A modified π rough k-means algorithm for web page recommendation system by Zidane, Khaled Ali Othman

“…Secondly, the CTI dataset, which has been proven by the existing research work as a more suitable Web server logs in the term of Web page recommendation quality, is used for measuring the performance of the proposed modified algorithm for Web page recommendation system. …”
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Nucleocapsid and matrix proteins of nipah virus produced in Pichia pastoris and their interaction by Narcisse Mary, Sither Joseph Vesudian

“…Therefore, the structures of the two proteins were predicted based on an ab initio method using the I-TASSER web server. The predicted 3D structures generated using ITASSER had a confidence score (C-score) of -0.82 and 0.56 for N and M proteins, respectively. …”
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Identification and characterisation of thiamine pyrophosphate riboswitch in oil palm (Elaeis guineensis Jacq.) by Subki, Atiqah

“…The secondary structure analysis was also carried out using Mfold Web server and it showed a stem- loop structure manifested with stems (P1-P5) with minimum free energy of -12.26 kcal/mol. …”
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Enhanced hypertext transfer protocol distributed denial of service detection scheme with get headers adoption by Jaafar, Abdul Ghafar

“…A transaction between a user and a web server involves several layers that are known as Open Systems Interconnection (OSI) layers. …”
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iProEP: A Computational Predictor for Predicting Promoter by Hong-Yan Lai, Zhao-Yue Zhang, Zhen-Dong Su, Wei Su, Hui Ding, Wei Chen, Hao Lin

“…Keywords: promoter, pseudo k-tuple nucleotide composition, position-correlation scoring function, feature selection, web server…”
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Scots pine defensins inhibit Ips acuminatus α-amylase activity by Yurii Yusypovych, Oleh Kit, Volodymyr Kramarets, Yuliia Shalovylo, Mykola Korol, Volodymyr Zaika, Hryhoriy Krynytskyy, Valentyna Kovaleva

“…The docking models of Scots pine defensins and Ips typographus L. α-amylase (AmyIp) complexes were predicted using the ClusPro 2.0 web server. Results and Discussion. As a result, we found the presence of α-amylase activity in the digestive systems of both larvae and adults of I. acuminatus, but not in pupae. …”
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A High-Performance Database Management System for Managing and Analyzing Large-Scale SNP Data in Plant Genotyping and Breeding Applications by Yikun Zhao, Bin Jiang, Yongxue Huo, Hongmei Yi, Hongli Tian, Haotian Wu, Rui Wang, Jiuran Zhao, Fengge Wang

“…Thus, we developed plant SNP database management system (PSNPdms) using an open-source web server and free software that is compatible with single nucleotide polymorphism (SNP), insertion–deletion (InDel) markers, Kompetitive Allele Specific PCR (KASP), SNP array platforms, and 23 species. …”
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The SWine IMputation (SWIM) haplotype reference panel enables nucleotide resolution genetic mapping in pigs by Rongrong Ding, Rodrigo Savegnago, Jinding Liu, Nanye Long, Cheng Tan, Gengyuan Cai, Zhanwei Zhuang, Jie Wu, Ming Yang, Yibin Qiu, Donglin Ruan, Jianping Quan, Enqin Zheng, Huaqiang Yang, Zicong Li, Suxu Tan, Mohammed Bedhane, Robert Schnabel, Juan Steibel, Cedric Gondro, Jie Yang, Wen Huang, Zhenfang Wu

“…We demonstrated in two case studies that genotype imputation using this resource can dramatically improve the resolution of genetic mapping. A public web server has been developed to allow the pig genetics community to fully utilize this resource. …”
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Prediction of base editor off-targets by deep learning by Chengdong Zhang, Yuan Yang, Tao Qi, Yuening Zhang, Linghui Hou, Jingjing Wei, Jingcheng Yang, Leming Shi, Sang-Ging Ong, Hongyan Wang, Hui Wang, Bo Yu, Yongming Wang

“…Finally, we develop an integrated tool that is freely accessible via an online web server http://www.deephf.com/#/bedeep/bedeepoff . …”
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Transient Receptor Potential Ankyrin 1 (TRPA1) Modulation by 4-Hydroxynonenal (4-HNE) in Pancreatic Adenocarcinoma Cell Lines: Putative Roles for Therapies by Florentina Piciu, Dan Domocos, Gabriela Chiritoiu, Marioara Chiritoiu-Butnaru, Maria Mernea, Cezar Gabriel Popescu, Dragos Paul Mihai, Bianca Galateanu, Ariana Hudita, Alexandru Babes, Dana Cucu

“…Also, we simulated the diffusion of 4-HNE through the membrane from the extracellular space with the Permeability of Molecules across Membranes (PerMM) web server. The analysis of cell migration was performed using the wound healing assay, and cell cycle progression was acquired using a Beckman Coulter CytoFlex flow cytometer. …”
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Zinc finger and SCAN domain-containing protein 18 is a potential DNA methylation-modified tumor suppressor and biomarker in breast cancer by Yu Wang, Yuhao Luo, Shaozhi Fu, Lijia He, Guangrui Pan, Dongmei Fan, Qinglian Wen, Yu Fan

“…ZSCAN18 expression was negatively correlated with infiltrating B cells and dendritic cells (DCs), as determined by the TIMER web server and reference to the TISIDB. ZSCAN18 DNA methylation was positively correlated with activated B cells, activated CD8+ and CD4+ T cells, macrophages, neutrophils, and activated DCs. …”
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PhageTailFinder: A tool for phage tail module detection and annotation by Fengxia Zhou, Han Yang, Yu Si, Rui Gan, Ling Yu, Chuangeng Chen, Chunyan Ren, Jiqiu Wu, Fan Zhang, Fan Zhang

“…The developed PhageTailFinder tool can be accessed either as a web server (http://www.microbiome-bigdata.com/PHISDetector/index/tools/PhageTailFinder) or as a stand-alone program on a standard desktop computer (https://github.com/HIT-ImmunologyLab/PhageTailFinder).…”
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Celastrol suppresses colorectal cancer via covalent targeting peroxiredoxin 1 by Heng Xu, Hongfang Zhao, Chunyong Ding, Defang Jiang, Zijie Zhao, Yang Li, Xiaoyu Ding, Jing Gao, Hu Zhou, Cheng Luo, Guoqiang Chen, Ao Zhang, Ying Xu, Hao Zhang

“…Here, we developed a text-mining-based web-server tool to enrich targets from omics data of inquired compounds. …”
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Identification of ST3GAL5 as a prognostic biomarker correlating with CD8+ T cell exhaustion in clear cell renal cell carcinoma by Jiakuan Liu, Jiakuan Liu, Meiqian Li, Meiqian Li, Jiajun Wu, Qi Qi, Yang Li, Simei Wang, Simei Wang, Shengjie Liang, Yuqing Zhang, Zhitao Zhu, Ruimin Huang, Ruimin Huang, Jun Yan, Jun Yan, Rujian Zhu

“…Then we revealed that ST3GAL5 expression showed a positive correlation with CD8+ T cell infiltration, using multiple tools on TIMER2.0 web server. Notably, ST3GAL5 overexpression was further identified to be associated with expression signature of CD8+ T cell exhaustion in ccRCC samples from three datasets (n = 867 in total; r > 0.3, p < 0.001). …”
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Autophagy and Mitophagy-Related Pathways at the Crossroads of Genetic Pathways Involved in Familial Sarcoidosis and Host-Pathogen Interactions Induced by Coronaviruses by Yves Pacheco, Dominique Valeyre, Thomas El Jammal, Maxime Vallee, Fabien Chevalier, Jérôme Lamartine, Dominique Sigaudo-Roussel, Bernard Verrier, Dominique Israel-Biet, Nathalie Freymond, Vincent Cottin, Alain Calender

“…Using ENRICH.R, a comprehensive gene set enrichment web server, we identified the functional pathways represented in the set of genes carrying deleterious mutations and confirmed the overrepresentation of autophagy- and mitophagy-related functions in familial cases of sarcoidosis. …”
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Identifying the Potential of miRNAs in Houttuynia cordata-Derived Exosome-Like Nanoparticles Against Respiratory RNA Viruses by Zhu H, Chang M, Wang Q, Chen J, Liu D, He W

“…The accessibility of miRNA target sites was determined through the MFOLD web server, and customized dual-luciferase reporter assays were administered to validate the computational findings.Results: A total of 12 highly enriched miRNAs were identified in both uHELNs and aHELNs. …”
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A Transformer-Based Ensemble Framework for the Prediction of Protein–Protein Interaction Sites by Minjie Mou, Ziqi Pan, Zhimeng Zhou, Lingyan Zheng, Hanyu Zhang, Shuiyang Shi, Fengcheng Li, Xiuna Sun, Feng Zhu

“…Moreover, pattern analysis based on the interpretability of EnsemPPIS demonstrated that EnsemPPIS was fully capable of learning residue interactions within the local structure of PPI sites using only sequence information. The web server of EnsemPPIS is freely available at http://idrblab.org/ensemppis.…”
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Expression of Eosinophilic Subtype Markers in Patients with Kawasaki Disease by Ling-Sai Chang, Kuang-Den Chen, Ying-Hsien Huang, Ho-Chang Kuo

“…Materials and Methods: The marker expressions of eosinophilic subtypes in the leukocytes of patients with KD were evaluated by the recently established KDmarkers online tool, a web server including gene expression data. Finally, the results were validated with a quantitative reverse transcriptase polymerase chain reaction (RT-PCR). …”
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USP5 facilitates bladder cancer progression by stabilizing the c-Jun protein by Hui-hui Zhang, An-qi Zhang, Peng Peng, Liang Huang, Cai-ying Liu, Xin-rui Nie, De-fu Hou, Xia Zhang, Shang-ze Li

“…Methods The USP5 expression was analysed using the web server GEPIA. To explore USP5 function in bladder cancer, we constructed USP5-knockout cell lines in T24 cells. …”
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RNAm5CPred: Prediction of RNA 5-Methylcytosine Sites Based on Three Different Kinds of Nucleotide Composition by Ting Fang, Zizheng Zhang, Rui Sun, Lin Zhu, Jingjing He, Bei Huang, Yi Xiong, Xiaolei Zhu

“…Thus, we selected the model based on Met240 as our final model, which was named RNAm5CPred. In addition, a web server for RNAm5CPred (http://zhulab.ahu.edu.cn/RNAm5CPred/) has been provided to facilitate experimental research. …”
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