Journal of bioinformatics and systems biology : Open access最新文献

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

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":"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.","PeriodicalId":73617,"journal":{"name":"Journal of bioinformatics and systems biology : Open access","volume":"7 1","pages":"81-91"},"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

Deciphering Collagen Phenotype Dynamics Regulators: Insights from In-Silico Analysis. 解密胶原表型动态调节因子：从模拟分析中获得启示

Journal of bioinformatics and systems biology : Open access Pub Date : 2024-01-01 Epub Date: 2024-09-19 DOI: 10.26502/jbsb.5107089

Resmi Rajalekshmi, Vikrant Rai, Devendra K Agrawal

{"title":"Deciphering Collagen Phenotype Dynamics Regulators: Insights from In-Silico Analysis.","authors":"Resmi Rajalekshmi, Vikrant Rai, Devendra K Agrawal","doi":"10.26502/jbsb.5107089","DOIUrl":"10.26502/jbsb.5107089","url":null,"abstract":"Collagen (Col) types I and III are integral components in wound healing and tissue regeneration, influencing tissue development, homeostasis, and related pathologies. Col I and Col III expression changes during different stages of wound healing and understanding the regulation of collagen phenotype determination is crucial for unraveling the complexities of these processes. Transcription factors and microRNAs, directly and indirectly, play a critical role in regulating collagen expression, however, a comprehensive understanding of the factors regulating Col I and III phenotypes remains elusive. This critically analyzed published reports with focuses on various factors regulating the expression of Col I and Col III at the transcriptional and translational levels. We performed bioinformatics analysis with an input of proinflammatory mediators, growth factors, elastases, and matrix metalloproteinases and predicted transcription factors and microRNAs involved in the regulation of collagen expression. Network analysis revealed an interaction between genes, transcription factors, and microRNAs and provided a holistic view of the regulatory landscape governing collagen expression and unveils intricate interconnections. This analysis lays a founda-tional framework for guiding future research and therapeutic interventions to promote extracellular matrix remodeling, wound healing, and tissue regeneration after an injury by modulating collagen expression. In essence, this scientific groundwork offers a comprehensive exploration of the regulatory dynamics in collagen synthesis, serving as a valuable resource for advancing both basic research and clinical interventions in tissue repair.","PeriodicalId":73617,"journal":{"name":"Journal of bioinformatics and systems biology : Open access","volume":"7 3","pages":"169-181"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11526781/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142559646","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

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

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

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.

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

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, Devendra K Agrawal","doi":"10.26502/jbsb.5107054","DOIUrl":"https://doi.org/10.26502/jbsb.5107054","url":null,"abstract":"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.","PeriodicalId":73617,"journal":{"name":"Journal of bioinformatics and systems biology : Open access","volume":"6 2","pages":"110-120"},"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

引用次数: 0