Current Genomics最新文献_第7页

IF 2.6 4区生物学

Current Genomics Pub Date : 2023-02-14 DOI: 10.2174/138920292306230209163617

引用次数: 0

Chromosome-level genome assembly and sex-specific differential transcriptome of the white-backed planthopper, Sogatella furcifera 白背飞虱的染色体水平基因组组装和性别特异性差异转录组

IF 2.6 4区生物学

Current Genomics Pub Date : 2023-01-02 DOI: 10.2174/1389202924666230102092822

C. Zhang, Yu-Xuan Ye, Dan-Ting Li, Si-Yu Zhang, Z. Shen

引用次数: 0

Preface 前言

IF 2.6 4区生物学

Current Genomics Pub Date : 2023-01-01 DOI: 10.2174/138920292401230610190952

C. Neri

引用次数: 0

A Deep Clustering-based Novel Approach for Binning of Metagenomics Data. 基于深度聚类的元基因组学数据分选新方法

IF 1.8 4区生物学

Current Genomics Pub Date : 2022-11-18 DOI: 10.2174/1389202923666220928150100

Sharanbasappa D Madival, Dwijesh Chandra Mishra, Anu Sharma, Sanjeev Kumar, Arpan Kumar Maji, Neeraj Budhlakoti, Dipro Sinha, Anil Rai

{"title":"A Deep Clustering-based Novel Approach for Binning of Metagenomics Data.","authors":"Sharanbasappa D Madival, Dwijesh Chandra Mishra, Anu Sharma, Sanjeev Kumar, Arpan Kumar Maji, Neeraj Budhlakoti, Dipro Sinha, Anil Rai","doi":"10.2174/1389202923666220928150100","DOIUrl":"10.2174/1389202923666220928150100","url":null,"abstract":"Background: One major challenge in binning Metagenomics data is the limited availability of reference datasets, as only 1% of the total microbial population is yet cultured. This has given rise to the efficacy of unsupervised methods for binning in the absence of any reference datasets.Objective: To develop a deep clustering-based binning approach for Metagenomics data and to evaluate results with suitable measures.Methods: In this study, a deep learning-based approach has been taken for binning the Metagenomics data. The results are validated on different datasets by considering features such as Tetra-nucleotide frequency (TNF), Hexa-nucleotide frequency (HNF) and GC-Content. Convolutional Autoencoder is used for feature extraction and for binning; the K-means clustering method is used.Results: In most cases, it has been found that evaluation parameters such as the Silhouette index and Rand index are more than 0.5 and 0.8, respectively, which indicates that the proposed approach is giving satisfactory results. The performance of the developed approach is compared with current methods and tools using benchmarked low complexity simulated and real metagenomic datasets. It is found better for unsupervised and at par with semi-supervised methods.Conclusion: An unsupervised advanced learning-based approach for binning has been proposed, and the developed method shows promising results for various datasets. This is a novel approach for solving the lack of reference data problem of binning in metagenomics.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"23 5","pages":"353-368"},"PeriodicalIF":1.8,"publicationDate":"2022-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/72/5e/CG-23-353.PMC9878855.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9484053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Circular RNA Involvement in Aging and Longevity. 环状RNA参与衰老和长寿。

IF 2.6 4区生物学

Current Genomics Pub Date : 2022-11-18 DOI: 10.2174/1389202923666220927110258

Ruize Niu, Jia Liu

{"title":"Circular RNA Involvement in Aging and Longevity.","authors":"Ruize Niu, Jia Liu","doi":"10.2174/1389202923666220927110258","DOIUrl":"https://doi.org/10.2174/1389202923666220927110258","url":null,"abstract":"Background: Circular RNAs (circRNAs) are transcribed by RNA polymerase II and are mostly generated by the back-splicing of exons in the protein-coding gene. Massive circRNAs are reported to be differentially expressed in different species, implicating their prospects as aging biomarkers or regulators in the aging progression.Methods: The possible role of circRNAs in aging and longevity was reviewed by the query of circRNAs from literature reports related to tissue, organ or cellular senescence, and individual longevity.Results: A number of circRNAs have been found to positively and negatively modulate aging and longevity through canonical aging pathways in the invertebrates Caenorhabditis elegans and Drosophila. Recent studies have also shown that circRNAs regulate age-related processes and pathologies such various mammalian tissues, as the brain, serum, heart, and muscle. Besides, three identified representative circRNAs (circSfl, circGRIA1, and circNF1-419) were elucidated to correlate with aging and longevity.Conclusion: This review outlined the current studies of circRNAs in aging and longevity, highlighting the role of circRNAs as a biomarker of aging and as a regulator of longevity.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"23 5","pages":"318-325"},"PeriodicalIF":2.6,"publicationDate":"2022-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/e3/38/CG-23-318.PMC9878857.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9484051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

An Update on Non-invasive Approaches for Genetic Testing of the Preimplantation Embryo. 植入前胚胎非侵入性基因检测方法的最新进展。

IF 2.6 4区生物学

Current Genomics Pub Date : 2022-11-18 DOI: 10.2174/1389202923666220927111158

Georgia Kakourou, Thalia Mamas, Christina Vrettou, Joanne Traeger-Synodinos

{"title":"An Update on Non-invasive Approaches for Genetic Testing of the Preimplantation Embryo.","authors":"Georgia Kakourou, Thalia Mamas, Christina Vrettou, Joanne Traeger-Synodinos","doi":"10.2174/1389202923666220927111158","DOIUrl":"https://doi.org/10.2174/1389202923666220927111158","url":null,"abstract":"Preimplantation Genetic Testing (PGT) aims to reduce the chance of an affected pregnancy or improve success in an assisted reproduction cycle. Since the first established pregnancies in 1990, methodological approaches have greatly evolved, combined with significant advances in the embryological laboratory. The application of preimplantation testing has expanded, while the accuracy and reliability of monogenic and chromosomal analysis have improved. The procedure traditionally employs an invasive approach to assess the nucleic acid content of embryos. All biopsy procedures require high technical skill, and costly equipment, and may impact both the accuracy of genetic testing and embryo viability. To overcome these limitations, many researchers have focused on the analysis of cell-free DNA (cfDNA) at the preimplantation stage, sampled either from the blastocoel or embryo culture media, to determine the genetic status of the embryo non-invasively. Studies have assessed the origin of cfDNA and its application in non-invasive testing for monogenic disease and chromosomal aneuploidies. Herein, we discuss the state-of-the-art for modern non-invasive embryonic genetic material assessment in the context of PGT. The results are difficult to integrate due to numerous methodological differences between the studies, while further work is required to assess the suitability of cfDNA analysis for clinical application.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"23 5","pages":"337-352"},"PeriodicalIF":2.6,"publicationDate":"2022-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ef/67/CG-23-337.PMC9878856.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9484054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Heuristic Analysis of Genomic Sequence Processing Models for High Efficiency Prediction: A Statistical Perspective. 高效预测基因组序列处理模型的启发式分析:统计学视角。

IF 2.6 4区生物学

Current Genomics Pub Date : 2022-11-18 DOI: 10.2174/1389202923666220927105311

Aditi R Durge, Deepti D Shrimankar, Ankush D Sawarkar

{"title":"Heuristic Analysis of Genomic Sequence Processing Models for High Efficiency Prediction: A Statistical Perspective.","authors":"Aditi R Durge, Deepti D Shrimankar, Ankush D Sawarkar","doi":"10.2174/1389202923666220927105311","DOIUrl":"https://doi.org/10.2174/1389202923666220927105311","url":null,"abstract":"Genome sequences indicate a wide variety of characteristics, which include species and sub-species type, genotype, diseases, growth indicators, yield quality, etc. To analyze and study the characteristics of the genome sequences across different species, various deep learning models have been proposed by researchers, such as Convolutional Neural Networks (CNNs), Deep Belief Networks (DBNs), Multilayer Perceptrons (MLPs), etc., which vary in terms of evaluation performance, area of application and species that are processed. Due to a wide differentiation between the algorithmic implementations, it becomes difficult for research programmers to select the best possible genome processing model for their application. In order to facilitate this selection, the paper reviews a wide variety of such models and compares their performance in terms of accuracy, area of application, computational complexity, processing delay, precision and recall. Thus, in the present review, various deep learning and machine learning models have been presented that possess different accuracies for different applications. For multiple genomic data, Repeated Incremental Pruning to Produce Error Reduction with Support Vector Machine (Ripper SVM) outputs 99.7% of accuracy, and for cancer genomic data, it exhibits 99.27% of accuracy using the CNN Bayesian method. Whereas for Covid genome analysis, Bidirectional Long Short-Term Memory with CNN (BiLSTM CNN) exhibits the highest accuracy of 99.95%. A similar analysis of precision and recall of different models has been reviewed. Finally, this paper concludes with some interesting observations related to the genomic processing models and recommends applications for their efficient use.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"23 5","pages":"299-317"},"PeriodicalIF":2.6,"publicationDate":"2022-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f3/6a/CG-23-299.PMC9878859.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9484055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Non-invasive Prenatal Testing in Pregnancies Following Assisted Reproduction. 辅助生殖后妊娠的无创产前检测。

IF 1.8 4区生物学

Current Genomics Pub Date : 2022-11-18 DOI: 10.2174/1389202923666220518095758

Vandana Kamath, Mary Purna Chacko, Mohan S Kamath

引用次数: 0

Construction of PARPi Resistance-related Competing Endogenous RNA Network. PARPi耐药相关竞争内源RNA网络的构建

IF 2.6 4区生物学

Current Genomics Pub Date : 2022-08-11 DOI: 10.2174/1389202923666220527114108

Lili Kong, Jiaqi Xu, Lijun Yu, Shuo Liu, Zongjian Liu, Juanjuan Xiang

{"title":"Construction of PARPi Resistance-related Competing Endogenous RNA Network.","authors":"Lili Kong, Jiaqi Xu, Lijun Yu, Shuo Liu, Zongjian Liu, Juanjuan Xiang","doi":"10.2174/1389202923666220527114108","DOIUrl":"https://doi.org/10.2174/1389202923666220527114108","url":null,"abstract":"Objective: Ovarian cancer is a kind of common gynecological malignancy in women. PARP inhibitors (PARPi) have been approved for ovarian cancer treatment. However, the primary and acquired resistance have limited the application of PARPi. The mechanisms remain to be elucidated. Methods: In this study, we characterized the expression profiles of mRNA and nonconding RNAs (ncRNAs) and constructed the regulatory networks based on RNA sequencing in PARPi Olaparib-induced ovarian cancer cells. Results: We found that the functions of the differentially expressed genes were enriched in \"PI3K/AKT signaling pathway,\" \"MAPK signaling pathway\" and \"metabolic process\". The functions of DELs (cis) were enriched in \"Human papillomavirus infection\"\"tight junction\" \"MAPK signaling pathway\". As the central regulator of ceRNAs, the differentially expressed miRNAs were enriched in \"Human papillomavirus infection\" \"MAPK signaling pathway\" \"Ras signaling pathway\". According to the degree of interaction, we identified 3 lncRNAs, 2 circRNAs, 7 miRNAs, and 12 mRNA as the key regulatory ceRNA axis, in which miR-320b was the important mediator. Conclusion: Here, we revealed the key regulatory lncRNA (circRNA)-miRNA-mRNA axis and their involved pathways in the PARPi resistant ovarian cancer cells. These findings provide new insights into exploring the ceRNA regulatory networks and developing new targets for PARPi resistance.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"23 4","pages":"262-274"},"PeriodicalIF":2.6,"publicationDate":"2022-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/20/a8/CG-23-262.PMC9875538.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10704604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Establishment of New Genetic Markers and Methods for Sex Determination of Mouse and Human Cells using Polymerase Chain Reactions and Crude DNA Samples. 利用聚合酶链反应和粗DNA样本建立新的遗传标记及小鼠和人细胞性别测定方法。

IF 2.6 4区生物学

Current Genomics Pub Date : 2022-08-11 DOI: 10.2174/1389202923666220610121344

Keyin Zhang, Jianglin Yang, Zhenwei Qin, Tianzu Lu, Didong Lou, Qianchuan Ran, Hai Huang, Shuqiang Cheng, Lucas Zellmer, Hong Ma, Dezhong J Liao

{"title":"Establishment of New Genetic Markers and Methods for Sex Determination of Mouse and Human Cells using Polymerase Chain Reactions and Crude DNA Samples.","authors":"Keyin Zhang, Jianglin Yang, Zhenwei Qin, Tianzu Lu, Didong Lou, Qianchuan Ran, Hai Huang, Shuqiang Cheng, Lucas Zellmer, Hong Ma, Dezhong J Liao","doi":"10.2174/1389202923666220610121344","DOIUrl":"https://doi.org/10.2174/1389202923666220610121344","url":null,"abstract":"Background: The currently available methods for sexing human or mouse cells have weaknesses. Therefore, it is necessary to establish new methods. Methods: We used bioinformatics approach to identify genes that have alleles on both the X and Y chromosomes of mouse and human genomes and have a region showing a significant difference between the X and Y alleles. We then used polymerase chain reactions (PCR) followed by visualization of the PCR amplicons in agarose gels to establish these genomic regions as genetic sex markers. Results: Our bioinformatics analyses identified eight mouse sex markers and 56 human sex markers that are new, i.e. are previously unreported. Six of the eight mouse markers and 14 of the 56 human markers were verified using PCR and ensuing visualization of the PCR amplicons in agarose gels. Most of the tested and untested sex markers possess significant differences in the molecular weight between the X- and Y-derived PCR amplicons and are thus much better than most, if not all, previously-reported genetic sex markers. We also established several simple and essentially cost-free methods for extraction of crude genomic DNA from cultured cells, blood samples, and tissues that could be used as template for PCR amplification. Conclusion: We have established new sex genetic markers and methods for extracting genomic DNA and for sexing human and mouse cells. Our work may also lend some methodological strategies to the identification of new genetic sex markers for other organismal species.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"23 4","pages":"275-288"},"PeriodicalIF":2.6,"publicationDate":"2022-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/91/04/CG-23-275.PMC9875541.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10704598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0