[HTML][HTML] A review of transformers in drug discovery and beyond

J Jiang, L Chen, L Ke, B Dou, C Zhang, H Feng… - Journal of …, 2024 - Elsevier
Transformer models have emerged as pivotal tools within the realm of drug discovery,
distinguished by their unique architectural features and exceptional performance in …

Application of deep learning in cancer epigenetics through DNA methylation analysis

M Yassi, A Chatterjee, M Parry - Briefings in bioinformatics, 2023 - academic.oup.com
DNA methylation is a fundamental epigenetic modification involved in various biological
processes and diseases. Analysis of DNA methylation data at a genome-wide and high …

Deep learning methods for omics data imputation

L Huang, M Song, H Shen, H Hong, P Gong, HW Deng… - Biology, 2023 - mdpi.com
Simple Summary Missing values are common in omics data and can arise from various
causes. Imputation approaches offer a different means of handling missing data instead of …

Multi-scale attention flow for probabilistic time series forecasting

S Feng, C Miao, K Xu, J Wu, P Wu… - IEEE Transactions on …, 2023 - ieeexplore.ieee.org
The probability prediction of multivariate time series is a notoriously challenging but practical
task. On the one hand, the challenge is how to effectively capture the cross-series …

MetaTransformer: deep metagenomic sequencing read classification using self-attention models

A Wichmann, E Buschong, A Müller… - NAR Genomics and …, 2023 - academic.oup.com
Deep learning has emerged as a paradigm that revolutionizes numerous domains of
scientific research. Transformers have been utilized in language modeling outperforming …

Recall DNA methylation levels at low coverage sites using a CNN model in WGBS

X Luo, Y Wang, Q Zou, L Xu - PLOS Computational Biology, 2023 - journals.plos.org
DNA methylation is an important regulator of gene transcription. WGBS is the gold-standard
approach for base-pair resolution quantitative of DNA methylation. It requires high …

ASHFormer: axial and sliding window based attention with high-resolution transformer for automatic stratigraphic correlation

N Liu, Z Li, R Liu, H Zhang, J Gao… - IEEE Transactions on …, 2023 - ieeexplore.ieee.org
The stratigraphic correlation of well logs is crucial for characterizing subsurface reservoirs.
However, due to the complexity of well logs and the huge amount of well data, manual …

Computational methods for single-cell DNA methylome analysis

W Iqbal, W Zhou - Genomics, Proteomics & Bioinformatics, 2023 - academic.oup.com
Dissecting intercellular epigenetic differences is key to understanding tissue heterogeneity.
Recent advances in single-cell DNA methylome profiling have presented opportunities to …

GraphCpG: imputation of single-cell methylomes based on locus-aware neighboring subgraphs

Y Deng, J Tang, J Zhang, J Zou, Q Zhu, S Fan - Bioinformatics, 2023 - academic.oup.com
Motivation Single-cell DNA methylation sequencing can assay DNA methylation at single-
cell resolution. However, incomplete coverage compromises related downstream analyses …

Research progress and application of single-cell sequencing in head and neck malignant tumors

S Qu, M Gong, Y Deng, Y Xiang, D Ye - Cancer Gene Therapy, 2024 - nature.com
Single-cell sequencing (SCS) is a technology that separates thousands of cells from the
organism and accurately analyzes the genetic material expressed in each cell using high …