Search Results - "Sequence analysis"

Unlocking the full potential of nanopore sequencing: tips, tricks, and advanced data analysis techniques.

Authors: Meyer D Goettsch W Spangenberg J et al.

Source: Nucleic acids research [Nucleic Acids Res] 2026 Jan 22; Vol. 54 (3).

Publication Type: Journal Article; Review

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

Integration of gene expression profiling and mutation analysis via RNA sequencing: transitioning the 95-gene classifier to a next-generation platform in early-stage HR+/HER2- breast cancer.

Authors: Kato C Sota Y Kitano S et al.

Source: Breast cancer (Tokyo, Japan) [Breast Cancer] 2026 May; Vol. 33 (3), pp. 722-735. Date of Electronic Publication: 2026 Apr 01.

Publication Type: Journal Article

Journal Info: Publisher: Maruzen Co Country of Publication: Japan NLM ID: 100888201 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1880-4233 (Electronic) Linking ISSN: 13406868 NLM ISO Abbreviation: Breast Cancer Subsets: MEDLINE

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

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

Early Screening for Cervical Squamous Cell Carcinoma and Precancerous Lesions Based on Surface-Enhanced Raman Spectroscopy Microarray Chips.

Authors: Xia J Sun J Lu D

Source: International journal of nanomedicine [Int J Nanomedicine] 2026 Jun 04; Vol. 21, pp. 606920. Date of Electronic Publication: 2026 Jun 04 (Print Publication: 2026).

Publication Type: Journal Article

Journal Info: Publisher: DOVE Medical Press Country of Publication: New Zealand NLM ID: 101263847 Publication Model: eCollection Cited Medium: Internet ISSN: 1178-2013 (Electronic) Linking ISSN: 11769114 NLM ISO Abbreviation: Int J Nanomedicine Subsets: MEDLINE

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

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

Genome misassembly detection using Stash: A data structure based on stochastic tile hashing.

Authors: Sarvar A Coombe L Birol I

Source: PloS one [PLoS One] 2026 Jul 13; Vol. 21 (7), pp. e0333729. Date of Electronic Publication: 2026 Jul 13 (Print Publication: 2026).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

In Silico Fragment Size Selection for Enhanced Fetal Fraction and Abnormality Origin Discernment Using Pair-End Sequencing of Maternal Plasma DNA.

Authors: Yang L Zhang J Jin Q et al.

Source: Journal of clinical laboratory analysis [J Clin Lab Anal] 2026 Jul; Vol. 40 (13), pp. e70233. Date of Electronic Publication: 2026 May 25.

Publication Type: Journal Article

Journal Info: Publisher: Wiley Country of Publication: United States NLM ID: 8801384 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1098-2825 (Electronic) Linking ISSN: 08878013 NLM ISO Abbreviation: J Clin Lab Anal Subsets: MEDLINE

LORA: a polymorphic multi-sample long read assembly pipeline.

Authors: Desvillechabrol D Ouazahrou R da Fonseca JP et al.

Source: NAR genomics and bioinformatics [NAR Genom Bioinform] 2026 Jun 23; Vol. 8 (2), pp. lqag062. Date of Electronic Publication: 2026 Jun 23 (Print Publication: 2026).

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

De novo direct sequencing of small therapeutic RNAs by layer-by-layer intensity-resolved mass spectrometry.

Authors: Lin S Jiang S Tang L et al.

Source: Nucleic acids research [Nucleic Acids Res] 2026 Jun 22; Vol. 54 (12).

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

GrassSV - hybrid method to detect structural variants in high throughput DNA-seq data.

Authors: Witczak D Sychla K Wysocka J et al.

Source: PLoS computational biology [PLoS Comput Biol] 2026 Jun 22; Vol. 22 (6), pp. e1014406. Date of Electronic Publication: 2026 Jun 22 (Print Publication: 2026).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

Systematic benchmarking of dorado basecalling models for RNA modification detection with highly multiplexed nanopore sequencing.

Authors: Diensthuber G Milenkovic I Llovera L et al.

Source: Nucleic acids research [Nucleic Acids Res] 2026 Jun 08; Vol. 54 (11).

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

High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences.

Authors: Hertz LM Arce A Rivas E et al.

Source: Nucleic acids research [Nucleic Acids Res] 2026 Jun 08; Vol. 54 (11).

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

Heuristic multi-site optimization for protein sequence design using Masked Protein Language Models.

Authors: Wang L Wang Y Qiu C et al.

Source: PLoS computational biology [PLoS Comput Biol] 2026 Jun 05; Vol. 22 (6), pp. e1014365. Date of Electronic Publication: 2026 Jun 05 (Print Publication: 2026).

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

Immune Landscape and Tumour Heterogeneity in Ovarian Cancer: Insights From Single-Cell RNA Sequencing.

Authors: Chen S Elhessewi GMS Cai H et al.

Source: Journal of cellular and molecular medicine [J Cell Mol Med] 2026 Jun; Vol. 30 (11), pp. e71235.

Publication Type: Journal Article; Review; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Wiley-Blackwell Country of Publication: England NLM ID: 101083777 Publication Model: Print Cited Medium: Internet ISSN: 1582-4934 (Electronic) Linking ISSN: 15821838 NLM ISO Abbreviation: J Cell Mol Med Subsets: MEDLINE

Barbell reveals and resolves demultiplexing and trimming issues in Nanopore data.

Authors: Beeloo R Groot Koerkamp R Jia X et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2026 Jun 01; Vol. 42 (6).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

Challenges and progress in RNA velocity: Comparative analysis across multiple biological contexts.

Authors: Ancheta S Dorman L Le Treut G et al.

Source: PLoS computational biology [PLoS Comput Biol] 2026 Jun 01; Vol. 22 (6), pp. e1014303. Date of Electronic Publication: 2026 Jun 01 (Print Publication: 2026).

Publication Type: Journal Article; Comparative Study

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

MethyNano: supervised contrastive pretraining enables robust and generalizable methylation detection from nanopore sequencing.

Authors: Yan J Chen Y Gong Y et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2026 Jun 01; Vol. 42 (6).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

MarkerMatch: a proximity-based probe-matching algorithm for joint analysis of copy-number variants from different genotyping arrays.

Authors: Ivankovic F Yu D Shen J et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2026 Jun 01; Vol. 42 (6).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE