Search Results - "Bioinformatics Software"

Formal verification of bioinformatics software using model checking and theorem proving Open Access.

Authors: Weerasena, Hansika Jayasena, Aruna Boucher, Christina et al.

Source: Briefings in Bioinformatics. Jul2025, Vol. 26 Issue 4, p1-13. 13p.

Subject Terms: *SOFTWARE libraries (Computer programming), *SOFTWARE reliability, *LOGIC, BIOINFORMATICS software, SOFTWARE verification, BIOINFORMATICS, SOFTWARE validation

TelOMpy enables single-molecule resolution of telomere length from optical genome mapping data.

Authors: Pokrovac, Ivan Stipoljev, Sunčica Pezer, Željka

Source: BMC Biology. 11/5/2025, Vol. 23 Issue 1, p1-14. 14p.

Subject Terms: *TELOMERES, *BIOINFORMATICS software, *DATA analysis, *GENE mapping, *HIGH-fat diet, *REPRODUCIBLE research, *NUCLEIC acid isolation methods

Advance in the assembly of the plant mitochondrial genomes using high‐throughput DNA sequencing data of total cellular DNAs.

Authors: Ni, Yang Li, Jingling Tan, Yihui et al.

Source: Plant Biotechnology Journal. Nov2025, Vol. 23 Issue 11, p4944-4965. 22p.

Subject Terms: *MITOCHONDRIAL DNA, *BIOINFORMATICS software, *MITOCHONDRIAL DNA abnormalities, *NUCLEOTIDE sequencing

BioSet2Vec: extraction of k-mer dictionaries from multiple sets of biological sequences via big data technologies.

Authors: Galluzzo, Ylenia Giancarlo, Raffaele Rombo, Simona E. et al.

Source: BMC Bioinformatics. 10/27/2025, Vol. 26 Issue 1, p1-23. 23p.

Subject Terms: *BIG data, *BIOINFORMATICS software, *NUCLEOTIDE sequence, *GENOMICS, *PATTERN perception, *SEQUENCE analysis, *BIOLOGICAL research methodology

Comparative evaluation of MG-RAST, MEGAN6 and Kraken2 for whole metagenome analysis of saffron corms for bacterial community structure and function.

Authors: Sharma, Nitika Verma, Ayushi Ambardar, Sheetal et al.

Source: Molecular Genetics & Genomics. 10/14/2025, Vol. 300 Issue 1, p1-18. 18p.

Subject Terms: *BIOINFORMATICS software, *BACTERIAL communities, *SAFFRON crocus, *SPECIES diversity, *METAGENOMICS, *BIOINFORMATICS

vvv2_align_SE, vvv2_align_PE/vvv2_display: Galaxy-Based Workflows and Tool Designed to Perform, Summarize and Visualize Variant Calling and Annotation in Viral Genome Assemblies.

Authors: Flageul, Alexandre Hirchaud, Edouard Courtillon, Céline et al.

Source: Viruses (1999-4915). Oct2025, Vol. 17 Issue 10, p1385. 11p.

Subject Terms: *VIRAL genomes, *BIOINFORMATICS software, *NUCLEOTIDE sequencing, *DATA visualization, *OPEN source software, *DNA mutational analysis, *GENETIC variation

Variant scoring tools for deep mutational scanning.

Authors: Çubuk, Hasan Jin, Xinyi Phipson, Belinda et al.

Source: Molecular Systems Biology. Oct2025, Vol. 21 Issue 10, p1293-1305. 13p.

Subject Terms: *DATA analysis, *BIOINFORMATICS software, *COMPUTER software, *NUCLEOTIDE sequencing, *PROTEOMICS, *EXPERIMENTAL design, *BIOLOGICAL systems, *DNA mutational analysis

Parsing GTF and FASTA files using the eccLib Library Open Access.

Authors: Chady, Tomasz Filutowska, Zuzanna Karolina

Source: Bioinformatics. Oct2025, Vol. 41 Issue 10, p1-5. 5p.

Subject Terms: *BIOINFORMATICS software, *SOFTWARE libraries (Computer programming), *NUCLEOTIDE sequence, *APPLICATION program interfaces, *BIOINFORMATICS

Arthropod: A Tool for Phylogenomic Research in Arthropods.

Authors: Wang, Jiajia Gao, Shichen Chen, Renfeng et al.

Source: Molecular Ecology Resources. Oct2025, Vol. 25 Issue 7, p1-11. 11p.

Subject Terms: *ARTHROPODA, *BIOINFORMATICS software, *TRANSCRIPTOMES, *MOLECULAR phylogeny, *BIOLOGICAL evolution, *NUCLEOTIDE sequencing, *PHYLOGENY, *BIOINFORMATICS

Evaluation of cell type annotation reliability using a large language model-based identifier.

Authors: Ye, Wenjin Ma, Yuanchen Xiang, Junkai et al.

Source: Communications Biology. 9/25/2025, Vol. 8 Issue 1, p1-14. 14p.

Subject Terms: *BIOINFORMATICS software, *RNA sequencing, *LANGUAGE models, *PHENOTYPES, *REPRODUCIBLE research, *BIOLOGICAL research methodology

AQuA Tools: clear and reliable BEDPE operations for 3D genomics Open Access.

Authors: Chakraborty, Maharshi Morgan, Laura Scacheri, Quin et al.

Source: Bioinformatics. Sep2025, Vol. 41 Issue 9, p1-9. 9p.

Subject Terms: *GENOMICS, *BIOINFORMATICS software, *CANCER research, *BIOINFORMATICS, *DNA-protein interactions, *GENE mapping

ERSAtool: A User‐Friendly R/Shiny Comprehensive Transcriptomic Analysis Interface Suitable for Education.

Authors: Taridalu, Sujith Kameshwar, Ayyappa Kumar Sista Suzuki, Masako

Source: Genes to Cells. Sep2025, Vol. 30 Issue 5, p1-9. 9p.

Subject Terms: *RNA sequencing, *BIOINFORMATICS software, *TRANSCRIPTOMES, *EDUCATIONAL resources, *BIOINFORMATICS, *DATA visualization, *GENE ontology

An enhanced gene function analysis platform for Gastrodia Elata integrating further omics data and analysis tools.

Authors: Pan, Bingbing Zhang, Jingjie Yang, Jiangxin et al.

Source: BMC Plant Biology. 8/22/2025, p1-13. 13p.

Subject Terms: *TRANSCRIPTOMES, *BIOINFORMATICS software, *GENE regulatory networks, *CHINESE medicine, *FLAVONOIDS, *METABOLITES, *GENE expression profiling

Functional Characterization and In Silico Prediction Tools Improve the Pathogenicity Prediction of Novel Bile Acid Transporter Variants.

Authors: Peng, Ziyue Wang, Xin Li, Ying et al.

Source: Clinical Genetics. Jul2025, Vol. 108 Issue 1, p3-13. 11p.

Subject Terms: *GENETIC profile, *BIOINFORMATICS software, *BIOLOGICAL assay, *MULTIDRUG resistance-associated proteins, *BILIOUS diseases & biliousness, *INTERDISCIPLINARY research, *FORECASTING

Geographic Terms: CHINA

CAGEcleaner: reducing genomic redundancy in gene cluster mining Open Access.

Authors: Vrieze, Lucas De Biltjes, Miguel Lukashevich, Sofya et al.

Source: Bioinformatics. Jul2025, Vol. 41 Issue 7, p1-4. 4p.

Subject Terms: *GENE clusters, *BIOINFORMATICS software, *INFORMATION filtering, *GENOMICS, *BIOINFORMATICS, *LOCUS (Genetics)

Fast and flexible minimizer digestion with digestOpen Access.

Authors: Zheng, Alan Lee, Ishmeal Shivakumar, Vikram S et al.

Source: Bioinformatics. Jul2025, Vol. 41 Issue 7, p1-4. 4p.

Subject Terms: *BIOINFORMATICS, *BIOINFORMATICS software, *SEQUENCE analysis, *NUCLEOTIDE sequence, *C++, *PYTHON programming language, *DE Bruijn graph, *OPEN source software

AI-HOPE: an AI-driven conversational agent for enhanced clinical and genomic data integration in precision medicine research Open Access.

Authors: Yang, Ei-Wen Velazquez-Villarreal, Enrique

Source: Bioinformatics. Jul2025, Vol. 41 Issue 7, p1-4. 4p.

Subject Terms: *BIOINFORMATICS software, *DATA integration, *DATA analysis, *INDIVIDUALIZED medicine, *NATURAL language processing, *CHATBOTS

Enable, empower, succeed: a bioinformatics workshop Harnessing open web-based tools for surveillance of bacterial antimicrobial resistance.

Authors: Founou, Luria Leslie Lawal, Opeyemi U. Djiyou, Armando et al.

Source: BMC Microbiology. 3/19/2025, Vol. 25 Issue 1, p1-11. 11p.

Subject Terms: *BIOINFORMATICS software, *DRUG resistance in bacteria, *DRUG resistance in microorganisms, *LIFE sciences, *RESEARCH personnel

Geographic Terms: AFRICA

Computational Tools for Studying Genome Structural Variation.

Authors: Chen, Xingyu Wei, Siyu Sun, Chen et al.

Source: OMICS: A Journal of Integrative Biology. Feb2025, Vol. 29 Issue 2, p36-48. 13p.

Subject Terms: *GENOMICS, *BIOINFORMATICS software, *DNA structure, *GENE rearrangement, *NUCLEOTIDE sequencing, *PUBLIC health

Comparative Evaluation of AI-Based Pathogenicity Prediction Tools for BRCA Variants.

Authors: Matkerim, Bazargul Murat, Nazerke Nurtas, Marat et al.

Source: Procedia Computer Science. 2025, Vol. 272, p311-317. 7p.

Subject Terms: BRCA genes, Hereditary cancer syndromes, Genetic variation, Bioinformatics software, Benchmarking (Management), Medical genomics, Artificial intelligence