Explanipedia

Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer Open

Heather Karner, Tabea Mittmann, Vicky Chen, Ashir A. Borah, Adrianus J. de Langen , et al. · 2025

Heterogeneity in cancer gene expression is typically linked to genetic and epigenetic alterations, yet post-transcriptional regulation likely influences these patterns as well. However, the quantitative contribution of post-transcriptional…

Discovery of a tRNA-regulatory transcription factor that suppresses breast cancer metastasis Open

Siyu Chen, Daniel Markett, Mehran Karimzadeh, Yikai Luo, Matvei Khoroshkin , et al. · 2025

Transfer RNAs (tRNAs), once viewed as static adaptors in translation, are now recognized as dynamic regulators of gene expression. While recent studies have illuminated roles for tRNA stability, the upstream mechanisms governing tRNA trans…

Decoy-seq unlocks scalable genetic screening for regulatory small noncoding RNAs Open

Bong Gun Choi, Sushil Sobti, Larisa M. Soto, Trey Charbonneau, Aiden M Sababi , et al. · 2025

Small noncoding RNAs (smRNAs) play critical roles in regulating various cellular processes, including development, stress response, and disease pathogenesis. However, functional characterization of smRNAs remains limited by the scale and s…

A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation Open

Alex Y. Ge, Abolfazl Arab, Raymond Dai, Albertas Navickas, Lisa Fish , et al. · 2024

Author Correction: Systematic identification of post-transcriptional regulatory modules Open

Matvei Khoroshkin, Andrey Buyan, Martin Dodel, Albertas Navickas, Johnny Yu , et al. · 2024

Systematic identification of post-transcriptional regulatory modules Open

Matvei Khoroshkin, Andrey Buyan, Martin Dodel, Albertas Navickas, Johnny Yu , et al. · 2024

In our cells, a limited number of RNA binding proteins (RBPs) are responsible for all aspects of RNA metabolism across the entire transcriptome. To accomplish this, RBPs form regulatory units that act on specific target regulons. However, …

Integrative identification of non-coding regulatory regions driving metastatic prostate cancer Open

Brian Woo, Ruhollah Moussavi-Baygi, Heather Karner, Mehran Karimzadeh, Hassan Yousefi , et al. · 2024

Large-scale sequencing efforts have been undertaken to understand the mutational landscape of the coding genome. However, the vast majority of variants occur within non-coding genomic regions. We designed an integrative computational and e…

A systematic search for RNA structural switches across the human transcriptome Open

Matvei Khoroshkin, Daniel Asarnow, Shaopu Zhou, Albertas Navickas, Aidan Winters , et al. · 2024

Accurate isoform quantification by joint short- and long-read RNA-sequencing Open

Michael Apostolides, Man Hung Choi, Albertas Navickas, Alihossein Saberi, Larisa M. Soto , et al. · 2024

Accurate quantification of transcript isoforms is crucial for understanding gene regulation, functional diversity, and cellular behavior. Existing RNA sequencing methods have significant limitations: short-read (SR) sequencing provides hig…

Post-transcriptional gene regulation: From mechanisms to RNA chemistry and therapeutics Open

Clara Bonnet, Ana Luisa Dian, Tristan Espie-Caullet, Lucilla Fabbri, Lucie Lagadec , et al. · 2024

Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers Open

Jeffrey Wang, Jung Min Suh, Brian J Woo, Albertas Navickas, Kristle Garcia , et al. · 2024

From extrachromosomal DNA to neo-peptides, the broad reprogramming of the cancer genome leads to the emergence of molecules that are specific to the cancer state. We recently described orphan non-coding RNAs (oncRNAs) as a class of cancer-…

Revealing the grammar of small RNA secretion using interpretable machine learning Open

Bahar Zirak, Mohsen Naghipourfar, Alihossein Saberi, Delaram Pouyabahar, Amirhossein Zarezadeh , et al. · 2024

Translational adaptation in breast cancer metastasis and emerging therapeutic opportunities Open

Siyu Chen, Albertas Navickas, Hani Goodarzi · 2024

A bi-steric mTORC1-selective inhibitor overcomes drug resistance in breast cancer Open

Delong Meng, Xin Zhao, Yu Chi Yang, Albertas Navickas, Ciara Helland , et al. · 2023

Activation of the PI3K-mTOR pathway is central to breast cancer pathogenesis including resistance to many targeted therapies. The mTOR kinase forms two distinct complexes, mTORC1 and mTORC2, and understanding which is required for the surv…

A sense-antisense RNA interaction promotes breast cancer metastasis via regulation of NQO1 expression Open

Bruce Culbertson, Kristle Garcia, Daniel Markett, Hosseinali Asgharian, Li Chen , et al. · 2023

An mRNA processing pathway suppresses metastasis by governing translational control from the nucleus Open

Albertas Navickas, Hosseinali Asgharian, Juliane Winkler, Lisa Fish, Kristle Garcia , et al. · 2023

Cancer cells often co-opt post-transcriptional regulatory mechanisms to achieve pathologic expression of gene networks that drive metastasis. Translational control is a major regulatory hub in oncogenesis; however, its effects on cancer pr…

Integrative identification of non-coding regulatory regions driving metastatic prostate cancer Open

Brian J Woo, Ruhollah Moussavi-Baygi, Heather Karner, Mehran Karimzadeh, Kristle Garcia , et al. · 2023

Large-scale sequencing efforts of thousands of tumor samples have been undertaken to understand the mutational landscape of the coding genome. However, the vast majority of germline and somatic variants occur within non-coding portions of …

Revealing the Grammar of Small RNA Secretion Using Interpretable Machine Learning Open

Bahar Zirak, Mohsen Naghipourfar, Alihossein Saberi, Delaram Pouyabahar, Amirhossein Zarezadeh , et al. · 2023

Small non-coding RNAs can be secreted through a variety of mechanisms, including exosomal sorting, in small extracellular vesicles, and within lipoprotein complexes 1,2 . However, the mechanisms that govern their sorting and secretion are …

Table S2 from RBMS1 Suppresses Colon Cancer Metastasis through Targeted Stabilization of Its mRNA Regulon Open