A5039544050- Machine Learning in Bioinformatics
- Acute Myeloid Leukemia Research
- Bioinformatics and Genomic Networks
- Cancer Genomics and Diagnostics
- Ferroptosis and cancer prognosis
- Computational Drug Discovery Methods
- Metabolomics and Mass Spectrometry Studies
- Cancer, Lipids, and Metabolism
- Protein Degradation and Inhibitors
- HIV/AIDS drug development and treatment
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Chronic Myeloid Leukemia Treatments
- Biomedical Text Mining and Ontologies
- Single-cell and spatial transcriptomics
- COVID-19 Clinical Research Studies
- Monoclonal and Polyclonal Antibodies Research
- Histone Deacetylase Inhibitors Research
- PARP inhibition in cancer therapy
- SARS-CoV-2 and COVID-19 Research
- Neuroinflammation and Neurodegeneration Mechanisms
- Gene expression and cancer classification
- Genomics and Chromatin Dynamics
- Influenza Virus Research Studies
- Genetics, Bioinformatics, and Biomedical Research
Institute for Systems Biology
2019-2025
InSysBio (Russia)
2019-2024
Shanghai Center For Bioinformation Technology
2014-2020
Shanghai Academy of Science & Technology
2016-2020
Shanghai Institute of Materia Medica
2008-2017
Chinese Academy of Sciences
2008-2016
Shanghai Institutes for Biological Sciences
2010
Dalian Institute of Chemical Physics
2010
East China University of Science and Technology
2010
We present an integrated analysis of the clinical measurements, immune cells, and plasma multi-omics 139 COVID-19 patients representing all levels disease severity, from serial blood draws collected during first week infection following diagnosis. identify a major shift between mild moderate disease, at which point elevated inflammatory signaling is accompanied by loss specific classes metabolites metabolic processes. Within this stressed environment multiple unusual cell phenotypes emerge...
Lipid metabolism reprogramming is a hallmark for tumor which contributes to tumorigenesis and progression, but the commonality difference of lipid among pan-cancer not fully investigated. Increasing evidences suggest that alterations in metabolism, including metabolite abundance accumulation metabolic products, lead local immunosuppression microenvironment. An integrated analysis cancers from different tissues using multiple omics data may provide novel insight into understanding...
Elucidating the origin of microglia is crucial for understanding their functions and homeostasis. Previous study has indicated that Nestin-positive progenitor cells differentiate into replenish brain after depleting most microglia. Microglia have also shown capacity to repopulate retina eliminating all retinal However, origin(s) repopulated is/are unknown. In this study, we aim investigate origins in retina. Interestingly, find are not derived from cells. Instead, they two origins:...
Abstract Purpose: The inherent genetic heterogeneity of acute myeloid leukemia (AML) has challenged the development precise and effective therapies. objective this study was to elucidate genomic basis drug resistance or sensitivity, identify signatures for response prediction, provide resources research community. Experimental Design: We performed targeted sequencing, high-throughput screening, single-cell profiling on cell samples derived from patients with AML. Statistical approaches...
The recently discovered 150-cavity (formed by loop residues 147–152, N2 numbering) adjacent to the enzymatic active site of group 1 influenza A neuraminidase (NA) has introduced a novel target for design next-generation NA inhibitors. However, only NAs, with exception 2009 pandemic H1N1 NA, possess and no been observed in 2 NAs. role played activity inhibitor binding is not well understood. Here, we demonstrate first time that oseltamivir carboxylate can induce opening rigid closed 150-loop...
Introduction A digital twin is a virtual representation of patient's disease, facilitating real-time monitoring, analysis, and simulation. This enables the prediction disease progression, optimization care delivery, improvement outcomes. Methods Here, we introduce framework for type 2 diabetes (T2D) that integrates machine learning with multiomic data, knowledge graphs, mechanistic models. By analyzing substantial clinical dataset, constructed predictive models to forecast progression....
Abstract Biological and biomedical research relies on comprehensive understanding of protein-coding transcripts. However, the total number human proteins is still unknown due to prevalence alternative splicing. In this paper, we detected 31,566 novel transcripts with coding potential by filtering our ab initio predictions 50 RNA-seq datasets from diverse tissues/cell lines. PCR followed MiSeq sequencing showed that at least 84.1% these predicted splice sites could be validated. contrast...
Abstract Most low GC Gram-positive bacteria possess an essential walKR two-component system (TCS) for signal transduction involved in regulating cell wall homoeostasis. Despite the well-established intracellular regulatory mechanism, role of this TCS extracellular recognition and factors that modulate activity remain largely unknown. Here we identify receptor kinase ‘WalK’ (erWalK) as a key hub bridging input modulation Staphylococcus aureus . Characterization crystal structure erWalK...
Abstract Introduction. The current approved drugs for myelodysplastic syndrome (MDS) are limited, with a few targeted agents such as IDH and BCL-2 inhibitors, hypomethylating (HMAs), growth factors. To identify new effective combinations, evaluate individual patient responses develop predictive models, we have developed multiparameter flow cytometry based high throughput drug screen (MFC-HTS) using the iQue 3 (Sartorius) MDS novel immunotherapy combinations. Methods. Blood bone marrow...
Acute myeloid leukemia (AML) is a highly aggressive and heterogeneous disease, underscoring the need for improved therapeutic options methods to optimally predict responses. With wealth of available data resources, including clinical features, multiomics analysis,
<h3>Objective:</h3> Pancreatic ductal adenocarcinoma (PDAC) is a disease with high mortality. Many so-called "junk" noncoding RNAs need to be discovered in PDAC. The purpose of this study was therefore investigate the function and regulatory mechanism long RNA MEG3 <h3>Methods:</h3> Gene Expression Omnibus database (GEO database) used determine differential expression PDAC, selected for subsequent verification. Tissue cell samples were verify expression, followed by functional detection...
Patients with cancer different molecular characterization and subtypes result in response to anticancer therapeutics survival. To identify features that are associated prognosis is essential precision medicine by providing clues for target identification, drug discovery. Here, we developed a tumor online prognostic analysis platform (ToPP) which integrated eight multi-omics clinical data from 68 projects. It provides multiple approaches customized studies, including 1) Prognostic based on...
ErbB4, a receptor tyrosine kinase of the ErbB family, plays crucial roles in cell growth and differentiation, especially development heart nervous system. Ligand binding to its extracellular region could modulate activation process. To understand mechanism ErbB4 induced by ligand binding, we performed one microsecond molecular dynamics (MD) simulations on (ECR) with without endogenous neuregulin1β (NRG1β). The conformational transition ECR-ErbB4/NRG1β complex from tethered inactive...
Chromosomal translocation, which generates fusion proteins in blood tumor or solid tumor, is considered as one of the major causes leading to cancer. Recent studies suggested that disordered fragments a protein might contribute its carcinogenicity. Here, we investigated sequence feature near breakpoints partner genes, structure features proteins, and posttranslational modification preference proteins. Results show genes have both structural preference. At level, nucleotide combination AG...
Host immune responses play central roles in controlling SARS-CoV2 infection, yet remain incompletely characterized and understood. Here, we present a comprehensive response map spanning 454 proteins 847 metabolites plasma integrated with single-cell multi-omic assays of PBMCs which whole transcriptome, 192 surface proteins, T B cell receptor sequence were co-analyzed within the context clinical measures from 50 COVID19 patient samples. Our study reveals novel cellular subpopulations, such as...