International Symposium on Bioinformatics Research and Applications最新文献

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stEnTrans: Transformer-Based Deep Learning for Spatial Transcriptomics Enhancement stEnTrans:基于变压器的深度学习用于空间转录组学增强
International Symposium on Bioinformatics Research and Applications Pub Date : 2024-07-11 DOI: 10.1007/978-981-97-5128-0_6
Shuailin Xue, Fangfang Zhu, Changmiao Wang, Wenwen Min
{"title":"stEnTrans: Transformer-Based Deep Learning for Spatial Transcriptomics Enhancement","authors":"Shuailin Xue, Fangfang Zhu, Changmiao Wang, Wenwen Min","doi":"10.1007/978-981-97-5128-0_6","DOIUrl":"https://doi.org/10.1007/978-981-97-5128-0_6","url":null,"abstract":"","PeriodicalId":354035,"journal":{"name":"International Symposium on Bioinformatics Research and Applications","volume":"63 3","pages":"63-75"},"PeriodicalIF":0.0,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141834741","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Sequence-Based Nanobody-Antigen Binding Prediction 基于序列的纳米体抗原结合预测
International Symposium on Bioinformatics Research and Applications Pub Date : 2023-07-15 DOI: 10.48550/arXiv.2308.01920
Usama Sardar, Sarwan Ali, Muhammad Sohaib Ayub, Muhammad Shoaib, Khurram Bashir, Imdadullah Khan, Murray Patterson
{"title":"Sequence-Based Nanobody-Antigen Binding Prediction","authors":"Usama Sardar, Sarwan Ali, Muhammad Sohaib Ayub, Muhammad Shoaib, Khurram Bashir, Imdadullah Khan, Murray Patterson","doi":"10.48550/arXiv.2308.01920","DOIUrl":"https://doi.org/10.48550/arXiv.2308.01920","url":null,"abstract":"Nanobodies (Nb) are monomeric heavy-chain fragments derived from heavy-chain only antibodies naturally found in Camelids and Sharks. Their considerably small size (~3-4 nm; 13 kDa) and favorable biophysical properties make them attractive targets for recombinant production. Furthermore, their unique ability to bind selectively to specific antigens, such as toxins, chemicals, bacteria, and viruses, makes them powerful tools in cell biology, structural biology, medical diagnostics, and future therapeutic agents in treating cancer and other serious illnesses. However, a critical challenge in nanobodies production is the unavailability of nanobodies for a majority of antigens. Although some computational methods have been proposed to screen potential nanobodies for given target antigens, their practical application is highly restricted due to their reliance on 3D structures. Moreover, predicting nanobodyantigen interactions (binding) is a time-consuming and labor-intensive task. This study aims to develop a machine-learning method to predict Nanobody-Antigen binding solely based on the sequence data. We curated a comprehensive dataset of Nanobody-Antigen binding and nonbinding data and devised an embedding method based on gapped k-mers to predict binding based only on sequences of nanobody and antigen. Our approach achieves up to 90% accuracy in binding prediction and is significantly more efficient compared to the widely-used computational docking technique.","PeriodicalId":354035,"journal":{"name":"International Symposium on Bioinformatics Research and Applications","volume":"13 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124854678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A k-mer Based Approach for SARS-CoV-2 Variant Identification 基于k-mer的SARS-CoV-2变异鉴定方法
International Symposium on Bioinformatics Research and Applications Pub Date : 2021-08-07 DOI: 10.1007/978-3-030-91415-8_14
Sarwan Ali, Bikram Sahoo, N. Ullah, Alexander Zelikovskiy, M. Patterson, Imdadullah Khan
{"title":"A k-mer Based Approach for SARS-CoV-2 Variant Identification","authors":"Sarwan Ali, Bikram Sahoo, N. Ullah, Alexander Zelikovskiy, M. Patterson, Imdadullah Khan","doi":"10.1007/978-3-030-91415-8_14","DOIUrl":"https://doi.org/10.1007/978-3-030-91415-8_14","url":null,"abstract":"","PeriodicalId":354035,"journal":{"name":"International Symposium on Bioinformatics Research and Applications","volume":"28 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125021035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 29
A New Network-Based Tool to Analyse Competing Endogenous RNAs 一个新的基于网络的工具来分析竞争的内源性rna
International Symposium on Bioinformatics Research and Applications Pub Date : 2020-12-01 DOI: 10.1007/978-3-030-57821-3_24
Selcen Ari Yuka, Alper Yilmaz
{"title":"A New Network-Based Tool to Analyse Competing Endogenous RNAs","authors":"Selcen Ari Yuka, Alper Yilmaz","doi":"10.1007/978-3-030-57821-3_24","DOIUrl":"https://doi.org/10.1007/978-3-030-57821-3_24","url":null,"abstract":"","PeriodicalId":354035,"journal":{"name":"International Symposium on Bioinformatics Research and Applications","volume":"102 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115646021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Estimating Enzyme Participation in Metabolic Pathways for Microbial Communities from RNA-seq Data 从RNA-seq数据估计微生物群落代谢途径中的酶参与
International Symposium on Bioinformatics Research and Applications Pub Date : 2020-12-01 DOI: 10.1007/978-3-030-57821-3_32
F. Rondel, A. Hosseini, Bikram Sahoo, S. Knyazev, Igor Mandric, F. Stewart, I. Măndoiu, B. Pasaniuc, A. Zelikovsky
{"title":"Estimating Enzyme Participation in Metabolic Pathways for Microbial Communities from RNA-seq Data","authors":"F. Rondel, A. Hosseini, Bikram Sahoo, S. Knyazev, Igor Mandric, F. Stewart, I. Măndoiu, B. Pasaniuc, A. Zelikovsky","doi":"10.1007/978-3-030-57821-3_32","DOIUrl":"https://doi.org/10.1007/978-3-030-57821-3_32","url":null,"abstract":"","PeriodicalId":354035,"journal":{"name":"International Symposium on Bioinformatics Research and Applications","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125493207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of Essential Genes with NemoProfile and Various Machine Learning Models 用NemoProfile和各种机器学习模型鉴定必需基因
International Symposium on Bioinformatics Research and Applications Pub Date : 2020-12-01 DOI: 10.1007/978-3-030-57821-3_30
Yangxiao Wang, Wooyoung Kim
{"title":"Identification of Essential Genes with NemoProfile and Various Machine Learning Models","authors":"Yangxiao Wang, Wooyoung Kim","doi":"10.1007/978-3-030-57821-3_30","DOIUrl":"https://doi.org/10.1007/978-3-030-57821-3_30","url":null,"abstract":"","PeriodicalId":354035,"journal":{"name":"International Symposium on Bioinformatics Research and Applications","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128526453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
HiChew: a Tool for TAD Clustering in Embryogenesis HiChew:胚胎发生中TAD聚类的工具
International Symposium on Bioinformatics Research and Applications Pub Date : 2020-12-01 DOI: 10.1007/978-3-030-57821-3_37
Nikolai S. Bykov, Olga M. Sigalova, M. Gelfand, Aleksandra Galitsyna
{"title":"HiChew: a Tool for TAD Clustering in Embryogenesis","authors":"Nikolai S. Bykov, Olga M. Sigalova, M. Gelfand, Aleksandra Galitsyna","doi":"10.1007/978-3-030-57821-3_37","DOIUrl":"https://doi.org/10.1007/978-3-030-57821-3_37","url":null,"abstract":"","PeriodicalId":354035,"journal":{"name":"International Symposium on Bioinformatics Research and Applications","volume":"98 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124188997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Diagnosis of ASD from rs-fMRI Images Based on Brain Dynamic Networks 基于脑动态网络的rs-fMRI图像诊断ASD
International Symposium on Bioinformatics Research and Applications Pub Date : 2020-12-01 DOI: 10.1007/978-3-030-57821-3_15
Hongyu Guo, Wutao Yin, Sakib Mostafa, Fang-Xiang Wu
{"title":"Diagnosis of ASD from rs-fMRI Images Based on Brain Dynamic Networks","authors":"Hongyu Guo, Wutao Yin, Sakib Mostafa, Fang-Xiang Wu","doi":"10.1007/978-3-030-57821-3_15","DOIUrl":"https://doi.org/10.1007/978-3-030-57821-3_15","url":null,"abstract":"","PeriodicalId":354035,"journal":{"name":"International Symposium on Bioinformatics Research and Applications","volume":"306 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121281225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Ess-NEXG: Predict Essential Proteins by Constructing a Weighted Protein Interaction Network Based on Node Embedding and XGBoost Ess-NEXG:基于节点嵌入和XGBoost的加权蛋白质相互作用网络预测必需蛋白质
International Symposium on Bioinformatics Research and Applications Pub Date : 2020-12-01 DOI: 10.1007/978-3-030-57821-3_9
Nian Wang, Min Zeng, Jiashuai Zhang, Yiming Li, Min Li
{"title":"Ess-NEXG: Predict Essential Proteins by Constructing a Weighted Protein Interaction Network Based on Node Embedding and XGBoost","authors":"Nian Wang, Min Zeng, Jiashuai Zhang, Yiming Li, Min Li","doi":"10.1007/978-3-030-57821-3_9","DOIUrl":"https://doi.org/10.1007/978-3-030-57821-3_9","url":null,"abstract":"","PeriodicalId":354035,"journal":{"name":"International Symposium on Bioinformatics Research and Applications","volume":"158 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114805538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Automated Detection of Sleep Apnea from Abdominal Respiratory Signal Using Hilbert-Huang Transform 基于Hilbert-Huang变换的腹部呼吸信号自动检测睡眠呼吸暂停
International Symposium on Bioinformatics Research and Applications Pub Date : 2020-12-01 DOI: 10.1007/978-3-030-57821-3_35
Xingfeng Lv, Jinbao Li, Qin Yan
{"title":"Automated Detection of Sleep Apnea from Abdominal Respiratory Signal Using Hilbert-Huang Transform","authors":"Xingfeng Lv, Jinbao Li, Qin Yan","doi":"10.1007/978-3-030-57821-3_35","DOIUrl":"https://doi.org/10.1007/978-3-030-57821-3_35","url":null,"abstract":"","PeriodicalId":354035,"journal":{"name":"International Symposium on Bioinformatics Research and Applications","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134207153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
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