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Bioinformatics (Oxford, England)
Jun 1, 2023
MOTIVATION: Recent advances in multimodal single-cell omics technologies enable multiple modalities of molecular attributes, such as gene expression, chromatin accessibility, and protein abundance, to be profiled simultaneously at a global level in i...
Briefings in bioinformatics
Mar 19, 2023
Identifying the function of DNA sequences accurately is an essential and challenging task in the genomic field. Until now, deep learning has been widely used in the functional analysis of DNA sequences, including DeepSEA, DanQ, DeepATT and TBiNet. Ho...
Nucleic acids research
Jan 6, 2023
Aging is a complex process that accompanied by molecular and cellular alterations. The identification of tissue-/cell type-specific biomarkers of aging and elucidation of the detailed biological mechanisms of aging-related genes at the single-cell le...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
Here we describe an approach that uses deep learning neural networks such as CNN and RNN to aggregate information from DNA sequence; physical, chemical, and structural properties of nucleotides; and omics data on histone modifications, methylation, c...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
DNA accessibility has been a powerful tool in locating active regulatory elements in a cell type, but dissecting the combinatorial logic within these regulatory elements has been a continued challenge in the field. Deep learning models have been show...
Bioinformatics (Oxford, England)
Jan 1, 2023
MOTIVATION: Promoter-centered chromatin interactions, which include promoter-enhancer (PE) and promoter-promoter (PP) interactions, are important to decipher gene regulation and disease mechanisms. The development of next-generation sequencing techno...
Nucleic acids research
Oct 28, 2022
Cancer is a disease of gene dysregulation, where cells acquire somatic and epigenetic alterations that drive aberrant cellular signaling. These alterations adversely impact transcriptional programs and cause profound changes in gene expression. Inter...
Bioinformatics (Oxford, England)
Sep 30, 2022
MOTIVATION: Three-dimensional (3D) genome organization is of vital importance in gene regulation and disease mechanisms. Previous studies have shown that CTCF-mediated chromatin loops are crucial to studying the 3D structure of cells. Although variou...
Bioinformatics (Oxford, England)
Jul 11, 2022
MOTIVATION: The importance of chromatin loops in gene regulation is broadly accepted. There are mainly two approaches to predict chromatin loops: transcription factor (TF) binding-dependent approach and genomic variation-based approach. However, neit...
Bioinformatics (Oxford, England)
Apr 28, 2022
MOTIVATION: Sequence models based on deep neural networks have achieved state-of-the-art performance on regulatory genomics prediction tasks, such as chromatin accessibility and transcription factor binding. But despite their high accuracy, their con...