Shuyan Li

Xuzhou Medical University · College of Medical Information and Engineering

Background Cholangiocarcinoma (CCA) is a highly aggressive malignant tumor, and its diagnosis is still a challenge. This study aimed to identify a novel bile marker for CCA diagnosis based on proteomics and establish a diagnostic model with deep learning. Methods A total of 644 subjects (236 CCA and 408 non-CCA) from two independent centers were d...

We report the discovery and functional characterization of a new bacterial tRNA species. The tRNA-Asp-AUC, from a fast-growing desert streptomycete, decodes GAU codons. In the absence of queuosine tRNA anticodon modification in streptomycetes, the new tRNA circumvents inefficient wobble base-pairing during translation. The tRNA, which is constituti...

Background Endoscopic retrograde cholangiopancreatography (ERCP) is an established treatment for common bile duct (CBD) stones. Post- ERCP cholecystitis (PEC) is a known complication of such procedure and there are no effective models and clinical applicable tools for PEC prediction. Methods A random forest (RF) machine learning model was develope...

Activation of EGFR is a major risk factor for non-small cell lung cancer (NSCLC). Understanding the molecular events promoting EGFR activation can help us gain more insights into the progression of NSCLC. In this study, we demonstrate that collagen type VIII alpha 1 chain (COL8A1), an extracellular matrix component, was overexpressed in NSCLC. In N...

Gastric cancer (GC) is one of the most common cancers in the world. In cancer detection, liquid biopsy, as a noninvasive and rapid method, is growing in importance. Different from traditional liquid biopsy using a single biomarker, this study integrated a variety of blood biochemical indices and established an identification system by means of deep...

Breast cancer is a malignant tumor that occurs in the glandular epithelium of the breast, and more than 15% of the patients are triple-negative breast cancer (TNBC). Therefore, finding new targets and targeted therapeutic drugs for TNBC is urgent. Overexpression of the AXL is associated with motility and invasiveness of the TNBC cells, which is a p...

Background: The current focus is largely on whole course medical management of coronavirus disease-19 (COVID-19) with real-time polymerase chain reaction (RT-PCR) and radiological features, while the mild cases are usually missed. Thus, combination of multiple diagnostic methods is urgent to understand COVID-19 fully and to monitor the progression...

Currently, preoperative diagnosis and differentiation of renal clear cell carcinoma and other subtypes remain a serious challenge for doctors. The liquid biopsy technique and artificial intelligence have inspired the pursuit of distinguishing clear cell renal cell carcinoma using clinically available test data. In this work, a method called liq_ccR...

In order to extract useful information from a huge amount of biological data nowadays, simple and convenient tools are urgently needed for data analysis and modeling. In this paper, an automatic data mining tool, termed as ABCModeller (Automatic Binary Classification Modeller), with a user-friendly graphical interface was developed here, which incl...

Since the sudden outbreak of coronavirus disease 2019 (COVID-19), it has rapidly evolved into a momentous global health concern. Due to the lack of constructive information on the pathogenesis of COVID-19 and specific treatment, it highlights the importance of early diagnosis and timely treatment. In this study, 11 key blood indices were extracted...

Gastric cancer (GC) continues to be one of the major causes of cancer deaths worldwide. Meanwhile, liquid biopsies have received extensive attention in the screening and detection of cancer along with better understanding and clinical practice of biomarkers. In this work, 58 routine blood biochemical indices were tentatively used as integrated mark...

Tuberculosis remains one of the deadliest infectious disease worldwide. Only 5-15% of people infected with M. tuberculosis develop active TB disease (ATB) while others remain latently infected (LTBI) during their lifetime, which has completely different clinical treatment schedule. However, most current clinical diagnostic methods are based on the...

Background: Liquid biopsies based on blood samples have been widely accepted as a diagnostic and monitoring tool for cancers, but extremely high sensitivity is frequently needed due to the very low levels of the specially selected DNA, RNA, or protein biomarkers that are released into blood. However, routine blood indices tests are frequently orde...

To discover drugs for toxoplasmosis with less side effects and less probability to get drug resistance is eagerly appealed for pregnant women, infant or immunocompromised patients. In this work, using TgCDPK1 as drug target, we design a method to discover new inhibitors for CDPK1 as potential drug lead for toxoplasmosis with novel scaffolds based o...

Objective: To identify the genetic causes of male infertility characterized by teratozoospermia. Design: Genetic studies. Setting: Medical university. Patient(s): Two infertile brothers with teratozoospermia in a consanguineous Chinese family, another 124 sporadic infertile male patients presenting with teratozoospermia, and 200 male control...

BACKGROUND Liquid biopsies based on blood samples have been widely accepted as a diagnostic and monitoring tool for cancers, but extremely high sensitivity is frequently needed due to the very low level of the specially selected DNA/RNA/protein biomarkers released into blood. On the other hand, routine blood indices tests are frequently ordered by...

Background Quercetin is a natural bioactive flavonoid that is present in a wide variety of vegetables and fruits and exhibits a promising anti-metastasis property in various human cancer cells. However, the effect of quercetin on human HCCLM3 cells is unclear. Material/Methods In the current study, a wound-healing assay was performed using quercet...

Drug-induced liver injury (DILI) is one of the major causes of drug attrition and failure. Currently, there is increasing evidence that direct inhibition of the human bile salt export pump (BSEP/ABCB11) by drugs and/or metabolites is one of the most important mechanisms of cholestatic DILI. In the present study, we employ two in silico methods, ran...

Glacier forelands, where the initially exposed area is unvegetated with minimal human influence, are an ideal place for research on the distributions and biogeography of microbial communities. Actinobacteria produce many bioactive substances and have important roles in soil development and biogeochemical cycling. However, little is known about the...

Pseudarthrobacter sulfonivorans strain Ar51, a psychotrophic bacterium isolated from the Tibet permafrost of China, can degrade crude oil and multi benzene compounds efficiently in low temperature. Here we report the complete genome sequence of this bacterium. The complete genome sequence of Pseudarthrobacter sulfonivorans strain Ar51, consisting o...

Arthrobacter strain A3, a psychotrophic bacterium isolated from the Tian Shan Mountain of China, can degrade the cellulose and synthesis the long-chain hydrocarbons efficiently in low temperature. Here we report the complete genome sequence of this bacterium. The complete genome sequence of Arthrobacter strain A3, consisting of a cycle chromosome w...

B-RAF protein is a clinically validated target implicated in melanoma and advanced renal cell carcinoma (RCC). PLX4720 and TAK-632 are two promising inhibitors targeting B-RAF with good inhibition activities and different dissociation rates (koff), but the specific mechanism of the difference of dissociation rates remains unclear. In order to eluci...

The disruption of protein hydroxylation is highly associated with several serious diseases and consequently the identification of protein hydroxylation sites has attracted significant attention recently. Here, we report the development of an improved method, called HydPred, to identify protein hydroxylation sites (hydroxyproline and hydroxylysine)...

R-Bicalutamide is a first generation antiandrogen used to treat prostate cancer, which inhibits androgen action by competitively binding to the androgen receptor (AR). However, R-bicalutamide was discovered to exhibit some agonistic properties in clinical application. According to reports, the W741L AR mutation may lead to resistance towards R-bica...

S-palmitoylation is a key regulatory mechanism controlling protein targeting, localization, stability and activity. Since increasing evidence shows that its disruption is implicated in many human diseases, the identification of palmitoylation sites is attracting more attention. However, the computational methods that are published so far for this p...

ABSTRACT Background: As an essential protein for bacterial cell division, the tubulin-like FtsZ protein has been selected as a target for development of next generation antimicrobials. PC190723 is a fluoride-containing benzamide compound developed as a FtsZ inhibitor that selectively inhibits growth of multidrug resistant Gram-positive bacteria. Ou...

Matrix metalloproteinase 13 (MMP-13) plays an important role in the degradation of articular cartilage and has been considered as an attractive target for the treatment of osteoarthritis; hence, the development of efficient inhibitors of MMP-13 has become a hot study field. Taking a series of carboxylic acid-based MMP-13 inhibitors as research obje...

Malaria is a fatal tropical and subtropical disease caused by the protozoal species Plasmodium. Many commonly available antimalarial drugs and therapies are becoming ineffective because of the emergence of multidrug resistant Plasmodium falciparum, which drives the need for the development of new antimalarial drugs. Recently, a series of 3-carboxyl...

The formula that life process follows is a major scientific mystery during centuries. Some people put programming thoughts into this field like Gates brought the idea that “Human DNA is like a computer program but far, far more advanced than any software we’ve ever created”[1]. Here we proposed a more specific hypothesis on this topic as that DNA i...

Because of the high conservation of ATP-binding sites in kinases, the quest for selective kinase inhibitors has been increasingly urgent in recent years. The Aurora kinase family represents attractive targets in cancer therapy and several small molecule inhibitors targeting Aurora kinases are undergoing clinical trials. Among them, MLN8054 has been...

Predicting the solvent accessible surface area (ASA) of transmembrane (TM) residues is of great importance for experimental researchers to elucidate diverse physiological processes. TM residues fall into two major structural classes (α-helix membrane protein and β-barrel membrane protein). The reported solvent ASA prediction models were developed f...

Molecular cause of human disease retains as one of the most attractive scientific research targets for decades. An effective approach toward this topic is analysis and identification of disease-related amino acid polymorphisms. In this work, we developed a concise and promising deleterious amino acid polymorphism identification method SeqSubPred ba...

Predicting the burial status (the residue exposure to the lipid bilayer or buried within the protein core) of transmembrane (TM) residues of α-helix membrane protein (αHMP) is of great importance for genome-wide annotation and for experimental researchers to elucidate diverse physiological processes. In this work, we developed a new computational m...

To understand the folding behavior of proteins is an important and challenging problem in modern molecular biology. In the present investigation, a large number of features representing protein sequences were developed based on sequence autocorrelation weighted by properties of amino acid residues. Genetic algorithm (GA) combined with multiple line...

Zinc-dependent matrix metalloproteinase (MMP) family is considered to be an attractive target because of its important role in many physiological and pathological processes. In the present work, a molecular modeling study combining protein-, ligand- and complex-based computational methods was performed to analyze a new series of beta-N-biaryl ether...

Understanding and predicting molecular cause of disease is one of the major challenges for biology and medicine. One particular area of interest continues to be computational analyses of disease-associated amino acid substitutions. To this end, various studies have been performed to identify molecular functions disrupted by disease-causing mutation...

In this paper, a fast method for the study on the interactions of a series of drugs used in the treatment of hypertension with human serum albumin (HSA) by flow injection-capillary electrophoresis (FI-CE) was developed based on the principle of frontal analysis (FA). The binding parameters were determined by FI-CE-FA from Scatchard equation and com...

In the quantitative structure-activity relationship (QSAR) study, local lazy regression (LLR) can predict the activity of a query molecule by using the information of its local neighborhood without need to produce QSAR models a priori. When a prediction is required for a query compound, a set of local models including different number of nearest ne...

In this study, a novel method was developed to predict the binding affinity of protein-ligand based on a comprehensive set of structurally diverse protein-ligand complexes (PLCs). The 1300 PLCs with binding affinity (493 complexes with K(d) and 807 complexes with K(i)) from the refined dataset of PDBbind Database (release 2007) were studied in the...

The base sequence autocorrelation (BSA) descriptors were used to describe structures of oligonucleotides and to develop accurate quantitative structure-retention relationship (QSRR) models of oligonucleotides in ion-pair reversed-phase high-performance liquid chromatography. Through the combination use of multiple linear regression (MLR) and geneti...

In this work, an accurate and validated Quantitative Structure–Activity Relationship (QSAR) model was developed for the caspase-mediated apoptosis-inducing effect of 52 substituted phenolic compounds in a murine leukemia cell line (L1210). All molecules were optimized by the Density Functional Theory (DFT) to obtain lowest energy conformations. The...

Quantitative structure-activity relationship (QSAR) of a series of structural diverse malonyl-CoA decarboxylase (MCD) inhibitors have been investigated by using the predictive single model as well as the consensus analysis based on a new strategy proposed by us. Self-organizing map (SOM) neural network was employed to divide the whole data set into...

Three-dimensional quantitative structure-activity relationship (3D-QSAR) models for a series of thiazolone derivatives as novel inhibitors bound to the allosteric site of hepatitis C virus (HCV) NS5B polymerase were developed based on CoMFA and CoMSIA analyses. Two different conformations of the template molecule and the combinations of different C...

Quantitative structure-activity relationship (QSAR) has been applied to a set of thyroid hormone receptor beta(1) (TRbeta(1)) antagonists, which are of special interest because of their potential role in safe therapies for nonthyroid disorders while avoiding the cardiac side effects. Using the calculated structural descriptors by CODESSA program, p...

T-lymphocyte (T-cell) is a very important component in human immune system. It possesses a receptor (TCR) that is specific for the foreign epitopes which are in a form of short peptides bound to the major histocompatibility complex (MHC). When T-cell receives the message about the peptides bound to MHC, it makes the immune system active and results...