MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics.

Protein structure prediction is a longstanding issue crucial for identifying new drug targets and providing a mechanistic understanding of protein functions. To enhance the progress in this field, a spectrum of computational methodologies has been cultivated. AlphaFold2 has exhibited exceptional precision in predicting wild-type protein structures, with performance exceeding that of other methods.

Understanding common human driving semantics for autonomous vehicles.

Autonomous vehicles will share roads with human-driven vehicles until the transition to fully autonomous transport systems is complete. The critical challenge of improving mutual understanding between both vehicle types cannot be addressed only by feeding extensive driving data into data-driven models but by enabling autonomous vehicles to understand and apply common driving behaviors analogous to human drivers. Therefore, we designed and conducted two electroencephalography experiments for comparing the cerebral activities of human linguistics and driving understanding.

Elevated CHCHD4 orchestrates mitochondrial oxidative phosphorylation to disturb hypoxic pulmonary hypertension.

Background: Pulmonary arterial hypertension (PAH) is a highly prevalent cardiopulmonary disorder characterized by vascular remodeling and increased resistance in pulmonary artery. Mitochondrial coiled-coil-helix-coiled-coil-helix domain (CHCHD)-containing proteins have various important pathophysiological roles. However, the functional roles of CHCHD proteins in hypoxic PAH is still ambiguous.

RNAenrich: a web server for non-coding RNA enrichment.

Motivation: With the rapid advances of RNA sequencing and microarray technologies in non-coding RNA (ncRNA) research, functional tools that perform enrichment analysis for ncRNAs are needed. On the one hand, because of the rapidly growing interest in circRNAs, snoRNAs, and piRNAs, it is essential to develop tools for enrichment analysis for these newly emerged ncRNAs. On the other hand, due to the key role of ncRNAs' interacting target in the determination of their function, the interactions between ncRNA and its corresponding target should be fully considered in functional enrichment.

Identification of hub genes and transcription factor regulatory network for heart failure using RNA-seq data and robust rank aggregation analysis.

Background: Heart failure (HF) is the end stage of various cardiovascular diseases with a high mortality rate. Novel diagnostic and therapeutic biomarkers for HF are urgently required. Our research aims to identify HF-related hub genes and regulatory networks using bioinformatics and validation assays.

DrugMAP: molecular atlas and pharma-information of all drugs.

The efficacy and safety of drugs are widely known to be determined by their interactions with multiple molecules of pharmacological importance, and it is therefore essential to systematically depict the molecular atlas and pharma-information of studied drugs. However, our understanding of such information is neither comprehensive nor precise, which necessitates the construction of a new database providing a network containing a large number of drugs and their interacting molecules. Here, a new database describing the molecular atlas and pharma-information of drugs (DrugMAP) was therefore constructed.

ConSIG: consistent discovery of molecular signature from OMIC data.

The discovery of proper molecular signature from OMIC data is indispensable for determining biological state, physiological condition, disease etiology, and therapeutic response. However, the identified signature is reported to be highly inconsistent, and there is little overlap among the signatures identified from different biological datasets. Such inconsistency raises doubts about the reliability of reported signatures and significantly hampers its biological and clinical applications.

Biological activities of drug inactive ingredients.

In a drug formulation (DFM), the major components by mass are not Active Pharmaceutical Ingredient (API) but rather Drug Inactive Ingredients (DIGs). DIGs can reach much higher concentrations than that achieved by API, which raises great concerns about their clinical toxicities. Therefore, the biological activities of DIG on physiologically relevant target are widely demanded by both clinical investigation and pharmaceutical industry.

PFmulDL: a novel strategy enabling multi-class and multi-label protein function annotation by integrating diverse deep learning methods.

Bioinformatic annotation of protein function is essential but extremely sophisticated, which asks for extensive efforts to develop effective prediction method. However, the existing methods tend to amplify the representativeness of the families with large number of proteins by misclassifying the proteins in the families with small number of proteins. That is to say, the ability of the existing methods to annotate proteins in the 'rare classes' remains limited.

Cardiovascular-specific PSEN1 deletion leads to abnormalities in calcium homeostasis.

Mutations of PSEN1 have been reported in dilated cardiomyopathy pedigrees. Understanding the effects and mechanisms of PSEN1 in cardiomyocytes might have important implications for treatment of heart diseases. Here, we showed that PSEN1 was downregulated in ischemia-induced failing hearts.

MicroRNA-199a acts as a potential suppressor of cardiomyocyte autophagy through targeting .

Autophagy is an adaptive response to cardiomyocytes survival under stress conditions. MicroRNAs (miRNAs, miR) have been described to act as potent modulators of autophagy. To investigate whether and how miR-199a modulated autophagy , primary cardiomyocytes were treated under starvation to induce autophagy.

Alternative splicing in cancers: From aberrant regulation to new therapeutics.

Alternative splicing is one of the most common mechanisms for gene regulation in humans, and plays a vital role to increase the complexity of functional proteins. In this article, we seek to provide a general review on the relationships between alternative splicing and tumorigenesis. We briefly introduce the basic rules for regulation of alternative splicing, and discuss recent advances on dynamic regulation of alternative splicing in cancers by highlighting the roles of a variety of RNA splicing factors in tumorigenesis.

Conditionally targeted deletion of PSEN1 leads to diastolic heart dysfunction.

Recently, PSEN1 has been reported to have mutations in dilated cardiomyopathy pedigrees. However, the function and mechanism of PSEN1 in cardiomyopathy remains unresolved. Here, we established four types of genetically modified mice to determine the function of PSEN1 in cardiac development and pathology.

Se-methylselenocysteine inhibits apoptosis induced by clusterin knockdown in neuroblastoma N2a and SH-SY5Y cell lines.

Apoptosis, as a programmed cell death process, is essential for the maintenance of tissue function in organisms. Alteration of this process is linked to many diseases. Over-expression of clusterin (Clu) can antagonize apoptosis in various cells.