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Article
Open AccessAttSiOff: a self-attention-based approach on siRNA design with inhibition and off-target effect prediction
Small interfering RNA (siRNA) is often used for function study and expression regulation of specific genes, as well as the development of small molecule drugs. Selecting siRNAs with high inhibition and low off...
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Article
Open AccessTFvelo: gene regulation inspired RNA velocity estimation
RNA velocity is closely related with cell fate and is an important indicator for the prediction of cell states with elegant physical explanation derived from single-cell RNA-seq data. Most existing RNA velocit...
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Article
Open AccessZeroBind: a protein-specific zero-shot predictor with subgraph matching for drug-target interactions
Existing drug-target interaction (DTI) prediction methods generally fail to generalize well to novel (unseen) proteins and drugs. In this study, we propose a protein-specific meta-learning framework ZeroBind w...
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Article
Open AccessDG-Affinity: predicting antigen–antibody affinity with language models from sequences
Antibody-mediated immune responses play a crucial role in the immune defense of human body. The evolution of bioengineering has led the progress of antibody-derived drugs, showing promising efficacy in cancer ...
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Chapter and Conference Paper
Evaluation Method of Physical Education Teaching Quality in Higher Vocational Colleges Using Mobile Teaching Terminal
At present, there is a problem of single subject and mode in the evaluation of physical education teaching quality in higher vocational colleges, which affects the accuracy of the evaluation results. In order ...
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Chapter and Conference Paper
Physical Movement Monitoring Method of College Physical Education Students Based on Genetic Algorithm
In order to better improve the physical fitness and comprehensive quality of college physical education students, this paper puts forward the physical fitness mobile monitoring method of college physical educa...
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Article
Cell clustering for spatial transcriptomics data with graph neural networks
Spatial transcriptomics data can provide high-throughput gene expression profiling and the spatial structure of tissues simultaneously. Most studies have relied on only the gene expression information but cann...
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Article
Lentiviral delivery of co-packaged Cas9 mRNA and a Vegfa-targeting guide RNA prevents wet age-related macular degeneration in mice
Therapeutic genome editing requires effective and targeted delivery methods. The delivery of Cas9 mRNA using adeno-associated viruses has led to potent in vivo therapeutic efficacy, but can cause sustained Cas9 e...
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Article
Open AccessRBPsuite: RNA-protein binding sites prediction suite based on deep learning
RNA-binding proteins (RBPs) play crucial roles in various biological processes. Deep learning-based methods have been demonstrated powerful on predicting RBP sites on RNAs. However, the training of deep learni...
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Article
Inferring novel genes related to oral cancer with a network embedding method and one-class learning algorithms
Oral cancer (OC) is one of the most common cancers threatening human lives. However, OC pathogenesis has yet to be fully uncovered, and thus designing effective treatments remains difficult. Identifying genes ...
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Article
HIV infection alters the human epigenetic landscape
Many complex diseases or traits are the results of both genetic and environmental factors. The environmental factors affect the human body by modifying its epigenetics, which controls the activity of genomes w...
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Article
Identification of the copy number variant biomarkers for breast cancer subtypes
Breast cancer is a common and threatening malignant disease with multiple biological and clinical subtypes. It can be categorized into subtypes of luminal A, luminal B, Her2 positive, and basal-like. Copy numb...
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Protocol
LabCaS for Ranking Potential Calpain Substrate Cleavage Sites from Amino Acid Sequence
Calpains are a family of Ca2+-dependent cysteine proteases involved in many important biological processes, where they selectively cleave relevant substrates at specific cleavage sites to regulate the function of...
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Chapter and Conference Paper
CNNPSP: Pseudouridine Sites Prediction Based on Deep Learning
Pseudouridine (ψ) is a kind of RNA modification, which is formed at specific site of RNA sequence due to the catalytic action of Pseudouridine synthase in the process of gene transcription. It is the most prev...
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Article
Identifying RNA-binding proteins using multi-label deep learning
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Article
Open AccessPrediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks
RNA regulation is significantly dependent on its binding protein partner, known as the RNA-binding proteins (RBPs). Unfortunately, the binding preferences for most RBPs are still not well characterized. Interd...
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Article
Discriminating cirRNAs from other lncRNAs using a hierarchical extreme learning machine (H-ELM) algorithm with feature selection
As non-coding RNAs, circular RNAs (cirRNAs) and long non-coding RNAs (lncRNAs) have attracted an increasing amount of attention. They have been confirmed to participate in many biological processes, including ...
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Article
Open AccessObservation of aggregation triggered by Resonance Energy Transfer (RET) induced intermolecular pairing force
In this report, we showed the existence of RET induced intermolecular pairing force by comparing their fluorescence behaviors under room illumination vs standing in dark area for either PFluAnt solution or PFluAn...
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Article
Open AccessRNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach
RNAs play key roles in cells through the interactions with proteins known as the RNA-binding proteins (RBP) and their binding motifs enable crucial understanding of the post-transcriptional regulation of RNAs....
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Article
Open AccessIPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction
Non-coding RNAs (ncRNAs) play crucial roles in many biological processes, such as post-transcription of gene regulation. ncRNAs mainly function through interaction with RNA binding proteins (RBPs). To understa...
