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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....
RNA sequencing reveals that calorie restriction drives dose-responsive alternative splicing across multiple tissues, affecting mitochondrial, translational, and RNA quality-control...
Long-read RNA sequencing and APALORD reveal how alternative polyadenylation changes during neuronal differentiation and identify new patterns of RNA processing across species...
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...
RNA sequencing benchmarking across 42 laboratories identifies data quality, sequencing depth, and bioinformatics choices that improve alternative splicing and isoform analysis...
RNA Variant Imaging is attracting attention because it addresses a persistent blind spot in cancer diagnostics: many clinically relevant RNA isoforms, splice events, and fusion tra...
RNA sequencing reveals cancer-associated transcriptional alleles and differences between prostate cancer stem cells and other tumor cells, identifying candidate alterations for fur...
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...
A new RNA sequencing analysis method uses the Lomb-Scargle periodogram to efficiently identify genes associated with pseudotime across complex single-cell trajectories...
RNA sequencing reveals two opposing patterns of brain gene activity across genetically diverse autism-risk mouse models, with differences...
Single-cell RNA sequencing combined with GP-DHT helps predict transcription factor and target gene relationships, providing a...
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....
Long-read RNA sequencing analysis shows that handling biological replicates differently can influence transcript reconstruction and the discovery of novel RNA isoforms...
by Yi Qiu, Emilie Hebraud, Fanny Pouyet, Alexander F. Palazzo In the human genome, mutation rates vary along genes, yet how their fine-scale structure contributes to gene evolutio...
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...
by Rafael Riudavets Puig, Denise G. O’Mahony, Ina Skaara Brorson, Ksenia Sokolova, Vessela N. Kristensen, Anthony Mathelier Transcription is regulated through the sequence-specifi...
Short-read RNA sequencing reporting the modifications that alter protein output is starting to make epitranscriptomics indispensable for patient selection in precision medicines. T...
by Alicia Lou, Juan F. Poyatos, Monica Chagoyen Housekeeping genes are commonly defined as broadly expressed genes that support essential cellular function. However, their identif...
Researchers developed CASREL, a machine learning framework that uses single-cell RNA sequencing to identify potential regulators of alternative splicing across different tissues an...
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...
RNA sequencing combined with qMAP reveals regulatory RNA fragmentation patterns associated with cell reprogramming, ulcerative colitis, implantation failure, and aging...
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...
by Penghui Song, Lijuan Ma, Dong Yan N6-methyladenosine (m6A), one of the most abundant chemical modifications on RNA, is installed by METTL3 and several other methyltransferases,...
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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