Representation learning applications in biological sequence analysis

H Iuchi, T Matsutani, K Yamada, N Iwano… - Computational and …, 2021 - Elsevier
Although remarkable advances have been reported in high-throughput sequencing, the
ability to aptly analyze a substantial amount of rapidly generated biological …

Similarity regression predicts evolution of transcription factor sequence specificity

SA Lambert, AWH Yang, A Sasse, G Cowley, M Albu… - Nature …, 2019 - nature.com
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 …

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 …

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 …

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 …

[HTML][HTML] High-throughput affinity measurements of transcription factor and DNA mutations reveal affinity and specificity determinants

AK Aditham, CJ Markin, DA Mokhtari, N DelRosso… - Cell Systems, 2021 - cell.com
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 …

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 …

Distributed algorithms of solving linear matrix equations via double-layered networks

Y Huang, X Zeng, Z Meng, D Meng - Automatica, 2024 - Elsevier
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 …

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 …

Specifying RNA-binding regions in proteins by peptide cross-linking and affinity purification

M Mullari, D Lyon, LJ Jensen… - Journal of proteome …, 2017 - ACS Publications
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 …