Representation learning applications in biological sequence analysis
Although remarkable advances have been reported in high-throughput sequencing, the
ability to aptly analyze a substantial amount of rapidly generated biological …
ability to aptly analyze a substantial amount of rapidly generated biological …
Similarity regression predicts evolution of transcription factor sequence specificity
Transcription factor (TF) binding specificities (motifs) are essential for the analysis of gene
regulation. Accurate prediction of TF motifs is critical, because it is infeasible to assay all TFs …
regulation. Accurate prediction of TF motifs is critical, because it is infeasible to assay all TFs …
Multi-target prediction: a unifying view on problems and methods
W Waegeman, K Dembczyński… - Data Mining and …, 2019 - Springer
Many problem settings in machine learning are concerned with the simultaneous prediction
of multiple target variables of diverse type. Amongst others, such problem settings arise in …
of multiple target variables of diverse type. Amongst others, such problem settings arise in …
Diversification of transcription factor–DNA interactions and the evolution of gene regulatory networks
JM Rogers, ML Bulyk - Wiley Interdisciplinary Reviews …, 2018 - Wiley Online Library
Sequence‐specific transcription factors (TFs) bind short DNA sequences in the genome to
regulate the expression of target genes. In the last decade, numerous technical advances …
regulate the expression of target genes. In the last decade, numerous technical advances …
Learning distributed representations of RNA sequences and its application for predicting RNA-protein binding sites with a convolutional neural network
X Pan, HB Shen - Neurocomputing, 2018 - Elsevier
RNA-binding proteins (RBPs) play a crucial role in gene regulation. Unfortunately,
experimental approaches for detecting the RNA-protein binding sites on RNAs are still high …
experimental approaches for detecting the RNA-protein binding sites on RNAs are still high …
[HTML][HTML] High-throughput affinity measurements of transcription factor and DNA mutations reveal affinity and specificity determinants
Transcription factors (TFs) bind regulatory DNA to control gene expression, and mutations to
either TFs or DNA can alter binding affinities to rewire regulatory networks and drive …
either TFs or DNA can alter binding affinities to rewire regulatory networks and drive …
DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues
KH Kock, PK Kimes, SS Gisselbrecht, S Inukai… - Nature …, 2024 - nature.com
Homeodomains (HDs) are the second largest class of DNA binding domains (DBDs) among
eukaryotic sequence-specific transcription factors (TFs) and are the TF structural class with …
eukaryotic sequence-specific transcription factors (TFs) and are the TF structural class with …
Distributed algorithms of solving linear matrix equations via double-layered networks
This paper focuses on designing distributed algorithms for solving the linear matrix equation
in the form of AXB= F via a double-layered multi-agent network. Firstly, we equivalently …
in the form of AXB= F via a double-layered multi-agent network. Firstly, we equivalently …
Pedestrian heading estimation based on spatial transformer networks and hierarchical LSTM
Q Wang, H Luo, L Ye, A Men, F Zhao, Y Huang… - IEEE …, 2019 - ieeexplore.ieee.org
Accurate heading estimation is the foundation of numerous applications, including
augmented reality, pedestrian dead reckoning, and human-computer interactions. While …
augmented reality, pedestrian dead reckoning, and human-computer interactions. While …
Specifying RNA-binding regions in proteins by peptide cross-linking and affinity purification
RNA-binding proteins (RBPs) allow cells to carry out pre-RNA processing and post-
transcriptional regulation of gene expression, and aberrations in RBP functions have been …
transcriptional regulation of gene expression, and aberrations in RBP functions have been …