Journal of Integrative Bioinformatics最新文献_第9页

A hybrid of Bees algorithm and regulatory on/off minimization for optimizing lactate and succinate production. 混合蜜蜂算法和调节开/关最小化优化乳酸和琥珀酸盐生产。

IF 1.9

Journal of Integrative Bioinformatics Pub Date : 2022-07-19 eCollection Date: 2022-09-01 DOI: 10.1515/jib-2022-0003

Mohd Izzat Yong, Mohd Saberi Mohamad, Yee Wen Choon, Weng Howe Chan, Hasyiya Karimah Adli, Khairul Nizar Syazwan Wsw, Nooraini Yusoff, Muhammad Akmal Remli

{"title":"A hybrid of Bees algorithm and regulatory on/off minimization for optimizing lactate and succinate production.","authors":"Mohd Izzat Yong, Mohd Saberi Mohamad, Yee Wen Choon, Weng Howe Chan, Hasyiya Karimah Adli, Khairul Nizar Syazwan Wsw, Nooraini Yusoff, Muhammad Akmal Remli","doi":"10.1515/jib-2022-0003","DOIUrl":"https://doi.org/10.1515/jib-2022-0003","url":null,"abstract":"Metabolic engineering has expanded in importance and employment in recent years and is now extensively applied particularly in the production of biomass from microbes. Metabolic network models have been employed extravagantly in computational processes developed to enhance metabolic production and suggest changes in organisms. The crucial issue has been the unrealistic flux distribution presented in prior work on rational modelling framework adopting Optknock and OptGene. In order to address the problem, a hybrid of Bees Algorithm and Regulatory On/Off Minimization (BAROOM) is used. By employing Escherichia coli as the model organism, the most excellent set of genes in E. coli that can be removed and advance the production of succinate can be decided. Evidences shows that BAROOM outperforms alternative strategies used to escalate in succinate production in model organisms like E. coli by selecting the best set of genes to be removed.","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2022-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9521821/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40518181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Automatic curation of LTR retrotransposon libraries from plant genomes through machine learning. 通过机器学习从植物基因组中自动管理LTR反转录转座子文库。

IF 1.9

Journal of Integrative Bioinformatics Pub Date : 2022-07-12 eCollection Date: 2022-09-01 DOI: 10.1515/jib-2021-0036

Simon Orozco-Arias, Mariana S Candamil-Cortes, Paula A Jaimes, Estiven Valencia-Castrillon, Reinel Tabares-Soto, Gustavo Isaza, Romain Guyot

{"title":"Automatic curation of LTR retrotransposon libraries from plant genomes through machine learning.","authors":"Simon Orozco-Arias, Mariana S Candamil-Cortes, Paula A Jaimes, Estiven Valencia-Castrillon, Reinel Tabares-Soto, Gustavo Isaza, Romain Guyot","doi":"10.1515/jib-2021-0036","DOIUrl":"https://doi.org/10.1515/jib-2021-0036","url":null,"abstract":"Transposable elements are mobile sequences that can move and insert themselves into chromosomes, activating under internal or external stimuli, giving the organism the ability to adapt to the environment. Annotating transposable elements in genomic data is currently considered a crucial task to understand key aspects of organisms such as phenotype variability, species evolution, and genome size, among others. Because of the way they replicate, LTR retrotransposons are the most common transposable elements in plants, accounting in some cases for up to 80% of all DNA information. To annotate these elements, a reference library is usually created, a curation process is performed, eliminating TE fragments and false positives and then annotated in the genome using the homology method. However, the curation process can take weeks, requires extensive manual work and the execution of multiple time-consuming bioinformatics software. Here, we propose a machine learning-based approach to perform this process automatically on plant genomes, obtaining up to 91.18% F1-score. This approach was tested with four plant species, obtaining up to 93.6% F1-score (Oryza granulata) in only 22.61 s, where bioinformatics methods took approximately 6 h. This acceleration demonstrates that the ML-based approach is efficient and could be used in massive sequencing projects.","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2022-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9521825/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40498603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Colors in the representation of biological structures. 表现生物结构的颜色

IF 1.5

Journal of Integrative Bioinformatics Pub Date : 2022-07-04 DOI: 10.1515/jib-2022-0021

Monica Zoppè

引用次数: 0

Design considerations for representing systems biology information with the Systems Biology Graphical Notation. 用系统生物学图形符号表示系统生物学信息的设计考虑。

IF 1.9

Journal of Integrative Bioinformatics Pub Date : 2022-07-04 DOI: 10.1515/jib-2022-0024

Falk Schreiber, Tobias Czauderna

引用次数: 1

Design - a new way to look at old molecules. 设计——一种看待旧分子的新方法。

IF 1.9

Journal of Integrative Bioinformatics Pub Date : 2022-07-01 DOI: 10.1515/jib-2022-0020

Davide Spalvieri, Anne-Marine Mauviel, Matthieu Lambert, Nicolas Férey, Sophie Sacquin-Mora, Matthieu Chavent, Marc Baaden

引用次数: 3

Integrative illustration of a JCVI-syn3A minimal cell. JCVI-syn3A 最小细胞的综合图示。

IF 1.5

Journal of Integrative Bioinformatics Pub Date : 2022-06-27 DOI: 10.1515/jib-2022-0013

David S Goodsell

引用次数: 0

Considering best practices in color palettes for molecular visualizations. 考虑分子可视化调色板的最佳实践。

IF 1.9

Journal of Integrative Bioinformatics Pub Date : 2022-06-22 DOI: 10.1515/jib-2022-0016

Laura Garrison, Stefan Bruckner

{"title":"Considering best practices in color palettes for molecular visualizations.","authors":"Laura Garrison, Stefan Bruckner","doi":"10.1515/jib-2022-0016","DOIUrl":"https://doi.org/10.1515/jib-2022-0016","url":null,"abstract":"Biomedical illustration and visualization techniques provide a window into complex molecular worlds that are difficult to capture through experimental means alone. Biomedical illustrators frequently employ color to help tell a molecular story, e.g., to identify key molecules in a signaling pathway. Currently, color use for molecules is largely arbitrary and often chosen based on the client, cultural factors, or personal taste. The study of molecular dynamics is relatively young, and some stakeholders argue that color use guidelines would throttle the growth of the field. Instead, content authors have ample creative freedom to choose an aesthetic that, e.g., supports the story they want to tell. However, such creative freedom comes at a price. The color design process is challenging, particularly for those without a background in color theory. The result is a semantically inconsistent color space that reduces the interpretability and effectiveness of molecular visualizations as a whole. Our contribution in this paper is threefold. We first discuss some of the factors that contribute to this array of color palettes. Second, we provide a brief sampling of color palettes used in both industry and research sectors. Lastly, we suggest considerations for developing best practices around color palettes applied to molecular visualization.","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":"19 2","pages":""},"PeriodicalIF":1.9,"publicationDate":"2022-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9377702/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40192929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Integrative analysis of chemical properties and functions of drugs for adverse drug reaction prediction based on multi-label deep neural network 基于多标签深度神经网络的药物化学性质和功能综合分析用于药物不良反应预测

IF 1.9

Journal of Integrative Bioinformatics Pub Date : 2022-05-19 DOI: 10.1515/jib-2022-0007

Pranab Das, Yogita, V. Pal

引用次数: 3

Genome-wide expression reveals potential biomarkers in breast cancer bone metastasis 全基因组表达揭示了乳腺癌症骨转移的潜在生物标志物

IF 1.9

Journal of Integrative Bioinformatics Pub Date : 2022-04-08 DOI: 10.1515/jib-2021-0041

Yashbir Singh, N. Subbarao, Abhinav Jaimini, Quincy A. Hathaway, Amina Kunovac, Bradley J. Erickson, V. Swarup, H. Singh

{"title":"Genome-wide expression reveals potential biomarkers in breast cancer bone metastasis","authors":"Yashbir Singh, N. Subbarao, Abhinav Jaimini, Quincy A. Hathaway, Amina Kunovac, Bradley J. Erickson, V. Swarup, H. Singh","doi":"10.1515/jib-2021-0041","DOIUrl":"https://doi.org/10.1515/jib-2021-0041","url":null,"abstract":"Abstract Breast cancer metastases are most commonly found in bone, an indication of poor prognosis. Pathway-based biomarkers identification may help elucidate the cellular signature of breast cancer metastasis in bone, further characterizing the etiology and promoting new therapeutic approaches. We extracted gene expression profiles from mouse macrophages from the GEO dataset, GSE152795 using the GEO2R webtool. The differentially expressed genes (DEGs) were filtered by log2 fold-change with threshold 1.5 (FDR < 0.05). STRING database and Enrichr were used for GO-term analysis, miRNA and TF analysis associated with DEGs. Autodock Vienna was exploited to investigate interaction of anti-cancer drugs, Actinomycin-D and Adriamycin. Sensitivity and specificity of DEGs was assessed using receiver operating characteristic (ROC) analyses. A total of 61 DEGs, included 27 down-regulated and 34 up-regulated, were found to be significant in breast cancer bone metastasis. Major DEGs were associated with lipid metabolism and immunological response of tumor tissue. Crucial DEGs, Bcl3, ADGRG7, FABP4, VCAN, and IRF4 were regulated by miRNAs, miR-497, miR-574, miR-138 and TFs, CCDN1, STAT6, IRF8. Docking analysis showed that these genes possessed strong binding with the drugs. ROC analysis demonstrated Bcl3 is specific to metastasis. DEGs Bcl3, ADGRG7, FABP4, IRF4, their regulating miRNAs and TFs have strong impact on proliferation and metastasis of breast cancer in bone tissues. In conclusion, present study revealed that DEGs are directly involved in of breast tumor metastasis in bone tissues. Identified genes, miRNAs, and TFs can be possible drug targets that may be used for the therapeutics. However, further experimental validation is necessary.","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2022-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46059130","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 review on methods for predicting miRNA–mRNA regulatory modules miRNA-mRNA调控模块预测方法综述

IF 1.9

Journal of Integrative Bioinformatics Pub Date : 2022-04-01 DOI: 10.1515/jib-2020-0048

Madhumita Madhumita, Sushmita Paul

引用次数: 4