Long-read sequencing holds great potential for characterizing complex microbial communities, yet taxonomic profiling tools designed specifically for long reads remain lacking. We introduce Melon, a novel marker-based taxonomic profiler that capitalizes on the unique attributes of long reads. Melon employs a two-stage classification scheme to reduce computational time and is equipped with an expectation-maximization-based post-correction module to handle ambiguous reads. Melon achieves superior performance compared to existing tools in both mock and simulated samples. Using wastewater metagenomic samples, we demonstrate the applicability of Melon by showing it provides reliable estimates of overall genome copies, and species-level taxonomic profiles.

BACKGROUND: The utilization of long reads for single nucleotide polymorphism (SNP) phasing has become popular, providing substantial support for research on human diseases and genetic studies in animals and plants. However, due to the complexity of the linkage relationships between SNP loci and sequencing errors in the reads, the recent methods still cannot yield satisfactory results.
RESULTS: In this study, we present a graph-based algorithm, GCphase, which utilizes the minimum cut algorithm to perform phasing. First, based on alignment between long reads and the reference genome, GCphase filters out ambiguous SNP sites and useless read information. Second, GCphase constructs a graph in which a vertex represents alleles of an SNP locus and each edge represents the presence of read support; moreover, GCphase adopts a graph minimum-cut algorithm to phase the SNPs. Next, GCpahse uses two error correction steps to refine the phasing results obtained from the previous step, effectively reducing the error rate. Finally, GCphase obtains the phase block. GCphase was compared to three other methods, WhatsHap, HapCUT2, and LongPhase, on the Nanopore and PacBio long-read datasets. The code is available from https://github.com/baimawjy/GCphase .
CONCLUSIONS: Experimental results show that GCphase under different sequencing depths of different data has the least number of switch errors and the highest accuracy compared with other methods.

Vital signs are important indicators to evaluate the health status of patients. Channel state information (CSI) can sense the displacement of the chest wall caused by cardiorespiratory activity in a non-contact manner. Due to the influence of clutter, DC components, and respiratory harmonics, it is difficult to detect reliable heartbeat signals. To address this problem, this paper proposes a robust and novel method for simultaneously extracting breath and heartbeat signals using software defined radios (SDR). Specifically, we model and analyze the signal and propose singular value decomposition (SVD)-based clutter suppression method to enhance the vital sign signals. The DC is estimated and compensated by the circle fitting method. Then, the heartbeat signal and respiratory signal are obtained by the modified variational modal decomposition (VMD). The experimental results demonstrate that the proposed method can accurately separate the respiratory signal and the heartbeat signal from the filtered signal. The Bland-Altman analysis shows that the proposed system is in good agreement with the medical sensors. In addition, the proposed system can accurately measure the heart rate variability (HRV) within 0.5m. In summary, our system can be used as a preferred contactless alternative to traditional contact medical sensors, which can provide advanced patient-centered healthcare solutions.

The microRNAs (miRNAs) play crucial roles in several biological processes. It is essential for a deeper insight into their functions and mechanisms by detecting their subcellular localizations. The traditional methods for determining miRNAs subcellular localizations are expensive. The computational methods are alternative ways to quickly predict miRNAs subcellular localizations. Although several computational methods have been proposed in this regard, the incomplete representations of miRNAs in these methods left the room for improvement. In this study, a novel computational method for predicting miRNA subcellular localizations, named PMiSLocMF, was developed. As lots of miRNAs have multiple subcellular localizations, this method was a multi-label classifier. Several properties of miRNA, such as miRNA sequences, miRNA functional similarity, miRNA-disease, miRNA-drug, and miRNA-mRNA associations were adopted for generating informative miRNA features. To this end, powerful algorithms [node2vec and graph attention auto-encoder (GATE)] and one newly designed scheme were adopted to process above properties, producing five feature types. All features were poured into self-attention and fully connected layers to make predictions. The cross-validation results indicated the high performance of PMiSLocMF with accuracy higher than 0.83, average area under the receiver operating characteristic curve (AUC) and area under the precision-recall curve (AUPR) exceeding 0.90 and 0.77, respectively. Such performance was better than all previous methods based on the same dataset. Further tests proved that using all feature types can improve the performance of PMiSLocMF, and GATE and self-attention layer can help enhance the performance. Finally, we deeply analyzed the influence of miRNA associations with diseases, drugs, and mRNAs on PMiSLocMF. The dataset and codes are available at https://github.com/Gu20201017/PMiSLocMF.

The rapid rise in the availability and scale of scRNA-seq data needs scalable methods for integrative analysis. Though many methods for data integration have been developed, few focus on understanding the heterogeneous effects of biological conditions across different cell populations in integrative analysis. Our proposed scalable approach, scParser, models the heterogeneous effects from biological conditions, which unveils the key mechanisms by which gene expression contributes to phenotypes. Notably, the extended scParser pinpoints biological processes in cell subpopulations that contribute to disease pathogenesis. scParser achieves favorable performance in cell clustering compared to state-of-the-art methods and has a broad and diverse applicability.

Protein-encoding circular RNAs (circRNAs) are newly identified RNA molecules characterized by intense interaction with translating ribosome. Emerging evidence has implicated physiological and pathological significance of these non-canonical RNAs, yet a large body of them remains unidentified. Due to limited tools at hand, we developed CircProPlus, an automated computational pipeline for de novo detection of translated circRNAs. In comparison to previously established CircPro, CircProPlus adjusts the overall workflow and integrates more robust implements for achieving easier accessibility, higher flexibility and productivity. In present study, we tested the performance of CircProPlus when using different circRNA-detecting implements (i.e., CIRI2, CirComPara2) in the evaluation of coding ability of circRNAs. Results showed that CirComPara2, a state-of-the-art algorithm, consistently outperformed CIRI2 when coupled with CircProPlus in testing real data collected from different RNA libraries and species, which highlighted its potency in data mining of circRNAs with protein-coding potential.

Genome sequencing has become a routine task for biologists, but the challenge of gene structure annotation persists, impeding accurate genomic and genetic research. Here, we present a bioinformatics toolkit, SynGAP (Synteny-based Gene structure Annotation Polisher), which uses gene synteny information to accomplish precise and automated polishing of gene structure annotation of genomes. SynGAP offers exceptional capabilities in the improvement of gene structure annotation quality and the profiling of integrative gene synteny between species. Furthermore, an expression variation index is designed for comparative transcriptomics analysis to explore candidate genes responsible for the development of distinct traits observed in phylogenetically related species.

BACKGROUND: Orofacial clefts are one of the most common congenital malformations of the fetal face and ultrasound is mainly responsible for its diagnosis. It is difficult to view the fetal palate, so there is currently no unified standard for fetal palate screening, and the diagnosis of cleft palate is not included in the relevant prenatal ultrasound screening guidelines. Many prenatal diagnoses for cleft palate are missed due to the lack of effective screening methods. Therefore, it is imperative to increase the display rate of the fetal palate, which would improve the detection rate and diagnostic accuracy for cleft palate. We aim to introduce a fetal palate screening software based on the \"sequential sector scan though the oral fissure\", an effective method for fetal palate screening which was verified by our follow up results and three-dimensional ultrasound and to evaluate its feasibility and clinical practicability.
METHODS: A software was designed and programmed based on \"sequential sector scan through the oral fissure\" and three-dimensional ultrasound. The three-dimensional ultrasound volume data of the fetal face were imported into the software. Then, the median sagittal plane was taken as the reference interface, the anterior upper margin of the mandibular alveolar bone was selected as the fulcrum, the interval angles, and the number of layers of the sector scan were set, after which the automatic scan was performed. Thus, the sector scan sequential planes of the mandibular alveolar bone, pharynx, soft palate, hard palate, and maxillary alveolar bone were obtained in sequence to display and evaluate the palate. In addition, the feasibility and accuracy of the software in fetal palate displaying and screening was evaluated by actual clinical cases.
RESULTS: Full views of the normal fetal palates and the defective parts of the cleft palates were displayed, and relatively clear sequential tomographic images and continuous dynamic videos were formed after the three-dimensional volume data of 10 normal fetal palates and 10 cleft palates were imported into the software.
CONCLUSIONS: The software can display fetal palates more directly which might allow for a new method of fetal palate screening and cleft palate diagnosis.

Digital reconstruction of neuronal structures from 3D neuron microscopy images is critical for the quantitative investigation of brain circuits and functions. Currently, neuron reconstructions are mainly obtained by manual or semiautomatic methods. However, these ways are labor-intensive, especially when handling the huge volume of whole brain microscopy imaging data. Here, we present a deep-learning-based neuron morphology analysis toolbox (DNeuroMAT) for automated analysis of neuron microscopy images, which consists of three modules: neuron segmentation, neuron reconstruction, and neuron critical points detection.

Navigating the complex landscape of high-dimensional omics data with machine learning models presents a significant challenge. The integration of biological domain knowledge into these models has shown promise in creating more meaningful stratifications of predictor variables, leading to algorithms that are both more accurate and generalizable. However, the wider availability of machine learning tools capable of incorporating such biological knowledge remains limited. Addressing this gap, we introduce BioM2, a novel R package designed for biologically informed multistage machine learning. BioM2 uniquely leverages biological information to effectively stratify and aggregate high-dimensional biological data in the context of machine learning. Demonstrating its utility with genome-wide DNA methylation and transcriptome-wide gene expression data, BioM2 has shown to enhance predictive performance, surpassing traditional machine learning models that operate without the integration of biological knowledge. A key feature of BioM2 is its ability to rank predictor variables within biological categories, specifically Gene Ontology pathways. This functionality not only aids in the interpretability of the results but also enables a subsequent modular network analysis of these variables, shedding light on the intricate systems-level biology underpinning the predictive outcome. We have proposed a biologically informed multistage machine learning framework termed BioM2 for phenotype prediction based on omics data. BioM2 has been incorporated into the BioM2 CRAN package (https://cran.r-project.org/web/packages/BioM2/index.html).