Latest updates for Differential Transcript Usage

Fresh curated links around differential transcript usage are collected here so marketers can spot useful updates and turn timely ideas into posts faster.

Recent items include:

  • A functionally integrated cross-tissue alternative splicing program during short-term calorie restriction
  • Accurate <i>de novo</i> transcription unit annotation from run-on and sequencing data
  • The Lomb–Scargle periodogram-based differentially expressed gene detection along pseudotime

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rna-seqblog.com /2 weeks 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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journals.plos.org /1 month ago

Accurate &lt;i&gt;de novo&lt;/i&gt; 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

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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journals.plos.org /1 day ago

Not every gene is special: Modelling scale controls the false discovery rate when analysing high-throughput sequencing d...

by Scott J. Dos Santos, Andreea C. Murariu, Justin D. Silverman, Gregory B. Gloor Differential expression/abundance analyses are commonplace in studies employing high-throughput s...

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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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journals.plos.org /1 week ago

ASPIRE: Accurate alternative splicing prediction from limited RNA sequencing data and a minimal gene set

by Ran Eisenberg, Efraim Rahamim, Eli Kopel, Miri Danan-Gotthold, Erez Y. Levanon, Ofir Lindenbaum Alternative splicing is a fundamental biological mechanism that increases protei...

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journals.plos.org /1 month ago

Comparative single-nucleus transcriptomics reveals asymmetric evolution of the &lt;i&gt;Drosophila&lt;/i&gt; male and fe...

by Imtiyaz E. Hariyani, Sudeshna Das, Emma M. Le, Carmen Gamero-Castano, Tina Soroudi, Joshua Choi, Spring Momeni, Justin C. Kim, Rongying Lu, Vivek Swarup, José M. Ranz Reproduct...

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rna-seqblog.com /1 week ago

scLS – a computationally efficient differentially expressed gene detection algorithm

A new RNA sequencing analysis method uses the Lomb-Scargle periodogram to efficiently identify genes associated with pseudotime across complex single-cell trajectories...

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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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journals.plos.org /1 week ago

Characterization of METTL3/14-mediated m&lt;sup&gt;6&lt;/sup&gt;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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journals.plos.org /1 month ago

Neuronal protein Sex-lethal modulates tRNA synthesis via the polymerase III subunit Polr3E in male &lt;i&gt;Drosophila&l...

by Freya Storer, Colin D. McClure, Alicia Estacio Gomez, Lucy J. Minkley, Tsz Lam Wong, Nina Markevych, Tony D. Southall The RNA-binding protein Sex-lethal (Sxl) is classically kn...

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journals.plos.org /4 weeks ago

Social isolation upregulates &lt;i&gt;takeout&lt;/i&gt; expression in female &lt;i&gt;Drosophila melanogaster&lt;/i&gt;...

by Elisabeth A. Tawa, Lisa Schneper, Katherine I. Cho, Mindy Sim, Eve Schoeffler, Daniel A. Notterman Previous research suggests that social isolation induces changes in gene expr...

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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 /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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journals.plos.org /1 week ago

A Bayesian framework for multivariate differential analysis

by Marie Chion, Arthur Leroy Differential analysis is a routine procedure in the statistical analysis toolbox across many applied fields, including quantitative proteomics, the ma...

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journals.plos.org /1 month ago

Disruption of small RNAs and mechanistic variation in &lt;i&gt;Segregation Distorter:&lt;/i&gt; A sperm-killing drive sy...

by Logan T. Edvalson, Xiaolu Wei, Ching-Ho Chang, Amanda M. Larracuente Meiotic drivers achieve biased transmission to the next generation, often at the expense of their host. Dri...

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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

Assessing scale and predictive diversity in models for single-cell transcriptomics based on Geneformer

by Junfan Chen, Fabian Schmidt, Ricardo Henao Single-cell transcriptomic data provide critical insights into cellular states and disease mechanisms, and foundation models have rec...

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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 /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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Sources covering Differential Transcript Usage

journals.plos.org

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journals.plos.org

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journals.plos.org

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rna-seqblog.com

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Publications rna sequencing gene expression bioinformatics transcriptomics Analysis Pipelines Annotation Commentary Computational Biology Expression and Quantification Machine learning Single-cell RNA sequencing

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