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A comparative evaluation of computational models for RNA modification detection using nanopore sequencing with RNA004 chemistry.

• Authors : Zou Y; Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, 3501 Civic Center Boulevard, Philadelphia, PA 19104, United States.; Bioengineering Graduate Program, University of Pennsylvania, Skirkanich Hall 210 South 33rd Street, Philadelphia, PA 19104, United States.

Subjects: Nanopore Sequencing*/Nanopore Sequencing*/Nanopore Sequencing*/methods ; RNA*/RNA*/RNA*/genetics ; RNA*/RNA*/RNA*/chemistry

• Source: Briefings in bioinformatics [Brief Bioinform] 2025 Jul 02; Vol. 26 (4).Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN:

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NASTRA: accurate analysis of short tandem repeat markers by nanopore sequencing with repeat-structure-aware algorithm.

• Authors : Ren Z; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, No. 573 Yujinxiang Street, Jingyue District, Changchun 130012, China.; School of Information Science and Technology, Northeast Normal University, No. 2555 Jingyue Street, Jingyue District, Changchun 130117, China.

Subjects: Nanopore Sequencing*/Nanopore Sequencing*/Nanopore Sequencing*/methods ; Microsatellite Repeats* ; Algorithms*

• Source: Briefings in bioinformatics [Brief Bioinform] 2024 Sep 23; Vol. 25 (6).Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN:

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DeepBAM: a high-accuracy single-molecule CpG methylation detection tool for Oxford nanopore sequencing.

• Authors : Bai X; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 7 Jinsui Road, Tianhe District, Guangzhou 510060, China.; Yao HC

Subjects: Nanopore Sequencing*/Nanopore Sequencing*/Nanopore Sequencing*/methods ; DNA Methylation* ; CpG Islands*

• Source: Briefings in bioinformatics [Brief Bioinform] 2024 Jul 25; Vol. 25 (5).Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN:

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miniSNV: accurate and fast single nucleotide variant calling from nanopore sequencing data.

• Authors : Cui M; Faculty of Computing, Harbin Institute of Technology, 92 Xidazhi Street, Nangang District, Harbin, Heilongjiang 150001, China.; Liu Y

Subjects: Nanopore Sequencing*/Nanopore Sequencing*/Nanopore Sequencing*/methods ; Polymorphism, Single Nucleotide* ; Algorithms*

• Source: Briefings in bioinformatics [Brief Bioinform] 2024 Sep 23; Vol. 25 (6).Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN:

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A Comparative Evaluation of Computational Models for RNA modification detection using Nanopore sequencing with RNA004 Chemistry

• Authors : Yongji Zou; Mian Umair Ahsan; Joe Chan

Subjects: Nanopore Sequencing; HEK293 Cells; Adenosine

• Source: bioRxivBrief Bioinform

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Correction to: A comparative evaluation of computational models for RNA modification detection using nanopore sequencing with RNA004 chemistry

Subjects: Correction

• Source: Brief Bioinform

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CircRM: profiling circular RNA modifications from nanopore direct RNA sequencing.

• Authors : Li J; Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, China.; Center for Intelligent RNA Therapeutics, Suzhou Key Laboratory of Cancer Biology and Chronic Disease, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, China.

Subjects: RNA, Circular*/RNA, Circular*/RNA, Circular*/genetics ; RNA, Circular*/RNA, Circular*/RNA, Circular*/metabolism ; Sequence Analysis, RNA*/Sequence Analysis, RNA*/Sequence Analysis, RNA*/methods

• Source: Briefings in bioinformatics [Brief Bioinform] 2026 Jan 07; Vol. 27 (1).Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN:

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Ab initio detection of multiple epitranscriptomic modifications from Oxford nanopore technology direct RNA sequencing data.

• Authors : Fonzino A; Department of Biosciences, Biotechnology, and Environment, University of Bari Aldo Moro, Via Orabona 4, 70125, Bari, Italy.; Fosso B

Subjects: Sequence Analysis, RNA*/Sequence Analysis, RNA*/Sequence Analysis, RNA*/methods ; Nanopore Sequencing*/Nanopore Sequencing*/Nanopore Sequencing*/methods ; RNA*/RNA*/RNA*/genetics

• Source: Briefings in bioinformatics [Brief Bioinform] 2026 Jan 07; Vol. 27 (1).Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN:

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NanoPrePro: a fully equipped, fast, and memory-efficient preprocessor for nanopore transcriptomic sequencing.

• Authors : Chu CC; Department of Life Science and Institute of Plant Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Daan Dist., Taipei 10617, Taiwan.; Department of Pharmacy, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong St. Beitou Dist., Taipei 11221, Taiwan.

Subjects: Nanopore Sequencing*/Nanopore Sequencing*/Nanopore Sequencing*/methods ; Gene Expression Profiling*/Gene Expression Profiling*/Gene Expression Profiling*/methods ; High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/High-Throughput Nucleotide Sequencing*/methods

• Source: Briefings in bioinformatics [Brief Bioinform] 2026 Jan 07; Vol. 27 (1).Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN:

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Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions

• Authors : Damla Senol Cali; Jeremie S. Kim; Saugata Ghose

Subjects: Genomics (q-bio.GN); 0301 basic medicine; Nanopore sequencing

• Source: Briefings in Bioinformatics.-Oxford University Press (OUP).-2018, vol. 20, no. 4, p. 1542-1559Briefings in Bioinformatics, 20 (4)

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