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Draft Genome Sequence of Pantoea sp. Strain MHSD4, a Bacterial Endophyte With Bioremediation Potential Evol. Bioinf. (IF 2.6) Pub Date : 2024-03-14 Dimpho Michelle Morobane, Khuthadzo Tshishonga, Mahloro Hope Serepa-Dlamini
Pantoea sp. strain MHSD4 is a bacterial endophyte isolated from the leaves of the medicinal plant Pellaea calomelanos. Here, we report on strain MHSD4 draft whole genome sequence and annotation. The draft genome size of Pantoea sp. strain MHSD4 is 4 647 677 bp with a G+C content of 54.2% and 41 contigs. The National Center for Biotechnology Information Prokaryotic Genome Annotation Pipeline tool predicted
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A Comprehensive Analysis of 3 Moroccan Genomes Revealed Contributions From Both African and European Ancestries Evol. Bioinf. (IF 2.6) Pub Date : 2024-02-07 Nasma Boumajdi, Houda Bendani, Souad Kartti, Tarek Alouane, Lahcen Belyamani, Azeddine Ibrahimi
Genetic variations in the human genome represent the differences in DNA sequence within individuals. This highlights the important role of whole human genome sequencing which has become the keystone for precision medicine and disease prediction. Morocco is an important hub for studying human population migration and mixing history. This study presents the analysis of 3 Moroccan genomes; the variant
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Screening and Validation of Key Genes of Autophagy in Acute Myocardial Infarction Based on Bioinformatics Evol. Bioinf. (IF 2.6) Pub Date : 2024-01-31 Yingjie Geng, Yu’e Han, Shujuan Wang, Jia Qi, Xiaoli Bi
Aims:Autophagy plays a significant role in the development of acute myocardial infarction (AMI), and cardiomyocyte autophagy is of major importance in maintaining cardiac function. We aimed to identify key genes associated with autophagy in AMI through bioinformatics analysis and verify them through clinical validation.Materials and Methods:We downloaded an AMI expression profile dataset GSE166780
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Multi-omics Analysis of Prognostic Significance and Immune Infiltration of FASTK Family Members in Kidney Renal Clear Cell Carcinoma. Evol. Bioinf. (IF 2.6) Pub Date : 2023-11-27 Guanghui Zhong,Dali Wu,Haiping Chen,Lingfei Yan,Qi Xiang,Yufeng Liu,Tao Wang
Objective The Fas-activated serine/threonine kinase (FASTK) family of proteins has been recently found to be able to regulate mitochondrial gene expression post-transcriptionally. Nonetheless, there is a paucity of study about the role of the FASTK family in kidney renal clear cell carcinoma (KIRC). This study was conducted to explore the correlation of FASTK family genes with expression, prognosis
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Retrospective Phylodynamic and Phylogeographic Analysis of the Bluetongue Virus in Tunisia. Evol. Bioinf. (IF 2.6) Pub Date : 2023-11-27 Oussema Souiai,Marwa Arbi,Mariem Hanachi,Ameny Sallami,Imen Larbi,Melek Chaouch,Emna Harigua-Souiai,Alia Benkahla
Bluetongue virus (BTV) is an arbovirus considered as a major threat for the global livestock economy. Since 1999, Tunisia has experienced several incursions of BTV, during which numerous cases of infection and mortality have been reported. However, the geographical origin and epidemiological characteristics of these incursions remained unclear. To understand the evolutionary history of BTV emergence
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Utilizing In Silico Approaches to Investigate the Signaling Pathway's Crucial Function in Pennisetum glaucum Under Thermal Stress. Evol. Bioinf. (IF 2.6) Pub Date : 2023-11-15 Faten Dhawi
Pearl millet (Pennisetum glaucum (L.)) is a remarkable cereal crop known for its ability to thrive in challenging environmental conditions. Despite its resilience, the intricate molecular mechanisms behind its toughness remain a mystery. To address this knowledge gap, we conducted advanced next-generation RNA sequencing. This approach allowed us to compare the gene expression profiles of pearl millet
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Molecular Mechanisms of the miR396b-GRF1 Module Underlying Rooting Regulation in Acer rubrum L. Evol. Bioinf. (IF 2.6) Pub Date : 2023-11-15 Manyu Zhang,Huiju Li,Huiyu Zhu,Hewen Zhao,Kezhong Zhang,Wei Ge
Rooting and root development in Acer rubrum have important effects on overall growth. A. rubrum does not take root easily in natural conditions. In this study, the mechanisms of the miR396b-GRF1 module underlying rooting regulation in A. rubrum were studied. The subcellular localization and transcriptional activation of miR396b and its target gene growth regulating factor 1 (GRF1) were investigated
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New Insights Into The Evolution of Chloroplast Genomes in Ochna Species (Ochnaceae, Malpighiales). Evol. Bioinf. (IF 2.6) Pub Date : 2023-11-15 Nguyen Nhat Nam,Nguyen Hoang Danh,Vu Minh Thiet,Hoang Dang Khoa Do
Ochnaceae DC. includes more than 600 species that exhibit potential values for environmental ecology, ornamental, pharmaceutical, and timber industries. Although studies on phylogeny and phytochemicals have been intensively conducted, chloroplast genome data of Ochnaceae species have not been fully explored. In this study, the next-generation sequencing method was used to sequence the chloroplast genomes
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Transposable Elements-Derived MicroRNA Expression Patterns in TCGA Dataset for 10 Species. Evol. Bioinf. (IF 2.6) Pub Date : 2023-08-14 Chan-Mi Lee,Sang Woo Jin,Byunghyun Jang,Young Kyung Ko,Jeong-An Gim
MicroRNAs (miRNAs) are a class of non-coding RNAs that act as regulators of disease. An evolutionary approach to the disease could reveal factors such as diagnosis, treatment, and prognosis prediction. The expression patterns of transposable element (TEs)-derived miRNAs could help elucidate diseases, and their evolutionary patterns are also valuable. The 34 miRNAs were compared in terms of stage survival
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The Pan-Genomic Analysis of Corynebacterium striatum Revealed its Genetic Characteristics as an Emerging Multidrug-Resistant Pathogen. Evol. Bioinf. (IF 2.6) Pub Date : 2023-08-10 Junhui Qiu,Yulan Shi,Fei Zhao,Yi Xu,Hui Xu,Yan Dai,Yi Cao
Corynebacterium striatum is a Gram-positive bacterium that is straight or slightly curved and non-spore-forming. Although it was originally believed to be a part of the normal microbiome of human skin, a growing number of studies have identified it as a cause of various chronic diseases, bacteremia, and respiratory infections. However, despite its increasing importance as a pathogen, the genetic characteristics
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Beta, Delta, and Omicron, Deadliest Among SARS-CoV-2 Variants: A Computational Repurposing Approach. Evol. Bioinf. (IF 2.6) Pub Date : 2023-07-11 Mohammad Mamun Alam,Sumaiya Binte Hannan,Tanvir Ahmed Saikat,Md Belayet Hasan Limon,Md Raihan Topu,Md Jowel Rana,Asma Salauddin,Sagar Bosu,Mohammed Ziaur Rahman
SARS-CoV-2 has been highly susceptible to mutations since its emergence in Wuhan, China, and its subsequent propagation due to containing an RNA as its genome. The emergence of variants with improved transmissibility still poses a grave threat to global health. The spike protein mutation is mainly responsible for higher transmissibility and risk severity. This study retrieved SARS-CoV-2 variants structural
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Effects of Antibiotic Treatment on the Development and Bacterial Community of the Wolbachia-Infected Diamondback Moth. Evol. Bioinf. (IF 2.6) Pub Date : 2023-06-06 Xiangyu Zhu,Ling Zhang,Jinyang Li,Ao He,Minsheng You,Shijun You
Based on the important role of antibiotic treatment in the research of the interaction between Wolbachia and insect hosts, this study aimed to identify the most suitable antibiotic and concentration for Wolbachia elimination in the P. xylostella, and to investigate the effect of Wolbachia and antibiotic treatment on the bacterial community of P. xylostella. Our results showed that the Wolbachia-infected
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In Silico Analyses of All STAT3 Missense Variants Leading to Explore Divergent AD-HIES Clinical Phenotypes Evol. Bioinf. (IF 2.6) Pub Date : 2023-04-24 Mariam Mansouri, Ghyzlane El Haddoumi, Houda Bendani, Nasma Boumajdi, Mohammed Hakmi, Hanane Abbou, El Mehdi Bouricha, Boutaina Elgharbaoui, Souad Kartti, Rachid El Jaoudi, Lahcen Belyamani, Ilham Kandoussi, Azeddine Ibrahimi, Naima El Hafidi
Autosomal dominant hyper-IgE syndrome (AD-HIES) is linked to dominant negative mutations of the STAT3 protein whose molecular basis for dysfunction is unclear and presenting with a variety of clini...
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Worldwide Correlations Support COVID-19 Seasonal Behavior and Impact of Global Change Evol. Bioinf. (IF 2.6) Pub Date : 2023-04-17 Nicolas Hernandez, Gustavo Caetano-Anollés
Many viral diseases exhibit seasonal behavior and can be affected by environmental stressors. Using time-series correlation charts extrapolated from worldwide data, we provide strong support for th...
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The Biological Processes of Ferroptosis Involved in Pathogenesis of COVID-19 and Core Ferroptoic Genes Related With the Occurrence and Severity of This Disease Evol. Bioinf. (IF 2.6) Pub Date : 2023-02-13 Zhengzhong Zhang, Tingting Pang, Min Qi, Gengyun Sun
Background:A worldwide outbreak of coronavirus disease 2019 (COVID-19) has resulted in millions of deaths. Ferroptosis is a form of iron-dependent cell death which is characterized by accumulation ...
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G-SAIP: Graphical Sequence Alignment Through Parallel Programming in the Post-Genomic Era Evol. Bioinf. (IF 2.6) Pub Date : 2023-01-20 Johan S. Piña, Simon Orozco-Arias, Nicolas Tobón-Orozco, Leonardo Camargo-Forero, Reinel Tabares-Soto, Romain Guyot
A common task in bioinformatics is to compare DNA sequences to identify similarities between organisms at the sequence level. An approach to such comparison is the dot-plots, a 2-dimensional graphi...
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The Prognostic Value of a lncRNA Risk Model Consists of 9 m6A Regulator-Related lncRNAs in Hepatocellular Carcinoma (HCC) Evol. Bioinf. (IF 2.6) Pub Date : 2023-01-12 Zhen Deng, Jiaxing Hou, Hongbo Xu, Zhao Lei, Zhiqiang Li, Hongwei Zhu, Xiao Yu, Zhi Yang, Xiaoxin Jin, Jichun Sun
Hepatocellular carcinoma (HCC) is the most common primary malignancy of the liver. Although the RNA modification N6-methyladenine (m6A) has been reported to be involved in HCC carcinogenesis, early...
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Characterization and Expression Analysis of B12D-Like Gene From Pearl Millet Evol. Bioinf. (IF 2.6) Pub Date : 2022-12-22 Zainab M Almutairi
B12D-Like is a member of the B12D domain-containing protein family, which includes several transmembrane proteins in plants. In this study, the cDNA of PgB12D-Like from Pennisetum glaucum subsp. mo...
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Diversity in Expression Biases of Lineage-Specific Genes During Development and Anhydrobiosis Among Tardigrade Species Evol. Bioinf. (IF 2.6) Pub Date : 2022-12-21 Jean-Christophe Metivier, Frédéric J J Chain
Lineage-specific genes can contribute to the emergence and evolution of novel traits and adaptations. Tardigrades are animals that have adapted to tolerate extreme conditions by undergoing a form o...
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Further Quantifying the Niche-Neutral Continuum of Human Digestive Tract Microbiomes with Near Neutral Model and Stochasticity Analysis Evol. Bioinf. (IF 2.6) Pub Date : 2022-11-23 Hongju (Daisy) Chen, Zhanshan (Sam) Ma
It is postulated that the human digestive tract (DT) from mouth to intestine is differentiated into diverse niches. For example, Segata et al. discovered that the microbiomes of diverse habitats al...
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Distribution, Phylogeny and Evolution of Clinical and Environmental Vibrio vulnificus Antibiotic-Resistant Genes Evol. Bioinf. (IF 2.6) Pub Date : 2022-11-15 Nan Geng, Guojin Sun, Wen-Jia Liu, Bin-Cheng Gao, Cong Sun, Cundong Xu, Ertian Hua, Lin Xu
Vibrio vulnificus is an emergent marine pathogen and is the cause of a deadly septicemia. However, the evolution mechanism of antibiotic-resistant genes (ARGs) is still unclear. Twenty-two high-qua...
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Bioinformatics-based Characterization of the Sequence Variability of Zika Virus Polyprotein and Envelope Protein (E) Evol. Bioinf. (IF 2.6) Pub Date : 2022-10-27 Carlos Polanco, Vladimir N Uversky, Alberto Huberman, Gilberto Vargas-Alarcón, Jorge Alberto Castañón González, Thomas Buhse, Enrique Hernández Lemus, Martha Rios Castro, Erika Jeannette López Oliva, Sergio Enrique Solís Nájera
Background:Zika virus, which is widely spread and infects humans through the bites of Aedes albopictus and Aedes aegypti female mosquitoes, represents a serious global health issue.Objective:The ob...
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Integrated Analysis of Multi-Omics Data to Establish a Hypoxia-Related Prognostic Model in Osteosarcoma Evol. Bioinf. (IF 2.6) Pub Date : 2022-10-26 Ye Tong, Xiaoqing Zhang, Ye Zhou
Background:Osteosarcoma (OS) is the most common malignant bone tumor in clinical practice, and currently, the ability to predict prognosis in the diagnosis of OS is limited. There is an urgent need...
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Stability of scRNA-Seq Analysis Workflows is Susceptible to Preprocessing and is Mitigated by Regularized or Supervised Approaches Evol. Bioinf. (IF 2.6) Pub Date : 2022-09-29 Arda Durmaz, Jacob G Scott
Background:Statistical methods developed to address various questions in single-cell datasets show increased variability to different parameter regimes. In order to delineate further the robustness...
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Construction of a Prognostic Nomogram Based on Autophagy-Related Genes for Children With Neuroblastoma Evol. Bioinf. (IF 2.6) Pub Date : 2022-08-26 Guogang Ye, Yue Wang
Neuroblastoma (NB) is the most common solid malignancy in children. MYCN gene amplification is the most relevant genetic alteration in patients with NB and is associated with poor prognosis. Autoph...
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Biological Computation and Compatibility Search in the Possibility Space as the Mechanism of Complexity Increase During Progressive Evolution Evol. Bioinf. (IF 2.6) Pub Date : 2022-08-19 AP Kozlov
The idea of computational processes, which take place in nature, for example, DNA computation, is discussed in the literature. DNA computation that is going on in the immunoglobulin locus of verteb...
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Transcriptomics of a Greenlandic Snailfish Reveals Exceptionally High Expression of Antifreeze Protein Transcripts Evol. Bioinf. (IF 2.6) Pub Date : 2022-08-16 John A Burns, David F Gruber, Jean P Gaffney, John S Sparks, Mercer R Brugler
Polar fishes have evolved antifreeze proteins (AFPs) that allow them to survive in subzero temperatures. We performed deep transcriptomic sequencing on a postlarval/juvenile variegated snailfish, L...
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Bioinformatics Analysis Identifies Potential Related Genes in the Pathogenesis of Intrauterine Fetal Growth Retardation Evol. Bioinf. (IF 2.6) Pub Date : 2022-07-28 Chao Xiao, Yao Wang, Yuchao Fan
Background:Intrauterine growth retardation (IUGR) affects approximately 10% to 15% of all pregnancies worldwide. IUGR is not only associated with stillbirth and newborn death, but also the delay of...
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BioAlign: An Accurate Global PPI Network Alignment Algorithm Evol. Bioinf. (IF 2.6) Pub Date : 2022-07-20 Umair Ayub, Hammad Naveed
Motivation:The advancement of high-throughput PPI profiling techniques results in generating a large amount of PPI data. The alignment of the PPI networks uncovers the relationship between the spec...
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Analysis of Competitive Endogenous RNA Regulatory Network of Exosomal Breast Cancer Based on exoRBase Evol. Bioinf. (IF 2.6) Pub Date : 2022-07-20 Kangle Zhu, Qingqing Wang, Lian Wang
Objective:To construct a competitive endogenous RNA (ceRNA) regulatory network derived from exosomes of human breast cancer (BC) by using the exoRbase database, to explore the possible pathogenesis...
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Metagenomic Sequencing and Histology on a Chronic Wound Identified Epstein-Barr Virus-Associated Lymphoma Evol. Bioinf. (IF 2.6) Pub Date : 2022-07-18 Wan-Ting Yang, I Chiang, Chien-Hao Tseng, Chun Cheng, Jyun-Hong Lin, Po-Yu Liu, Yao-Ting Huang
Accurate diagnosis of chronic, non-healing wounds is challenging and time-consuming because it can be caused by a variety of etiologies. This brief report presents an unusual case of a chronic woun...
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Mononucleotide A-repeats may Play a Regulatory Role in Endothermic Housekeeping Genes Evol. Bioinf. (IF 2.6) Pub Date : 2022-07-15 Jatuphol Pholtaisong, Nachol Chaiyaratana, Chatchawit Aporntewan, Apiwat Mutirangura
Background:Coding and non-coding short tandem repeats (STRs) facilitate a great diversity of phenotypic traits. The imbalance of mononucleotide A-repeats around transcription start sites (TSSs) was...
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Computational Structural and Functional Analyses of ORF10 in Novel Coronavirus SARS-CoV-2 Variants to Understand Evolutionary Dynamics Evol. Bioinf. (IF 2.6) Pub Date : 2022-07-07 Seema Mishra
Introduction:In an effort to combat SARS-CoV-2 through multi-subunit vaccine design, during studies using whole genome and immunome, ORF10, located at the 3′ end of the genome, displayed unique fea...
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In Silico Identification and Characterization of B12D Family Proteins in Viridiplantae Evol. Bioinf. (IF 2.6) Pub Date : 2022-06-14 Zainab M Almutairi
B12D family proteins are transmembrane proteins that contain the B12D domain involved in membrane trafficking. Plants comprise several members of the B12D family, but these members’ numbers and spe...
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Investigating the Genomic Background of CRISPR-Cas Genomes for CRISPR-Based Antimicrobials Evol. Bioinf. (IF 2.6) Pub Date : 2022-06-08 Hyunjin Shim
CRISPR-Cas systems are an adaptive immunity that protects prokaryotes against foreign genetic elements. Genetic templates acquired during past infection events enable DNA-interacting enzymes to recognize foreign DNA for destruction. Due to the programmability and specificity of these genetic templates, CRISPR-Cas systems are potential alternative antibiotics that can be engineered to self-target antimicrobial
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Wenxiang 3.0: Evolutionary Visualization of α, π, and 3/10 Helices Evol. Bioinf. (IF 2.6) Pub Date : 2022-05-31 John R Jungck, Metehan Cebeci
Wenxiang diagrams illustrate protein helices as spirals on a plane and thus have the advantage over helical wheels of being planar graphs. Wenxiang 3.0 extends the original version by adding 3 major features: (1) individual amino acid residues can be colored according to their evolutionary conservation in comparative multiple sequence alignments using CONSURF encoding; (2) α, π, and 3/10 helices can
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Host-Population Microbial Diversity Scaling of Chinese Gut Microbiomes in Gout Patients Evol. Bioinf. (IF 2.6) Pub Date : 2022-05-13 Jieshang Zhou, Yali Yuan, Pengli Xu, Bin Yi, Hongju Chen, Wei Su
Gout is a prevalent chronic inflammatory disease that affects the life of tens of millions of people worldwide, and it typically presents as gout arthritis, gout stone, or even kidney damage. Research has revealed its connection with the gut microbiome, although exact mechanism is still unclear. Studies have shown the decline of microbiome diversity in gout patients and change of microbiome compositions
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Identification of Phosphorylated Proteins Regulated by SDF2L1 in Nasopharyngeal Carcinoma Cells Evol. Bioinf. (IF 2.6) Pub Date : 2022-04-28 Chengchang Luo, Zunni Zhang, Qisheng Su, Wuning Mo
SDF2L1 is a new type of endoplasmic reticulum stress inducible protein, which is related to poor prognosis of various cancer, we initially studied the low expression level of SDF2L1 in NPC, but the molecular mechanism of SDF2L1 in NPC needs further elucidation. To identify phosphorylated proteins regulated by SDF2L1 in nasopharyngeal carcinoma (NPC), Label-free Quantitative (LFQ) Proteomics and 2D-LC-MS/MS
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The Prevalence of Pharmacogenomics Variants and Their Clinical Relevance Among the Pakistani Population Evol. Bioinf. (IF 2.6) Pub Date : 2022-04-24 Abdul Rafay Khan, Sayed Hajan Shah, Sadia Ajaz, Sadaf Firasat, Aiysha Abid, Ali Raza
Background: Pharmacogenomics (PGx), forming the basis of precision medicine, has revolutionized traditional medical practice. Currently, drug responses such as drug efficacy, drug dosage, and drug adverse reactions can be anticipated based on the genetic makeup of the patients. The pharmacogenomic data of Pakistani populations are limited. This study investigates the frequencies of pharmacogenetic
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The Prevalence of Pharmacogenomics Variants and Their Clinical Relevance Among the Pakistani Population. Evol. Bioinf. (IF 2.6) Pub Date : 2022-04-24 Abdul Rafay Khan,Sayed Hajan Shah,Sadia Ajaz,Sadaf Firasat,Aiysha Abid,Ali Raza
Background Pharmacogenomics (PGx), forming the basis of precision medicine, has revolutionized traditional medical practice. Currently, drug responses such as drug efficacy, drug dosage, and drug adverse reactions can be anticipated based on the genetic makeup of the patients. The pharmacogenomic data of Pakistani populations are limited. This study investigates the frequencies of pharmacogenetic variants
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Transcriptome Analysis of MYB Genes and Patterns of Anthocyanin Accumulation During Seed Development in Wheat Evol. Bioinf. (IF 2.6) Pub Date : 2022-04-13 Paulina Calderon Flores, Jin Seok Yoon, Dae Yeon Kim, Yong Weon Seo
Plants accumulate key metabolites as a response of biotic/abiotic stress conditions. In seed coats, anthocyanins, carotenoids, and chlorophylls can be found. They have been associated as important antioxidants that affect germination. In wheat, anthocyanins can impart the seed coat color which have been recognized as health-promoting nutrients. Transcription factors act as master regulators of cellular
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Transcriptome Analysis of MYB Genes and Patterns of Anthocyanin Accumulation During Seed Development in Wheat. Evol. Bioinf. (IF 2.6) Pub Date : 2022-04-13 Paulina Calderon Flores,Jin Seok Yoon,Dae Yeon Kim,Yong Weon Seo
Plants accumulate key metabolites as a response of biotic/abiotic stress conditions. In seed coats, anthocyanins, carotenoids, and chlorophylls can be found. They have been associated as important antioxidants that affect germination. In wheat, anthocyanins can impart the seed coat color which have been recognized as health-promoting nutrients. Transcription factors act as master regulators of cellular
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Metatranscriptomics Analysis Reveals Diverse Viral RNA in Cutaneous Papillomatous Lesions of Cattle Evol. Bioinf. (IF 2.6) Pub Date : 2022-03-14 Adriana O Fernandes, Gerlane S Barros, Marcus VA Batista
Bovine papillomavirus (BPV) is associated with bovine papillomatosis, a disease that forms benign warts in epithelial tissues, as well as malignant lesions. Previous studies have detected a co-infection between BPV and other viruses, making it likely that these co-infections could influence disease progression. Therefore, this study aimed to identify and annotate viral genes in cutaneous papillomatous
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Corrigendum to “Optimized Next-Generation Sequencing Genotype-Haplotype Calling for Genome Variability Analysis” Evol. Bioinf. (IF 2.6) Pub Date : 2022-03-14
Navarro J, Nevado B, Hernández P, et al. Optimized Next-Generation Sequencing Genotype-Haplotype Calling for Genome Variability Analysis. Evolutionary Bioinformatics. 2017;13: 1–11. DOI: 10.1177/1176934317723884
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SPINK5 is a Prognostic Biomarker Associated With the Progression and Prognosis of Laryngeal Squamous Cell Carcinoma Identified by Weighted Gene Co-Expression Network Analysis Evol. Bioinf. (IF 2.6) Pub Date : 2022-02-04 Jian Liu, Jing Zhao, Jiaran Xu, Qing Sun, Xuemei Qin, Guohui Chen, Tianle Gao, Guangping Bai, Zhiqiang Guo
Laryngeal squamous cell carcinoma (LSCC) is one of the most common types of head and neck squamous cell carcinomas (HNSCC) and is the second most prevalent malignancy occurring in the head and neck or respiratory tract, with a high incidence and mortality rate. Survival is limited for patients with LSCC. To identify more biomarkers associated with the prognosis of patients with LSCC, using bioinformatics
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SPINK5 is a Prognostic Biomarker Associated With the Progression and Prognosis of Laryngeal Squamous Cell Carcinoma Identified by Weighted Gene Co-Expression Network Analysis. Evol. Bioinf. (IF 2.6) Pub Date : 2022-02-04 Jian Liu,Jing Zhao,Jiaran Xu,Qing Sun,Xuemei Qin,Guohui Chen,Tianle Gao,Guangping Bai,Zhiqiang Guo
Laryngeal squamous cell carcinoma (LSCC) is one of the most common types of head and neck squamous cell carcinomas (HNSCC) and is the second most prevalent malignancy occurring in the head and neck or respiratory tract, with a high incidence and mortality rate. Survival is limited for patients with LSCC. To identify more biomarkers associated with the prognosis of patients with LSCC, using bioinformatics
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Screening of Important Markers in Peripheral Blood Mononuclear Cells to Predict Female Osteoporosis Risk Using LASSO Regression Algorithm and SVM Method Evol. Bioinf. (IF 2.6) Pub Date : 2022-01-28 Hongwei Tang, Qingtian Han, Yong Yin
Background: Osteoporosis is a bone disease that increases the patient’s risk of fracture. We aimed to identify robust marker genes related to osteoporosis based on different bioinformatic methods and multiple datasets. Methods: Three datasets from Gene Expression Omnibus (GEO) were utilized for analysis separately. Significantly differentially expressed genes (DEGs) from comparing high hip and low
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Draft Genome Sequence of Oceanobacillus jordanicus Strain GSFE11, a Halotolerant Plant Growth-Promoting Bacterial Endophyte Isolated From the Jordan Valley Evol. Bioinf. (IF 2.6) Pub Date : 2022-01-25 Tareq Alhindi, Randa Albdaiwi
The bacterium Oceanobacillus jordanicus strain GSFE11 is a halotolerant endophyte isolated from sterilized roots of Durum wheat (Triticum turgidum ssp. Durum) growing in hot and arid environments of Ghor Safi area in the Jordan Valley. The draft genome sequence and annotation of this plant growth-promoting endophytic bacterium are reported in this study. The draft genome sequence of Oceanobacillus
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Seasonal Diversity of Microeukaryotes in the Han River, Korea Through 18S rRNA Gene Metabarcoding Evol. Bioinf. (IF 2.6) Pub Date : 2022-01-25 Tae-June Choi, Adeel Malik, Hyung-Eun An, Jung-Il Kim, Thinh Dinh Do, Chang-Bae Kim
Freshwater ecosystems contain a large diversity of microeukaryotes that play important roles in maintaining their structure. Microeukaryote communities vary in composition and abundance on the basis of temporal and environmental variables and may serve as useful bioindicators of environmental changes. In the present study, 18S rRNA metabarcoding was employed to investigate the seasonal diversity of
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Seasonal Diversity of Microeukaryotes in the Han River, Korea Through 18S rRNA Gene Metabarcoding. Evol. Bioinf. (IF 2.6) Pub Date : 2022-01-25 Tae-June Choi,Adeel Malik,Hyung-Eun An,Jung-Il Kim,Thinh Dinh Do,Chang-Bae Kim
Freshwater ecosystems contain a large diversity of microeukaryotes that play important roles in maintaining their structure. Microeukaryote communities vary in composition and abundance on the basis of temporal and environmental variables and may serve as useful bioindicators of environmental changes. In the present study, 18S rRNA metabarcoding was employed to investigate the seasonal diversity of
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Draft Genome Sequence of Oceanobacillus jordanicus Strain GSFE11, a Halotolerant Plant Growth-Promoting Bacterial Endophyte Isolated From the Jordan Valley. Evol. Bioinf. (IF 2.6) Pub Date : 2022-01-25 Tareq Alhindi,Randa Albdaiwi
The bacterium Oceanobacillus jordanicus strain GSFE11 is a halotolerant endophyte isolated from sterilized roots of Durum wheat (Triticum turgidum ssp. Durum) growing in hot and arid environments of Ghor Safi area in the Jordan Valley. The draft genome sequence and annotation of this plant growth-promoting endophytic bacterium are reported in this study. The draft genome sequence of Oceanobacillus
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Evolutionary Dynamics of Indels in SARS-CoV-2 Spike Glycoprotein Evol. Bioinf. (IF 2.6) Pub Date : 2021-12-06 R Shyama Prasad Rao, Nagib Ahsan, Chunhui Xu, Lingtao Su, Jacob Verburgt, Luca Fornelli, Daisuke Kihara, Dong Xu
SARS-CoV-2, responsible for the current COVID-19 pandemic that claimed over 5.0 million lives, belongs to a class of enveloped viruses that undergo quick evolutionary adjustments under selection pressure. Numerous variants have emerged in SARS-CoV-2, posing a serious challenge to the global vaccination effort and COVID-19 management. The evolutionary dynamics of this virus are only beginning to be
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The Power of Universal Contextualized Protein Embeddings in Cross-species Protein Function Prediction Evol. Bioinf. (IF 2.6) Pub Date : 2021-12-03 Irene van den Bent, Stavros Makrodimitris, Marcel Reinders
Computationally annotating proteins with a molecular function is a difficult problem that is made even harder due to the limited amount of available labeled protein training data. Unsupervised protein embeddings partly circumvent this limitation by learning a universal protein representation from many unlabeled sequences. Such embeddings incorporate contextual information of amino acids, thereby modeling
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Screening of Important Factors in the Early Sepsis Stage Based on the Evaluation of ssGSEA Algorithm and ceRNA Regulatory Network Evol. Bioinf. (IF 2.6) Pub Date : 2021-11-26 Liou Huang, Chunrong Wu, Dan Xu, Yuhui Cui, Jianguo Tang
Background: Sepsis is a dysregulated host response to pathogens. Delay in sepsis diagnosis has become a primary cause of patient death. This study determines some factors to prevent septic shock in its early stage, contributing to the early treatment of sepsis. Methods: The sequencing data (RNA- and miRNA-sequencing) of patients with septic shock were obtained from the NCBI GEO database. After re-annotation
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AURKB as a Promising Prognostic Biomarker in Hepatocellular Carcinoma Evol. Bioinf. (IF 2.6) Pub Date : 2021-11-24 Jingchuan Xiao, Yingai Zhang
The Aurora kinases form a family of 3 genes encoding serine/threonine kinases and are involved in the regulation of cell division during the mitosis. This study was designed to investigate the prognostic role of Aurora kinases in hepatocellular carcinoma (HCC). In this study, we analyzed the expression, overall survival (OS) data, promoter methylation level, and relationship with immunoinhibitors of
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Comparison of the Gut Microbiota in Patients with Benign and Malignant Breast Tumors: A Pilot Study Evol. Bioinf. (IF 2.6) Pub Date : 2021-11-13 Peidong Yang, Zhitang Wang, Qingqin Peng, Weibin Lian, Debo Chen
The microbiome plays diverse roles in many diseases and can potentially contribute to cancer development. Breast cancer is the most commonly diagnosed cancer in women worldwide. Thus, we investigated whether the gut microbiota differs between patients with breast carcinoma and those with benign tumors. The DNA of the fecal microbiota community was detected by Illumina sequencing and the taxonomy of
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Exploration of Prognostic Biomarkers of Muscle-Invasive Bladder Cancer (MIBC) by Bioinformatics Evol. Bioinf. (IF 2.6) Pub Date : 2021-10-28 Xianglai Xu, Yelin Wang, Sihong Zhang, Yanjun Zhu, Jiajun Wang
We aimed to discover prognostic factors of muscle-invasive bladder cancer (MIBC) and investigate their relationship with immune therapies. Online data of MIBC were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus database (GEO) database. Weighted gene co-expression network analysis (WGCNA) and univariate Cox analysis were applied to classify genes into different groups. Venn
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Identification of Conserved Pappalysin 1-Derived Circular RNA-Mediated Competing Endogenous RNA in Osteosarcoma Evol. Bioinf. (IF 2.6) Pub Date : 2021-10-21 Guang-Fu Ming, Bo-Hua Gao, Peng Chen
The etiology of osteosarcoma (OS) is complex and not fully understood till now. This study aimed to identify the miRNAs, circRNAs, and genes (mRNAs) that are differentially expressed in OS cell lines to investigate the mechanism of circRNA-associated competing endogenous RNAs (ceRNAs) in OS. Microarray datasets reporting mRNA (GSE70414), miRNA (GSE70367), and circRNA changes (GSE96964) in human OS
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Sequence-Based Prediction of Plant Protein-Protein Interactions by Combining Discrete Sine Transformation With Rotation Forest Evol. Bioinf. (IF 2.6) Pub Date : 2021-10-12 Jie Pan, Li-Ping Li, Chang-Qing Yu, Zhu-Hong You, Yong-Jian Guan, Zhong-Hao Ren
Protein-protein interactions (PPIs) in plants are essential for understanding the regulation of biological processes. Although high-throughput technologies have been widely used to identify PPIs, they are usually laborious, expensive, and suffer from high false-positive rates. Therefore, it is imperative to develop novel computational approaches as a supplement tool to detect PPIs in plants. In this
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Compelling Evidence Suggesting the Codon Usage of SARS-CoV-2 Adapts to Human After the Split From RaTG13 Evol. Bioinf. (IF 2.6) Pub Date : 2021-10-08 Yanping Zhang, Xiaojie Jin, Haiyan Wang, Yaoyao Miao, Xiaoping Yang, Wenqing Jiang, Bin Yin
SARS-CoV-2 needs to efficiently make use of the resources from hosts in order to survive and propagate. Among the multiple layers of regulatory network, mRNA translation is the rate-limiting step in gene expression. Synonymous codon usage usually conforms with tRNA concentration to allow fast decoding during translation. It is acknowledged that SARS-CoV-2 has adapted to the codon usage of human lungs