Opening the black box: interpretable machine learning for geneticists

CB Azodi, J Tang, SH Shiu - Trends in genetics, 2020 - cell.com
Because of its ability to find complex patterns in high dimensional and heterogeneous data,
machine learning (ML) has emerged as a critical tool for making sense of the growing …

mRNA therapeutics deliver a hopeful message

Z Zhong, S Mc Cafferty, F Combes, H Huysmans… - Nano today, 2018 - Elsevier
Messenger RNA based therapeutics have the potential to cause a big revolution in medicine
as they can facilitate personalized medicines and allow patients to produce their own …

CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs

S Zhong, J Feng - BMC bioinformatics, 2022 - Springer
Abstract Background Some circular RNAs (circRNAs) can be translated into functional
peptides by small open reading frames (ORFs) in a cap-independent manner. Internal …

Translation acrobatics: how cancer cells exploit alternate modes of translational initiation

A Sriram, J Bohlen, AA Teleman - EMBO reports, 2018 - embopress.org
Recent work has brought to light many different mechanisms of translation initiation that
function in cells in parallel to canonical cap‐dependent initiation. This has important …

Internal ribosome entry site (IRES)-mediated translation and its potential for novel mRNA-based therapy development

R Marques, R Lacerda, L Romão - Biomedicines, 2022 - mdpi.com
Many conditions can benefit from RNA-based therapies, namely, those targeting internal
ribosome entry sites (IRESs) and their regulatory proteins, the IRES trans-acting factors …

IRESpy: an XGBoost model for prediction of internal ribosome entry sites

J Wang, M Gribskov - BMC bioinformatics, 2019 - Springer
Background Internal ribosome entry sites (IRES) are segments of mRNA found in
untranslated regions that can recruit the ribosome and initiate translation independently of …

Human IRES Atlas: an integrative platform for studying IRES-driven translational regulation in humans

TH Yang, CY Wang, HC Tsai, CT Liu - Database, 2021 - academic.oup.com
It is now known that cap-independent translation initiation facilitated by internal ribosome
entry sites (IRESs) is vital in selective cellular protein synthesis under stress and different …

RNA-binding proteins as regulators of internal initiation of viral mRNA translation

B López-Ulloa, Y Fuentes, MS Pizarro-Ortega… - Viruses, 2022 - mdpi.com
Viruses are obligate intracellular parasites that depend on the host's protein synthesis
machinery for translating their mRNAs. The viral mRNA (vRNA) competes with the host …

DeepIRES: a hybrid deep learning model for accurate identification of internal ribosome entry sites in cellular and viral mRNAs

J Zhao, Z Chen, M Zhang, L Zou, S He… - Briefings in …, 2024 - academic.oup.com
The internal ribosome entry site (IRES) is a cis-regulatory element that can initiate
translation in a cap-independent manner. It is often related to cellular processes and many …

DeepCIP: a multimodal deep learning method for the prediction of internal ribosome entry sites of circRNAs

Y Zhou, J Wu, S Yao, Y Xu, W Zhao, Y Tong… - Computers in Biology …, 2023 - Elsevier
Circular RNAs (circRNAs) have been found to have the ability to encode proteins through
internal ribosome entry sites (IRESs), which are essential RNA regulatory elements for cap …