Latest updates for Rna-Seq

Fresh curated links around RNA-Seq are collected here so marketers can spot useful updates and turn timely ideas into posts faster.

Recent items include:

  • An end-to-end computational framework for “Record-seq” transcriptional recording data
  • From bench to bytes: a practical guide to RNA sequencing data analysis
  • NanoncRNA-seq – an rRNA-depleted full-length transcriptome strategy for identification of novel lncRNA isoforms

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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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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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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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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

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

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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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 /1 month ago

Amaranth – enhanced single-cell transcript assembly via discriminative modelling of UMI reads and internal reads

Amaranth improves transcript reconstruction from RNA sequencing data by modeling different read types, enabling more accurate isoform analysis at single-cell resolution...

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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 /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 /4 weeks ago

The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance

Long-read RNA sequencing combined with practical quality-control measures reduces mapping bias and improves the accuracy of allele-specific gene expression measurements...

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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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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 /1 week ago

Ultrafast and reference-free sequence discovery in single-cell data

Malva enables ultrafast, reference-free searches across massive single-cell RNA sequencing datasets for mutations, splice junctions, pathogens, transcripts, and other sequence-leve...

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rna-seqblog.com /6 days ago

RNA sequencing reveals functional chimeric mRNAs in mammalian immunity

Direct RNA sequencing revealed thousands of chimeric mRNAs in mammalian cells, uncovering previously unknown proteins with roles in immunity, inflammation, and potential drug disco...

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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

ISAtools improves full-length RNA isoform analysis from long-read RNA sequencing

RNA sequencing with ISAtools enables accurate reconstruction and quantification of full-length RNA isoforms while efficiently processing large PacBio sequencing datasets...

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rna-seqblog.com /5 days ago

Single-cell and single-embryo RNA sequencing

Single-cell and single-embryo RNA sequencing enables detailed analysis of gene expression and cell identity during the earliest stages of embryonic development...

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rna-seqblog.com /4 weeks ago

NextLongIso – a comprehensive Nextflow pipeline for multi-dimensional long-read RNA-seq analysis

NextLongIso provides a unified RNA sequencing pipeline for analyzing transcript isoforms, alternative splicing, promoter usage, and...

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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 month ago

STGBench – sequencing-level spatial DNA-RNA simulation for multimodal and virtual cell-oriented benchmarking of genomic...

STGBench generates realistic paired DNA and RNA sequencing datasets with known genetic alterations, enabling accurate benchmarking of spatial genomics and transcriptomics analysis....

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rna-seqblog.com /1 month ago

DeepDETAILS – high-resolution reconstruction of cell-type-specific transcriptional regulatory processes from bulk sequen...

DeepDETAILS combines artificial intelligence with RNA sequencing and chromatin data to reconstruct cell-specific gene regulation from bulk tissue sequencing experiments...

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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

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

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