Human IRES Atlas: an integrative platform for studying IRES-driven translational regulation in humans
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 …
entry sites (IRESs) is vital in selective cellular protein synthesis under stress and different …
Integration of metabolic, regulatory and signaling networks towards analysis of perturbation and dynamic responses
The expanding generation of dynamic biological data requires approaches that integrate
and analyze information from different types of cellular processes–metabolism, regulation …
and analyze information from different types of cellular processes–metabolism, regulation …
Three topological features of regulatory networks control life-essential and specialized subsystems
Gene regulatory networks (GRNs) play key roles in development, phenotype plasticity, and
evolution. Although graph theory has been used to explore GRNs, associations amongst …
evolution. Although graph theory has been used to explore GRNs, associations amongst …
[HTML][HTML] regCNN: identifying Drosophila genome-wide cis-regulatory modules via integrating the local patterns in epigenetic marks and transcription factor binding …
TH Yang, YC Yang, KC Tu - Computational and Structural Biotechnology …, 2022 - Elsevier
Transcription regulation in metazoa is controlled by the binding events of transcription
factors (TFs) or regulatory proteins on specific modular DNA regulatory sequences called cis …
factors (TFs) or regulatory proteins on specific modular DNA regulatory sequences called cis …
Functional redundancy of transcription factors explains why most binding targets of a transcription factor are not affected when the transcription factor is knocked out
WS Wu, FJ Lai - BMC systems biology, 2015 - Springer
Background Biologists are puzzled by the extremely low percentage (3%) of the binding
targets of a yeast transcription factor (TF) affected when the TF is knocked out, a …
targets of a yeast transcription factor (TF) affected when the TF is knocked out, a …
Transcription factor regulatory modules provide the molecular mechanisms for functional redundancy observed among transcription factors in yeast
TH Yang - BMC bioinformatics, 2019 - Springer
Background Current technologies for understanding the transcriptional reprogramming in
cells include the transcription factor (TF) chromatin immunoprecipitation (ChIP) experiments …
cells include the transcription factor (TF) chromatin immunoprecipitation (ChIP) experiments …
Bow-tie architecture of gene regulatory networks in species of varying complexity
The gene regulatory network (GRN) architecture plays a key role in explaining the biological
differences between species. We aim to understand species differences in terms of some …
differences between species. We aim to understand species differences in terms of some …
Identifying piRNA targets on mRNAs in C. elegans using a deep multi-head attention network
Abstract Background Piwi-interacting RNAs (piRNAs) are the small non-coding RNAs
(ncRNAs) that silence genomic transposable elements. And researchers found out that …
(ncRNAs) that silence genomic transposable elements. And researchers found out that …
Inferring Gene Regulatory Networks from RNA-seq Data Using Kernel Classification
Simple Summary Understanding the relationships between genes is crucial to identify the
genetic program of organisms. This research could potentially have implications for this …
genetic program of organisms. This research could potentially have implications for this …
[HTML][HTML] YTLR: Extracting yeast transcription factor-gene associations from the literature using automated literature readers
Cells adapt to environmental stresses mainly via transcription reprogramming. Correct
transcription control is mediated by the interactions between transcription factors (TF) and …
transcription control is mediated by the interactions between transcription factors (TF) and …