MSIQ: Joint Modeling of Multiple RNA-seq Samples for Accurate Isoform Quantification [PDF]
Ann. Appl. Stat. 12(1) (2018) 510-539, 2016 Next-generation RNA sequencing (RNA-seq) technology has been widely used to assess full-length RNA isoform abundance in a high-throughput manner. RNA-seq data offer insight into gene expression levels and transcriptome structures, enabling us to better understand the regulation of gene expression and fundamental biological processes.
Li, Jingyi Jessica +3 more
arxiv +4 more sources
Methods to study splicing from high-throughput RNA Sequencing data [PDF]
Methods Mol Biol. 2014;1126:357-97, 2013 The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be analyzed has turned this into a challenging task.
A Ameur +131 more
arxiv +3 more sources
Transcription of a 5’ extended mRNA isoform directs dynamic chromatin changes and interference of a downstream promoter [PDF]
eLife, 2017 Cell differentiation programs require dynamic regulation of gene expression. During meiotic prophase in Saccharomyces cerevisiae, expression of the kinetochore complex subunit Ndc80 is downregulated by a 5’ extended long undecoded NDC80 transcript ...
Minghao Chia +6 more
doaj +3 more sources
An expectation-maximization framework for comprehensive prediction of isoform-specific functions. [PDF]
, 2023 MOTIVATION: Advances in RNA sequencing technologies have achieved an unprecedented accuracy in the quantification of mRNA isoforms, but our knowledge of isoform-specific functions has lagged behind.
Carmody, Leigh +8 more
core +2 more sources
TAGET: a toolkit for analyzing full-length transcripts from long-read sequencing
Nature Communications, 2023 Single-molecule Real-time Isoform Sequencing (Iso-seq) of transcriptomes by PacBio can generate very long and accurate reads, thus providing an ideal platform for full-length transcriptome analysis.
Yuchao Xia +10 more
doaj +1 more source
Frontiers in Genetics, 2021 The SALL2 transcription factor, an evolutionarily conserved gene through vertebrates, is involved in normal development and neuronal differentiation. In disease, SALL2 is associated with eye, kidney, and brain disorders, but mainly is related to cancer ...
Carlos Farkas +9 more
doaj +1 more source
A large-scale comparative study of isoform expressions measured on four platforms
BMC Genomics, 2020 Background Most eukaryotic genes produce different transcripts of multiple isoforms by inclusion or exclusion of particular exons. The isoforms of a gene often play diverse functional roles, and thus it is necessary to accurately measure isoform ...
Wei Zhang +6 more
doaj +1 more source
Investigating isoform switching in RHBDF2 and its role in neoplastic growth in breast cancer [PDF]
PeerJ, 2022 Background Breast cancer is the second leading cause of cancer-related deaths globally, and its prevalence rates are increasing daily. In the past, studies predicting therapeutic drug targets for cancer therapy focused on the assumption that one gene is ...
Mehar Masood +5 more
doaj +2 more sources
Improved prediction of smoking status via isoform-aware RNA-seq deep learning models.
PLoS Computational Biology, 2021 Most predictive models based on gene expression data do not leverage information related to gene splicing, despite the fact that splicing is a fundamental feature of eukaryotic gene expression.
Zifeng Wang +11 more
doaj +1 more source
Regulatory Divergence of Transcript Isoforms in a Mammalian Model System. [PDF]
PLoS ONE, 2015 Phenotypic differences between species are driven by changes in gene expression and, by extension, by modifications in the regulation of the transcriptome.
Sarah Leigh-Brown +8 more
doaj +1 more source