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Analysis of protein determinants of genotype-specific properties of group a rotaviruses using machine learning

Computers in Biology and Medicine 2025年 191卷 110143-110143页

作者： Cho, Myeongji Been, Nara Son, Hyeon S. Laboratory of Computational Virology & Viroinformatics of Public Health Seoul National University 1 Gwanak-ro Gwanak-gu Seoul08826 Korea Republic of Public Health AI Lab of Public Health Seoul National University 1 Gwanak-ro Gwanak-gu Seoul08826 Korea Republic of Institute of Health and Environment Seoul National University 1 Gwanak-ro Gwanak-gu Seoul08826 Korea Republic of Interdisciplinary Graduate Program in Bioinformatics College of Natural Science Seoul National University 1 Gwanak-ro Gwanak-gu Seoul08826 Korea Republic of

Group A rotaviruses (RVAs) are the leading cause of viral diarrhoea across various host species, including mammals and birds. The VP7 and VP4 proteins of these viruses play critical roles in determining genotype specificity, influencing viral infectivity and host adaptation. This study employed machine-learning techniques to classify RVA genotypes based on the molecular and physicochemical properties of these proteins. A dataset of 94 VP7 and 68 VP4 protein sequences was collected from various host species. Seven machine-learning algorithms—Naïve Bayes (NB), logistic regression (LR), decision tree (DT), random forest (RF), k-nearest neighbour (kNN), support vector machine (SVM), and artificial neural network (ANN)—were used for genotype classification. Feature subsets were configured using ranking-based attribute selection, and classification performance was evaluated using accuracy (ACC), precision, recall, Matthews’ correlation coefficient (MCC), and the area under the curve (AUC). kNN demonstrated the highest classification accuracy for both VP7 (ACC = 97.87 %) and VP4 (ACC = 100 %), outperforming NB, LR, DT, RF, SVM, and ANN. For VP7 sequences, key properties influencing genotype classification included hydrophobicity, normalised van der Waals volume, and leucine composition. For VP4, polarity, normalised van der Waals volume, and polarizability were the most significant factors. In summary, the genotype-specific molecular features of VP7 and VP4 proteins served as reliable markers for RVA classification. Our findings highlight the potential of machine-learning approaches to predict RVA genotypes based on the physicochemical properties of amino acids, providing valuable insights into the molecular mechanisms that drive viral evolution, host specificity, and immune evasion. © 2025 Elsevier Ltd

关键词： Adversarial machine learning

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How to build a system that manages bioinformatics content

How to build a system that manages bioinformatics content

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2007 International Conference on Enterprise Information Systems and Web Technologies, EISWT 2007

作者： Phan, Vinhthuy Thomas, Allen Department of Computer Science Bioinformatics Program University of Memphis TN 38152 United States

ISBN: (纸本)9781615677245

We discuss how to build systems with sophisticated features based on a core set of bioinformatics tools. Beside from being the front-end server to the core analyses, such a system can manage users, bioinformatics content and shared data. Using tools available in the open-source community, we show how to build a system with such sophisticated features with a relatively minimal effort, especially in comparison to building such a system from scratch. We discuss the notion of Model-Content Management-View, under whose framework similar applications with such desirable features beyond the field bioinformatics can be built. Our system can be viewed at http://***/rnamotif.

关键词： bioinformatics

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Overview of guide RNA design tools for CRISPR-Cas9 genome editing technology

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Frontiers in Biology 2015年第4期10卷 289-296页

作者： Lihua Julie Zhu Department of Molecular Cell and Cancer Biology Program in Bioinformatics and Integrated Biology Program in Molecular MedicineUniversity of Massachusetts Medical School Worcester MA O1605 USA

CRISPR-Cas （Clustered, Regularly Interspaced, Short Palindromic Repeats - CRISPR-associated （Cas）） RNA guided endonuclease has emerged as the most effective and widely used genome editing technology, which has become the most exciting and rapidly advancing research field. Efficient genome editing by the CRISPR-Cas9 system has been demonstrated in many species, and several laboratories have established CRISPR-Cas9 as a screening tool for systematic genetic analysis, similar to sbRNA screening. At least three companies have been founded to leverage this technology for therapeutic uses. To facilitate the implementation of this technology, many software tools have been developed to identify guide RNAs that effectively target a desired genomic region. Here, I provide an overview of the technology, focusing on guide RNA design principles, available software tools and their strengths and weaknesses.

关键词： CRISPR-Cas9 genome editing gRNA design off-target analysis gRNA efficacy

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BIOPEN: A proposed web application for implementing the biological electronic protocol system of enteropathogens characterization: Personalized web sites and services

BIOPEN: A proposed web application for implementing the biol...

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作者： Kamada, Terumi Paula Bonfim Suzuki, Danielle Forbeci Costa, Maicon Silva Cruz, Leonardo Magalhes Neves, Luiz Antônio Pereira Bioinformatics Master Program Federal University of Paraná - UFPR Curitiba Brazil

ISBN: (纸本)9789898425515

In the present work, we have developed a Biological Electronic Protocol System for Enteropathogens Characterization (BIOPEN) with a Web Application interface that allows users to query data for characterization and analysis of pathogens through an integrated management of accurate collection, storage and retrieval of data, which aids decisions in health actions to combat diseases caused by these microorganisms. The proposed tool is an electronic protocol that aims to facilitate data sharing in health care, using a structured database to store information concerning about clinical assays and molecular characterizations of pathogenic strains and clinical isolates. BIOPEN was developed using open source facilities and is freely distributed, allowing a particular laboratory create a customized, reliable, and low cost database. Thus, the principal contribution of this work is to provide a tool that store and integrate results of physiological, biochemical, and molecular clinical tests that can help researchers in taxonomic identification of clinical isolates and prospective epidemiological studies.

关键词： Search engines

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Pursuit-evasion Voronoi diagrams in 1

Pursuit-evasion Voronoi diagrams in 1

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4th International Symposium on Voronoi Diagrams in Science and Engineering 2007, ISVD 2007

作者： Cheung, Warren Evans, William Department of Computer Science University of British Columbia University of British Columbia Bioinformatics Program

ISBN: (纸本)0769528694

We are given m pursuers and one evader. Each pursuer and the evader has an associated starting point in the plane, a maximum speed, and a start time. We also have a set of line segment obstacles with a total of n endpoints. Our task is to find those points in the plane, called the evader's region, that the evader can reach via evasive paths. A path is evasive if the evader can traverse the path from its starting point without encountering a pursuer along the way. The evader and the pursuers must obey their start time and speed constraints, and cannot go through obstacles. The partition of the plane into the evader's region and the remaining pursuers' region is called the pursuit-evasion Voronoi diagram. We study pursuit-evasion Voronoi diagrams for the 1 metric. We show that the complexity of the diagram is O((n + m)2(mn + m)) and that it can be calculated in polynomial time. © 2007 IEEE.

关键词： Graphic methods

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Monascus pilosus-fermented black soybean inhibits lipid accumulation in adipocytes and in high-fat diet-induced obese mice

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Asian Pacific Journal of Tropical Medicine 2015年第4期8卷 276-282页

作者： Young-Sil Lee Bong-Keun Choi Hae Jin Lee Dong-Ryung Lee Jinhua Cheng Won-Keun Lee Seung Hwan Yang Joo-Won Suh Center for Nutraceutical and Pharmaceutical Materials Myongji University Interdisciplinary Program of Biomodulation Myongji University Division of Bioscience and Bioinformatics College of Natural ScienceMyongji University

Objective:To explore the anti-obesity effects and the mechanism of action of Monascus pilosus(***)-fermented black soybean(MFBS)extracts(MFBSE)and MFBS powders(MFBSP)in adipocytes and high-fat diet(HFD)-induced obese mice,***:Black soybean was fermented with ***,and the main constituents in MFBS were analyzed by HPLC *** vitro,MFBSE were examined for anti-adipogenic effects using Oil-Red O *** vivo,mice were fed a normal-fat diet(NFD)control,HFD control or HFD containing 1 g/kg MFBSP for 12 weeks,and then body weight gain and tissues weight ***-time PCR and western blot assay were used to determine the mechanism of anti-adipogenic ***:MFBSE inhibited lipid accumulation in 3T3-L1 adipocytes without exerting cell *** treatment in HFD-fed mice significantly decreased the body weight gain compared with the HFD control *** and MFBSP treatment resulted in significantly lower mRNA levels of adipogenesis-related genes,such as peroxisome proliferator-activated receptorγ(PPARγ),fatty acid-binding protein 4(FABP4),and fatty acid synthase(FAS),in adipocytes and in white adipose tissue(WAT)of HFD-induced obese ***:These results suggest that the anti-obesity effects of MFBS are elicited by regulating the expression of adipogenesis-related genes in adipocytes and WAT of HFDinduced obese mice.

关键词： Monascus pilosus Black soybean Adipocytes High-fat diet-induced obese mice Anti-obesity Adipogenesis-related genes

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Detection of Gene Fusions and Rearrangements in Formalin-Fixed, Paraffin-Embedded Solid Tumor Specimens Using High-Throughput Chromosome Conformation Capture

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Journal of Molecular Diagnostics 2025年第5期27卷 346-359页

作者： Galbraith, Kristyn Wu, Jamin Sikkink, Kristin Mohamed, Hussein Reid, Derek Perez-Arreola, Michelle Belton, Jon-Matthew Nomikou, Sofia Melnyk, Shadi Yang, Yiying Liechty, Benjamin L. Jour, George Tsirigos, Aristotelis Hermel, David J. Beck, Alyssa Sigal, Darren Dahl, Nathan A. Vibhakar, Rajeev Schmitt, Anthony Snuderl, Matija Department of Pathology NYU Langone Health and NYU Grossman School of Medicine New York New York United States Arima Genomics Inc. Carlsbad California United States Department of Pathology Weill Cornell School of Medicine New York New York United States Division of Precision Medicine Department of Medicine NYU School of Medicine New York New York United States Applied Bioinformatics Laboratories NYU School of Medicine New York New York United States Scripps Clinic/Scripps Cancer Center La Jolla California United States Moores Cancer Center University of California San Diego San Diego California United States Morgan Adams Foundation Pediatric Brain Tumor Research Program Department of Pediatrics University of Colorado School of Medicine Aurora Colorado United States Brain and Spine Tumor Center Laura and Isaac Perlmutter Cancer Center NYU Langone Health New York New York United States

Chromosomal structural variants (SVs) are major contributors to cancer development. Although multiple methods exist for detecting SVs, they are limited in throughput, such as fluorescent in situ hybridization and targeted panels, and use RNA, which degrades in formalin-fixed, paraffin-embedded (FFPE) blocks and is unable to detect SVs that do not produce a fusion transcript. High-throughput chromosome conformation capture (Hi-C) is a DNA-based next-generation sequencing (NGS) method that preserves the spatial conformation of the genome, capturing long-range genetic interactions and SVs. Herein, a retrospective study analyzing 71 FFPE specimens from 10 different solid tumors was performed. Results showed high concordance (98%) with clinical fluorescent in situ hybridization and RNA NGS in detecting known SVs. Furthermore, Hi-C provided insight into the mechanism of SV formation, including chromothripsis and extrachromosomal DNA, and detected rearrangements between genes and regulatory regions, all of which are undetectable by RNA NGS. Lastly, SVs were detected in 71% of cases in which previous clinical methods failed to identify a driver. Of these, 14% were clinically actionable based on current medical guidelines, and an additional 14% were not in medical guidelines but involve targetable biomarkers. Current data suggest that Hi-C is a robust and accurate method for genome-wide SV analyses from FFPE tissue and can be incorporated into current clinical NGS workflows. © 2025 Association for Molecular Pathology and American Society for Investigative Pathology

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Synthesis of transcriptomic studies reveals a core response to heat stress in abalone (genus Haliotis)

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BMC genomics 2025年第1期26卷 474页

作者： Roy Barkan Ira Cooke Sue-Ann Watson Jan M Strugnell Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia. roy.barkan@my.jcu.edu.au. Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia. roy.barkan@my.jcu.edu.au. College of Science and Engineering James Cook University Townsville QLD Australia. roy.barkan@my.jcu.edu.au. Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia. Department of Molecular and Cell Biology James Cook University Townsville QLD Australia. College of Science and Engineering James Cook University Townsville QLD Australia. Biodiversity and Geosciences Program Queensland Museum Tropics Queensland Museum Townsville QLD Australia. Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia.

BACKGROUND:As climate change causes marine heat waves to become more intense and frequent, marine species increasingly suffer from heat stress. This stress can result in reduced growth, disrupted breeding cycles, vulnerability to diseases and pathogens, and increased mortality rates. Abalone (genus Haliotis) are an ecologically significant group of marine gastropods and are among the most highly valued seafood products. However, heat stress events have had devastating impacts on both farmed and wild populations. Members of this genus are among the most susceptible marine species to climate change impacts, with over 40% of all abalone species listed as threatened with extinction. This has motivated researchers to explore the genetics linked to heat stress in abalone. A substantial portion of publicly available studies has employed transcriptomic approaches to investigate abalone genetic response to heat stress. However, to date, no meta-analysis has been conducted to determine the common response to heat stress (i.e. the core response) across the genus. This study uses a standardized bioinformatic pipeline to reanalyze and compare publicly available RNA-seq datasets from different heat stress studies on abalone. RESULTS:Nine publicly available RNA-seq datasets from nine different heat-stress studies on abalone from seven different abalone species and three hybrids were included in the meta-analysis. We identified a core set of 74 differentially expressed genes (DEGs) in response to heat stress in at least seven out of nine studies. This core set of DEGs mainly included genes associated with alternative splicing, heat shock proteins (HSPs), Ubiquitin-Proteasome System (UPS), and other protein folding and protein processing pathways. CONCLUSIONS:The detection of a consistent set of genes that respond to heat stress across various studies, despite differences in experimental design (e.g. stress intensity, species studied-geographical distribution, preferred temperature

关键词： Climate change Gene expression Meta-analysis RNA-seq Thermal stress

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Reverse engineering for a dynamic model of the drosophila circadian oscillator

Reverse engineering for a dynamic model of the drosophila ci...

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International Conference on Computational Intelligence for Modelling, Control and Automation/International Conference on Intelligent Agents Web Technologies and International Commerce

作者： Tanaka, Shin Kurata, Hiroyuki Ohashi, Takeshi Program of Creation Informatics Kyushu Institute of Technology Japan Department of Bioscience and Bioinformatics Kyushu Institute of Technology Japan

ISBN: (纸本)0769525040

In the field of bioinformatics, biochemical networks have been reconstructed in computer to understand their dynamic features. A problem is how to estimate the values of many kinetic parameters that are hard to measure experimentally. In this study, we have proposed a novel parameter estimation method based on genetic algorithms (GAs) and applied it to the Drosophila circadian oscillator. We defined two evaluation functions that represent two features of the dynamic model. To optimize the two functions simultaneously, we proposed the survival ratio GA, which has a gene's lifetime as a new concept, that is, the population holds previous search histories. By alternating between two evaluation functions every generation, the population holds both previously evaluated genes and children inherit both properties. In the two-evaluation problem of the Drosophila circadian oscillation system, the survival ratio GA exhibited a considerably better optimizing performance. than traditional GA methods.

关键词： Reverse engineering

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ChromActivity: integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types

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Genome biology 2025年第1期26卷 123页

作者： Tevfik Umut Dincer Jason Ernst Bioinformatics Interdepartmental Program University of California Los Angeles Los Angeles CA 90095 USA. Department of Biological Chemistry University of California Los Angeles Los Angeles CA 90095 USA. Bioinformatics Interdepartmental Program University of California Los Angeles Los Angeles CA 90095 USA. jason.ernst@ucla.edu. Department of Biological Chemistry University of California Los Angeles Los Angeles CA 90095 USA. jason.ernst@ucla.edu. Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at University of California Los Angeles Los Angeles CA 90095 USA. jason.ernst@ucla.edu. Computer Science Department University of California Los Angeles Los Angeles CA 90095 USA. jason.ernst@ucla.edu. Jonsson Comprehensive Cancer Center University of California Los Angeles Los Angeles CA 90095 USA. jason.ernst@ucla.edu. Molecular Biology Institute University of California Los Angeles Los Angeles CA 90095 USA. jason.ernst@ucla.edu. Department of Computational Medicine University of California Los Angeles Los Angeles CA 90095 USA. jason.ernst@ucla.edu.

We introduce ChromActivity, a computational framework for predicting and annotating regulatory activity across the genome through integration of multiple epigenomic maps and various functional characterization datasets. ChromActivity generates genomewide predictions of regulatory activity associated with each functional characterization dataset across many cell types based on available epigenomic data. It then for each cell type produces ChromScoreHMM genome annotations based on the combinatorial and spatial patterns within these predictions and ChromScore tracks of overall predicted regulatory activity. ChromActivity provides a resource for analyzing and interpreting the human regulatory genome across diverse cell types.

关键词： CRISPR screens Epigenome Gene regulation Genome annotation Hidden Markov model Machine learning Massively parallel reporter assays

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