Challenges and best practices in omics benchmarking
TG Brooks, NF Lahens, A Mrčela, GR Grant - Nature Reviews Genetics, 2024 - nature.com
Technological advances enabling massively parallel measurement of biological features—
such as microarrays, high-throughput sequencing and mass spectrometry—have ushered in …
such as microarrays, high-throughput sequencing and mass spectrometry—have ushered in …
[HTML][HTML] Leveraging multi-omics data to infer regulators of mRNA 3'end processing in glioblastoma
Alterations in mRNA 3'end processing and polyadenylation are widely implicated in the
biology of many cancer types, including glioblastoma (GBM), one the most aggressive tumor …
biology of many cancer types, including glioblastoma (GBM), one the most aggressive tumor …
Alternative Transcripts Diversify Genome Function for Phenome Relevance to Health and Diseases
SA Carrion, JJ Michal, Z Jiang - Genes, 2023 - mdpi.com
Manipulation using alternative exon splicing (AES), alternative transcription start (ATS), and
alternative polyadenylation (APA) sites are key to transcript diversity underlying health and …
alternative polyadenylation (APA) sites are key to transcript diversity underlying health and …
PolyASite v3. 0: a multi-species atlas of polyadenylation sites inferred from single-cell RNA-sequencing data
Y Moon, CJ Herrmann, A Mironov… - Nucleic Acids …, 2025 - academic.oup.com
The broadly used 10X Genomics technology for single-cell RNA sequencing (scRNA-seq)
captures RNA 3′ ends. Thus, some reads contain part of the non-templated polyadenosine …
captures RNA 3′ ends. Thus, some reads contain part of the non-templated polyadenosine …
[HTML][HTML] TDP-43 loss induces extensive cryptic polyadenylation in ALS/FTD
Nuclear depletion and cytoplasmic aggregation of the RNA-binding protein TDP-43 is the
hallmark of ALS, occurring in over 97% of cases. A key consequence of TDP-43 nuclear loss …
hallmark of ALS, occurring in over 97% of cases. A key consequence of TDP-43 nuclear loss …
Alternative 3′ UTR expression induced by T cell activation is regulated in a temporal and signal dependent manner
The length of 3′ untranslated regions (3′ UTR) is highly regulated during many transitions
in cell state, including T cell activation, through the process of alternative polyadenylation …
in cell state, including T cell activation, through the process of alternative polyadenylation …
TDP-43 dysregulation of polyadenylation site selection is a defining feature of RNA misprocessing in ALS/FTD and related disorders
Nuclear clearance and cytoplasmic aggregation of the RNA-binding protein TDP-43 are
observed in many neurodegenerative disorders, including amyotrophic lateral sclerosis …
observed in many neurodegenerative disorders, including amyotrophic lateral sclerosis …
ZARP: A user-friendly and versatile RNA-seq analysis workflow
Background RNA sequencing (RNA-seq) is a widely used technique in many scientific
studies. Given the plethora of models and software packages that have been developed for …
studies. Given the plethora of models and software packages that have been developed for …
[HTML][HTML] InPAS: An R/Bioconductor Package for Identifying Novel Polyadenylation Sites and Alternative Polyadenylation from Bulk RNA-seq Data
Background: Alternative cleavage and polyadenylation (APA) is a crucial post-transcriptional
gene regulation mechanism that regulates gene expression in eukaryotes by increasing the …
gene regulation mechanism that regulates gene expression in eukaryotes by increasing the …
Deep Learning Models of Polyadenylation Regulation and Applications in Genetics
EK Stroup - 2024 - search.proquest.com
RNA processing tightly couples transcription to the 5'cap**, intron splicing, and 3'-end
formation of pre-mRNA to produce a mature mRNA prepared for export to the cytoplasm and …
formation of pre-mRNA to produce a mature mRNA prepared for export to the cytoplasm and …