Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635983 | PMC |
| http://dx.doi.org/10.1105/tpc.17.00742 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Unraveling new avenues in pancreatic cancer treatment: A comprehensive exploration of drug repurposing using transcriptomic data.
Comput Biol Med
February 2025
Department of Mechatronics Engineering, Jeju National University, Republic of Korea. Electronic address:
Pancreatic cancer, a malignancy notorious for its late-stage diagnosis and low patient survival rates, remains a formidable global health challenge. The currently available FDA-approved treatments for pancreatic cancer, notably chemotherapeutic agents, exhibit suboptimal efficacy, often accompanied by concerns regarding toxicity. Given the intricate nature of pancreatic cancer pathogenesis and the time-intensive nature of in silico drug discovery approaches, drug repurposing emerges as a compelling strategy to expedite the development of novel therapeutic interventions.
View Article and Find Full Text PDFModeling APOE ε4 familial Alzheimer's disease in directly converted 3D brain organoids.
Front Aging Neurosci
August 2024
Department of Chemistry, Dongguk University, Seoul, Republic of Korea.
Brain organoids have become a valuable tool for studying human brain development, disease modeling, and drug testing. However, generating brain organoids with mature neurons is time-intensive and often incomplete, limiting their utility in studying age-related neurodegenerative diseases such as Alzheimer's disease (AD). Here, we report the generation of 3D brain organoids from human fibroblasts through direct reprogramming, with simplicity, efficiency, and reduced variability.
View Article and Find Full Text PDFUnsupervised Single-Cell Clustering with Asymmetric Within-Sample Transformation and Per-Cluster Supervised Features Selection.
Methods Mol Biol
July 2024
Department of Science and Technology, Università degli Studi del Sannio, Benevento, Italy.
This chapter shows applying the Asymmetric Within-Sample Transformation to single-cell RNA-Seq data matched with a previous dropout imputation. The asymmetric transformation is a special winsorization that flattens low-expressed intensities and preserves highly expressed gene levels. Before a standard hierarchical clustering algorithm, an intermediate step removes noninformative genes according to a threshold applied to a per-gene entropy estimate.
View Article and Find Full Text PDFPrecision nuclear run-on (PRO) sequencing (PRO-seq) is a powerful technique for mapping polymerase active sites with nucleotide resolution and measuring newly synthesized transcripts at both promoters and enhancer elements. The current PRO-seq protocol is time-intensive, technically challenging, and requires a large amount of starting material. To overcome these limitations, we developed rapid PRO-seq (rPRO-seq) which utilizes pre-adenylated single-stranded DNAs (AppDNA), a dimer blocking oligonucleotide (DBO), on-bead 5' RNA end repair, and column-based purification.
View Article and Find Full Text PDFDecoding Transcription Regulatory Mechanisms Associated with Phase Transition Using Total RNA.
mSystems
February 2022
Department of Medicine, Division of Infectious Disease, UC San Diego School of Medicine, La Jolla, California, USA.
New or emerging infectious diseases are commonly caused by pathogens that cannot be readily manipulated or studied under common laboratory conditions. These limitations hinder standard experimental approaches and our abilities to define the fundamental molecular mechanisms underlying pathogenesis. The advance of capped small RNA sequencing (csRNA-seq) now enables genome-wide mapping of actively initiated transcripts from genes and other regulatory transcribed start regions (TSRs) such as enhancers at a precise moment from total RNA.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!