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Genomic and Metagenomic Insights into the Distribution of Nicotine-Degrading Enzymes in Human Microbiota Curr. Genomics (IF 2.6) Pub Date : 2024-03-21 Ying Guan, Zhouhai Zhu, Qiyuan Peng, Meng Li, Xuan Li, Jia-Wei Yang, Yan-Hong Lu, Meng Wang, Bin-Bin Xie
Introduction: Nicotine degradation is a new strategy to block nicotine-induced pathology. The potential of human microbiota to degrade nicotine has not been explored. Aims: This study aimed to uncover the genomic potentials of human microbiota to degrade nicotine. Method: To address this issue, we performed a systematic annotation of Nicotine-Degrading Enzymes (NDEs) from genomes and metagenomes of
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Prediction of Deleterious Single Amino Acid Polymorphisms with a Consensus Holdout Sampler Curr. Genomics (IF 2.6) Pub Date : 2024-03-18 Óscar Álvarez-Machancoses, Eshel Faraggi, Enrique deAndrés-Galiana, Juan Fernández-Martínez, Andrzej Kloczkowski
Background: Single Amino Acid Polymorphisms (SAPs) or nonsynonymous Single Nucleotide Variants (nsSNVs) are the most common genetic variations. They result from missense mutations where a single base pair substitution changes the genetic code in such a way that the triplet of bases (codon) at a given position is coding a different amino acid. Since genetic mutations sometimes cause genetic diseases
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Testing the Significance of Ranked Gene Sets in Genome-Wide Transcriptome Profiling Data Using Weighted Rank Correlation Statistics Curr. Genomics (IF 2.6) Pub Date : 2024-03-15 Min Yao, Hao He, Binyu Wang, Xinmiao Huang, Sunli Zheng, Jianwu Wang, Xuejun Gao, Tinghua Huang
Objective: Ignoring the rank information during the enrichment analysis will lead to improper statistical inference. We address this issue by developing of new method to test the significance of ranked gene sets in genome-wide transcriptome profiling data. Methods: A method was proposed by first creating ranked gene sets and gene lists and then applying weighted Kendall's tau rank correlation statistics
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Effect of Calebin-A on Critical Genes Related to NAFLD: A Protein-Protein Interaction Network and Molecular Docking Study Curr. Genomics (IF 2.6) Pub Date : 2024-02-22 Ali Mahmoudi, Mohammad Mahdi Hajihasani, Muhammed Majeed, Tannaz Jamialahmadi, Amirhossein Sahebkar
Background: Calebin-A is a minor phytoconstituent of turmeric known for its activity against inflammation, oxidative stress, cancerous, and metabolic disorders like Non-alcoholic fatty liver disease(NAFLD). Based on bioinformatic tools. Subsequently, the details of the interaction of critical proteins with Calebin-A were investigated using the molecular docking technique. Methods: We first probed the
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DHFS-ECM: Design of a Dual Heuristic Feature Selection-based Ensemble Classification Model for the Identification of Bamboo Species from Genomic Sequences Curr. Genomics (IF 2.6) Pub Date : 2024-02-21 Aditi R. Durge, Deepti D. Shrimankar
Problem: Analyzing genomic sequences plays a crucial role in understanding biological diversity and classifying Bamboo species. Existing methods for genomic sequence analysis suffer from limitations such as complexity, low accuracy, and the need for constant reconfiguration in response to evolving genomic datasets. Aim: This study addresses these limitations by introducing a novel Dual Heuristic Feature
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Expression Profiling of EMT Transcriptional Regulators ZEB1 and ZEB2 in Different Histopathological Grades of Oral Squamous Cell Carcinoma Patients Curr. Genomics (IF 2.6) Pub Date : 2024-02-15 Neha Baqai, Rafat Amin, Tehseen Fatima, Zeba Ahmed, Nousheen Faiz
Background: Pakistan has a high burden of oral cancers, with a prevalence rate of around 9%. Oral Squamous Cell Carcinoma (OSCC) accounts for about 90% of oral cancer cases. Epithelial to Mesenchymal Transition (EMT) gets highly stimulated in tumor cells by adopting subsequent malignant features of highly invasive cancer populations. Zinc Finger E-Box binding factors, ZEB1 and ZEB2, are regulatory
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COVID-19: Recent Insight in Genomic Feature, Pathogenesis, Immunological Biomarkers, Treatment Options and Clinical Updates on SARS-CoV-2 Curr. Genomics (IF 2.6) Pub Date : 2024-02-07 Rohitas Deshmukh, Ranjit Kumar Harwansh, Akash Garg, Sakshi Mishra, Rutvi Agrawal, Rajendra Jangde
SARS-CoV-2 is a highly contagious and transmissible viral infection that first emerged in 2019 and since then has sparked an epidemic of severe respiratory problems identified as “coronavirus disease 2019” (COVID-19) that causes a hazard to human life and safety. The virus developed mainly from bats. The current epidemic has presented a significant warning to life across the world by showing mutation
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Tertiary Lymphoid Structures Gene Signature Predicts Prognosis and Immune Infiltration Analysis in Head and Neck Squamous Cell Carcinoma Curr. Genomics (IF 2.6) Pub Date : 2024-01-29 Aiyan Xing, Dongxiao Lv, Changshun Wu, Kai Zhou, Tianhui Zhao, Lihua Zhao, Huaqing Wang, Hong Feng
Objectives: This study aims to assess the prognostic implications of gene signature of the tertiary lymphoid structures (TLSs) in head and neck squamous cell carcinoma (HNSCC) and scrutinize the influence of TLS on immune infiltration. Methods: Patients with HNSCC from the Cancer Genome Atlas were categorized into high/low TLS signature groups based on the predetermined TLS signature threshold. The
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Analysis of the Expression of PRDX6 in Patients with Hepatocellular Carcinoma and its Effect on the Phenotype of Hepatocellular Carcinoma Cells Curr. Genomics (IF 2.6) Pub Date : 2024-01-22 Runhong Mu, Mingzhu Chang, Chuanbo Feng, Yunhe Cui, Tingyu Li, Chang Liu, Yilin Wang, Xiao Guo
Objective: This research aimed to study the expression of PRDX6 mRNA in hepatocellular carcinoma (HCC) and its effect on the prognosis of HCC. Moreover, the effect of PRDX6 gene knockdown on the proliferation, migration, and invasion of HepG2 cells mediated by lentivirus was also examined. This study offers a theoretical and experimental basis for further research on the mechanism of PRDX6 in liver
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Plasma Virome of HIV-infected Subjects on Suppressive Antiretroviral Therapy Reveals Association of Differentially Abundant Viruses with Distinct T-cell Phenotypes and Inflammation Curr. Genomics (IF 2.6) Pub Date : 2024-01-22 Tannu Bhagchandani, Mohammad M.U. Haque, Shilpa Sharma, Md Zubbair Malik, Ashwini K. Ray, Urvinder S. Kaur, Ankita Rai, Anjali Verma, Kamal K. Sawlani, Rupesh Chaturvedi, Himanshu Dandu, Abhishek Kumar, Ravi Tandon
Background: The plasma virome represents the overall composition of viral sequences present in it. Alteration in plasma virome has been reported in treatment naïve and immunocompromised (CD4 count < 200) people with HIV (PWH). However, the effect of ART on virome composition in PWH on ART with preserved CD4 counts is poorly understood. Objectives: We aimed to assess the alterations in plasma virome
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Exploring the Role of Non-synonymous and Deleterious Variants Identified in Colorectal Cancer: A Multi-dimensional Computational Scrutiny of Exomes Curr. Genomics (IF 2.6) Pub Date : 2024-01-22 Karunakaran Chandrashekar, Vidya Niranjan, Anagha S. Setlur, Dhanya Pradeep, Jitendra Kumar
Introduction: Colorectal cancers are the world’s third most commonly diagnosed type of cancer. Currently, there are several diagnostic and treatment options to combat it. However, a delay in detection of the disease is life-threatening. Additionally, a thorough analysis of the exomes of cancers reveals potential variation data that can be used for early disease prognosis. Method: By utilizing a comprehensive
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A Novel Methylation-based Model for Prognostic Prediction in Lung Adenocarcinoma Curr. Genomics (IF 2.6) Pub Date : 2024-01-22 Manyuan Li, Xufeng Deng, Dong Zhou, Xiaoqing Liu, Jigang Dai, Quanxing Liu
Objective: Specific methylation sites have shown promise in the early diagnosis of lung adenocarcinoma (LUAD). However, their utility in predicting LUAD prognosis remains unclear. This study aimed to construct a reliable methylation-based predictor for accurately predicting the prognosis of LUAD patients. Method: DNA methylation data and survival data from LUAD patients were obtained from the TCGA
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Molecular Determination of Tumor Necrosis Factor-alpha, Interleukin-8, Interleukin-10, and C-X-C Chemokine Receptor-2 Genetic Variations and their Association with Disease Susceptibility and Mortality in COVID-19 Patients Curr. Genomics (IF 2.6) Pub Date : 2024-01-17 Badr A. Alsayed, Rashid Mir, Mohammad M. Mir, Tarig M.S. Alnour, Shereen Fawzy, Mesaik M. Ahmed, Dnyanesh Amle
Background: Altered cytokine levels have been associated with poor outcomes among COVID-19 patients. TNF-α, IL-8 and IL-10 are key cytokines in COVID-19 pathogenesis, and CXCR-2 is a major chemokine receptor involved in inflammatory response. Polymorphisms in the genes of these proteins are proposed to influence disease outcomes. In this study, we aimed to find out the association of genetic polymorphisms
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Towards an Analytical Biology Curr. Genomics (IF 2.6) Pub Date : 2024-01-10 Max H. Garzon, Fredy A. Coloradodo
This article draws a perspective on the increasingly unavoidable question of whether steps can be taken in genomics and biology at large to move them more rapidly towards more analytical and deductive biology, akin to similar developments that occurred in other natural sciences, such as physics and chemistry, centuries ago. It provides a summary of recent advances in other relevant sciences in the
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Epigenetic Diversity Underlying Seasonal and Annual Variations in Brown Planthopper (BPH) Populations as Revealed by Methylationsensitive Restriction Assay Curr. Genomics (IF 2.6) Pub Date : 2023-12-07 Ayushi Gupta, Suresh Nair
Background: The brown planthopper (BPH) is a monophagous sap-sucking insect pest of rice that is responsible for massive yield loss. BPH populations, even when genetically homogenous, can display a vast range of phenotypes, and the development of effective pest-management strategies requires a good understanding of what generates this phenotypic variation. One potential source could be epigenetic differences
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Oxford Nanopore Technology and its Application in Liquid Biopsies Curr. Genomics (IF 2.6) Pub Date : 2023-11-30 Mariya Levkova, Trifon Chervenkov, Lyudmila Angelova, Deyan Dzenkov
Advanced medical technologies are transforming the future of healthcare, in particular, the screening and detection of molecular-genetic changes in patients suspected of having a neoplasm. They are based on the assumption that neoplasms release small amounts of various neoplasm- specific molecules, such as tumor DNA, called circulating DNA (cirDNA), into the extracellular space and subsequently into
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A Study and Analysis of Disease Identification using Genomic Sequence Processing Models: An Empirical Review Curr. Genomics (IF 2.6) Pub Date : 2023-11-29 Sony K. Ahuja, Deepti D. Shrimankar, Aditi R. Durge
: Human gene sequences are considered a primary source of comprehensive information about different body conditions. A wide variety of diseases including cancer, heart issues, brain issues, genetic issues, etc. can be pre-empted via efficient analysis of genomic sequences. Researchers have proposed different configurations of machine learning models for processing genomic sequences, and each of these
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Aberrant Expressions of PSMD14 in Tumor Tissue are the Potential Prognostic Biomarkers for Hepatocellular Carcinoma after Curative Resection Curr. Genomics (IF 2.6) Pub Date : 2023-11-28 Yi-Mei Xiong, Fang Zhou, Jia-Wen Zhou, Fei Liu, Si-Qi Zhou, Bo Li, Zhong-Jian Liu, Yang Qin
Introduction: Hepatocellular carcinoma (HCC) has a high mortality rate, with curative resection being the primary treatment. However, HCC patients have a large possibility of recurrence within 5 years after curative resection Method: Thus, identifying biomarkers to predict recurrence is crucial. In our study, we analyzed data from CCLE, GEO, and TCGA, identifying eight oncogenes associated with HCC
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Identification of Two Novel Pathogenic Variants of the ATM Gene in the Iranian-Azeri Turkish Ethnic Group by Applying Whole Exome Sequencing Curr. Genomics (IF 2.6) Pub Date : 2023-11-22 Amir-Reza Dalal Amandi, Neda Jabbarpour, Shadi Shiva, Mortaza Bonyadi
Background: The ATM gene encodes a multifunctional kinase involved in important cellular functions, such as checkpoint signaling and apoptosis, in response to DNA damage. Bi-allelic pathogenic variants in this gene cause Ataxia Telangiectasia (AT), while carriers of ATM pathogenic variants are at increased risk of cancer depending on the pathogenicity of the variant they carry. Identifying pathogenic
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Identification of Plausible Candidates in Prostate Cancer Using Integrated Machine Learning Approaches Curr. Genomics (IF 2.6) Pub Date : 2023-11-21 Bhumandeep Kour, Nidhi Shukla, Harshita Bhargava, Devendra Sharma, Amita Sharma, Anjuvan Singh, Jayaraman Valadi, Trilok Chand Sadasukhi, Sugunakar Vuree, Prashanth Suravajhala
Background: Currently, prostate-specific antigen (PSA) is commonly used as a prostate cancer (PCa) biomarker. PSA is linked to some factors that frequently lead to erroneous positive results or even needless biopsies of elderly people. Objectives: In this pilot study, we undermined the potential genes and mutations from several databases and checked whether or not any putative prognostic biomarkers
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Current Advances in Genetic Testing for Spinal Muscular Atrophy Curr. Genomics (IF 2.6) Pub Date : 2023-11-10 Yulin Zhou, Yu Jiang
Spinal muscular atrophy (SMA) is one of the most common genetic disorders worldwide, and genetic testing plays a key role in its diagnosis and prevention. The last decade has seen a continuous flow of new methods for SMA genetic testing that, along with traditional approaches, have affected clinical practice patterns to some degree. Targeting different application scenarios and selecting the appropriate
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Taxonomic Status and Phylogenetic Relationship of the Charadriidae Family Based on Complete Mitogenomes Curr. Genomics (IF 2.6) Pub Date : 2023-10-27 Weiya Qian, Yizheng Liu, Keer Miao, Qing Chang, Chaochao Hu
Background: The Charadriiformes provide a good source for researching evolution owing to their diverse distribution, behavior, morphology, and ecology. However, in the Charadrii, family-level relationships remain understudied, and the monophyly of Charadriidae is also a subject of controversy. Method: In the present study, we generated complete mitogenomes for two species, Charadrius leschenaultii
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Genome Sequencing and Organization of Three Geographically Different Isolates of Nucleopolyhedrovirus from the Gypsy Moth Reveal Significant Genomic Differences Curr. Genomics (IF 2.6) Pub Date : 2023-10-25 Donus Gencer, Cihan Inan, Zeynep Bayramoglu, Remziye Nalcacioglu, Feifei Yin, Zheng Zhu, Jun Wang, Zhihong Hu, Lillian Pavlik, Basil Arif, Zihni Demirbag, Ismail Demir
Background: The gypsy moth (Lymantria dispar L., Lepidoptera: Erebidae) is a worldwide pest of trees and forests. Lymantria dispar nucleopolyhedrovirus (LdMNPV) belongs to the Baculoviridae family and is an insect virus specific to gypsy moth larvae. In this study, we describe the complete genome sequences of three geographically diverse isolates, H2 (China), J2 (Japan), and T3 (Turkey), of Lymantria
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Complete Chloroplast Genomes of Pterodon emarginatus Vogel and Pterodon pubescens Benth: Comparative and Phylogenetic Analyses Curr. Genomics (IF 2.6) Pub Date : 2023-10-25 Juliana Borges Pereira Brito, Adriana Maria Antunes, Ramilla dos Santos Braga Ferreira, Mariana Pires de Campos Telles, Cíntia Pelegrineti Targueta, Thannya Nascimento Soares
Background: The species Pterodon emarginatus and P. pubescens, popularly known as white sucupira or faveira, are native to the Cerrado biome and have the potential for medicinal use and reforestation. They are sister species with evolutionary proximity. Objective: Considering that the chloroplast genome exhibits a conserved structure and genes, the analysis of its sequences can contribute to the understanding
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Pan-cancer Analysis Identifies AIMP2 as a Potential Biomarker for Breast Cancer Curr. Genomics (IF 2.6) Pub Date : 2023-10-25 Jie Qiu, Tao Zhou, Danhong Wang, Weimin Hong, Da Qian, Xuli Meng, Xiaozhen Liu
Introduction: Aminoacyl tRNA synthetase complex interacting with multifunctional protein 2 (AIMP2) is a significant regulator of cell proliferation and apoptosis. Despite its abnormal expression in various tumor types, the specific functions and effects of AIMP2 on tumor immune cell infiltration, proliferation, and migration remain unclear. Materials and Methods: To assess AIMP2's role in tumor immunity
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Unraveling the Concealed Transcriptomic Landscape of PTEN in Human Malignancies Curr. Genomics (IF 2.6) Pub Date : 2023-10-25 Michaela A. Boti, Panagiotis G. Adamopoulos, Dido Vassilacopoulou, Andreas Scorilas
Background: Phosphatase and tensin homolog, widely known as PTEN, is a major negative regulator of the PI3K/AKT/mTOR signaling pathway, involved in the regulation of a variety of important cellular processes, including cell proliferation, growth, survival, and metabolism. Since most of the molecules involved in this biological pathway have been described as key regulators in cancer, the study of the
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High Prevalence of a c.5979dupA Variant in the Dysferlin Gene (DYSF) in Individuals from a Semiarid Region of Brazil Curr. Genomics (IF 2.6) Pub Date : 2023-10-25 Isabella A. Motta, Maria L.A. Gouveia, Ana P.M. Braga, Rafael S. Andrade, Mayra F.F. Montenegro, Sandra N. Gurgel, Keila M.F. Albuquerque, Priscilla A.N.G. Souto, Flávia P.B.F. Cardoso, Joseane S. Araujo, Mirella C.L. Pinheiro, Carlos E.P. da Silva, Pamella A.S. Gurgel, David Feder, Matheus M. Perez, Glaucia L. da Veiga, Beatriz C.A. Alves, Fernando L.A. Fonseca, Alzira A.S. Carvalho
Background: Dysferlinopathies represent a group of limb girdle or distal muscular dystrophies with an autosomal-recessive inheritance pattern resulting from the presence of pathogenic variants in the dysferlin gene (DYSF). Objective: In this work, we describe a population from a small city in Brazil carrying the c.5979dupA pathogenic variant of DYSF responsible for limb girdle muscular dystrophy type
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Deacetylation of Histones and Non-histone Proteins in Inflammatory Diseases and Cancer Therapeutic Potential of Histone Deacetylase Inhibitors Curr. Genomics (IF 2.6) Pub Date : 2023-10-24 Ezgi Man, Serap EVRAN
Epigenetic changes play an important role in the pathophysiology of autoimmune diseases such as allergic asthma, multiple sclerosis, lung diseases, diabetes, cystic fibrosis, atherosclerosis, rheumatoid arthritis, and COVID-19. There are three main classes of epigenetic alterations: posttranslational modifications of histone proteins, control by non-coding RNA and DNA methylation. Since histone modifications
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Modulation of Plant MicroRNA Expression: Its Potential Usability in Wheat (Triticum aestivum L.) Improvement Curr. Genomics (IF 2.6) Pub Date : 2023-10-24 Louie Cris Lopos, Urbashi Panthi, Igor Kovalchuk, Andriy Bilichak
Wheat, a crucial crop for the pursuit of food security, is faced with a plateauing yield projected to fall short of meeting the demands of the exponentially increasing human population. To raise global wheat productivity levels, strong efforts must be made to overcome the problems of (1) climate change-induced heat and drought stress and (2) the genotype-dependent amenability of wheat to tissue culture
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Using Chaos-Game-Representation for Analysing the SARS-CoV-2 Lineages, Newly Emerging Strains and Recombinants Curr. Genomics (IF 2.6) Pub Date : 2023-10-24 Amarinder Singh Thind, Somdatta Sinha
Background: Viruses have high mutation rates, facilitating rapid evolution and the emergence of new species, subspecies, strains and recombinant forms. Accurate classification of these forms is crucial for understanding viral evolution and developing therapeutic applications. Phylogenetic classification is typically performed by analyzing molecular differences at the genomic and sub-genomic levels
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DLC-ac4C: A Prediction Model for N4-acetylcytidine Sites in Human mRNA Based on DenseNet and Bidirectional LSTM Methods Curr. Genomics (IF 2.6) Pub Date : 2023-10-19 Jianhua Jia, Xiaojing Cao, Zhangying Wei
Introduction: N4 acetylcytidine (ac4C) is a highly conserved nucleoside modification that is essential for the regulation of immune functions in organisms. Currently, the identification of ac4C is primarily achieved using biological methods, which can be time-consuming and laborintensive. In contrast, accurate identification of ac4C by computational methods has become a more effective method for classification
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Lentiviral Transduction-based CRISPR/Cas9 Editing of Schistosoma mansoni Acetylcholinesterase Curr. Genomics (IF 2.6) Pub Date : 2023-10-09 Xiaofeng Du, Donald P. McManus, Juliet D. French, Haran Sivakumaran, Rebecca L. Johnston, Olga Kondrashova, Conor E. Fogarty, Malcolm K. Jones, Hong You
Background: Recent studies on CRISPR/Cas9-mediated gene editing in Schistosoma mansoni have shed new light on the study and control of this parasitic helminth. However, the gene editing efficiency in this parasite is modest. Methods: To improve the efficiency of CRISPR/Cas9 genome editing in schistosomes, we used lentivirus, which has been effectively used for gene editing in mammalian cells, to deliver
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Insights into Metabolic Engineering of Bioactive Molecules in Tetrastigma Hemsleyanum Diels & Gilg: A Traditional Medicinal Herb Curr. Genomics (IF 2.6) Pub Date : 2023-09-26 T.P. Ajeesh Krishna, T. Maharajan, T.P. Adarsh Krishna, S. Antony Ceasar
Plants are a vital source of bioactive molecules for various drug development processes. Tetrastigma hemsleyanum is one of the endangered medicinal plant species well known to the world due to its wide range of therapeutic effects. Many bioactive molecules have been identified from this plant, including many classes of secondary metabolites such as flavonoids, phenols, terpenoids, steroids, alkaloids
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Mitochondrial Lipid Metabolism Genes as Diagnostic and Prognostic Indicators in Hepatocellular Carcinoma Curr. Genomics (IF 2.6) Pub Date : 2023-09-25 Xuejing Li, Ying Tan, Bihan Liu, Houtian Guo, Yongjian Zhou, Jianhui Yuan, Feng Wang
Background: Due to the heterogeneity of Hepatocellular carcinoma (HCC), there is an urgent need for reliable diagnosis and prognosis. Mitochondria-mediated abnormal lipid metabolism affects the occurrence and progression of HCC. Objective: This study aims to investigate the potential of mitochondrial lipid metabolism (MTLM) genes as diagnostic and independent prognostic biomarkers for HCC. Methods:
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Circular RNA Translation in Cardiovascular Diseases Curr. Genomics (IF 2.6) Pub Date : 2023-09-13 Lijun Wang, Xinxin Cui, Fei Jiang, Yuxue Hu, Wensi Wan, Guoping Li, Yanjuan Lin, Junjie Xiao
Circular RNAs (circRNAs) are a class of endogenous functional RNA generated by backsplicing. Recently, circRNAs have been found to have certain coding potential. Proteins/peptides translated from circRNAs play essential roles in various diseases. Here, we briefly summarize the basic knowledge and technologies that are usually applied to study circRNA translation. Then, we focus on the research progress
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Application of Feature Definition and Quantification in Biological Sequence Analysis Curr. Genomics (IF 2.6) Pub Date : 2023-08-22 Weiyang Chen, Weiwei Li
Biological sequence analysis is the most fundamental work in bioinformatics. Many research methods have been developed in the development of biological sequence analysis. These methods include sequence alignment-based methods and alignment-free methods. In addition, there are also some sequence analysis methods based on the feature definition and quantification of the sequence itself. This editorial
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Deciphering Target Protein Cascade in Salmonella typhi Biofilm using Genomic Data Mining, and Protein-protein Interaction Curr. Genomics (IF 2.6) Pub Date : 2023-08-18 Aditya Upadhyay, Dharm Pal, Awanish Kumar
Background: Salmonella typhi biofilm confers a serious public health issue for lengthy periods and the rise in antibiotic resistance and death rate. Biofilm generation has rendered even the most potent antibiotics ineffective in controlling the illness, and the S. typhi outbreak has turned into a fatal disease typhoid. S. typhi infection has also been connected to other deadly illnesses, such as a
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Identification of Potential Genes and Critical Pathways in Postoperative Recurrence of Crohn’s Disease by Machine Learning And WGCNA Network Analysis Curr. Genomics (IF 2.6) Pub Date : 2023-06-13 Aruna Rajalingam, Kanagaraj Sekar, Anjali Ganjiwale
Background: Crohn's disease (CD) is a chronic idiopathic inflammatory bowel disease affecting the entire gastrointestinal tract from the mouth to the anus. These patients often experience a period of symptomatic relapse and remission. A 20–30% symptomatic recurrence rate is reported in the first year after surgery, with a 10% increase each subsequent year. Thus, surgery is done only to relieve symptoms
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The Era of Plant Breeding: Conventional Breeding to Genomics-assisted Breeding for Crop Improvement Curr. Genomics (IF 2.6) Pub Date : 2023-05-30 Thumadath Palayullaparambil Ajeesh Krishna, Duraipandiyan Veeramuthu, Theivanayagam Maharajan, Mariapackiam Soosaimanickam
Plant breeding has made a significant contribution to increasing agricultural production. Conventional breeding based on phenotypic selection is not effective for crop improvement. Because phenotype is considerably influenced by environmental factors, which will affect the selection of breeding materials for crop improvement. The past two decades have seen tremendous progress in plant breeding research
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Comprehensive Analysis of Alternative Polyadenylation Events Associated with the Tumor Immune Microenvironment in Colon Adenocarcinoma Curr. Genomics (IF 2.6) Pub Date : 2023-05-26 Fangning Pang, Peng Yang, Tongfei Wang, Xuzhao Li, Xiaoyong Wu, Rong Yue, Bin Bai, Qingchuan Zhao
Objective: Colon adenocarcinoma (COAD) is one of the leading causes of cancer death worldwide. Alternative polyadenylation (APA) is relevant to the variability of the 3'-UTR of mRNA. However, the posttranscriptional dysregulation of APA in COAD is poorly understood. Methods: We collected APA data from The Cancer Genome Atlas (TCGA) COAD (n =7692). APA events were evaluated using PDUI values, and the
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Nonsynonymous Synonymous Variants Demand for a Paradigm Shift in Genetics Curr. Genomics (IF 2.6) Pub Date : 2023-04-27 Mauno Vihinen
Synonymous (also known as silent) variations are by definition not considered to change the coded protein. Still many variations in this category affect either protein abundance or properties. As this situation is confusing, we have recently introduced systematics for synonymous variations and those that may on the surface look like synonymous, but these may affect the coded protein in various ways
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Draft Genome Sequence of Enterobacter cloacae S23 a Plant Growthpromoting Passenger Endophytic Bacterium Isolated from Groundnut Nodule Possesses Stress Tolerance Traits Curr. Genomics (IF 2.6) Pub Date : 2023-04-19 Pavithra Ramakrishnan, Manikandan Ariyan, Anandham Rangasamy, Raghu Rajasekaran, Krishnamoorthy Ramasamy, SenthilKumar Murugaiyan, Veeranan Janahiraman
Aim: This study aims to reveal the passenger endophytic bacterium Enterobacter cloacae S23 isolated from groundnut nodules and to underpin the molecular mechanism and genes responsible for abiotic stress tolerance. Background: A variety of microorganisms that contribute to nodulation and encourage plant development activity in addition to the nodulating Rhizobium. Passenger endophytes (PE) are endophytes
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An Insight into Emerging Begomoviruses and their Satellite Complex Causing Papaya Leaf Curl Disease Curr. Genomics (IF 2.6) Pub Date : 2023-02-15 Aarshi Srivastava, Vineeta Pandey, Abdullah. M. Al-Sadi, Muhammad S. Shahid, R.K. Gaur
Papaya leaf curl disease (PaLCD) was primarily detected in India and causes major economic damage to agriculture crops grown globally, seriously threatening food security. Begomoviruses are communicated by the vector Bemisia tabaci, and their transmission efficiency and persistence in the vector are the highest, exhibiting the widest host range due to adaptation and evolution. Symptoms induced during
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New Short RNA Motifs Potentially Relevant in the SARS-CoV-2 Genome Curr. Genomics (IF 2.6) Pub Date : 2023-02-07 Miguel Angel Fuertes, Carlos Alonso
Background: The coronavirus disease has led to an exhaustive exploration of the SARSCoV- 2 genome. Despite the amount of information accumulated, the prediction of short RNA motifs encoding peptides mediating protein-protein or protein-drug interactions has received limited attention. Objective: The study aims to predict short RNA motifs that are interspersed in the SARS-CoV-2 genome. Methods: A method
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Long Noncoding RNA and mRNA Expression Profiles in Rats with LPSInduced Myocardial Dysfunction Curr. Genomics (IF 2.6) Pub Date : 2023-01-27 Ye-Chen Han, Zhu-Jun Shen, Ruo-Lan Xiang, Bo Lu, Hao Qian, Jing-Yi Li, Hong-Zhi Xie
Background: Sepsis is an uncontrolled systemic inflammatory response. Long noncoding RNAs (lncRNAs) are involved in the pathogenesis of sepsis. However, little is known about the roles of lncRNAs in sepsis-induced myocardial dysfunction. Objective: We aimed to determine the regulatory mechanism of lncRNAs in sepsis-induced myocardial dysfunction. Methods: In this study, we analysed the lncRNA and mRNA
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Chromosome-Level Genome Assembly and Sex-Specific Differential Transcriptome of the White-Backed Planthopper, Sogatella furcifera Curr. Genomics (IF 2.6) Pub Date : 2023-01-17 Yu-Xuan Ye, Dan-Ting Li, Si-Yu Zhang, Zhi-Cheng Shen, Chuan-Xi Zhang
Background: The white-backed planthopper (WBPH), Sogatella furcifera, causes great damage to many crops (mainly rice) by direct feeding or transmitting plant viruses. The previous genome assembly was generated by second-generation sequencing technologies, with a contig N50 of only 51.5 kb, and contained a lot of heterozygous sequences. Methods: We utilized third-generation sequencing technologies and
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Integrative Approaches of DNA Methylation Patterns According to Age, Sex and Longitudinal Changes Curr. Genomics (IF 2.6) Pub Date : 2022-12-19 Jeong-An Gim
Background: In humans, age-related DNA methylation has been studied in blood, tissues, buccal swabs, and fibroblasts, and changes in DNA methylation patterns according to age and sex have been detected. To date, approximately 137,000 samples have been analyzed from 14,000 studies, and the information has been uploaded to the NCBI GEO database. Methods: A correlation between age and methylation level
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Poaceae Chloroplast Genome Sequencing: Great Leap Forward in Recent Ten Years Curr. Genomics (IF 2.6) Pub Date : 2022-12-13 Yiyu Hu, Yanqing Sun, Qian-Hao Zhu, Longjiang Fan, Jianhua Li
The first complete chloroplast genome of rice (Oryza sativa) was published in 1989, ushering in a new era of studies of chloroplast genomics in Poaceae. Progresses in Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) technologiesand in the development of genome assembly software, have significantly advanced chloroplast genomics research. Poaceae is one of the most targeted families
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An Update on Non-invasive Approaches for Genetic Testing of the Preimplantation Embryo Curr. Genomics (IF 2.6) Pub Date : 2022-10-17 Georgia Kakourou, Thalia Mamas, Christina Vrettou, Joanne Traeger-Synodinos
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
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A Deep Clustering-based Novel Approach for Binning of Metagenomics Data Curr. Genomics (IF 2.6) Pub Date : 2022-10-17 Sharanbasappa D. Madival, Dwijesh Chandra Mishra, Anu Sharma, Sanjeev Kumar, Arpan Kumar Maji, Neeraj Budhlakoti, Dipro Sinha, Anil Rai
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
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Circular RNA Involvement in Aging and Longevity Curr. Genomics (IF 2.6) Pub Date : 2022-10-14 Ruize Niu, Jia Liu
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
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Heuristic Analysis of Genomic Sequence Processing Models for High Efficiency Prediction: A Statistical Perspective Curr. Genomics (IF 2.6) Pub Date : 2022-10-07 Aditi R. Durge, Deepti D. Shrimankar, Ankush D. Sawarkar
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
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Non-invasive Prenatal Testing in Pregnancies Following Assisted Reproduction Curr. Genomics (IF 2.6) Pub Date : 2022-07-05 Vandana Kamath, Mary Purna Chacko, Mohan S. Kamath
In the decade since non-invasive prenatal testing (NIPT) was first implemented as a prenatal screening tool, it has gained recognition for its sensitivity and specificity in the detection of common aneuploidies. This review mainly focuses on the emerging role of NIPT in pregnancies following assisted reproductive technology (ART) in the light of current evidence and recommendations. It also deals with
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Establishment of New Genetic Markers and Methods for Sex Determination of Mouse and Human Cells using Polymerase Chain Reactions and Crude DNA Samples Curr. Genomics (IF 2.6) Pub Date : 2022-06-13 Hong Ma, Dezhong J. Liao, Keyin Zhang, Jianglin Yang, Zhenwei Qin, Tianzu Lu, Didong Lou, Qianchuan Ran, Hai Huang, Shuqiang Cheng, Lucas Zellmer
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GAAP: A GUI-based Genome Assembly and Annotation Package Curr. Genomics (IF 2.6) Pub Date : 2022 Deepak Singla
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Integrating LASSO Feature Selection and Soft Voting Classifier to Identify Origins of Replication Sites Curr. Genomics (IF 2.6) Pub Date : 2022 Yingying Yao
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Prospective Analysis of Proteins Carried in Extracellular Vesicles with Clinical Outcome in Hepatocellular Carcinoma Curr. Genomics (IF 2.6) Pub Date : 2022 Wenbiao Chen
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Draft Genome Sequence of the Earthworm Eudrilus eugeniae Curr. Genomics (IF 2.6) Pub Date : 2022 Arun Arumugaperumal
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Infestation of Rice by Gall Midge Influences Density and Diversity of Pseudomonas and Wolbachia in the Host Plant Microbiome Curr. Genomics (IF 2.6) Pub Date : 2022 Deepak K. Sinha