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17 articles for “Comparative genomics”
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Tools and Techniques for Whole-Genome Alignments
Abstract: The prediction of evolutionary relationships between two or more genomes at the nucleotide level is known as whole-genome alignment (WGA). It possesses characteristics of both gene orthology prediction and collinear sequence alignment. WGAs are useful for genome-wide analyses like phylogenetic inference, genome annotation, and function prediction. So many solutions have been developed despite the fact that this problem is difficult. This article provides an overview of the approaches used to …
Published in Research and Reviews : Journal of Computational Biology · Vol. 11, Issue 2, 2022 · pp. 36–38 Read article
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Bioinformatics Tools and Databases for Functional Annotation of Genomes
Abstract: Functional annotation of genomes plays a crucial role in understanding the functions and characteristics of genes. Bioinformatics tools and databases have greatly contributed to this field by providing valuable resources for gene function prediction, pathway analysis, and comparative genomics. This abstract provides an overview of these tools and databases and highlights their significance in functional annotation. Ensembl is a popular bioinformatics tool that offers comprehensive genome annotation and browsing capabilities. …
Published in Research and Reviews : Journal of Computational Biology · Vol. 12, Issue 1, 2023 · pp. 31–35 Read article
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Comparative Evaluation of Pedigree-Based and Genomic BLUP Models for Wheat Grain Yield Prediction
Abstract: Before genome-wide molecular markers became affordable, plant and animal breeding relied on pedigree-based prediction (P-BLUP), using the expected additive relationship matrix (A) derived from recorded ancestry. Genomic selection replaced or augmented this with a marker-derived genomic relationship matrix (G; GBLUP), and single-step methods combining A and G are now standard when only a subset of a breeding population is genotyped. It is less clear whether pedigree information retains any predictive …
Published in Research and Reviews : Journal of Computational Biology · Vol. 15, Issue 2, 2026 · pp. 1–9 Read article
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Genomic Selection for Grain Yield in Wheat Using Machine Learning on DArT Molecular Markers: A Comparative Evaluation Across Multi-Environment Trials
Abstract: Genomic selection (GS) predicts complex quantitative traits directly from genome-wide molecular markers, bypassing the need for extensive phenotypic trials and accelerating plant breeding cycles. We conducted a comparative evaluation of seven regression approaches — ridge regression (the machine-learning equivalent of RR-BLUP), Lasso, Elastic Net, Partial Least Squares, linear Support Vector Regression, Random Forest, and Gradient Boosting — for predicting grain yield from 1,279 Diversity Array Technology (DArT) molecular markers genotyped …
Published in Research and Reviews : Journal of Computational Biology · Vol. 15, Issue 2, 2026 Read article
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An Overview of Fanconi Anemia: A Genetic Disorder
Abstract: Fanconi Anemia (FA) is a rare genetic disorder caused by DNA repair defects due to pathogenic variants in one of 21 genes. It is the primary cause of inherited bone marrow failure, marked by pancytopenia. Clinically, Fanconi Anemia (FA) is associated with congenital malformations in multiple systems, resulting in progressive bone marrow failure and heightened cancer risk, especially in the urogenital region and the head and neck. There are approximately …
Published in International Journal of Oncological Nursing and Practices · Vol. 2, Issue 2, 2024 · pp. 19–25 Read article
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Computational Biology and Intellectual Property Rights: A Need of the Hour
Abstract: The possibility of the discovery of drugs and cures based on genetic studies that may have the potential to treat diseases hereto considered incurable, has meant an investment of huge amounts in research and development of bioinformatics tools of a more sophisticated, nature which would aid in the field of comparative genomics and such. In this scenario, there has already been a copious amount of funding into research and development …
Published in Research and Reviews : Journal of Computational Biology · Vol. 10, Issue 1, 2021 Read article
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A Factorial Investigation of Hyperparameter Tuning Strategies for Lasso- Based Genomic Prediction
Abstract: In an earlier comparative study of machine-learning methods for genomic prediction of wheat grain yield, we reported a counter-intuitive result: automated nested-cross-validation tuning of the Lasso regularization penalty reduced mean predictive ability relative to a fixed, arbitrarily chosen penalty (mean Pearson r falling from 0.408 to 0.349 across four environments), the opposite of the expected effect of hyperparameter tuning. We hypothesized two possible explanations at the time — high-variance penalty …
Published in Research and Reviews : Journal of Computational Biology · Vol. 15, Issue 2, 2026 · pp. 42–51 Read article
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To Explore and Download the Genome Sequence of Drosophila Melanogaster at NCBI
Abstract: Drosophila melanogaster is one of the most intensively studied organisms in biology, serving as a model system for many developmental and cellular processes shared by higher eukaryotes, including humans. A shotgun whole-genome sequencing strategy was used to sequence almost the entire nucleotide of the approximately 120-megamegabase euchromatic portion of the Drosophila genome. It is supported by extensive clone-based sequences and high quality bacterial artificial chromosome maps. Work is being done …
Published in Research and Reviews : Journal of Computational Biology · Vol. 10, Issue 3, 2021 · pp. 4–6 Read article
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From Ancient DNA to Modern Livestock: Paleogenomics
Abstract: Paleogenomics, an interdisciplinary blend of paleontology and genomics, has revolutionized our understanding of ancient DNA and its applications across various fields. In Animal Genetics and Breeding, this field has emerged as a pivotal tool providing invaluable insights into the historical genetics of domesticated animals. By reconstructing and analyzing the genomes of long-extinct organisms, paleogenomics sheds light on genetic diversity, evolutionary dynamics, and adaptations of ancient species. Paleogenomics significantly impacts animal …
Published in International Journal of Genetic Modifications and Recombinations · Vol. 1, Issue 2, 2023 · pp. 1–6 Read article
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GenChrome-ML: A Machine Learning Framework for Early Detection of Chromosomal Disorders Using Genomic Data
Abstract: The increasing burden of chronic disease and cancer demands innovative, more rapid and effective diagnostic tools in the field of healthcare. The majority of current diagnostic tools are dependent upon clinical symptomology and manual evaluation, leading to delays in early detection and treatment. The development of artificial intelligence (AI) and machine learning (ML), in recent years, has offered opportunities for the enhancement of disease prediction, diagnosis and personalization of treatment …
Published in International Journal of Bioinformatics and Computational Biology · Vol. 4, Issue 2, 2026 Read article
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Nitric Oxide Synthase (NOS) in Breast Carcinoma
Abstract: Breast cancer is the most alarming problem of the current time. Nitric oxide, a free radical gas is synthesized by isoenzymes called nitric oxide synthase. Nitric oxide synthase consists of three isoforms; Nitric oxide produced is cytotoxic which is known to inhibit the DNA synthesis causing its damage. Keeping this in mind, nitric oxide synthase was determined in breast cancer and normal breast tissue. For this tissue from 60 breast …
Published in Research and Reviews: Journal of Oncology and Hematology · Vol. 7, Issue 1, 2018 · pp. 23–28 Read article
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The Relationship Between LOH Severity and Androgen Receptor Gene CAG Repeat Length of Korean Men Affected with LOH
Abstract: Context: There have been no investigations on the severity of late-onset hypogonadism (LOH) of Korean male according to their androgen receptor gene CAG repeat length. Aim: To investigate the relationship between late-onset hypogonadism (LOH) and androgen receptor gene CAG repeat length in Korean men. A total of 106 patients with LOH from Pyongyang City participated in this study. LOH was diagnosed in individuals who had a serum testosterone level below …
Published in Research and Reviews: A Journal of Medicine · Vol. 15, Issue 1, 2025 · pp. 32–37 Read article
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A Comparative Study of different Techniques to predict Maternal Morbidity and Mortality Model
Abstract: Artificial intelligence (AI) encompasses a range of techniques, including machine learning and deep learning, which are increasingly utilized in the healthcare sector for tasks such as disease diagnosis and drug discovery. To achieve accurate disease diagnosis through AI, it is essential to integrate data from multiple medical sources, including ultrasound imaging, magnetic resonance imaging (MRI), mammography, genomics, and computed tomography (CT) scans, among others. This article presents a comprehensive review …
Published in Research and Reviews: A Journal of Health Professions · Vol. 15, Issue 1, 2025 Read article
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RsaI polymorphisms of ER-β and Idiopathic Male Infertility
Abstract: Purpose: Study on association between estrogen receptor gene polymorphism and male infertility has been interested, but highly specific genetic markers have been reported to be variable according to regions and nations. Herein we studied to figure out whether ERβ gene1082 G>A polymorphism could influence on sperm indices or not.Method: We dealt with 100 Korean patients with idiopathic male infertility diagnosed at our university hospital as a study group and 127 …
Published in Research and Reviews: A Journal of Medicine · Vol. 12, Issue 3, 2022 · pp. 34–41 Read article
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Efficacy of Combination Therapy with Osimertinib and Afatinib in epidermal growth factor receptor-mutant non-small-cell lung cancer Patients
Abstract: Treatment options for patients with non-small-cell lung cancer who have epidermal growth factor receptor mutations are constrained by the emergence of resistance to epidermal growth factor receptor tyrosine kinase inhibitors. Osimertinib or afatinib alone, when tested in a laboratory model, led to the formation of drug-resistant clones harboring epidermal growth factor receptor secondary mutations. However, combining these drugs prevented the emergence of such mutations. In a Phase II clinical trial, …
Published in Research and Reviews: Journal of Oncology and Hematology · Vol. 13, Issue 1, 2024 · pp. 13–24 Read article
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CRISPR-Cas9: Revolutionizing the Genetic Frontier
Abstract: The rapid development of CRISPR/CRISPR-associated enzyme (Cas) technology has enabled truly customised treatment of human genetic disorders, paving the way for recent developments in the field of gene therapy. Because CRISPR/Cas can accurately target and edit individual genes within a genome, it has established itself as a formidable tool for genetic manipulation. CRISPR/Cas9 technology allows for precise editing of specific DNA sequences in an organism's genome. This method uses three …
Published in International Journal of Genetic Modifications and Recombinations · Vol. 3, Issue 2, 2025 Read article
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Seroprevalence of Hepatitis E Virus and Serum Level of Serum Aspartate Transaminase (AST) and Alkaline Phosphatase (ALP) Among Jaundice Patients in Kathmandu Valley, Nepal
Abstract: Hepatitis E is an acute disease caused by hepatitis E virus that usually manifest as acute jaundice. It is a waterborne infection and occurs sporadically or as epidemic outbreaks. Hepatitis E virus (HEV) is a positive-stranded RNA virus with a 7.2 kb genome with three open reading frames In this study we report the seroprevalence of HEV in different categories of jaundice patients along with their elevation of serum bilirubin, …
Published in Research and Reviews: A Journal of Medicine · Vol. 4, Issue 3, 2014 · pp. 37–42 Read article