Search Results - "Sequence analysis"

scooby: modeling multimodal genomic profiles from DNA sequence at single-cell resolution.

Authors: Hingerl JC Martens LD Karollus A et al.

Source: Nature methods [Nat Methods] 2025 Nov; Vol. 22 (11), pp. 2275-2285. Date of Electronic Publication: 2025 Oct 22.

Publication Type: Journal Article

Journal Info: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE

MeSH Terms: Single-Cell Analysis*/methods , Genomics*/methods , Sequence Analysis, DNA*/methods, Humans ; Chromatin/genetics ; Quantitative Trait Loci ; Sequence Analysis, RNA/methods ; Gene Expression Regulation ; Gene Expression Profiling/methods

[Will nanopores also sequence proteins ?]

Transliterated Title: Séquençage par nanopores : les protéines aussi ?

Authors: Jordan B; Biologiste, généticien et immunologiste, Président d'Aprogène (Association pour la promotion de la Génomique), 13007, Marseille, France.

Source: Medecine sciences : M/S [Med Sci (Paris)] 2025 Aug-Sep; Vol. 41 (8-9), pp. 703-705. Date of Electronic Publication: 2025 Sep 08.

Publication Type: English Abstract; Journal Article

Journal Info: Publisher: EDK Country of Publication: France NLM ID: 8710980 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1958-5381 (Electronic) Linking ISSN: 07670974 NLM ISO Abbreviation: Med Sci (Paris) Subsets: MEDLINE

MeSH Terms: Nanopore Sequencing*/methods , Nanopores* , Nanotechnology*/methods , Nanotechnology*/trends , Proteins*/chemistry , Proteins*/genetics , Sequence Analysis, Protein*/methods , Sequence Analysis, Protein*/trends, Animals ; Humans ; Sequence Analysis, DNA/methods

Targeted decontamination of sequencing data with CLEAN.

Authors: Lataretu M Krautwurst S Huska MR et al.

Source: NAR genomics and bioinformatics [NAR Genom Bioinform] 2025 Jul 24; Vol. 7 (3), pp. lqaf105. Date of Electronic Publication: 2025 Jul 24 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 101756213 Publication Model: eCollection Cited Medium: Internet ISSN: 2631-9268 (Electronic) Linking ISSN: 26319268 NLM ISO Abbreviation: NAR Genom Bioinform Subsets: MEDLINE

MeSH Terms: High-Throughput Nucleotide Sequencing*/methods , Decontamination*/methods , Software* , Sequence Analysis, DNA*/methods, Humans ; Metagenomics/methods ; RNA, Ribosomal/genetics ; Sequence Analysis, RNA/methods

[Expert consensus on combined DNA and RNA next-generation sequencing of common driver genes in solid tumors (2025 version)].

Corporate Authors: Chinese Society of Pathology, Pathology Quality Control Center

Source: Zhonghua bing li xue za zhi = Chinese journal of pathology [Zhonghua Bing Li Xue Za Zhi] 2025 Jul 08; Vol. 54 (7), pp. 701-709.

Publication Type: Consensus Development Conference; Journal Article

Journal Info: Publisher: Zhonghua Yixuehui Country of Publication: China NLM ID: 0005331 Publication Model: Print Cited Medium: Print ISSN: 0529-5807 (Print) Linking ISSN: 05295807 NLM ISO Abbreviation: Zhonghua Bing Li Xue Za Zhi Subsets: MEDLINE

MeSH Terms: High-Throughput Nucleotide Sequencing*/methods , High-Throughput Nucleotide Sequencing*/standards , Neoplasms*/genetics , Neoplasms*/diagnosis , Sequence Analysis, RNA*/methods, Humans ; Consensus ; Quality Control ; Sequence Analysis, DNA/methods

MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF files.

Authors: Patsakis M Provatas K Karatzikos A et al.

Source: BMC bioinformatics [BMC Bioinformatics] 2025 May 30; Vol. 26 (1), pp. 142. Date of Electronic Publication: 2025 May 30.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE

MeSH Terms: Software* , Sequence Alignment*/methods , Sequence Analysis, DNA*/methods , Computational Biology*/methods, Algorithms ; Sequence Analysis, Protein/methods

An updated comparison of microarray and RNA-seq for concentration response transcriptomic study: case studies with two cannabinoids, cannabichromene and cannabinol.

Authors: Gao X Yourick MR Campasino K et al.

Source: BMC genomics [BMC Genomics] 2025 Apr 23; Vol. 26 (1), pp. 392. Date of Electronic Publication: 2025 Apr 23.

Publication Type: Journal Article; Comparative Study

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE

MeSH Terms: Cannabinoids*/pharmacology , Cannabinoids*/toxicity , Gene Expression Profiling*/methods , RNA-Seq*/methods , Transcriptome*/drug effects , Oligonucleotide Array Sequence Analysis*/methods, Humans ; Sequence Analysis, RNA

Design and verification of a 25 K multiple-SNP liquid-capture chip by target sequencing for dairy goat.

Authors: Zhao J Wang Y Kamalibieke J et al.

Source: BMC genomics [BMC Genomics] 2025 Apr 15; Vol. 26 (1), pp. 377. Date of Electronic Publication: 2025 Apr 15.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE

MeSH Terms: Goats*/genetics , Polymorphism, Single Nucleotide* , Oligonucleotide Array Sequence Analysis*/methods, Animals ; Sequence Analysis, DNA ; Genome-Wide Association Study ; Dairying ; High-Throughput Nucleotide Sequencing ; Genotype ; Birth Weight/genetics ; Litter Size/genetics ; Female ; Breeding

From dual nucleic acid co-extraction to co-sequencing: A highly integrated next-generation forensic DNA and RNA sequencing experimental workflow.

Authors: Miao L Lou DN Kang KL et al.

Source: Forensic science international. Genetics [Forensic Sci Int Genet] 2025 Mar; Vol. 76, pp. 103229. Date of Electronic Publication: 2025 Jan 25.

Publication Type: Journal Article

Journal Info: Publisher: Elsevier Country of Publication: Netherlands NLM ID: 101317016 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1878-0326 (Electronic) Linking ISSN: 18724973 NLM ISO Abbreviation: Forensic Sci Int Genet Subsets: MEDLINE

MeSH Terms: High-Throughput Nucleotide Sequencing*/methods , DNA*/isolation & purification , DNA*/genetics , Sequence Analysis, RNA*/methods , Forensic Genetics*/methods , RNA*/isolation & purification , RNA*/genetics, Humans ; Microsatellite Repeats ; Workflow ; DNA Fingerprinting/methods ; Polymorphism, Single Nucleotide ; Electrophoresis, Capillary ; Sequence Analysis, DNA ; Genetic Markers

Comparison of the BluePoint MoldID oligonucleotide array and Bruker Biotyper MALDI-TOF MS for the identification of filamentous fungi.

Authors: Chou C-H Chao Q-T Lu Y-S et al.

Source: Journal of clinical microbiology [J Clin Microbiol] 2025 Jan 31; Vol. 63 (1), pp. e0104824. Date of Electronic Publication: 2024 Dec 05.

Publication Type: Journal Article; Comparative Study; Evaluation Study

Journal Info: Publisher: American Society for Microbiology Country of Publication: United States NLM ID: 7505564 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1098-660X (Electronic) Linking ISSN: 00951137 NLM ISO Abbreviation: J Clin Microbiol Subsets: MEDLINE

MeSH Terms: Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization*/methods , Fungi*/classification , Fungi*/isolation & purification , Fungi*/genetics , Fungi*/chemistry , Mycoses*/diagnosis , Mycoses*/microbiology , Oligonucleotide Array Sequence Analysis*/methods , Microbiological Techniques*/methods, Humans ; Taiwan ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; DNA, Ribosomal Spacer/chemistry ; Sensitivity and Specificity ; Sequence Analysis, DNA

Massively parallel homogeneous amplification of chip-scale DNA for DNA information storage (MPHAC-DIS).

Authors: Weng Z Li J Wu Y et al.

Source: Nature communications [Nat Commun] 2025 Jan 14; Vol. 16 (1), pp. 667. Date of Electronic Publication: 2025 Jan 14.

Publication Type: Journal Article

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

MeSH Terms: DNA*/genetics , High-Throughput Nucleotide Sequencing*/methods , Information Storage and Retrieval*/methods , Oligonucleotide Array Sequence Analysis*/methods , Nucleic Acid Amplification Techniques*/methods, Sequence Analysis, DNA/methods ; DNA Primers/genetics ; Machine Learning

Functional phenotyping of genomic variants using joint multiomic single-cell DNA-RNA sequencing.

Authors: Lindenhofer D Bauman JR Hawkins JA et al.

Source: Nature methods [Nat Methods] 2025 Oct; Vol. 22 (10), pp. 2032-2041. Date of Electronic Publication: 2025 Sep 01.

Publication Type: Journal Article

Journal Info: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE

MeSH Terms: Single-Cell Analysis*/methods , Sequence Analysis, RNA*/methods , Genetic Variation* , Sequence Analysis, DNA*/methods , Genomics*/methods, Humans ; Induced Pluripotent Stem Cells/metabolism ; Phenotype ; Lymphoma, B-Cell/genetics

Evaluation of false positive and false negative errors in targeted next generation sequencing.

Authors: Moon Y Kim YH Kim JK et al.

Source: Genome biology [Genome Biol] 2025 Dec 01; Vol. 26 (1), pp. 409. Date of Electronic Publication: 2025 Dec 01.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 100960660 Publication Model: Electronic Cited Medium: Internet ISSN: 1474-760X (Electronic) Linking ISSN: 14747596 NLM ISO Abbreviation: Genome Biol Subsets: MEDLINE

MeSH Terms: High-Throughput Nucleotide Sequencing*/methods , High-Throughput Nucleotide Sequencing*/standards , Sequence Analysis, DNA*/methods , Sequence Analysis, DNA*/standards, Humans ; False Positive Reactions ; False Negative Reactions ; Female

Enhancing the Feature Representation of Protein Sequence Descriptors in Protein-Protein Interaction Prediction.

Authors: Tran HN Quynh NP Zhao H et al.

Source: Interdisciplinary sciences, computational life sciences [Interdiscip Sci] 2025 Dec; Vol. 17 (4), pp. 1018-1037. Date of Electronic Publication: 2025 Jun 02.

Publication Type: Journal Article

Journal Info: Publisher: Springer-Verlag Country of Publication: Germany NLM ID: 101515919 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1867-1462 (Electronic) Linking ISSN: 18671462 NLM ISO Abbreviation: Interdiscip Sci Subsets: MEDLINE

MeSH Terms: Proteins*/chemistry , Proteins*/metabolism , Computational Biology*/methods , Protein Interaction Mapping*/methods , Sequence Analysis, Protein*/methods, Databases, Protein ; Amino Acid Sequence ; Software ; Machine Learning ; Algorithms

Development and validation of a high-density SNP chip tailored for genomic analysis in Indian backyard chickens.

Authors: Vijh RK Arora R Sharma U et al.

Source: British poultry science [Br Poult Sci] 2025 Dec; Vol. 66 (6), pp. 758-766. Date of Electronic Publication: 2025 May 28.

Publication Type: Journal Article; Validation Study

Journal Info: Publisher: Taylor & Francis Country of Publication: England NLM ID: 15740290R Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1466-1799 (Electronic) Linking ISSN: 00071668 NLM ISO Abbreviation: Br Poult Sci Subsets: MEDLINE

MeSH Terms: Chickens*/genetics , Polymorphism, Single Nucleotide* , Genomics*/methods , Oligonucleotide Array Sequence Analysis*/veterinary , Oligonucleotide Array Sequence Analysis*/methods, Animals ; India ; Genotype ; Genetic Variation ; Breeding

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes.

Authors: Rupp O Roessner LH Kong D et al.

Source: Journal of visualized experiments : JoVE [J Vis Exp] 2025 Nov 07 (225). Date of Electronic Publication: 2025 Nov 07.

Publication Type: Journal Article; Video-Audio Media

Journal Info: Publisher: MYJoVE Corporation Country of Publication: United States NLM ID: 101313252 Publication Model: Electronic Cited Medium: Internet ISSN: 1940-087X (Electronic) Linking ISSN: 1940087X NLM ISO Abbreviation: J Vis Exp Subsets: MEDLINE

MeSH Terms: RNA-Seq*/methods , RNA-Seq*/standards , RNA, Plant*/genetics , Sequence Analysis, RNA*/methods , Sequence Analysis, RNA*/standards , Software* , Eukaryota*/genetics, Quality Control

Current trends in single-cell RNA sequencing applications in diabetes mellitus.

Authors: Zadian SS Jahanbin K Nikooei S et al.

Source: FEBS open bio [FEBS Open Bio] 2025 Nov; Vol. 15 (11), pp. 1738-1761. Date of Electronic Publication: 2025 Jun 19.

Publication Type: Journal Article; Review

Journal Info: Publisher: John Wiley & Sons Ltd Country of Publication: England NLM ID: 101580716 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2211-5463 (Electronic) Linking ISSN: 22115463 NLM ISO Abbreviation: FEBS Open Bio Subsets: MEDLINE

MeSH Terms: Single-Cell Analysis*/methods , Single-Cell Analysis*/trends , Diabetes Mellitus*/genetics , Diabetes Mellitus*/diagnosis , Sequence Analysis, RNA*/methods , Sequence Analysis, RNA*/trends, Humans ; Animals

DNA sequencing in newborn screening.

Authors: Tinkle MB; University of New Mexico College of Nursing, Albuquerque, New Mexico.

Source: Journal of the American Association of Nurse Practitioners [J Am Assoc Nurse Pract] 2025 Nov 01; Vol. 37 (11), pp. 597-602. Date of Electronic Publication: 2025 Nov 01.

Publication Type: Journal Article

Journal Info: Publisher: Wolters Kluwer Country of Publication: United States NLM ID: 101600770 Publication Model: Electronic Cited Medium: Internet ISSN: 2327-6924 (Electronic) Linking ISSN: 23276886 NLM ISO Abbreviation: J Am Assoc Nurse Pract Subsets: MEDLINE

MeSH Terms: Neonatal Screening*/methods , Neonatal Screening*/trends , Sequence Analysis, DNA*/methods , Sequence Analysis, DNA*/trends, Humans ; Infant, Newborn ; Genetic Testing/methods

Methylation reference datasets from quartet DNA materials for benchmarking epigenome sequencing.

Authors: Guo X Chen Q Zhang Y et al.

Source: Nature communications [Nat Commun] 2025 Oct 16; Vol. 16 (1), pp. 9202. Date of Electronic Publication: 2025 Oct 16.

Publication Type: Journal Article

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

MeSH Terms: DNA Methylation*/genetics , Epigenome*/genetics , Epigenomics*/methods , Epigenomics*/standards , Sequence Analysis, DNA*/methods , Sequence Analysis, DNA*/standards , DNA*/genetics, Humans ; Benchmarking ; Reproducibility of Results ; CpG Islands/genetics ; High-Throughput Nucleotide Sequencing/methods ; Reference Standards

Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard.

Authors: Lin YY Breuer K Weichenhan D et al.

Source: Nucleic acids research [Nucleic Acids Res] 2025 Oct 14; Vol. 53 (19).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

MeSH Terms: DNA Methylation* , Software* , Sequence Analysis, DNA*/methods , Sequence Analysis, DNA*/standards , Computational Biology*/methods, Workflow ; Benchmarking ; Humans ; Whole Genome Sequencing/methods ; Whole Genome Sequencing/standards ; Epigenesis, Genetic ; Epigenomics/methods

Commentary: a review of technical considerations for planning an RNA-Sequencing experiment.

Authors: Verma R Savaria-Butler A Enguita FJ et al.

Source: BMC genomics [BMC Genomics] 2025 Oct 14; Vol. 26 (1), pp. 918. Date of Electronic Publication: 2025 Oct 14.

Publication Type: Journal Article; Review

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE

MeSH Terms: Sequence Analysis, RNA*/methods , Sequence Analysis, RNA*/economics , RNA-Seq*/methods , RNA-Seq*/economics, Humans ; Gene Library ; RNA/genetics