The placenta, as a unique exchange organ between mother and fetus, is essential for successful human pregnancy fetal health. Preeclampsia (PE) caused by placental dysfunction contributes to both maternal infant morbidity mortality. Accurate identification of PE patients plays vital role in the formulation treatment plans. However, traditional clinical methods have high misdiagnosis rate.Here, we first designed computational biology method that used single-cell transcriptome (scRNA-seq)...

Abstract Lactic acid bacteria consortia are commonly present in food, and some of these possess probiotic properties. However, discovery experimental validation probiotics require extensive time effort. Therefore, it is great interest to develop effective screening methods for identifying probiotics. Advances sequencing technology have generated massive genomic data, enabling us create a machine learning-based platform such purpose this work. This study first selected comprehensive genome...

The increasing emergence of the time-series single-cell RNA sequencing (scRNA-seq) data, inferring developmental trajectory by connecting transcriptome similar cell states (i.e., types or clusters) has become a major challenge. Most existing computational methods are designed for individual cells and do not take into account available time series information. We present IDTI based on Increment Diversity Trajectory Inference, which combines information minimum increment diversity method to...

miR-126, an endothelial-specific microRNA, is associated to vascular integrity and angiogenesis. It well established that angiogenesis plays a critical role in burn wound healing. However, there was lack of understanding the mechanism by which miR-126 regulates during HOX transcript antisense intergenic RNA (HOTAIR) well-characterized long non-coding (lncRNA) involved cell proliferation, apoptosis, migration, invasion cancer cells. Sciellin (SCEL), precursor cornified envelope human...

Hematopoietic stem cells (HSCs) give rise to all blood and play a vital role throughout the whole lifespan through their pluripotency self-renewal properties. Accurately identifying stages of early HSCs is extremely important, as it may open up new prospects for extracorporeal research. Existing experimental techniques development are time-consuming expensive. Machine learning has shown its excellence in massive single-cell data processing desirable develop related computational models good...

Abstract Chronic diseases, because of insidious onset and long latent period, have become the major global disease burden. However, current chronic diagnosis methods based on genetic markers or imaging analysis are challenging to promote completely due high costs cannot reach universality popularization. This study analyzed massive data from routine blood biochemical test 32 448 patients developed a novel framework for cost-effective prediction with accuracy (AUC 87.32%). Based...

Human preimplantation development is a complex process involving dramatic changes in transcriptional architecture. For better understanding of their time-spatial development, it indispensable to identify key genes. Although the single-cell RNA sequencing (RNA-seq) techniques could provide detailed clustering signatures, identification decisive factors remains difficult. Additionally, requires high experimental cost and long period. Thus, highly desired develop computational methods for...

The identification of underlying differences is crucial for understanding the embryogenesis species specificity. In this paper, a comparative transcriptome analysis multi-species (CTAMS) was first developed to detect genome activation among human, mouse, and bovine. annotation intra-species detection inter-species difference were separately avoid potential batch effects. profile clusters Pearson correlation showed human bovine embryos displayed high similarity in with dramatic maternal...

Abstract The emerging importance of embryonic development research rapidly increases the volume for a professional resource related to multi-omics data. However, lack global embryogenesis repository and systematic analysis tools limits preceding in stem cell research, human congenital diseases assisted reproduction. Here, we developed EmAtlas, which collects most comprehensive data provides multi-scale explore spatiotemporal activation during mammalian embryogenesis. EmAtlas contains on...

Myocardial ischemic preconditioning (IP) is defined as a brief period of myocardial ischemia/reperfusion (I/R) that significantly reduces injury during the subsequent exposure to long-term I/R. However, underlying mechanisms IP are yet be elucidated. This study investigated expression and roles long noncoding RNA (lncRNA) H19 in vitro vivo. LncRNA levels were analyzed by quantitative reverse-transcription polymerase chain reaction, cell viability was determined Cell Counting Kit-8 assay,...

Developmental pluripotency-associated 2 (Dppa2) and developmental 4 (Dppa4) as positive drivers were helpful for transcriptional regulation of zygotic genome activation (ZGA). Here, we systematically assessed the cooperative interplay Dppa2 Dppa4 in regulating cell pluripotency found that simultaneous overexpression Dppa2/4 can make induced pluripotent stem cells closer to embryonic (ESCs). Compared with other transcription factors, regulate majorities signaling pathways by binding on...

Background: Nucleolin is a multifunctional nucleolar protein with RNA-binding properties. Increased nucleolin expression protects cells from H2O2-induced damage, but the mechanism remains unknown. Long noncoding RNAs (lncRNAs) play crucial roles in cardiovascular diseases. However, biological functions and underlying mechanisms of lncRNAs myocardial injury remain unclear.Methods: In nucleolin-overexpressing cardiac cell line, high-throughput technology was used to identify controlled by...

ABSTRACT As a multifunctional protein, nucleolin can participate in variety of cellular processes. Nucleolin also has multiple protective effects on heart disease. Previous studies have shown that could not only resist oxidative stress damage and inflammatory damage, but regulate autophagy to play role cardiac ischemia. However, the specific mechanism been fully elucidated LPS-induced myocardial injury. Therefore, aim this study is explore underlying by which regulates protect against injury...

Background: Inferring feature importance is both a promise and challenge in bioinformatics computational biology. While multiple biological computation methods exist to identify decisive factors of single cell subpopulation, there need for comprehensive toolkit that presents an intuitive custom view the importance. Objective: We developed Feature-scML, scalable friendly allows users visualize reveal omics analysis. Method: Feature-scML incorporates following main three functions: (i) There...

Abstract The in-depth understanding of cellular fate decision human preimplantation embryos has prompted investigations on how changes in lineage allocation, which is far from trivial and remains a time-consuming task by experimental methods. It desirable to develop novel effective bioinformatics strategy consider transitions coordinated embryo allocation stage-specific patterns. There are rapidly growing applications machine learning models interpret complex datasets for identifying...

Abstract Our previous study confirmed the critical role of miR‐125b and vascular endothelial growth factor (VEGF) in burn wound repair., The present was aimed to identify long noncoding RNAs (lncRNAs) related function VEGF repair underlying mechanism. First, we found that lncRNA PDK1‐AS VEGFA expression significantly increased heat‐denatured dermal tissue samples human microvascular cells (HDMECs) umbilical vein (HUVECs) after thermal injury. knockdown inhibited cell viability, cumulative...

Breast cancer is a kind of malignant tumor that occurs in breast tissue, which the most common women. Cellular metabolism critical determinant viability and function cells microenvironment. In this study, based on gene expression profile metabolism-related genes, prognostic value 20 metabolic pathways patients with was identified. A universal risk stratification signature relies established validated training cohort, two testing cohorts The Cancer Genome Atlas pan cohort. Then, relationship...

The 2-oxoglutarate/Fe (II)-dependent (2OG) oxygenase superfamily is mainly responsible for protein modification, nucleic acid repair and/or and fatty metabolism plays important roles in cancer, cardiovascular disease, other diseases. They are likely to become new targets the treatment of cancer diseases, so accurate identification 2OG oxygenases great significance. Many computational methods have been proposed predict functional proteins compensate time-consuming expensive experimental...

<title>Abstract</title> <bold>Background</bold>: Despite the advent of new pharmacotherapies, statins remain a cornerstone in secondary prevention myocardial infarction (MI). However, cardiac adverse events (CAEs) linked to are not well-documented. <bold>Aim</bold>: This pharmacovigilance study used data from FDA Adverse Event Reporting System (FAERS) investigate association between statin use and CAEs MI patients. <bold>Method</bold>: Reports FAERS database (2004-2023) identifying as...