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rna-seqblog.com /1 month ago

seq2ribo – structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA...

New computational methods combine RNA sequencing knowledge with artificial intelligence to predict ribosome behavior directly from RNA sequences, supporting mRNA design and...

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rna-seqblog.com /1 day 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

Position-dependent codon occurrence is associated with patterns of translational efficiency and ribosomal occupancy in t...

by Kaavya Subramanian, Nathan Waugh, Cole Shanks, David A. Hendrix All life depends on the reliable translation of RNA to protein according to complex interactions between transla...

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rna-seqblog.com /4 weeks ago

Precursor tRNAs sense temperature changes: heat stress-induced capped pre-tRNAs suppress protein synthesis

RNA sequencing reveals how capped precursor tRNAs respond to heat stress and regulate protein synthesis by competing with messenger RNA for translation machinery...

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rna-seqblog.com /1 week 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 /5 days ago

New method allows scientists to follow gene activity over time in the same cells

Live-cell RNA sequencing uses engineered virus-like particles to repeatedly sample transcriptomes without destroying cells, enabling researchers to track gene expression changes ov...

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rna-seqblog.com /1 month ago

Seq-Scope-X pushes spatial transcriptomics beyond optical resolution

RNA sequencing combined with tissue expansion enabled ultra-high-resolution spatial transcriptomics, allowing researchers to map gene activity within individual cells with...

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journals.plos.org /1 week 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 /4 weeks ago

Machine learning improves RNA sequencing annotation of active genes

Machine learning improves interpretation of RNA sequencing data, helping researchers accurately identify active genes, non-coding RNAs, and other transcription units...

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rna-seqblog.com /1 month ago

The Lomb–Scargle periodogram-based differentially expressed gene detection along pseudotime

RNA sequencing combined with a new computational method improved detection of genes that change during cellular transitions, helping researchers better understand...

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rna-seqblog.com /2 weeks 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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bioengineer.org /2 weeks ago

RAS Rewires Ribosomes, Reshaping How Cells Read the Genetic Code

Cancer cells may be able to reprogram more than gene activity and signaling networks. A study led by researchers at Fudan University and Zhongshan Hospital in Shanghai reports that...

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rna-seqblog.com /1 month ago

Spatial transcriptomics benchmark compares leading platforms

RNA sequencing and spatial transcriptomics were combined to benchmark leading platforms, helping researchers compare how accurately each maps gene activity within complex tissues.....

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rna-seqblog.com /2 weeks ago

An end-to-end computational framework for “Record-seq” transcriptional recording data

A new framework adapts RNA sequencing analysis for Record-seq, improving spacer extraction, transcription-unit quantification, normalization, differential expression, and modeling...

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journals.plos.org /1 month ago

Accurate <i>de novo</i> transcription unit annotation from run-on and sequencing data

by Paul R. Munn, Jay Chia, Charles G. Danko Functional element annotations are critical tools used to provide insight into the molecular processes governing cell development, diff...

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rna-seqblog.com /1 month ago

Nanopore RNA sequencing maps mitochondrial tRNA modifications in yeast

RNA sequencing mapped chemical modifications across yeast mitochondrial tRNAs, providing new insight into RNA maturation and mechanisms that may influence human...

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rna-seqblog.com /1 month ago

Benchmarking long-read RNA sequencing tools for single-cell and spatial transcriptomics

RNA sequencing benchmark compares long-read bioinformatics tools for single-cell and spatial transcriptomics, helping researchers improve isoform detection and gene...

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rna-seqblog.com /3 weeks ago

MitoClipSplice – machine learning improves RNA sequencing analysis of mitochondrial RNA processing

RNA sequencing combined with machine learning identifies mitochondrial RNA cleavage sites from soft-clipped reads, providing a new approach for investigating mitochondrial RNA...

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rna-seqblog.com /3 weeks ago

Tidesurf improves RNA velocity analysis for modern single-cell RNA sequencing

Tidesurf improves RNA sequencing analysis by accurately quantifying spliced and unspliced transcripts across 3' and 5' protocols for more reliable RNA velocity estimates...

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rna-seqblog.com /3 weeks ago

From bench to bytes: a practical guide to RNA sequencing data analysis

A practical guide helps molecular biologists understand RNA sequencing data analysis, from quality control and normalization to differential expression and biological interpretatio...

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webwire.com /2 days ago

New method allows scientists to follow gene activity over time in the same cells

The following press release was issued by the Broad Institute of MIT and Harvard. - - In recent years, scientists have built methods to measure a cell's transcriptome, or all t...

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rna-seqblog.com /2 weeks ago

ExoShorkie – predicting RNA-seq coverage of exogenous genomes in yeast by transfer learning

ExoShorkie uses RNA sequencing data and transfer learning to predict expression from exogenous DNA, supporting more accurate gene-regulation models and synthetic biology...

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rna-seqblog.com /3 weeks ago

New RNA sequencing model improves sequencing depth planning for UMI transcriptomics

RNA sequencing model NB-Lib predicts sequencing depth requirements from shallow pilot data while accounting for library complexity, amplification differences, and molecular recover...

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rna-seqblog.com /1 month ago

NanoncRNA-seq – an rRNA-depleted full-length transcriptome strategy for identification of novel lncRNA isoforms

A new RNA sequencing workflow using nanopore technology improves full-length lncRNA isoform discovery, revealing many previously undetected transcripts missed by conventional short...

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