Bairong Shen

Bairong Shen
West China Hospital · Institutes for Systems Genetics

About

313
Publications
40,556
Reads
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4,670
Citations
Additional affiliations
July 2008 - present
Soochow University (PRC)
Position
  • Professor, Director
December 2005 - June 2009
Tongji University
Position
  • Professor (Full)
June 2000 - June 2008
Tampere University
Position
  • Pos-doc, assitant professor

Publications

Publications (313)
Article
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Background: Crowdsourcing is a low-cost, adaptable, and innovative method to collect ideas from numerous contributors with diverse backgrounds. Crowdsourcing from social media like Twitter can be used for generating ideas in a noticeably brief time based on contributions from globally distributed users. The world has been challenged by the COVID-19...
Article
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In this pilot study, we aimed to explore the feasibility of conducting a questionnaire-based health survey (on the preference of different systems of medicine for the treatment of various health problems) as a Twitter poll. We had a mean 4358.6±590.3 poll reach with the engagement of 108.2±36.87 Twitter users and 67.6±28.06 votes. Most of the respo...
Article
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Since 2020, we are witnessing a COVID-19 pandemic that has ruled out all other pandemics ever happened in our history. Countries are still not be able to manage the COVID-19 threat properly, and while we are still dealing with it, here comes another deadlyinfectious disease, monkeypox. Rapid circulation of monkeypox infections worldwide has forced...
Preprint
Cancer therapy resistance and recurrence (CTRR) are the dominant causes of death in cancer patients. Recent studies have indicated that non-coding RNAs (ncRNAs) can not only reverse the resistance to cancer therapy but also are crucial biomarkers for the evaluation and prediction of CTRR. Herein, we developed CTRR-ncRNA, a knowledgebase of CTRR-ass...
Article
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While frailty corresponds to a multisystem failure, geriatric assessment can recognize multiple pathophysiological lesions and age changes. Up to now, a few frailty indexes have been introduced, presenting definitions of psychological problems, dysregulations in nutritional intake, behavioral abnormalities, and daily functions, genetic, environment...
Article
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Breast cancer (BC) is the most prevalent neoplasm among women. Genetic and environmental factors lead to BC development and on this basis, several preventive – screening and therapeutic interventions have been developed. Hormones, both in the form of endogenous hormonal signaling or hormonal contraceptives, play an important role in BC pathogenesis...
Article
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Gastrointestinal cancers (GICs) are high-incidence malignant tumors that seriously threaten human health around the world. Their complexity and heterogeneity make the classic staging system insufficient to guide patient management. Recently, competing endogenous RNA (ceRNA) interactions that closely link the function of protein-coding RNAs with tha...
Article
Background CD93 is newly reported to normalize vasculature and attenuate pancreatic cancer therapy response, but its role in bladder cancer (BLCA) is unknown. Method The immunologic role of CD93 is analyzed across TCGA pan-cancers. The correlation between CD93 and BLCA clinical and tumor microenvironment features, predicted immunotherapy pathways,...
Preprint
BACKGROUND Disease ontologies facilitate the semantic organization and representation of domain-specific knowledge. In the case of prostate cancer, large volumes of research results and clinical data have been accumulated and needed to be standardized for sharing and translational researches. OBJECTIVE A formal representation of prostate cancer (P...
Article
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Ethnopharmacological relevance: The genus Alternanthera ( Amaranthaceae ) comprises 139 species including 14 species used traditionally for the treatment of various ailments such as hypertension, pain, inflammation, diabetes, cancer, microbial and mental disorders. Aim of the review: To search research gaps through critical assessment of pharmacolo...
Article
Personal lifestyle is an important cause of prostate cancer (PCa), hence establishing a corresponding knowledge graph (KG) and a chatbot is a convenient way for preventing and assessing risks. The chatbot based on a KG of PCa‐associated lifestyles will be helpful to PCa management, then save health care resources in the ageing society. Based on our...
Article
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Endometrial cancer (EC) is the sixth most prevalent type of cancer among women. Kinases, enzymes mediating the transfer of adenosine triphosphate (ATP) in several signaling pathways, play a significant role in carcinogenesis and cancer cells' survival and proliferation. Cyclin-dependent kinases (CDKs) are involved in EC pathogenesis; therefore, CDK...
Article
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We are an international group of biological scientists, conservationists, and environmentalists who have been closely following the plight and conservation of pangolins over a number of years. Pangolins comprise the mammalian Order Pholidota, which contains eight living species found in diverse habitats in Africa (4 species) and Asia (4 species), w...
Article
With the increasing demand for low-cost high-throughput sequencing of large genomes, next-generation sequencing (NGS) technology has developed rapidly. NGS can not only be used in basic scientific research but also in clinical diagnostics and healthcare. Numerous software systems and tools have been developed to analyze NGS data, and various data f...
Article
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Depression, a neurological disorder, is a universally common and debilitating illness where social and economic issues could also become one of its etiologic factors. From a global perspective, it is the fourth leading cause of long-term disability in human beings. For centuries, natural products have proven their true potential to combat various d...
Article
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Background MicroRNAs (miRNAs) are post-transcriptional regulators with the potential as biomarkers for cancer management. Data-driven competing endogenous RNA (ceRNA) network modeling is an effective way to decipher the complex interplay between miRNAs and spongers. However, no general rules are discovered for ceRNA network-based biomarker prioriti...
Article
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SARS-CoV-2 is a single-stranded RNA betacoronavirus with a high mutation rate. The rapidly emerging SARS-CoV-2 variants could increase transmissibility and diminish vaccine protection. However, whether coinfection with multiple SARS-CoV-2 variants exists remains controversial. This study collected 12,986 and 4,113 SARS-CoV-2 genomes from the GISAID...
Chapter
The host immune system recognizes and responds to the selective antigens or epitopes (immunome) of the intruding pathogen over an entire organism. The immune response so generated is ample to confer the desired immunity and protection to the host. This led to the conception of immunome-derived vaccines that exploit selective genome-derived antigens...
Chapter
Virus infection is a common social health issue. In the past decades, serious virus infectious events have caused great loss in people's life and the economics. The nature of rapid widespread and frequent variation increases the difficulty for precision viral prevention and treatment. In the era of big data and artificial intelligence (AI), advance...
Chapter
Viral infections have remained a serious public health burden despite significant improvements in medical and pharmaceutical research in recent years. In silico approaches for drug discovery and design are fruitful for the management of a plethora of viral diseases. Virtual screening of libraries is performed using various computational tools to se...
Article
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Background: Studies have demonstrated the significance of multiple biomarkers for bladder cancer. Here, we attempt to present biomarkers potentially predictive of the prognosis and immunotherapy response of muscle-invasive bladder cancer (MIBC). Method: Immune and stromal scores were calculated for MIBC patients from The Cancer Genome Atlas (TCGA)....
Article
Motivation In the era of big data and precision medicine, accurate risk assessment is a prerequisite for the implementation of risk screening and preventive treatment. A large number of studies have focused on the risk of cancer, and related risk prediction models have been constructed, but there is a lack of effective resource integration for syst...
Article
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Background: The world has been unprecedentedly hit by a global pandemic which broke the record of deadly pandemics that faced humanity ever since its existence. Even kids are well-versed in the terminologies and basics of the SARS-CoV-2 virus and COVID-19 now. The vaccination program has been successfully launched in various countries, given that t...
Article
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In the rural communities of sub-Saharan African (sSA) countries, malaria is being managed using phytocompounds. Artesunate is reported to inhibit Gephyrin E, a central, multi-domain scaffolding protein of inhibitory post-synapses. Neem plant and its metabolites like azadirachtin are being indicated for management of malaria by traditional healers....
Article
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Immunotherapy has been a milestone for muscle-invasive bladder cancer (MIBC), but only a small portion of patients can benefit from it. Therefore, it is crucial to develop a robust individualized immune-related signature of MIBC to identify patients potentially benefiting from immunotherapy. The current study identified patients from the Cancer Gen...
Article
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Prostate cancer is the most common type of cancer among men and the second most frequent cause of cancer-related mortality around the world. The progression of advanced prostate cancer to castration-resistant prostate cancer (CRPC) plays a major role in disease-associated morbidity and mortality, posing a significant therapeutic challenge. Resistan...
Article
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Myocardial infarction knowledge base (MIKB; http://www.sysbio.org.cn/mikb/; latest update: December 31, 2020) is an open-access and manually curated database dedicated to integrating knowledge about MI to improve the efficiency of translational MI research. MIKB is an updated and expanded version of our previous MI Risk Knowledge Base (MIRKB), whic...
Article
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Background: With prostate cancer being the fifth-greatest cause of cancer mortality in 2020, there is a dire need to expand the available treatment options. Castration-resistant prostate cancer (CRPC) progresses despite androgen depletion therapy. The mechanisms of resistance are yet to be fully discovered. However, it is hypothesized that androgen...
Article
Bergenin, 4-O-methyl gallic acid glucoside, is a bioactive compound present in various plants belonging to different families. The present work compiles scattered information on pharmacology, structure activity relationship and nanotechnological aspects of bergenin, collected from various electronic databases such as Sci Finder, PubMed, Google scho...
Article
Background Neurological disorder, depression is the globally 4th leading cause of chronic disabilities in human beings. Objective This study aimed to model a 2D-QSAR equation that can facilitate the researchers to design better aplysinopsin analogs with potent hMAO-A inhibition. Methods Aplysinopsin analogs dataset were subjected to ADME assessme...
Article
Background: The plant Acacia leucophloea (Roxb.) Wild. Family Fabaceae is of paramount importance in Indian medicine. Objectives: We sought to evaluate the in vitro antimicrobial activity of A. leucophloea stem bark extract together with its phytochemical characterization and exploration of drug-likeness attributes. Methods: In vitro Kirby-Bauer...
Article
The Congenital Heart Disease Genetic Knowledge Base (CHDGKB) was established in 2020 to provide comprehensive knowledge about the genetics and pathogenesis of non-syndromic CHD (NS-CHD). In addition to the genetic causes of NS-CHD, environmental factors such as maternal drug use and gene-environment interactions can also lead to CHD. There is a nee...
Article
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The natural product specialized metabolites produced by microbes and plants are the backbone of our current drugs. Ironically, we are in a golden age of understanding natural product biosynthesis, biochemistry, and engineering. These advances have the potential to usher in a new era of natural product exploration and development, taking full advant...
Preprint
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SARS-CoV-2 is a single-stranded RNA betacoronavirus with a high mutation rate. The rapidly emerged SARS-CoV-2 variants could increase the transmissibility, aggravate the severity, and even fade the vaccine protection. Although the coinfections of SARS-CoV-2 with other respiratory pathogens have been reported, whether multiple SARS-CoV-2 variants co...
Article
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Background Kidney transplantation is an optimal method for treatment of end-stage kidney failure. However, kidney transplant rejection (KTR) is commonly observed to have negative effects on allograft function. MicroRNAs (miRNAs) are small non-coding RNAs with regulatory role in KTR genesis, the identification of miRNA biomarkers for accurate diagno...
Article
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Background Colon cancer (CC) is a common gastrointestinal malignant tumor with high heterogeneity in clinical behavior and response to treatment, making individualized survival prediction challenging. Ferroptosis is a newly discovered iron-dependent cell death that plays a critical role in cancer biology. Therefore, identifying a prognostic biomark...
Article
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Background 6-Fluoro-3-(4H-1,2,4-triazol-3-yl)quinolin-4(1H)-ones are promising antitumor agents with enormous data on their profound cytotoxic effects on the human cancer cell lines. Objectives: We sought to perform a Quantitative structure cytotoxicity relationship (QSCR) analysis of a series of previously reported fluoroquinolone analogues using...
Article
Motivation Heart failure (HF) is a cardiovascular disease with a high incidence around the world. Accumulating studies have focused on the identification of biomarkers for HF precision medicine. To understand the HF heterogeneity and provide biomarker information for the personalized diagnosis and treatment of HF, a knowledge database collecting th...
Article
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Introduction Neurodegenerative diseases (NDDs) are a series of chronic diseases, which are associated with progressive loss of neuronal structure or function. The complex etiologies of the NDDs remain unclear, thus the prevention and early diagnosis of NDDs are critical to reducing the mortality and morbidity of these diseases. Objectives To provi...
Article
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The open innovation hub Digital Health and Patient Safety Platform (DHPSP) was recently established with the purpose to invigorate collaborative scientific research and the development of new digital products and personalized solutions aiming to improve human health and patient safety. In this study, we evaluated the effectiveness of a Twitter-base...
Article
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With the progression of modern information techniques, such as the next generation sequencing (NGS), Internet-of-Things (IoT) based smart sensors and artificial intelligence algorithms, the data-intensive research and application now is emerged as the fourth paradigm for scientific discovery. However, we are still facing many challenges to apply th...
Article
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The pathogenesis of cancer is influenced by interactions among genes, proteins, metabolites and other small molecules. Understanding cancer progression at the metabolic level is propitious to the visual decoding of changes in living organisms. To date, a large number of metabolic biomarkers in cancer have been measured and reported, which provide a...
Article
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Background Hepatocellular carcinoma (HCC) is a malignant disease with high morbidity and mortality, and the molecular mechanism for the genesis and progression is complex and heterogeneous. Biomarker discovery is crucial for the personalized and precision treatment of HCC. The accumulation of reported microRNA biomarkers makes it possible to combin...
Article
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Background: Prostate cancer (PCa) is occurred with increasing incidence and heterogeneous pathogenesis. Although clinical strategies are accumulated for PCa prevention, there is still a lack of sensitive biomarkers for the holistic management in PCa occurrence and progression. Based on systems biology and artificial intelligence, translational info...
Article
Background Researches on Lifestyle medicine (LM) have emerged in recent years to garner wide attention. Prostate cancer (PCa) could be prevented and treated by positive lifestyles, but the association between lifestyles and PCa is always personalized. Objectives In order to solve the heterogeneity and diversity of different data types related to P...
Article
The latest advances in the next generation sequencing technology have greatly facilitated the extensive research of genomics and transcriptomics, thereby promoting the decoding of carcinogenesis with unprecedented resolution. Considering the contribution of analyzing high-throughput multi-omics data to the exploration of cancer molecular mechanisms...
Article
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Amino acid network (AAN) models empower us to gain insights into protein structures and functions by describing a protein 3D structure as a graph, where nodes represent residues and edges as amino acid interactions. Here, we present the ANCA, an interactive Web server for Amino Acids Network Construction and Analysis based on a single structure or...
Article
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Background Neuropathic pain (NP) is an egregious problem worldwide. Due to the side-effects of oral drugs, drugs delivered directly to the affected area of pain are preferred. Objective Capsaicin, a chemical compound isolated from chili peppers, is used as an analgesic in topical ointments and dermal patches to alleviate pain. Objective of the stu...
Article
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Emerging evidence has shown a strong association between neuropathic pain and chronic diseases. In recent years, the treatment of neuropathic pain has attracted more attention. Natural products, such as capsaicin and resiniferatoxin, have been well utilized to treat this disease. In this study, we aim to compare the regulatory effects of capsaicin...
Article
Parkinson’s disease is one of the most common adult-onset, a chronic disorder involving neurodegeneration, pro-gressively leading to deprivation of dopaminergic neurons in substantia nigra, causing a subsequent reduction of dopa-mine levels in the striatum resulting in tremor, myotonia, and dyskinesia. Genetics and environmental factors are believe...
Article
Cardiovascular disease (CVD) is the most wide-spread disorder all over the world. The personalized and precision diagnosis, treatment and prevention of CVD is still a challenge. With the developing of metagenome sequencing technologies and the paradigm shifting to data-driven discovery in life science, the computer aided microbiota biomarker discov...