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Computational methods for identifying enhancer-promoter interactions 识别增强子-启动子相互作用的计算方法
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2023-01-01 DOI: 10.15302/j-qb-022-0322
{"title":"Computational methods for identifying enhancer-promoter interactions","authors":"","doi":"10.15302/j-qb-022-0322","DOIUrl":"https://doi.org/10.15302/j-qb-022-0322","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67351360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Secure and efficient implementation of facial emotion detection for smart patient monitoring system 智能病人监护系统中面部情绪检测的安全高效实现
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2023-01-01 DOI: 10.15302/j-qb-022-0312
{"title":"Secure and efficient implementation of facial emotion detection for smart patient monitoring system","authors":"","doi":"10.15302/j-qb-022-0312","DOIUrl":"https://doi.org/10.15302/j-qb-022-0312","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"15 1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67351451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Light-driven synthetic microbial consortia: playing with an oxygen dilemma 光驱动的合成微生物联合体:与氧的困境玩耍
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2023-01-01 DOI: 10.15302/j-qb-022-0314
{"title":"Light-driven synthetic microbial consortia: playing with an oxygen dilemma","authors":"","doi":"10.15302/j-qb-022-0314","DOIUrl":"https://doi.org/10.15302/j-qb-022-0314","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67351506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A cell marker-based clustering strategy (cmCluster) for precise cell type identification of scRNA-seq data 基于细胞标记的聚类策略(cmCluster)用于scRNA-seq数据的精确细胞类型鉴定
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2023-01-01 DOI: 10.15302/j-qb-022-0311
Yuwei Huang, Huidan Chang, Xiaoyi Chen, Jiayue Meng, Mengyao Han, Tao Huang, Liyun Yuan, Guoqing Zhang
{"title":"A cell marker-based clustering strategy (cmCluster) for precise cell type identification of scRNA-seq data","authors":"Yuwei Huang, Huidan Chang, Xiaoyi Chen, Jiayue Meng, Mengyao Han, Tao Huang, Liyun Yuan, Guoqing Zhang","doi":"10.15302/j-qb-022-0311","DOIUrl":"https://doi.org/10.15302/j-qb-022-0311","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67351781","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Pattern discovery of long non-coding RNAs associated with the herbal treatments in breast and prostate cancers 与乳腺癌和前列腺癌草药治疗相关的长链非编码rna的模式发现
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2023-01-01 DOI: 10.15302/j-qb-023-0333
{"title":"Pattern discovery of long non-coding RNAs associated with the herbal treatments in breast and prostate cancers","authors":"","doi":"10.15302/j-qb-023-0333","DOIUrl":"https://doi.org/10.15302/j-qb-023-0333","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67351942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Introduction to bioimaging-based spatial multi-omic novel methods 基于生物成像的空间多组学新方法简介
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2023-01-01 DOI: 10.15302/j-qb-023-0332
{"title":"Introduction to bioimaging-based spatial multi-omic novel methods","authors":"","doi":"10.15302/j-qb-023-0332","DOIUrl":"https://doi.org/10.15302/j-qb-023-0332","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67351936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Prediction of chromatin looping using deep hybrid learning (DHL) 基于深度混合学习的染色质环预测
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2023-01-01 DOI: 10.15302/j-qb-022-0315
{"title":"Prediction of chromatin looping using deep hybrid learning (DHL)","authors":"","doi":"10.15302/j-qb-022-0315","DOIUrl":"https://doi.org/10.15302/j-qb-022-0315","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67351567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Exploration on learning molecular docking with deep learning models 学习分子与深度学习模型对接的探索
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2023-01-01 DOI: 10.15302/j-qb-022-0321
{"title":"Exploration on learning molecular docking with deep learning models","authors":"","doi":"10.15302/j-qb-022-0321","DOIUrl":"https://doi.org/10.15302/j-qb-022-0321","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67351747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
3D genomic organization in cancers 癌症中的三维基因组组织
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2023-01-01 DOI: 10.15302/j-qb-022-0317
{"title":"3D genomic organization in cancers","authors":"","doi":"10.15302/j-qb-022-0317","DOIUrl":"https://doi.org/10.15302/j-qb-022-0317","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67351685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Tuning hyperparameters of doublet-detection methods for single-cell RNA sequencing data 单细胞RNA测序数据双检测方法的超参数调整
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2022-11-01 DOI: 10.15302/j-qb-022-0324
N. Xi, Angelos Vasilopoulos
{"title":"Tuning hyperparameters of doublet-detection methods for single-cell RNA sequencing data","authors":"N. Xi, Angelos Vasilopoulos","doi":"10.15302/j-qb-022-0324","DOIUrl":"https://doi.org/10.15302/j-qb-022-0324","url":null,"abstract":"The existence of doublets in single-cell RNA sequencing (scRNA-seq) data poses a great challenge in downstream data analysis. Computational doublet-detection methods have been developed to remove doublets from scRNA-seq data. Yet, the default hyperparameter settings of those methods may not provide optimal performance. Here, we propose a strategy to tune hyperparameters for a cutting-edge doublet-detection method. We utilize a full factorial design to explore the relationship between hyperparameters and detection accuracy on 16 real scRNA-seq datasets. The optimal hyperparameters are obtained by a response surface model and convex optimization. We show that the optimal hyperparameters provide top performance across scRNA-seq datasets under various biological conditions. Our tuning strategy can be applied to other computational doublet-detection methods. It also offers insights into hyperparameter tuning for broader computational methods in scRNA-seq data analysis.","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46420397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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