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Linear Regression of Sampling Distributions of the Mean. 平均值抽样分布的线性回归。
Journal of bioinformatics and systems biology : Open access Pub Date : 2024-01-01 Epub Date: 2024-03-04 DOI: 10.26502/jbsb.5107079
David J Torres, Ana Vasilic, Jose Pacheco
{"title":"Linear Regression of Sampling Distributions of the Mean.","authors":"David J Torres, Ana Vasilic, Jose Pacheco","doi":"10.26502/jbsb.5107079","DOIUrl":"10.26502/jbsb.5107079","url":null,"abstract":"<p><p>We show that the simple and multiple linear regression coefficients and the coefficient of determination R<sup>2</sup> computed from sampling distributions of the mean (with or without replacement) are equal to the regression coefficients and coefficient of determination computed with individual data. Moreover, the standard error of estimate is reduced by the square root of the group size for sampling distributions of the mean. The result has applications when formulating a distance measure between two genes in a hierarchical clustering algorithm. We show that the Pearson <math><mi>R</mi></math> coefficient can measure how differential expression in one gene correlates with differential expression in a second gene.</p>","PeriodicalId":73617,"journal":{"name":"Journal of bioinformatics and systems biology : Open access","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11108041/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141077380","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
Transcriptional and Translational Regulation of Differentially Expressed Genes in Yucatan Miniswine Brain Tissues following Traumatic Brain Injury. 创伤性脑损伤后尤卡坦小型犬脑组织中差异表达基因的转录和转译调控。
Journal of bioinformatics and systems biology : Open access Pub Date : 2024-01-01 Epub Date: 2024-03-05 DOI: 10.26502/jbsb.5107080
Vikrant Rai, Yssel Mendoza-Mari, Mohamed M Radwan, James Brazdzionis, David A Connett, Dan E Miulli, Devendra K Agrawal
{"title":"Transcriptional and Translational Regulation of Differentially Expressed Genes in Yucatan Miniswine Brain Tissues following Traumatic Brain Injury.","authors":"Vikrant Rai, Yssel Mendoza-Mari, Mohamed M Radwan, James Brazdzionis, David A Connett, Dan E Miulli, Devendra K Agrawal","doi":"10.26502/jbsb.5107080","DOIUrl":"10.26502/jbsb.5107080","url":null,"abstract":"<p><p>Traumatic brain injury (TBI) is a leading cause of morbidity, disability, and mortality worldwide. Motor and cognitive deficits and emotional disturbances are long-term consequences of TBI. A lack of effective treatment for TBI-induced neural damage, functional impairments, and cognitive deficits makes it challenging in the recovery following TBI. One of the reasons may be the lack of knowledge underlying the complex pathophysiology of TBI and the regulatory factors involved in the cellular and molecular mechanisms of inflammation, neural regeneration, and injury repair. These mechanisms involve a change in the expression of various proteins encoded by genes whose expression is regulated by transcription factors (TFs) at the transcriptional level and microRNA (miRs) at the mRNA level. In this pilot study, we performed the RNA sequencing of injured tissues and non-injured tissues from the brain of Yucatan miniswine and analyzed the sequencing data for differentially expressed genes (DEGs) and the TFs and miRs regulating the expression of DEGs using in-silico analysis. We also compared the effect of the electromagnetic field (EMF) applied to the injured miniswine on the expression profile of various DEGs. The results of this pilot study revealed a few DEGs that were significantly upregulated in the injured brain tissue and the EMF stimulation showed effect on their expression profile.</p>","PeriodicalId":73617,"journal":{"name":"Journal of bioinformatics and systems biology : Open access","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11138201/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141181806","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
MXP: Modular eXpandable framework for building bioinformatics Pipelines. MXP：用于构建生物信息学管道的模块化可扩展框架。
Journal of bioinformatics and systems biology : Open access Pub Date : 2023-01-01 Epub Date: 2023-08-07 DOI: 10.26502/jbsb.5107058
Mikhail Kovtun, Konstantin Arbeev, Anatoliy Yashin, Igor Akushevich
{"title":"MXP: Modular eXpandable framework for building bioinformatics Pipelines.","authors":"Mikhail Kovtun,&nbsp;Konstantin Arbeev,&nbsp;Anatoliy Yashin,&nbsp;Igor Akushevich","doi":"10.26502/jbsb.5107058","DOIUrl":"10.26502/jbsb.5107058","url":null,"abstract":"<p><p>Pipelines are a natural tool in bioinformatics applications. Virtually any meaningful processing of biological data involves the execution of multiple software tools, and this execution must be arranged in a coherent manner. Many tools for the building of pipelines were developed over time and used to facilitate work with increasing volume of bioinformatics data. Here we present a flexible and expandable framework for building pipelines, MXP, which we hope will find its own niche in bioinformatics applications. We developed MXP and tested it on various tasks in our organization, primarily for building pipelines for GWAS (Genome-Wide Association Studies) and post-GWAS analysis. It was proven to be sufficiently flexible and useful. MXP implements a number of novel features which, from our point of view, make it to be more suitable and more convenient for building bioinformatics pipelines.</p>","PeriodicalId":73617,"journal":{"name":"Journal of bioinformatics and systems biology : Open access","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10621886/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71429921","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
The Need for Visualization Tools in the Electronic Health Record and in Decision Aids 电子健康记录和决策辅助中可视化工具的需求
Journal of bioinformatics and systems biology : Open access Pub Date : 2023-01-01 DOI: 10.26502/jbsb.5107059
Jonathan Bidwell, A. Leviton, M. Jackson, K. Mane, Sayantan Das, T. Loddenkemper
{"title":"The Need for Visualization Tools in the Electronic Health Record and in Decision Aids","authors":"Jonathan Bidwell, A. Leviton, M. Jackson, K. Mane, Sayantan Das, T. Loddenkemper","doi":"10.26502/jbsb.5107059","DOIUrl":"https://doi.org/10.26502/jbsb.5107059","url":null,"abstract":"","PeriodicalId":73617,"journal":{"name":"Journal of bioinformatics and systems biology : Open access","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69367517","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
Cell Type Classification and Discovery across Diseases, Technologies and Tissues Reveals Conserved Gene Signatures of Immune Phenotypes 跨疾病、技术和组织的细胞类型分类和发现揭示了免疫表型的保守基因特征
Journal of bioinformatics and systems biology : Open access Pub Date : 2023-01-01 DOI: 10.26502/jbsb.5107057
Mathew Chamberlain, Nima Nouri, Andre H. Kurlovs, R. Hanamsagar, Frank O. Nestle, E. de Rinaldis, Virginia Savova
{"title":"Cell Type Classification and Discovery across Diseases, Technologies and Tissues Reveals Conserved Gene Signatures of Immune Phenotypes","authors":"Mathew Chamberlain, Nima Nouri, Andre H. Kurlovs, R. Hanamsagar, Frank O. Nestle, E. de Rinaldis, Virginia Savova","doi":"10.26502/jbsb.5107057","DOIUrl":"https://doi.org/10.26502/jbsb.5107057","url":null,"abstract":"","PeriodicalId":73617,"journal":{"name":"Journal of bioinformatics and systems biology : Open access","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69367954","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
Metadichol® Induced the Expression of Neuronal Transcription Factors in Human Fibroblast Dermal Cells. Metadichol®诱导人成纤维细胞真皮细胞神经元转录因子的表达。
Journal of bioinformatics and systems biology : Open access Pub Date : 2023-01-01 DOI: 10.26502/jbsb.5107066
Palayakotai Raghavan R.
{"title":"Metadichol® Induced the Expression of Neuronal Transcription Factors in Human Fibroblast Dermal Cells.","authors":"Palayakotai Raghavan R.","doi":"10.26502/jbsb.5107066","DOIUrl":"https://doi.org/10.26502/jbsb.5107066","url":null,"abstract":"Background: Producing neurons from fibroblast cells has the potential to treat neurodegenerative diseases, characterized by neuron loss. Neurodegenerative diseases are a growing problem in the current aging and developed world populations. Metadichol® is a nontoxic nanoemulsion of long-chain lipid alcohols currently available as an oral supplement.","PeriodicalId":73617,"journal":{"name":"Journal of bioinformatics and systems biology : Open access","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136260007","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
Denovo Structural Modeling and B cell and T cell Epitope Prediction against SARS-COV-2 PLpro to Cure COVID-19: Vaccinomics Based Approach 基于疫苗组学的SARS-COV-2 PLpro治疗COVID-19的Denovo结构建模和B细胞和T细胞表位预测
Journal of bioinformatics and systems biology : Open access Pub Date : 2023-01-01 DOI: 10.26502/jbsb.5107062
Carlos Eliel Maya Ramirez, Sajida Ashraf, Faiza Irshad, Tabish Rehman, Moayad Shahwan, Muhammad Sufyan
{"title":"Denovo Structural Modeling and B cell and T cell Epitope Prediction against SARS-COV-2 PLpro to Cure COVID-19: Vaccinomics Based Approach","authors":"Carlos Eliel Maya Ramirez, Sajida Ashraf, Faiza Irshad, Tabish Rehman, Moayad Shahwan, Muhammad Sufyan","doi":"10.26502/jbsb.5107062","DOIUrl":"https://doi.org/10.26502/jbsb.5107062","url":null,"abstract":"","PeriodicalId":73617,"journal":{"name":"Journal of bioinformatics and systems biology : Open access","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135952809","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
Role of Transcription Factors and MicroRNAs in Regulating Fibroblast Reprogramming in Wound Healing. 转录因子和microrna在伤口愈合过程中调节成纤维细胞重编程中的作用。
Journal of bioinformatics and systems biology : Open access Pub Date : 2023-01-01 DOI: 10.26502/jbsb.5107054
Vikrant Rai, Devendra K Agrawal
{"title":"Role of Transcription Factors and MicroRNAs in Regulating Fibroblast Reprogramming in Wound Healing.","authors":"Vikrant Rai,&nbsp;Devendra K Agrawal","doi":"10.26502/jbsb.5107054","DOIUrl":"https://doi.org/10.26502/jbsb.5107054","url":null,"abstract":"<p><p>Non-healing diabetic foot ulcer, a chronic inflammatory disease, is a sizable clinical and economic burden to healthcare systems around the world. Chronic inflammation plays a critical role in the nonhealing pattern due to the arrest of the cellular response during wound healing in the inflammatory phase without progressing to the proliferative and remodeling phase. Fibroblasts play a critical role in all three phases of wound healing. Activation of fibroblasts in the presence of cytokines results in the formation of myofibroblast that contributes to extracellular matrix formation. Additionally, few studies documented the presence of inflammatory, angiogenic, and angiostatic fibroblast subpopulation during wound healing. Various studies have discussed the role of transcription factors and microRNA in regulating the transdifferentiation of fibroblast to myofibroblast, however, what factors regulate the reprogramming of fibroblast to inflammatory, angiogenic, and angiostatic phenotypes have not been clearly addressed in the literature. This critical review article addresses the role of transcription factors and microRNAs in regulating fibroblast to myofibroblast transdifferentiation followed by the prediction of transcription factors and microRNAs, based on the bioinformatics analysis, in regulating transdifferentiation of fibroblasts to inflammatory, angiogenic, and angiostatic subtypes. The results of in-silico networking revealed multiple new transcription factors and microRNAs and their interaction with specific markers on other fibroblasts suggesting their role in the regulation of fibroblast reprogramming.</p>","PeriodicalId":73617,"journal":{"name":"Journal of bioinformatics and systems biology : Open access","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10358319/pdf/nihms-1910077.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9855107","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
Supervised learning of Plasmodium falciparum life cycle stages using single-cell transcriptomes identifies crucial proteins 利用单细胞转录组鉴定关键蛋白，对恶性疟原虫生命周期阶段进行监督学习
Journal of bioinformatics and systems biology : Open access Pub Date : 2023-01-01 DOI: 10.26502/jbsb.5107047
Swarnim Shukla, Soham Choudhuri, Gayathri Priya Iragavarapu, B. Ghosh
{"title":"Supervised learning of Plasmodium falciparum life cycle stages using single-cell transcriptomes identifies crucial proteins","authors":"Swarnim Shukla, Soham Choudhuri, Gayathri Priya Iragavarapu, B. Ghosh","doi":"10.26502/jbsb.5107047","DOIUrl":"https://doi.org/10.26502/jbsb.5107047","url":null,"abstract":"","PeriodicalId":73617,"journal":{"name":"Journal of bioinformatics and systems biology : Open access","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69367935","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
The Growing Liberality Observed in Primary Animal and Plant Cultures is Common to the Social Amoeba. 在原始动物和植物培养中观察到的日益增长的慷慨是社会变形虫的共同特点。
Journal of bioinformatics and systems biology : Open access Pub Date : 2023-01-01 DOI: 10.26502/jbsb.5107045
Norichika Ogata
{"title":"The Growing Liberality Observed in Primary Animal and Plant Cultures is Common to the Social Amoeba.","authors":"Norichika Ogata","doi":"10.26502/jbsb.5107045","DOIUrl":"https://doi.org/10.26502/jbsb.5107045","url":null,"abstract":"<p><p>Tissue culture environment liberates cells fromordinary laws of multi-cellular organisms. This liberation enables cells several behaviors, such as proliferation, dedifferentiation, acquisition of pluripotency, immortalization, and reprogramming. Recently, the quantitative value of cellular dedifferentiation and differentiation was defined as \"liberality\", which is measurable as Shannon entropy of numerical transcriptome data and Lempel-Zip complexity of nucleotide sequence transcriptome data. The increasing liberality induced by the culture environment had first been observed in animal cells and had reconfirmed in plant cells.The phenomena may be common across the kingdom, also in a social amoeba. We measured the liberality of the social amoeba which disaggregated from multicellular aggregates and transferred into a liquid medium.</p>","PeriodicalId":73617,"journal":{"name":"Journal of bioinformatics and systems biology : Open access","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10078981/pdf/nihms-1881285.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9326056","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: 1
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