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A comprehensive benchmarking study on computational tools for cross-omics label transfer from single-cell RNA to ATAC data.

• Authors : Wang Y; Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT 06511, United States.; Zhao H

Subjects: Single-Cell Analysis*/Single-Cell Analysis*/Single-Cell Analysis*/methods ; Computational Biology*/Computational Biology*/Computational Biology*/methods ; Genomics*/Genomics*/Genomics*/methods

• Source: G3 (Bethesda, Md.) [G3 (Bethesda)] 2026 Apr 01; Vol. 16 (4).Publisher: Oxford University Press Country of Publication: England NLM ID: 101566598 Publication Model: Print Cited Medium: Internet ISSN:

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Software and Programming Tools in Pharmaceutical Research

• Authors : Dilpreet, Singh; Prashant, Tiwari

Subjects: Chemistry; Computational biology; ScienceTECHNOLOGY & ENGINEERING / Pharmaceutical; SCIENCE / Chemistry / Computational & Molecular Modeling

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RhoMitoAnnotator and Polypods, Bioinformatics Tools for the Rhodiola Mitochondrial Gene Assembly, Annotation and Phylogenetic Analysis.

• Authors : Zang E; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China.; School of Pharmacy, Minzu University of China, Beijing 100081, China.

Subjects: Molecular Sequence Annotation*/Molecular Sequence Annotation*/Molecular Sequence Annotation*/methods ; Computational Biology*/Computational Biology*/Computational Biology*/methods ; Rhodiola*/Rhodiola*/Rhodiola*/genetics

• Source: International journal of molecular sciences [Int J Mol Sci] 2026 May 15; Vol. 27 (10). Date of Electronic Publication: 2026 May 15.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067

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Bioinformatics Tools and Approaches for Virus Discovery in Genomic Data: A Systematic Review.

• Authors : Galeeva J; Research Institute for Systems Biology and Medicine (RISBM), Department of Mathematical Biology and Bioinformatics, Moscow 117246, Russia.; Kuzmichenko P

Subjects: Computational Biology*/Computational Biology*/Computational Biology*/methods ; Genomics*/Genomics*/Genomics*/methods ; Metagenomics*/Metagenomics*/Metagenomics*/methods

• Source: Viruses [Viruses] 2025 Nov 24; Vol. 17 (12). Date of Electronic Publication: 2025 Nov 24.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101509722 Publication Model: Electronic Cited Medium: Internet ISSN: 1999-4915

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Micro- and Nanoplastics Act as Metal Carriers with the Potential to Alter Human Gene Expression Patterns-The Inferences from Bioinformatic Online Tools.

• Authors : Grabacka M; Department of Biotechnology and General Technology of Foods, Faculty of Food Technology, University of Agriculture, ul. Balicka 122, 30-149 Cracow, Poland.; Pierzchalska M

Subjects: Computational Biology*/Computational Biology*/Computational Biology*/methods ; Metals*/Metals*/Metals*/chemistry ; Microplastics*/Microplastics*/Microplastics*/chemistry

• Source: Biomolecules [Biomolecules] 2025 Oct 06; Vol. 15 (10). Date of Electronic Publication: 2025 Oct 06.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101596414 Publication Model: Electronic Cited Medium: Internet ISSN: 2218-273X

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Variant scoring tools for deep mutational scanning.

• Authors : Çubuk H; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK.; Jin X

Subjects: Computational Biology*/Computational Biology*/Computational Biology*/methods ; Computational Biology*/Computational Biology*/Computational Biology*/trends ; DNA Mutational Analysis*/DNA Mutational Analysis*/DNA Mutational Analysis*/methods

• Source: Molecular systems biology [Mol Syst Biol] 2025 Oct; Vol. 21 (10), pp. 1293-1305. Date of Electronic Publication: 2025 Aug 08.Publisher: EMBO Press Country of Publication: Germany NLM ID: 101235389 Publication Model: Print-Electronic Cited Medium: Internet ISSN:

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Identification and validation of stage-specific microRNAs and target genes for prostate cancer: Utilizing bioinformatics tools for diagnostic marker discovery.

• Authors : Yaghobinejad M; Department of Anatomy, Tehran University of Medical Sciences, Tehran, Iran.; Naji M

Subjects: Prostatic Neoplasms*/Prostatic Neoplasms*/Prostatic Neoplasms*/genetics ; Prostatic Neoplasms*/Prostatic Neoplasms*/Prostatic Neoplasms*/diagnosis ; Prostatic Neoplasms*/Prostatic Neoplasms*/Prostatic Neoplasms*/pathology

• Source: PloS one [PLoS One] 2025 Nov 04; Vol. 20 (11), pp. e0315366. Date of Electronic Publication: 2025 Nov 04 (Print Publication: 2025).Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet

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Identification of potential molecular targets of rhaponticin in the treatment of periodontitis using bioinformatics tools.

• Authors : Li S; Jiangxi University of Chinese Medicine, Nanchang, Jiangxi Province, 330006, China.; Key Laboratory of Traditional Chinese Medicine Oral and Dental Diseases [No. Gan Traditional Chinese Medicine Science and Education Word (2022) 8], Jiangxi University of Chinese Medicine, Nanchang, Jiangxi Province, 330036, China.

Subjects: Periodontitis*/Periodontitis*/Periodontitis*/drug therapy ; Periodontitis*/Periodontitis*/Periodontitis*/metabolism ; Periodontitis*/Periodontitis*/Periodontitis*/pathology

• Source: Scientific reports [Sci Rep] 2025 Nov 28; Vol. 15 (1), pp. 42686. Date of Electronic Publication: 2025 Nov 28.Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN:

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A bio. tools collection of online resources for GPCR research.

• Authors : Laasfeld T; Institute of Chemistry, University of Tartu, Tartu, Estonia.; Wunsch F

Subjects: Receptors, G-Protein-Coupled*/Receptors, G-Protein-Coupled*/Receptors, G-Protein-Coupled*/metabolism ; Receptors, G-Protein-Coupled*/Receptors, G-Protein-Coupled*/Receptors, G-Protein-Coupled*/chemistry ; Computational Biology*/Computational Biology*/Computational Biology*/methods

• Source: British journal of pharmacology [Br J Pharmacol] 2025 Jul; Vol. 182 (14), pp. 3301-3319. Date of Electronic Publication: 2025 Feb 24.Publisher: Wiley Country of Publication: England NLM ID: 7502536 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1476-5381

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Comparative study of tools for copy number variation detection using next-generation sequencing data.

• Authors : Du R; School of Computer Science and Technology, Liaocheng University, No. 34 Wenhua Road, Liaocheng, 252000, Shandong, China.; Dong J

Subjects: High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/methods ; Computational Biology*/Computational Biology*/Computational Biology*/methods ; DNA Copy Number Variations*

• Source: Scientific reports [Sci Rep] 2025 Jul 01; Vol. 15 (1), pp. 22145. Date of Electronic Publication: 2025 Jul 01.Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN:

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