发布求助
文献互助 智能选刊 最新文献

BMC Bioinformatics最新文献

筛选
英文 中文
MicroSSNet: an R package for microbial network construction and analysis at the single-sample and aggregated levels. MicroSSNet：一个R软件包，用于在单个样本和聚合水平上构建和分析微生物网络。
IF 3.3 3区 生物学
BMC Bioinformatics Pub Date : 2026-04-13 DOI: 10.1186/s12859-026-06444-w
Zecheng Tang, Daohua Zhuang, Xinmin Duan, Qingqing Gong, Chen Tian, Peicheng Jiang, Jiangkun Yu, Fei Li, Fangfang Zhao, Guolin Shi, Hang Yang, Qinghang Du, Tong Li, Zhiqiang Ye, Zhigang Zhang
{"title":"MicroSSNet: an R package for microbial network construction and analysis at the single-sample and aggregated levels.","authors":"Zecheng Tang, Daohua Zhuang, Xinmin Duan, Qingqing Gong, Chen Tian, Peicheng Jiang, Jiangkun Yu, Fei Li, Fangfang Zhao, Guolin Shi, Hang Yang, Qinghang Du, Tong Li, Zhiqiang Ye, Zhigang Zhang","doi":"10.1186/s12859-026-06444-w","DOIUrl":"https://doi.org/10.1186/s12859-026-06444-w","url":null,"abstract":"","PeriodicalId":8958,"journal":{"name":"BMC Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147670183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Efficient and interpretable DNA/RNA representation using Komlós-Hadamard transforms. 使用Komlós-Hadamard转换的高效和可解释的DNA/RNA表示。
IF 3.3 3区 生物学
BMC Bioinformatics Pub Date : 2026-04-13 DOI: 10.1186/s12859-026-06442-y
Kareem Kabbani, Samir B Belhaouari, Michaël Aupetit, Aisha Al-Qahtani, Ahmad Halabi, Sophia L Haoudi, Halima Bensmail
{"title":"Efficient and interpretable DNA/RNA representation using Komlós-Hadamard transforms.","authors":"Kareem Kabbani, Samir B Belhaouari, Michaël Aupetit, Aisha Al-Qahtani, Ahmad Halabi, Sophia L Haoudi, Halima Bensmail","doi":"10.1186/s12859-026-06442-y","DOIUrl":"https://doi.org/10.1186/s12859-026-06442-y","url":null,"abstract":"","PeriodicalId":8958,"journal":{"name":"BMC Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147670232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
GGAR: gradient guided adaptive regularization enhances deep learning classification of brassica species using codon usage bias. GGAR：基于密码子使用偏差的梯度引导自适应正则化增强了芸苔种的深度学习分类。
IF 3.3 3区 生物学
BMC Bioinformatics Pub Date : 2026-04-11 DOI: 10.1186/s12859-026-06440-0
Anjum Shahzad, Sheeraz Akram, Tahir Mehmood
{"title":"GGAR: gradient guided adaptive regularization enhances deep learning classification of brassica species using codon usage bias.","authors":"Anjum Shahzad, Sheeraz Akram, Tahir Mehmood","doi":"10.1186/s12859-026-06440-0","DOIUrl":"https://doi.org/10.1186/s12859-026-06440-0","url":null,"abstract":"","PeriodicalId":8958,"journal":{"name":"BMC Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147662047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
QStrain: an interactive platform for viral genome analysis and nucleic acid therapeutic design. QStrain：病毒基因组分析和核酸治疗设计的互动平台。
IF 3.3 3区 生物学
BMC Bioinformatics Pub Date : 2026-04-10 DOI: 10.1186/s12859-026-06424-0
Euna Jeong, Seungyean Lee, Sumin Jeong, Hansaem Lee, Kyung-Chang Kim, Joo-Yeon Lee, Minwook Shin, Sukjoon Yoon
{"title":"QStrain: an interactive platform for viral genome analysis and nucleic acid therapeutic design.","authors":"Euna Jeong, Seungyean Lee, Sumin Jeong, Hansaem Lee, Kyung-Chang Kim, Joo-Yeon Lee, Minwook Shin, Sukjoon Yoon","doi":"10.1186/s12859-026-06424-0","DOIUrl":"https://doi.org/10.1186/s12859-026-06424-0","url":null,"abstract":"","PeriodicalId":8958,"journal":{"name":"BMC Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147653479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Molecular contrastive learning with graph attention network (MoCL-GAT) for enhanced molecular representation. 分子对比学习与图注意网络（MoCL-GAT）增强分子表征。
IF 3.3 3区 生物学
BMC Bioinformatics Pub Date : 2026-04-09 DOI: 10.1186/s12859-026-06409-z
Alperen Dalkıran, Ahmet Sureyya Rifaioglu, Rengul Cetin-Atalay, Aybar C Acar, Tunca Doğan, M Volkan Atalay
{"title":"Molecular contrastive learning with graph attention network (MoCL-GAT) for enhanced molecular representation.","authors":"Alperen Dalkıran, Ahmet Sureyya Rifaioglu, Rengul Cetin-Atalay, Aybar C Acar, Tunca Doğan, M Volkan Atalay","doi":"10.1186/s12859-026-06409-z","DOIUrl":"https://doi.org/10.1186/s12859-026-06409-z","url":null,"abstract":"","PeriodicalId":8958,"journal":{"name":"BMC Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147653482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Biochef: a client-side WebAssembly-based workflow builder for genomic data analysis. Biochef：用于基因组数据分析的基于webassembly的客户端工作流构建器。
IF 3.3 3区 生物学
BMC Bioinformatics Pub Date : 2026-04-09 DOI: 10.1186/s12859-026-06431-1
Joaquim Rosa, João Andrade, Jorge Miguel Silva, José Luis Oliveira
{"title":"Biochef: a client-side WebAssembly-based workflow builder for genomic data analysis.","authors":"Joaquim Rosa, João Andrade, Jorge Miguel Silva, José Luis Oliveira","doi":"10.1186/s12859-026-06431-1","DOIUrl":"https://doi.org/10.1186/s12859-026-06431-1","url":null,"abstract":"<p><strong>Background: </strong>Genomics analyses often rely on command-line tools executed via remote servers, imposing usability barriers for non-technical users and raising privacy concerns. WebAssembly (WASM) enables native-code execution directly in web browsers, eliminating installations and data transfers.</p><p><strong>Results: </strong>We introduce BioChef, a client-side genomic workflow platform that uses WASM. BioChef compiles a genomics toolkit into browser-executable modules and exposes them through a drag-and-drop GUI designed to be intuitive. The system provides real-time validation, flexible input methods (form-based and JSON), intermediate step inspections, and reproducible workflows exportable as bash scripts or configuration files. Performance benchmarks across major browsers (Chromium, Gecko, WebKit) demonstrate rapid initialization (LCP 0.583 s), responsive interactivity (INP 30.5 ms), minimal layout shifts (CLS 0.01), and acceptable overhead (average 181.5 ms initial WASM module load). Although browser execution introduced performance penalties (<math><mo>∼</mo></math>130<math><mo>×</mo></math> slower than native), BioChef workflows still significantly outperformed traditional web services such as Galaxy by avoiding network delays and server-side queueing (11.3<math><mo>×</mo></math> faster in a standard pipeline benchmark).</p><p><strong>Conclusions: </strong>BioChef shows how WebAssembly on the client side can democratize genomic data processing, ensuring privacy, reproducibility and ease of use without external dependencies. To our knowledge, this is the first fully client-side, graphical genomic workflow environment powered by WASM.</p>","PeriodicalId":8958,"journal":{"name":"BMC Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147643813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Gradual spatial constraint feature selection for robust biomarker discovery in high-dimensional gene expression data. 在高维基因表达数据中发现稳健生物标志物的渐进空间约束特征选择。
IF 3.3 3区 生物学
BMC Bioinformatics Pub Date : 2026-04-09 DOI: 10.1186/s12859-026-06435-x
Hong Wang, Xiaolong Ou, Wenshuai Zhang, Ben Niu
{"title":"Gradual spatial constraint feature selection for robust biomarker discovery in high-dimensional gene expression data.","authors":"Hong Wang, Xiaolong Ou, Wenshuai Zhang, Ben Niu","doi":"10.1186/s12859-026-06435-x","DOIUrl":"https://doi.org/10.1186/s12859-026-06435-x","url":null,"abstract":"","PeriodicalId":8958,"journal":{"name":"BMC Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147643829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 new SNP comparison (SnpC) method for detecting unique/enriched gene-SNP variants and comparing population gene mutation diversity. 一种新的SNP比较（SnpC）方法，用于检测独特/富集的基因-SNP变异和比较群体基因突变多样性。
IF 3.3 3区 生物学
BMC Bioinformatics Pub Date : 2026-04-06 DOI: 10.1186/s12859-026-06381-8
Zhanshan Sam Ma, Lianwei Li, Ya-Ping Zhang
{"title":"A new SNP comparison (SnpC) method for detecting unique/enriched gene-SNP variants and comparing population gene mutation diversity.","authors":"Zhanshan Sam Ma, Lianwei Li, Ya-Ping Zhang","doi":"10.1186/s12859-026-06381-8","DOIUrl":"https://doi.org/10.1186/s12859-026-06381-8","url":null,"abstract":"","PeriodicalId":8958,"journal":{"name":"BMC Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147627120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
pyFLANK, a graph neural network based null distribution inference model for FST outlier detection. 基于图神经网络的零分布推断模型，用于FST异常值检测。
IF 3.3 3区 生物学
BMC Bioinformatics Pub Date : 2026-04-06 DOI: 10.1186/s12859-026-06430-2
Zhihai Zhang, Weijia Jia, Joao Paulo Gomes Viana, Ping-Hung Hsieh, Yasuo Yoshikuni, Matthew Hudson
{"title":"pyFLANK, a graph neural network based null distribution inference model for F<sub>ST</sub> outlier detection.","authors":"Zhihai Zhang, Weijia Jia, Joao Paulo Gomes Viana, Ping-Hung Hsieh, Yasuo Yoshikuni, Matthew Hudson","doi":"10.1186/s12859-026-06430-2","DOIUrl":"https://doi.org/10.1186/s12859-026-06430-2","url":null,"abstract":"","PeriodicalId":8958,"journal":{"name":"BMC Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147627130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Adaptive enhancement of chest X-ray images using tissue attenuation and local and global fusion. 基于组织衰减和局部与全局融合的胸部x线图像自适应增强。
IF 3.3 3区 生物学
BMC Bioinformatics Pub Date : 2026-04-02 DOI: 10.1186/s12859-026-06429-9
Zhen Zhao, Rui Tang, Qifeng Liu
{"title":"Adaptive enhancement of chest X-ray images using tissue attenuation and local and global fusion.","authors":"Zhen Zhao, Rui Tang, Qifeng Liu","doi":"10.1186/s12859-026-06429-9","DOIUrl":"https://doi.org/10.1186/s12859-026-06429-9","url":null,"abstract":"","PeriodicalId":8958,"journal":{"name":"BMC Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147607817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
首页 上一页 下一页 尾页
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整，为了账户安全，请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们：info@booksci.cn Book学术提供免费学术资源搜索服务，方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号：604180095
Book学术官方微信
小红书