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rna-seqblog.com /1 month ago

PotatoRTD and TomatoRTD: comprehensive reference transcript datasets for accurate transcriptome analysis and isoform dis...

RNA sequencing and Iso-Seq improve potato and tomato transcript annotations, revealing additional isoforms and enabling more accurate analysis of gene expression and alternative sp...

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rna-seqblog.com /1 month ago

Avoiding a sticky situation: how cells stop messenger RNAs from clumping together

RNA sequencing reveals how naturally occurring mRNA sequences may reduce harmful RNA aggregation, offering insights into transcriptome stability and the design of mRNA therapeutics...

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journals.plos.org /6 days ago

Computational deconvolution of drug sensitivity via single-cell–to–bulk transcriptome mapping

by Alexandre Coudray, Romain Forey, Benjamin Bejar Haro, Filipe Martins, Joana Carlevaro-Fita, Shaoline Sheppard, Sandra Eloise Offner, Gioele La Manno, Guillaume Obozinski, Didier...

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rna-seqblog.com /1 month ago

A real-data approach to evaluating RNA transcript analysis methods

RNA sequencing data provide a real-world framework for comparing differential transcript usage methods across bulk, single-cell, spatial, long-read, and short-read transcriptomics....

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journals.plos.org /1 month ago

AET5: A transcriptome-guided molecular generation framework with contrastive self-supervised learning

by Zhikang Yuan, Xin Zhang, Gaoming Lin, Quan Zou, Subhashisa Swain, Yijie Ding, Prayag Tiwari, Shuofeng Yuan, Xiaoyi Guo Gene expression profiles capture system-level drug respon...

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journals.plos.org /4 weeks ago

Glycan reachability analysis: A bottleneck-aware framework for inferring tissue-specific glycan biosynthetic potential f...

by Yusuke Matsui Glycan biosynthesis requires the coordinated expression of glycosyltransferases, modifying enzymes, and nucleotide-sugar synthesis and transport machinery. Existi...

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rna-seqblog.com /1 month ago

POND-seq enables non-destructive RNA sequencing in living cells

POND-seq enables non-destructive RNA sequencing of living cells, allowing repeated measurement of transcriptomes and RNA-binding protein interactions as cells respond to changing c...

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journals.plos.org /1 month ago

Characterization of METTL3/14-mediated m<sup>6</sup>A modification in human transcriptome using Nanopore dir...

by Emily Kurtyan, Andrew J. Stein, Kelly J. Abdalla, Zhangerjiao Yuan, Miten Jain, Fadia Ibrahim Post-transcriptional RNA modifications modulate diverse aspects of RNA metabolism....

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rna-seqblog.com /3 weeks ago

The Human RNome Project Consortium seeks to publish first-ever complete sequence of the bodyÐ²Ð‚â„¢s RNA

RNA sequencing efforts from the Human RNome Project aim to build a comprehensive reference of human RNA sequences, isoforms, processing states and chemical modifications...

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journals.plos.org /3 weeks ago

Integrating zero-inflation correction and transcriptional kinetics for single-cell transcriptomic analysis

by Chengkai Yang, Yu Liao, Ying Sheng, Feng Jiao Single-cell transcriptomic data exhibit pervasive zero inflation, while traditional models either neglect this issue or fail to ca...

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rna-seqblog.com /2 weeks ago

DeCoRE – a computational method to resolve RNA structural heterogeneity from RNA structure probing data by direct RNA se...

Direct RNA sequencing with DeCoRE reveals alternative RNA structures and folding dynamics at single-nucleotide resolution, providing a detailed view of transcript-level structural....

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fightaging.org /1 week ago

Transcriptomic Approaches to Guiding the Discovery of Geroprotective Compounds

A great deal of drug discovery starts by screening compounds from the vast libraries of molecules that exist. The libraries are too large to screen everything (and even then the sc...

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journals.plos.org /3 weeks ago

Genome wide transcriptional changes underlie gradual and recurrent adaptation to protein malnutrition in zebrafish

by Siyao Wang, Laura Childers, Fernando Martinez III, Michel Bagnat, Jieun Park Lysosome-rich enterocytes (LREs) are a specialized population of intestinal cells that mediate the...

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rna-seqblog.com /3 weeks ago

ResolVI improves accuracy in spatial transcriptomics analysis

ResolVI improves spatial RNA sequencing analysis by correcting RNA assignment errors and technical variation, helping researchers distinguish cell states and detect subtle gene exp...

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rna-seqblog.com /1 month ago

A functionally integrated cross-tissue alternative splicing program during short-term calorie restriction

RNA sequencing reveals that calorie restriction drives dose-responsive alternative splicing across multiple tissues, affecting mitochondrial, translational, and RNA quality-control...

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rna-seqblog.com /6 days ago

RNAmel simplifies RNA sequencing data analysis with a reproducible, integrated platform

RNAmel integrates RNA sequencing data analysis, gene expression profiling, pathway enrichment and visualization into a reproducible platform that simplifies...

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rna-seqblog.com /1 month ago

Benchmarking RNA sequencing for more accurate alternative splicing analysis

RNA sequencing benchmarking across 42 laboratories identifies data quality, sequencing depth, and bioinformatics choices that improve alternative splicing and isoform analysis...

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rna-seqblog.com /1 month ago

Spatial mapping of RNA turnover kinetics in the mouse brain

Spatial RNA sequencing maps RNA synthesis and degradation across the mouse brain, revealing how different regions rapidly adjust gene expression in response to stimulation...

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rna-seqblog.com /1 month ago

Immune cells offer insights on billion-dollar virus

Single-nucleus RNA sequencing reveals cell-specific immune responses to white spot syndrome virus in whiteleg shrimp, identifying genes that may support future disease-resistance s...

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journals.plos.org /1 month ago

Multi-organ single-cell transcriptomic atlas identifies <i>QrIAA14</i> as a candidate negative regulator of...

by Wenkai Hui, Jiayue Li, Hao Li, Hongyi Wu, Yi He, Shuangying Yang, Xiong Huang, Hanbo Yang, Gang Chen, Peng Zhu, Xiaohong Chen, Xingcui Xiao, Yu Zhong, Zhenfeng Xu, Fang He Plan...

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bioengineer.org /2 weeks ago

Rumen Fluke Parasite Reveals Its Molecular Playbook Across Life Stages

A new transcriptomic study of the rumen fluke Calicophoron daubneyi reveals that its eggs, rediae and cercariae each deploy distinct gene programs tuned to survival, proliferation...

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journals.plos.org /1 week ago

Sparse neuronal C4 elevation induces network-wide transcriptomic and lipid-droplet remodeling in the cortical microenvir...

by Marta Sánchez-Carbonell, Sonia Bolshakova, Juan E. Ávila-Pagán, Yaseer A. Sabir, Clay Griffin-Derr, Dominik G. Stich, Sofia V. Cieslewicz, Sheyla Esther Carmen Sifuentes, Rhushi...

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journals.plos.org /2 weeks ago

Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular hetero...

by Dee Velazquez, Caleb Hallinan, Roujin An, Kalen Clifton, Jean Fan Imaging-based spatially resolved transcriptomics (imSRT) technologies provide high-throughput molecular-resolu...

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rna-seqblog.com /4 weeks ago

Single-cell TimeLapse-seq reveals MTA is an essential retrotransposon

Very early in development, an embryo must begin using its own genome instead of relying only on RNA and proteins inherited from the egg. This transition is known as zygotic genome...

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