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

Genomics to Notebook (g2nb): Extending the Electronic Notebook to Address the Challenges of Bioinformatics Analysis. 基因组学到笔记本（g2nb）：扩展电子笔记本以解决生物信息学分析的挑战。

Journal of bioinformatics and systems biology : Open access Pub Date : 2025-01-01 Epub Date: 2025-01-27 DOI: 10.26502/jbsb.5107096

Michael Reich, Thorin Tabor, Ted Liefeld, Jayadev Joshi, Forrest Kim, Edwin Huang, Helga Thorvaldsdottir, Daniel Blankenberg, Jill P Mesirov

引用次数: 0

CDC42 Regulatory Patterns Related To Inflammatory Bowel Disease and Hyperglycemia. 与炎症性肠病和高血糖相关的CDC42调节模式

Journal of bioinformatics and systems biology : Open access Pub Date : 2025-01-01 Epub Date: 2025-02-20

Marija Stojanovic, Devendra K Agrawal

{"title":"CDC42 Regulatory Patterns Related To Inflammatory Bowel Disease and Hyperglycemia.","authors":"Marija Stojanovic, Devendra K Agrawal","doi":"","DOIUrl":"","url":null,"abstract":"As a member of the rat sarcoma virus homolog (Rho) guanosine triphosphatases (GTPases) family, Cdc42 represents a \"switch\" molecule, by changing from inactive (GDP-associated) to active form (GTP-associated) and vice versa. Cdc42 is activated by the guanine nucleotide exchange factors (GEFs), in contrast to GTPase-activating proteins (GAPs) which are responsable for formation of GDP-binding, inactive form of Cdc42. Some of the fundamental cellular functions are regulated by Cdc42 such as cytosceleton dynamics, cell cycling, transcription and cellular trafficking. In the gastrointestinal system, Cdc42 participates in maintenance of the functional epithelial barrier by controling intestinal epithelial cell polarity and interconnections. In addition, Cdc42 expression in pancreatic β-cells is of great importance for glucose-stimulated insulin secretion. From the pathophysiological point of view, literature data provide some evidence for Cdc42 sigaling in inflammatory bowel disease, as well as in hyperglycemic conditions related to diabetes mellitus. However, whether and by which mechanism Cdc42 contributes to the IBD patophysiology in hyperglycemic conditions is still not fully understood. Therefore, we performed bioinformatics analysis to predict transcriptional factor-gene interactions related to Cdc42 signaling in inflammatory bowel disease in hyperglycemic conditions. In silico analysis predicts various interactions between input genes and output transcriptional factors, and therefore reveals the molecules with the highest predicted effect on particular genes. Based on the predictive interactions with the intracellular molecules, carefully designed in vitro or in vivo studies are required to get better insight in the pathways of interest. Better understanding of Cdc42 molecular pathway in inflammatory bowel disease and hyperglycemia will help identifying potential targets for therapeutical modifications in clinical setting resulting in better control of the disease progression.","PeriodicalId":73617,"journal":{"name":"Journal of bioinformatics and systems biology : Open access","volume":"8 1","pages":"17-28"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11967731/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143782276","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

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

The Effects of Nitric Oxide on Choroidal Gene Expression.

Journal of bioinformatics and systems biology : Open access Pub Date : 2024-01-01 DOI: 10.26502/jbsb.5107077

Makenzie B Merkley, Diana Soriano, Kenneth L Jones, Jody A Summers

{"title":"The Effects of Nitric Oxide on Choroidal Gene Expression.","authors":"Makenzie B Merkley, Diana Soriano, Kenneth L Jones, Jody A Summers","doi":"10.26502/jbsb.5107077","DOIUrl":"10.26502/jbsb.5107077","url":null,"abstract":"Purpose: Nitric oxide (NO) is recognized as an important biological mediator that controls several physiological functions, and evidence is now emerging that this molecule may play a significant role in the postnatal control of ocular growth and myopia development. We therefore sought to understand the role that nitric oxide plays in visually-guided ocular growth in order to gain insight into the underlying mechanisms of this process.Methods: Choroids were incubated in organ culture in the presence of the NO donor, PAPA- NONOate (1.5 mM). Following RNA extraction, bulk RNA-seq was used to quantify and compare choroidal gene expression in the presence and absence of PAPA-NONOate. We used bioinformatics to identify enriched canonical pathways, predicted diseases and functions, and regulatory effects of NO in the choroid.Results: Upon treatment of normal chick choroids with the NO donor, PAPA-NONOate, we identified a total of 837 differentially expressed genes (259 upregulated genes, 578 down-regulated genes) compared with untreated controls. Among these, the top five upregulated genes were LSMEM1, STEAP4, HSPB9, and CCL19, and the top five down-regulated genes were CDCA3, SMC2, a novel gene (ENSALGALG00000050836), an uncharacterized gene (LOC107054158), and SPAG5. Bioinformatics predicted that NO treatment will activate pathways involved in cell and organismal death, necrosis, and cardiovascular system development, and inhibit pathways involved in cell proliferation, cell movement, and gene expression.Conclusions: The findings reported herein may provide insight into possible effects of NO in the choroid during visually regulated eye growth, and help to identify targeted therapies for the treatment of myopia and other ocular diseases.","PeriodicalId":73617,"journal":{"name":"Journal of bioinformatics and systems biology : Open access","volume":"7 1","pages":"39-51"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11759056/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143049025","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