Combination of Oxalobacter Formigenes and Veillonella Parvula in Gastrointestinal Microbiota Related to Bile-Acid Metabolism as a Biomarker for Hypertensive Nephropathy by Xin Li, Li Wang, Shaojun Ma, Shaohui Lin, Chunyan Wang, Haiya Wang

“…The subjects of this research were divided into three groups, healthy control group, hypertension group, and hypertensive nephropathy group. Sequencing, bioinformatics, and statistical analysis were performed on the 16S rRNA gene of the subjects’ stool samples. …”
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Clove and Thyme Essential Oils: From Molecular Docking to Food ApplicationA Study of Their Preservative Properties in Buttermilk by Mohamed Raafat Atteya, Ramy M Romeilah, Khaled M. A. Ramadan, Hossam S. El-Beltagi, Ahmed Maher Gaber, Sallah A. Al Hashedi, Nada Ali AboZaid, Mohamed A. A. Mahmoud, Rania Youssef, Rasha A. Mohamed, Eslam S.A. Bendary

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AutoPVPrimer: A comprehensive AI-Enhanced pipeline for efficient plant virus primer design and assessment. by Abozar Ghorbani, Mahsa Rostami, Elham Ashrafi-Dehkordi, Pietro Hiram Guzzi

“…Future developments aim to extend compatibility and incorporate user feedback to consolidate AutoPVPrimer as an innovative contribution to the bioinformatics toolbox and a promising resource for the advancement of plant virology research.…”
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Major Histocompatibility Complex Genes as Therapeutic Opportunity for Immune Cold Molecular Cancer Subtypes by Paweł Karpiński, Łukasz Łaczmański, Maria M. Sąsiadek

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HairSplitter: haplotype assembly from long, noisy reads by Faure, Roland, Lavenier, Dominique, Flot, Jean-François

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hsa_circWDR37_016 Regulates Hypoxia-Induced Proliferation of Pulmonary Arterial Smooth Muscle Cells by Shan-Shan Li, Shuang Liang, Yao Long, Xu Chen, Xin Jin

“…As evidenced by flow cytometry, 5-ethynyl-2′-deoxyuridine (EdU) incorporation, wound healing, and Tunel assay, silencing of endogenous circWDR37 attenuated proliferation and cell-cycle progression in hypoxia-exposed human PASMCs in vitro. Furthermore, bioinformatics and Luciferase assay showed that circWDR37 directly sponged hsa-miR-138-5p (miR-138) and was involved in the immunoregulatory and inflammatory processes of PAH. …”
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Sitagliptin: a potential drug for the treatment of COVID-19? by Bardaweel Sanaa K., Hajjo Rima, Sabbah Dima A.

“…Possible interaction of SARS-CoV-2 with DPP4 peptidase may partly contribute to the viral pathogenesis. An integrative bioinformatics approach starting with mining the biomedical literature for high confidence DPP4-protein/gene associations followed by functional analysis using network analysis and pathway enrichment was adopted. …”
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Noninteger Derivative Order Analysis on Plane Wave Reflection from Electro-Magneto-Thermo-Microstretch Medium with a Gravity Field within the Three-Phase Lag Model by S. H. Elhag, Fatimah S. Bayones, A. A. Kilany, S. M. Abo-Dahab, Emad A.-B. Abdel-Salam, M. Elsagheer, A. M. Abd-Alla

“…The main goal for this study is investigating the fractional order impact and the applications related to the orders, especially in biology, medicine, and bioinformatics, besides the integer order considering an external effect, such as electromagnetic, gravity, and phase lags in a microstretch medium. …”
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MicroRNA-877-5p Inhibits Cell Progression by Targeting FOXM1 in Lung Cancer by Zhiguang Liu, Xinlian Wang, Liqiang Cao, Xiaowei Yin, Qian Zhang, Lan Wang

“…The downstream targets of miR-877-5p were predicted by Bioinformatics software. RT-qPCR and western blot were employed to analyze the gene levels. …”
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Deciphering metabolic differentiation during Bacillus subtilis sporulation by Juan D. Tibocha-Bonilla, Jelani Lyda, Eammon Riley, Kit Pogliano, Karsten Zengler

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From Ontology to Semantic Similarity: Calculation of Ontology-Based Semantic Similarity by Mingxin Gan, Xue Dou, Rui Jiang

“…Ontologies, as abstract description systems for domain-specific knowledge composition, hence receive more and more attention in computational biology and bioinformatics. Particularly, many applications relying on domain ontologies require quantitative measures of relationships between terms in the ontologies, making it indispensable to develop computational methods for the derivation of ontology-based semantic similarity between terms. …”
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Ovarian Cancer Prognostic Prediction Model Using RNA Sequencing Data by Seokho Jeong, Lydia Mok, Se Ik Kim, TaeJin Ahn, Yong-Sang Song, Taesung Park

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Untargeted metabolomics of Aloe volatiles: Implications in pathway enrichments for improved bioactivities by Nehal Batra, Priyankar Dey

“…Through the application of appropriate bioinformatics tools, we identified distinct phytochemical classes and determined the enrichment of their corresponding biosynthetic pathways, associated the pathways with bioactivities, and also identified the inter-relation between the commonly enriched pathways. …”
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The complete mitogenomes of all four Cryptospiza species (Aves: Estrildidae) by J. Dylan Maddox, Erica Zahnle, Kit McDonnell, Felix Grewe, Thomas P. Gnoske, John M. Bates, Shannon J. Hackett

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Beyond DNA: An Integrated and Functional Approach for Classifying Germline Variants in Breast Cancer Genes by T. Pesaran, R. Karam, R. Huether, S. Li, S. Farber-Katz, A. Chamberlin, H. Chong, H. LaDuca, A. Elliott

“…The accuracy of an assay is reliant on not only the technology and bioinformatics analysis utilized but also the experience and infrastructure required to correctly classify genetic variants as disease-causing. …”
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Targeted Anticancer Immunotoxins and Cytotoxic Agents with Direct Killing Moieties by Koji Kawakami, Oumi Nakajima, Ryuichi Morishita, Ryozo Nagai

“…Despite the progress of the bioinformatics approach to characterize cell-surface antigens and receptors on tumor cells, it remains difficult to generate novel cancer vaccines or neutralizing monoclonal antibody therapeutics. …”
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Applications of Neuroimaging to Disease-Modification Trials in Alzheimer’s Disease by Adam S. Fleisher, Michael Donohue, Kewei Chen, James B. Brewer, Paul S. Aisen, the Alzheimer’s Disease Neuroimaging Initiative

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An Efficient Approach to Mining Maximal Contiguous Frequent Patterns from Large DNA Sequence Databases by Md. Rezaul Karim, Md. Mamunur Rashid, Byeong-Soo Jeong, Ho-Jin Choi

“…Mining interesting patterns from DNA sequences is one of the most challenging tasks in bioinformatics and computational biology. Maximal contiguous frequent patterns are preferable for expressing the function and structure of DNA sequences and hence can capture the common data characteristics among related sequences. …”
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Survey on Encoding Schemes for Genomic Data Representation and Feature Learning—From Signal Processing to Machine Learning by Ning Yu, Zhihua Li, Zeng Yu

“…Data-driven machine learning, especially deep learning technology, is becoming an important tool for handling big data issues in bioinformatics. In machine learning, DNA sequences are often converted to numerical values for data representation and feature learning in various applications. …”
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Investigating the Prospects of ChatGPT in Training Medicinal Chemists and the Development of Novel Drugs by Michell O. Almeida, Artur C. G. Soares, Gustavo H. M. Sousa, Witor R. Ferraz, Gustavo Trossini

“…Alongside other large language models, this tool exhibits the potential to directly or indirectly assist in a range of scientific areas including Computer Science, Chemistry, Biology/Bioinformatics, and Medicine. Some of the functionalities of ChatGPT include text translation, code improvement, data visualization, and database cleaning. …”
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