNA-seq (sc/snRNA-seq) reference data is an important strategy for estimating …

Affinity-tagged SMAD1 and SMAD5 mouse lines reveal transcriptional reprogramming mechanisms during early pregnancy

Z Liao, S Tang, K Nozawa, K Shimada, M Ikawa… - Elife, 2024 - elifesciences.org
Endometrial decidualization, a prerequisite for successful pregnancies, relies on
transcriptional reprogramming driven by progesterone receptor (PR) and bone …

TDC-2: Multimodal Foundation for Therapeutic Science

A Velez-Arce, K Huang, MM Li, X Lin, W Gao, T Fu… - bioRxiv, 2024 - biorxiv.org
Abstract Therapeutics Data Commons (tdcommons. ai) is an open science initiative with
unified datasets, AI models, and benchmarks to support research across therapeutic …

An overview of key online resources for human genomics: a powerful and open toolbox for in silico research

DA Forero, DA Bonilla… - Briefings in …, 2024 - academic.oup.com
Recent advances in high-throughput molecular methods have led to an extraordinary
volume of genomics data. Simultaneously, the progress in the computational implementation …

[HTML][HTML] Melanocortin-4 Receptor PLC Activation Is Modulated by an Interaction with the Monocarboxylate Transporter 8

L Anthofer, P Gmach, ZC Uretmen Kagiali… - International Journal of …, 2024 - mdpi.com
The melanocortin-4 receptor (MC4R) is a key player in the hypothalamic leptin–
melanocortin pathway that regulates satiety and hunger. MC4R belongs to the G protein …

The GPR84 Antagonist GLPG1205 Reduces Features of Disease in Experimental Severe Asthma

C Donovan, AE Thorpe, HM Gomez… - American Journal of …, 2024 - atsjournals.org
Recent evidence has highlighted the detrimental effects of fatty acid receptor dysfunction in
the lung, with a major focus on the roles of short-and long-chain fatty acid receptors and …

Mapping a New Course to Understand Lung Biology Mechanisms: LungMAP. net

S Yang, K Gaietto, W Chen - American Journal of Respiratory Cell …, 2024 - atsjournals.org
The lung is a highly complex human organ, harboring over forty different cell types with
specialized functions to facilitate gas exchange and host defense (1). Single-cell omics …

scX: a user-friendly tool for scRNAseq exploration

TV Waichman, ML Vercesi, AA Berardino… - Bioinformatics …, 2024 - academic.oup.com
Motivation Single-cell RNA sequencing (scRNAseq) has transformed our ability to explore
biological systems. Nevertheless, proficient expertise is essential for handling and …