Shi Xu

ORCID: 0000-0002-8815-9707
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About
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Research Areas
  • Machine Learning in Bioinformatics
  • Gene expression and cancer classification
  • vaccines and immunoinformatics approaches
  • Ferroelectric and Negative Capacitance Devices
  • Immune Response and Inflammation
  • RNA Research and Splicing
  • Nuclear Structure and Function
  • Ubiquitin and proteasome pathways
  • Wound Healing and Treatments
  • Treatment of Major Depression
  • Insect symbiosis and bacterial influences
  • Immunotherapy and Immune Responses
  • Glycosylation and Glycoproteins Research
  • Geological and Geophysical Studies
  • Invertebrate Immune Response Mechanisms
  • Tryptophan and brain disorders
  • Bioinformatics and Genomic Networks
  • Marine animal studies overview
  • Advanced Memory and Neural Computing
  • Geomechanics and Mining Engineering
  • Aquaculture disease management and microbiota
  • Seismic Imaging and Inversion Techniques
  • Molecular Biology Techniques and Applications
  • Seismic Waves and Analysis
  • Immune Cell Function and Interaction

Nanjing Tech University
2022

Nanjing Normal University
2009-2020

Longgang Central Hospital
2020

China National Administration of Coal Geology
2017

Nanjing University
2013

Nanjing General Hospital of Nanjing Military Command
2013

University of Chinese Academy of Sciences
2009

Precise neoepitope discovery is crucial for effective cancer therapeutic vaccines. Conventional approaches struggle to build a repertoire with sufficient immunogenic epitopes. We developed workflow leveraging full-length ribosome–nascent chain complex–bound mRNA sequencing (FL-RNC seq) and artificial intelligence–based predictive models accurately identify the landscape, especially large-scale transcript variants (LSTVs) missed by short-read sequencing. In MC38 mouse model, we identified 22...

10.1126/sciadv.ado5600 article EN cc-by-nc Science Advances 2025-01-31

In Spin-Transfer Torque Magnetic Random Access Memory (STT-MRAM), the most commonly used timing scheme for conventional Voltage-mode Sense Amplifier (VSA) is global activated timing. Obviously this method cannot obtain optimal yield because different bit-cells have its sensing latency respectively. This paper proposes a self-timed voltage-mode sense named ST-VSS which can enable depending on bit-cell discharging ability. Two circuit structures are proposed: The single SA structure uses...

10.1109/tcsi.2019.2960028 article EN IEEE Transactions on Circuits and Systems I Regular Papers 2020-01-08

Abstract BACKGROUND C‐type lectins (CTLs), a group of pattern recognition receptors, are involved in regulating the immune response insects and could be used as potential targets for pest control. However, information about roles CTLs innate immunity Tribolium castaneum , serious, worldwide that damages stored grain products, is relatively scarce. RESULTS Here, CTL with dual carbohydrate domains (CRDs) containing highly conserved WHD (Trp 53 ‐His 54 ‐Asp 55 ) motif was identified T. named...

10.1002/ps.5945 article EN Pest Management Science 2020-06-10

Abstract Predicting MHC-II restricted epitopes across species used to be challenging, but Alphafold (AF) may provide a structure-based pan-prediction solution. In this study, we established the new tool AF-pred with clear standard for quantitative prediction results. Compared sequence-based tools heavily trained human ligandome, does not show advantage in predicting binding patterns of HLA-II has far better performance other animals’ MHC-II. Using recently resolved bat structures, analyzed...

10.1101/2024.10.11.617946 preprint EN cc-by-nc-nd bioRxiv (Cold Spring Harbor Laboratory) 2024-10-15

Therapeutic effect of autologous concentrated growth factor on lower-extremity chronic refractory wounds: A case report

10.12998/wjcc.v9.i18.4797 article EN World Journal of Clinical Cases 2021-06-11

Hutchinson-Gilford Progeria syndrome (HGPS) is a rare lethal premature and accelerated aging disease caused by mutations in the lamin A/C gene. Nevertheless, mechanisms of cellular damage, senescence, HGPS are not fully understood. Therefore, we aimed to screen potential key genes, pathways, therapeutic agents using bioinformatics methods this study.The gene expression profile GSE113648 GSE41751 were retrieved from omnibus database analyzed identify differentially expressed genes (DEGs)...

10.1097/md.0000000000019022 article EN cc-by-nc Medicine 2020-02-01

Background: Genetic mutations that cause the inactivation or aberrant activation of essential proteins may trigger alterations even dysfunctions in cellular signaling pathways, culminating development precancerous lesions and cancer. Mutations such can result generation "novel proteins" are not part conventional human proteome. Identification these carries a profound potential for unraveling promising drug targets designing innovative therapeutic models. Despite emergence diverse tools...

10.1142/s0219720024500227 article EN Journal of Bioinformatics and Computational Biology 2024-08-30

Firstly, from the point of view frequency domain Helmholtz equation, a detailed description modeling process and blended seismic acquisition forward were given.By solving reverse-time migration method in is derived.Reverse time based on domain, least-squares technology.Based Marmousi model, typical representative, through mixing offset achieved good results.Comparative analysis factors effect advantages disadvantages.

10.2991/meic-15.2015.372 article EN cc-by-nc 2015-01-01

The crust of rock and ore bodies in the Earth's magnetic field, since they are formed from it by its magnetization with varying degrees magnetism, anomaly is caused differences surface [1]. Local aeromagnetic anomalies, generally considered likely to three geological factors, namely related basement uplift or bedrock block; distribution igneous rocks; sedimentary cover layer. With weathered, susceptibility about dikes granite porphyry will within 100×10-5SI; fresh, more than 1000×10-5SI....

10.1063/1.4971928 article EN AIP conference proceedings 2017-01-01

Genetic modifications that cause pivotal protein inactivation or abnormal activation may lead to cell signaling pathway change even dysfunction, resulting in cancer and other diseases. In turn, dysfunction will further produce “novel proteins” do not exist the canonical human proteome. Identification of novel proteins is meaningful for identifying promising drug targets developing new therapies. recent years, several tools have been developed DNA RNA variants with extensive application...

10.2139/ssrn.4271234 article EN SSRN Electronic Journal 2022-01-01
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