NPI-DCGNN: An Accurate Tool for Identifying ncRNA-Protein Interactions Using a Dual-Channel Graph Neural Network.

Noncoding RNA (NcRNA)-protein interactions (NPIs) play fundamentally important roles in carrying out cellular activities. Although various predictors based on molecular features and graphs have been published to boost the identification of NPIs, most of them often ignore the information between known NPIs or exhibit insufficient learning ability from graphs, posing a significant challenge in effectively identifying NPIs. To develop a more reliable and accurate predictor for NPIs, in this article, we propose NPI-DCGNN, an end-to-end NPI predictor based on a dual-channel graph neural network (DCGNN). NPI-DCGNN initially treats the known NPIs as an ncRNA-protein bipartite graph. Subsequently, for each ncRNA-protein pair, NPI-DCGNN extracts two local subgraphs centered around the ncRNA and protein, respectively, from the bipartite graph. After that, it utilizes a dual-channel graph representation learning layer based on GNN to generate high-level feature representations for the ncRNA-protein pair. Finally, it employs a fully connected network and output layer to predict whether an interaction exists between the pair of ncRNA and protein. Experimental results on four experimentally validated datasets demonstrate that NPI-DCGNN outperforms several state-of-the-art NPI predictors. Our case studies on the NPInter database further demonstrate the prediction power of NPI-DCGNN in predicting NPIs. With the availability of the source codes (https://github.com/zhangxin11111/NPI-DCGNN), we anticipate that NPI-DCGNN could facilitate the studies of ncRNA interactome by providing highly reliable NPI candidates for further experimental validation.

DeepOCR: A multi-species deep-learning framework for accurate identification of open chromatin regions in livestock.

A wealth of experimental evidence has suggested that open chromatin regions (OCRs) are involved in many critical biological activities, such as DNA replication, enhancer activity, and gene transcription. Accurately identifying OCRs in livestock species can provide critical insights into the distribution and characteristics of OCRs for disease treatment in livestock, thereby improving animal welfare. However, most current machine-learning methods for OCR prediction were originally designed for a limited number of model organisms, such as humans and some model organisms, and thus their performance on non-model organisms, specifically livestock, is often unsatisfactory. To bridge this gap, we propose DeepOCR, a lightweight depth-separable residual network model for predicting OCRs in livestock, including chicken, cattle, and sheep. DeepOCR integrates a single convolution layer and two improved residue structure blocks to extract and learn important features from the input DNA sequences. A fully connected layer was also employed to further process the extracted features and improve the robustness of the entire network. Our benchmarking experiments demonstrated superior prediction performance of DeepOCR compared to state-of-the-art approaches on testing datasets of the three species. The source code of DeepOCR is freely available for academic purposes at https://github.com/jasonzhao371/DeepOCR/. We anticipate DeepOCR servers as a practical and reliable computational tool for OCR-related studies in livestock species.

CTISL: a dynamic stacking multi-class classification approach for identifying cell types from single-cell RNA-seq data.

MOTIVATION: Effective identification of cell types is of critical importance in single-cell RNA-sequencing (scRNA-seq) data analysis. To date, many supervised machine learning-based predictors have been implemented to identify cell types from scRNA-seq datasets. Despite the technical advances of these state-of-the-art tools, most existing predictors were single classifiers, of which the performances can still be significantly improved. It is therefore highly desirable to employ the ensemble learning strategy to develop more accurate computational models for robust and comprehensive identification of cell types on scRNA-seq datasets. RESULTS: We propose a two-layer stacking model, termed CTISL (Cell Type Identification by Stacking ensemble Learning), which integrates multiple classifiers to identify cell types. In the first layer, given a reference scRNA-seq dataset with known cell types, CTISL dynamically combines multiple cell-type-specific classifiers (i.e. support-vector machine and logistic regression) as the base learners to deliver the outcomes for the input of a meta-classifier in the second layer. We conducted a total of 24 benchmarking experiments on 17 human and mouse scRNA-seq datasets to evaluate and compare the prediction performance of CTISL and other state-of-the-art predictors. The experiment results demonstrate that CTISL achieves superior or competitive performance compared to these state-of-the-art approaches. We anticipate that CTISL can serve as a useful and reliable tool for cost-effective identification of cell types from scRNA-seq datasets. AVAILABILITY AND IMPLEMENTATION: The webserver and source code are freely available at http://bigdata.biocie.cn/CTISLweb/home and https://zenodo.org/records/10568906, respectively.

Thermochemical study of amino acid imprinted polymer films.

Molecularly imprinted polymers provide an alternative to traditional methods of amino acid analysis. The imprinted polymers are more robust and significantly less expensive than, for example, ELISA analysis. Amino acid imprinted nylon-6 thin films were studied by differential scanning calorimetry and scanning electron microscopy. Endothermic peaks were observed for imprinted films at temperatures higher than that for pure nylon, indicating the formation of a more-ordered, hydrogen bonded polymer. Removal of the amino acid from the imprinted film resulted in reversion to the peak observed for pure nylon-6. Additives, ß-cyclodextrin and multiwalled carbon nanotubes, were added to the imprinted polymer solutions as a means to increase the porosity of the films. These studies resulted in alternative morphologies and calorimetric results that provide additional functionalities and applications for imprinted polymers.