Tianyi Qiu

• Tongji University

Background Norovirus (NoVs) is a foodborne pathogen that causes acute gastroenteritis. The diversity of its principal antigenic protein poses a significant challenge to vaccine development and the prevention of large-scale outbreaks globally. Currently, no licensed vaccines against norovirus have been approved. Methods We developed a novel pipelin...

The emergence of various SARS-CoV-2 variants presents challenges for antibody therapeutics, emphasizing the need for more potent and broadly neutralizing antibodies. Here, we employed an unbiased screening approach and successfully isolated two antibodies from individuals with only exposure to ancestral SARS-CoV-2. One of these antibodies, CYFN1006...

Nuclear receptors (NRs) are a class of essential proteins that regulate the expression of specific genes and are associated with multiple diseases. In silico methods for prescreening potential NR binders with predictive binding ability are highly desired for NR-related drug development but are rarely reported. Here, we present the PbsNRs (Predictin...

Vaccine development is one of the most promising fields, and multi-epitope vaccine, which does not need laborious culture processes, is an attractive alternative to classical vaccines with the advantage of safety, and efficiency. The rapid development of algorithms and the accumulation of immune data have facilitated the advancement of computer-aid...

Phages can specifically recognize and kill bacteria, which lead to important application value of bacteriophage in bacterial identification and typing, livestock aquaculture and treatment of human bacterial infection. Considering the variety of human-infected bacteria and the continuous discovery of numerous pathogenic bacteria, screening suitable...

Since the first human infection reported in 2013, H7N9 avian influenza virus (AIV) has been regarded as a serious threat to human health. In this study, we sought to identify the virulence determinant of the H7N9 virus in mammalian hosts. By comparing the virulence of the SH/4664 H7N9 virus, a non-virulent H9N2 virus, and various H7N9-H9N2 hybrid v...

The current SARS-CoV-2 variants strikingly evade all authorized monoclonal antibodies and threaten the efficacy of serum-neutralizing activity elicited by vaccination or prior infection, urging the need to develop antivirals against SARS-CoV-2 and related sarbecoviruses. Here, we identified both potent and broadly neutralizing antibodies from a fiv...

Bacteriophages can help the treatment of bacterial infections yet require in-silico models to deal with the great genetic diversity between phages and bacteria. Despite the tolerable prediction performance, the application scope of current approaches is limited to the prediction at the species level, which cannot accurately predict the relationship...

Classic chimeric hemagglutinin (cHA) was designed to induce immune responses against the conserved stalk domain of HA. However, it is unclear whether combining more than one HA head domain onto one stalk domain is immunogenic and further induce immune responses against influenza viruses. Here, we constructed numerous novel cHAs comprising two or th...

The COVID‐19 pandemic was characterized by multiple subsequent, overlapping outbreaks, as well as extremely rapid changes in viral genomes. The information about local epidemics spread and the epidemic control measures was shared on a daily basis (number of cases and deaths) via centralized repositories. The vaccines were developed within the first...

Neoantigen vaccines are one of the most effective immunotherapies for personalized tumour treatment. The current immunogen design of neoantigen vaccines is usually based on whole-genome sequencing (WGS) and bioinformatics prediction that focuses on the prediction of binding affinity between peptide and MHC molecules, ignoring other peptide-presenti...

Identifying the exact epitope positions for a monoclonal antibody (mAb) is of critical importance yet highly challenging to the Ab design of biomedical research. Based on previous versions of SEPPA 3.0, we present SEPPA-mAb for the above purpose with high accuracy and low false positive rate (FPR), suitable for both experimental and modelled struct...

SARS-CoV Spike (S) protein shares considerable homology with SARS-CoV-2 S, especially in the conserved S2 subunit (S2). S protein mediates coronavirus receptor binding and membrane fusion, and the latter activity can greatly influence coronavirus infection. We observed that SARS-CoV S is less effective in inducing membrane fusion compared with SARS...

Background Norovirus is a leading cause of acute gastroenteritis among children. Previous studies based on symptomatic infections indicated that mutations, rather than recombination drove the evolution of the norovirus ORF2. These characteristics were found in hospital-based symptomatic infections, whereas, asymptomatic infections are frequent and...

SARS-CoV Spike (S) protein shares considerable homology with SARS-CoV-2 S, especially in the conserved S2 subunit (S2). S protein mediates coronavirus receptor binding and membrane fusion, and the latter activity can greatly influence coronavirus infection. We observed that SARS-CoV S is less effective in inducing membrane fusion compared with SARS...

Background Norovirus, is the leading cause of acute gastroenteritis among children. Previous studies based on symptomatic infections indicated that mutations, rather than recombination drove the evolution of the ORF2 for norovirus. However, strains causing asymptomatic infection were not considered. Methods we conduct the first norovirus molecular...

Long noncoding RNAs (lncRNAs) play a critical role in the immune regulation and tumor microenvironment of pancreatic cancer (PaCa). To construct a novel immune-related prognostic risk model for PaCa and evaluate the prognostic prediction of lncRNAs, essential immune-related lncRNAs (IRlncRNAs) were identified by Pearson correlation analysis of diff...

Background Recently, Zika virus (ZIKV) re-emerged in India and was potentially associated with microcephaly. However, the molecular mechanisms underlying ZIKV pathogenesis remain to be explored. Results Herein, we performed a comprehensive RNA-sequencing analysis on ZIKV-infected JEG-3, U-251 MG, and HK-2 cells versus corresponding uninfected cont...

The rapid mutations on hemagglutinin (HA) of influenza A virus (IAV) can lead to significant antigenic variance and consequent immune mismatch of vaccine strains. Thus, rapid antigenicity evaluation is highly desired. The subtype-specific antigenicity models have been widely used for common subtypes such as H1 and H3. However, the continuous emergi...

It is important to detect foodborne pathogens in food and water, such as Listeria monocytogenes (L.monocytrogenes), which can cause foodborne illness in people with compromised immune systems. Volatile organic compounds (VOC) and 3‑hydroxy-2-butanone (3H-2B) produced by L.monocytrogenes can be used as biomarkers for indirect detection of microbial...

Background The G8 rotavirus genotype has been detected frequently in children in many countries and even became the predominant strain in sub-Saharan African countries, while there are currently no reports from China. In this study we described the genetic characteristics and evolutionary relationship between rotavirus strains from Guangzhou in Chi...

Background The G[8] genotype rotavirus has been detected frequently in children in many countries and even became the predominant strain in sub-Saharan Africa countries. While there are almost no reports from China. In our study, the whole genome sequences of G8 rotavirus strains in China was reported for the first time, and phylogenetic analysis w...

In this paper, mesoporous ZnO nanosheets were synthesized by the hydrothermal method using polystyrene-polyacrylic acid (PS-PAA) as the template. The morphology, structure, and composition of the samples were characterized by SEM, TEM, XRD, and XPS, and the physical properties of the samples were tested by N2 adsorption–desorption curve. The result...

The COVID-19 pandemic of 2020–21 has been a major challenge to public health systems worldwide. Mathematical models of epidemic are useful tools for assessment of the situation and for providing decision-making support for relevant authorities. We developed and implemented SEIR(MH) model that extends the conventional SEIR model with parameters that...

The mixed semiconductor metal oxides as the gas sensor can enhance the sensitivity compared with the metal oxide respectively. In this study, the mesoporous ZnO@Co 3 O 4 nanosphere was prepared through the simple hydrothermal synthesis method of ZIF-L-Zn@Co, the cage construction of mesoporous ZnO@Co 3 O 4 nanosphere was remained unchanged after th...

In this work, the Staphylococcus aureus (S. aureus) was firstly used as a template coupled with PVP in electrospinning experiments, Sn²⁺ bonded with S. aureus and PVP to form nanofiber through electrospinning. Finally, we got the hierarchical mesoporous SnO2 nanotube after calcination of the nanofiber. The hierarchical mesoporous SnO2 nanotube as a...

In this paper, an electrochemical sensing platform based on gold nanoparticle modified carbon nanofiber ([email protected]) as working electrode is proposed for the high sensitivity and selective determination of metronidazole. Meanwhile, the sensor has a large linear response range from 0.1 to 2000 μM, the limit of detection for metronidazole (MNZ...

Since the outbreak of SARS-CoV-2, antigenicity concerns continue to linger with emerging mutants. As recent variants have shown decreased reactivity to previously determined monoclonal antibodies (mAbs) or sera, monitoring the antigenicity change of circulating mutants is urgently needed for vaccine effectiveness. Currently, antigenic comparison is...

To overcome obstacles such as low response and poor selectivity of pure ZnO and SnO2 gas sensors, the ZnO@SnO2 sensor was synthesized by hydrothermal synthesis. The samples were characterized by XRD, XPS, SEM, HRTEM, N2 adsorption-desorption and other techniques. The results show that ZnO@SnO2 forms an n-n-type heterostructure and presents a double...

Drug-resistant cases of human immunodeficiency virus (HIV) nucleoside reverse transcriptase inhibitors (NRTI) are constantly accumulating due to the frequent mutations of the reverse transcriptase (RT). Predicting the potential drug resistance of HIV-1 NRTIs could provide instructions for the proper clinical use of available drugs. In this study, a...

Noroviruses (NoVs), a group of single-stranded RNA viruses causing epidemic acute gastroenteritis in humans, are highly diverse, consisting of multiple genogroups with >30 genotypes. Their continual evolutions make NoV vaccine design and development difficult. Here, we report a study of NoV sequences obtained from a population-based diarrhea survei...

The mutation pattern of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has changed constantly during worldwide community transmission of this virus. However, the reasons for the changes in mutation patterns are still unclear. Accordingly, in this study, we present a comprehensive analysis of over 300 million peptides derived from 13,4...

Though promising, identifying synergistic combinations from a large pool of candidate drugs remains challenging for cancer treatment. Due to unclear mechanism and limited confirmed cases, only a few computational algorithms are able to predict drug synergy. Yet they normally require the drug-cell treatment results as an essential input, thus exclud...

As the entry sites of many pathogens such as human immunodeficiency virus (HIV), mucosal sites are defended by rapidly reacting resident memory T cells (TRM). TRMs represent a special subpopulation of memory T cells that persist long term in non-lymphoid sites without entering the circulation and provide the “sensing and alarming” role in the first...

Zika virus (ZIKV) infection during pregnancy causes intrauterine growth defects and microcephaly, but knowledge of the mechanism through which ZIKV infects and replicates in the placenta remains elusive. Here, we found that ALPP, an alkaline phosphatase expressed primarily in placental tissue, promoted ZIKV infection in both human placental trophob...

Antigenicity measurement plays a fundamental role in vaccine design, which requires antigen selection from a large number of mutants. To augment traditional cross-reactivity experiments, computational approaches for predicting the antigenic distance between multiple protein antigens are highly valuable. The performance of in silico models relies he...

The spreading of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has impacted over 200 countries and regions in the last six month and greatly affected the public health worldwide. It is urgent to reveal the potential evolutionary directions based on mutation patterns to increase our understanding of SARS-CoV-2. Here, we comprehensivel...

Background Colon cancer is one of the most common health threats for humans since its high morbidity and mortality. Detecting potential prognosis risk biomarkers (PRBs) is essential for the improvement of therapeutic strategies and drug development. Currently, although an integrated prognostic analysis of multi-omics for colon cancer is insufficien...

Background The dysregulation of non-coding RNAs (ncRNAs) such as miRNAs and lncRNAs are associated with the pathogenesis and progression in multiple cancers including solid tumors. Comprehensive investigations of prognosis-related ncRNA markers could promote the development of therapeutic strategies for solid tumors, but rarely reported. Methods B...

Background The epidemic caused by SARS-CoV-2 was first reported in Wuhan, China, and now is spreading worldwide. The Chinese government responded to this epidemic with multiple public health policies including locking down the city of Wuhan, establishing multiple temporary hospitals, and prohibiting public gathering events. Here, we constructed a n...

Given that continuing antigenic shift and drift of influenza A viruses result in the escape from previous vaccine-induced immune protection, a universal influenza vaccine has been actively sought. However, there were very few vaccines capable of eliciting cross-group ant-influenza immunity. Here, we designed two novel composite immunogens containin...

Foot-and-mouth disease virus (FMDV) is an antigenic-variable RNA virus that is responsible for the recurrence of foot-and-mouth disease in livestock and can be prevented and controlled using a vaccine with broad-spectrum protection. Current anti-genicity evaluation methods, which involve animal immunity experiments and serum preparation, are unable...

B-cell epitope information is critical to immune therapy and vaccine design. Protein epitopes can be significantly affected by glycosylation, while no methods have considered this till now. Based on previous versions of Spatial Epitope Prediction of Protein Antigens (SEPPA), we here present an enhanced tool SEPPA 3.0, enabling glycoprotein antigens...

Emerging or re-emerging dengue virus (DENV) causes dengue fever epidemics globally. Current DENV serotypes are defined based on genetic clustering, while discrepancies are frequently observed between the genetic clustering and the antigenicity experiments. Rapid antigenicity determination of DENV mutants in high-throughput way is critical for vacci...

Flavonoids are the largest class of plant polyphenols, with common structure of diphenylpropanes, consisting of two aromatic rings linked through three carbons and are abundant in both daily diets and medicinal plants. Fueled by the recognition of consuming flavonoids to get better health, researchers became interested in deciphering how flavonoids...

Major challenges in vaccine development include rapidly selecting or designing immunogens for raising cross-protective immunity against different intra-or inter-subtypic pathogens, especially for the newly emerging varieties. Here we propose a computational method, Conformational Epitope (CE)-BLAST, for calculating the antigenic similarity among di...

Nuclear receptors (NR) are a class of proteins that are responsible for sensing steroid and thyroid hormones and certain other molecules. In that case, NR have the ability to regulate the expression of specific genes and associated with various diseases, which make it essential drug targets. Approaches which can predict the inhibition ability of co...

Therapeutic antibodies are widely used for disease detection and specific treatments. However, as an exogenous protein, these antibodies can be detected by the human immune system and elicit a response that can lead to serious illnesses. Therapeutic antibodies can be engineered through antibody humanization, which aims to maintain the specificity a...

Objective: To analyze the immunogenomic characteristics of antibody repertoire in response to influenza vaccine in order to provide a theoretical basis for further development of antibody. Methods: Based on a time-series immunoglobulin heavy chain (IGH) repertoire sequencing dataset, we analyzed the immunogenomic characteristics of antibody reperto...

The rapid and consistent mutation of influenza requires frequent evaluation of antigenicity variation among newly emerged strains, during which several in-silico methods have been reported to facilitate the assays. In this paper, we designed a structure-based antigenicity scoring model instead of those sequence-based previously published. Protein s...

As an extension of the conventional quantitative structure activity relationship models, proteochemometric (PCM) modelling is a computational method that can predict the bioactivity relations between multiple ligands and multiple targets. Traditional PCM modelling includes three essential elements: descriptors (including target descriptors, ligand...

Mutations of the influenza virus lead to antigenic changes that cause recurrent epidemics and vaccine resistance. Preventive measures would benefit greatly from the ability to predict the potential distribution of new antigenic sites in future strains. By leveraging the extensive historical records of HA sequences for 90 years, we designed a comput...

Despite the high specificity between antigen and antibody binding, similar epitopes can be recognized or cross-neutralized by paratopes of antibody with different binding affinities. How to accurately characterize this slight variation which may or may not change the antigen-antibody binding affinity is a key issue in this area. In this report, by...

Proton pump inhibitors (PPIs) are extensively used for the treatment of gastric acid-related disorders. PPIs appear to be well tolerated and almost have no short-term side effects. However, the clinical adverse reactions of long-term PPI usage are increasingly reported in recent years. So far, there is no study that elucidates the side effects mech...

Spatial Epitope Prediction server for Protein Antigens (SEPPA) has received lots of feedback since being published in 2009. In this improved version, relative ASA preference of unit patch and consolidated amino acid index were added as further classification parameters in addition to unit-triangle propensity and clustering coefficient which were pr...

Potassium channels participate in many critical biological functions and play important roles in a variety of diseases. In recent years, many significant discoveries have been made which motivate us to review these achievements. The focus of our review is mainly on three aspects. Firstly, we try to summarize the latest developments in structure det...