Suchergebnisse - "Sequence Analysis, RNA"

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

Autoren: Rupp O Roessner LH Kong D et al.

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

Publikationsart: Journal Article; Video-Audio Media

Info zur Zeitschrift: 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-Schlagworte: 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.

Autoren: Zadian SS Jahanbin K Nikooei S et al.

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

Publikationsart: Journal Article; Review

Info zur Zeitschrift: 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-Schlagworte: Single-Cell Analysis*/methods , Single-Cell Analysis*/trends , Diabetes Mellitus*/genetics , Diabetes Mellitus*/diagnosis , Sequence Analysis, RNA*/methods , Sequence Analysis, RNA*/trends, Humans ; Animals

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

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

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

Publikationsart: Journal Article; Review

Info zur Zeitschrift: 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-Schlagworte: Sequence Analysis, RNA*/methods , Sequence Analysis, RNA*/economics , RNA-Seq*/methods , RNA-Seq*/economics, Humans ; Gene Library ; RNA/genetics

Transcriptional and temporal heterogeneity of developing α cells revealed by single-cell RNA sequencing.

Autoren: Shimizu N Taguchi T Himuro M et al.

Quelle: Biochemical and biophysical research communications [Biochem Biophys Res Commun] 2025 Dec 15; Vol. 792, pp. 152996. Date of Electronic Publication: 2025 Nov 14.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Elsevier Country of Publication: United States NLM ID: 0372516 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1090-2104 (Electronic) Linking ISSN: 0006291X NLM ISO Abbreviation: Biochem Biophys Res Commun Subsets: MEDLINE

MeSH-Schlagworte: Glucagon-Secreting Cells*/metabolism , Glucagon-Secreting Cells*/cytology , Single-Cell Analysis*/methods , Sequence Analysis, RNA*/methods , Transcription, Genetic*, Animals ; Mice ; Insulin-Secreting Cells/metabolism ; Insulin-Secreting Cells/cytology ; Transcriptome ; Cell Differentiation/genetics ; Gene Expression Regulation, Developmental ; Glucagon/metabolism ; Glucagon/genetics ; Gene Expression Profiling

Isoformic: a workflow for transcript-level RNA-seq interpretation.

Autoren: Mamede I Queiroz LR Mata-Machado C et al.

Quelle: NAR genomics and bioinformatics [NAR Genom Bioinform] 2025 Dec 03; Vol. 7 (4), pp. lqaf176. Date of Electronic Publication: 2025 Dec 03 (Print Publication: 2025).

Publikationsart: Journal Article

Info zur Zeitschrift: 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-Schlagworte: RNA-Seq*/methods , Transcriptome* , Gene Expression Profiling*/methods , Sequence Analysis, RNA*/methods , Software*, Animals ; Humans ; Mice ; COVID-19/genetics ; COVID-19/virology ; Workflow ; Female ; Alternative Splicing ; Pre-Eclampsia/genetics ; SARS-CoV-2/genetics ; Pregnancy

Pan-cancer gene set discovery via scRNA-seq for optimal deep learning based downstream tasks.

Autoren: Kim JH Lee S Jang J

Quelle: Scientific reports [Sci Rep] 2025 Dec 02; Vol. 15 (1), pp. 43159. Date of Electronic Publication: 2025 Dec 02.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

MeSH-Schlagworte: Deep Learning* , Neoplasms*/genetics , Single-Cell Analysis*/methods , RNA-Seq*/methods , Sequence Analysis, RNA*/methods, Humans ; Gene Expression Profiling/methods ; Gene Expression Regulation, Neoplastic ; Neural Networks, Computer ; Mutation ; Transcriptome ; Computational Biology/methods ; Single-Cell Gene Expression Analysis

Long-read sequencing transcriptome quantification with lr-kallisto.

Autoren: Loving RK Sullivan DK Reese F et al.

Quelle: PLoS computational biology [PLoS Comput Biol] 2025 Dec 01; Vol. 21 (12), pp. e1013692. Date of Electronic Publication: 2025 Dec 01 (Print Publication: 2025).

Publikationsart: Journal Article

Info zur Zeitschrift: 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

MeSH-Schlagworte: Transcriptome*/genetics , High-Throughput Nucleotide Sequencing*/methods , Gene Expression Profiling*/methods , Sequence Analysis, RNA*/methods, Humans ; Computational Biology/methods ; Software ; RNA-Seq/methods ; Single-Cell Analysis/methods

D3Impute: Dropout-aware discrimination, distribution-aware modeling, and density-guide imputation for scRNA-seq data.

Autoren: Huang S Jiang L Yi M et al.

Quelle: PLoS computational biology [PLoS Comput Biol] 2025 Dec 01; Vol. 21 (12), pp. e1013744. Date of Electronic Publication: 2025 Dec 01 (Print Publication: 2025).

Publikationsart: Journal Article

Info zur Zeitschrift: 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

MeSH-Schlagworte: Single-Cell Analysis*/methods , Single-Cell Analysis*/statistics & numerical data , Sequence Analysis, RNA*/methods , RNA-Seq*/methods, Humans ; Computational Biology/methods ; Algorithms ; Software ; Gene Expression Profiling/methods ; Transcriptome/genetics ; Single-Cell Gene Expression Analysis

Unraveling Traditional Chinese Medicine with single-cell RNA sequencing: Current applications and future frontiers.

Autoren: Chen X Liu J Lu P et al.

Quelle: Phytomedicine : international journal of phytotherapy and phytopharmacology [Phytomedicine] 2025 Dec; Vol. 149, pp. 157556. Date of Electronic Publication: 2025 Nov 13.

Publikationsart: Journal Article; Review

Info zur Zeitschrift: Publisher: Urban & Fischer Verlag Country of Publication: Germany NLM ID: 9438794 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1618-095X (Electronic) Linking ISSN: 09447113 NLM ISO Abbreviation: Phytomedicine Subsets: MEDLINE

MeSH-Schlagworte: Medicine, Chinese Traditional*/methods , Single-Cell Analysis*/methods , Sequence Analysis, RNA*/methods, Humans ; Drugs, Chinese Herbal/pharmacology ; Animals ; Neoplasms/drug therapy ; Neoplasms/genetics

Integrated bulk and single-cell RNA sequencing analysis reveals cuproptosis-related proteins in Crohn's disease.

Autoren: Wu P Lin N Ke Y et al.

Quelle: International journal of biological macromolecules [Int J Biol Macromol] 2025 Dec; Vol. 333 (Pt 2), pp. 148990. Date of Electronic Publication: 2025 Nov 11.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Elsevier Country of Publication: Netherlands NLM ID: 7909578 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1879-0003 (Electronic) Linking ISSN: 01418130 NLM ISO Abbreviation: Int J Biol Macromol Subsets: MEDLINE

MeSH-Schlagworte: Crohn Disease*/genetics , Crohn Disease*/metabolism , Single-Cell Analysis*/methods , Sequence Analysis, RNA*/methods , Copper*/metabolism, Humans ; Gene Expression Profiling ; Biomarkers/metabolism ; Computational Biology/methods

Identification, assembly and characterization of tumor immunoglobulin transcripts from RNA sequencing data using IgSeqR.

Autoren: Bryant D Sale B Chiodin G et al.

Quelle: Nature protocols [Nat Protoc] 2025 Dec; Vol. 20 (12), pp. 3509-3527. Date of Electronic Publication: 2025 Apr 24.

Publikationsart: Journal Article; Review

Info zur Zeitschrift: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101284307 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1750-2799 (Electronic) Linking ISSN: 17502799 NLM ISO Abbreviation: Nat Protoc Subsets: MEDLINE

MeSH-Schlagworte: Sequence Analysis, RNA*/methods , Immunoglobulins*/genetics , Software*, Humans ; High-Throughput Nucleotide Sequencing/methods ; Leukemia, Lymphocytic, Chronic, B-Cell/genetics

DeepRNA-Reg: a deep-learning based approach for comparative analysis of CLIP experiments.

Autoren: Sekhon H Kageyama R Sprenkle NT et al.

Quelle: RNA biology [RNA Biol] 2025 Dec; Vol. 22 (1), pp. 1-18. Date of Electronic Publication: 2025 Oct 07.

Publikationsart: Journal Article; Comparative Study

Info zur Zeitschrift: Publisher: Taylor & Francis Country of Publication: United States NLM ID: 101235328 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1555-8584 (Electronic) Linking ISSN: 15476286 NLM ISO Abbreviation: RNA Biol Subsets: MEDLINE

MeSH-Schlagworte: Deep Learning* , MicroRNAs*/genetics , MicroRNAs*/chemistry , High-Throughput Nucleotide Sequencing*/methods , Immunoprecipitation*/methods , Sequence Analysis, RNA*/methods , Computational Biology*/methods , RNA*/genetics , RNA*/chemistry, Humans ; Argonaute Proteins/genetics ; Argonaute Proteins/metabolism ; Animals

Nano3P-seq: charting the coding and noncoding transcriptome at single-molecule resolution.

Autoren: Begik O Pryszcz LP Niazi AM et al.

Quelle: Nature protocols [Nat Protoc] 2025 Dec; Vol. 20 (12), pp. 3607-3628. Date of Electronic Publication: 2025 Jul 08.

Publikationsart: Journal Article; Review

Info zur Zeitschrift: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101284307 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1750-2799 (Electronic) Linking ISSN: 17502799 NLM ISO Abbreviation: Nat Protoc Subsets: MEDLINE

MeSH-Schlagworte: Transcriptome*/genetics , Sequence Analysis, RNA*/methods , RNA, Untranslated*/genetics , Nanopore Sequencing*/methods, Polyadenylation ; RNA, Messenger/genetics ; Humans ; Nanopores ; Software

Efficient RNA nucleotide encoding enhances the accurate prediction of ac4C modifications.

Autoren: Li N Wang X Zeng M et al.

Quelle: Methods (San Diego, Calif.) [Methods] 2025 Dec; Vol. 244, pp. 1-6. Date of Electronic Publication: 2025 Aug 31.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Academic Press Country of Publication: United States NLM ID: 9426302 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1095-9130 (Electronic) Linking ISSN: 10462023 NLM ISO Abbreviation: Methods Subsets: MEDLINE

MeSH-Schlagworte: Cytidine*/analogs & derivatives , Cytidine*/metabolism , Cytidine*/chemistry , RNA*/genetics , RNA*/chemistry , RNA*/metabolism , RNA Processing, Post-Transcriptional* , Sequence Analysis, RNA*/methods , Computational Biology*/methods, Algorithms ; Humans

Kidney diseases and single-cell sequencing research: a bibliometric analysis from 2015 to 2024.

Autoren: Li Y Hou J Zhang X et al.

Quelle: Renal failure [Ren Fail] 2025 Dec; Vol. 47 (1), pp. 2521457. Date of Electronic Publication: 2025 Jun 23.

Publikationsart: Journal Article; Review

Info zur Zeitschrift: Publisher: Informa Healthcare Country of Publication: England NLM ID: 8701128 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1525-6049 (Electronic) Linking ISSN: 0886022X NLM ISO Abbreviation: Ren Fail Subsets: MEDLINE

MeSH-Schlagworte: Bibliometrics* , Kidney Diseases*/genetics , Single-Cell Analysis* , Sequence Analysis, RNA* , Biomedical Research*/trends, Humans ; RNA-Seq

Single-cell RNA sequencing reveals oocyte-granulosa crosstalk and regulatory networks driving chicken primordial follicle assembly.

Autoren: Zhang X Li D He H et al.

Quelle: International journal of biological macromolecules [Int J Biol Macromol] 2025 Dec; Vol. 332 (Pt 2), pp. 148357. Date of Electronic Publication: 2025 Oct 16.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Elsevier Country of Publication: Netherlands NLM ID: 7909578 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1879-0003 (Electronic) Linking ISSN: 01418130 NLM ISO Abbreviation: Int J Biol Macromol Subsets: MEDLINE

MeSH-Schlagworte: Oocytes*/metabolism , Oocytes*/cytology , Granulosa Cells*/metabolism , Granulosa Cells*/cytology , Chickens*/genetics , Ovarian Follicle*/metabolism , Ovarian Follicle*/cytology , Ovarian Follicle*/growth & development , Single-Cell Analysis* , Gene Regulatory Networks* , Sequence Analysis, RNA*, Animals ; Female ; Transcriptome ; Gene Expression Profiling ; Gene Expression Regulation, Developmental

Integrated bulk and single-cell RNA sequencing identifies oxidative stress signatures of radiation-induced lung injury in mice through machine learning.

Autoren: Huang W Deng G Zhang Q et al.

Quelle: The international journal of biochemistry & cell biology [Int J Biochem Cell Biol] 2025 Dec; Vol. 189, pp. 106863. Date of Electronic Publication: 2025 Sep 16.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Elsevier Country of Publication: Netherlands NLM ID: 9508482 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1878-5875 (Electronic) Linking ISSN: 13572725 NLM ISO Abbreviation: Int J Biochem Cell Biol Subsets: MEDLINE

MeSH-Schlagworte: Oxidative Stress*/genetics , Oxidative Stress*/radiation effects , Machine Learning* , Single-Cell Analysis* , Sequence Analysis, RNA* , Lung Injury*/genetics , Lung Injury*/metabolism , Lung Injury*/pathology , Lung Injury*/etiology, Animals ; Mice ; Gene Regulatory Networks ; Mice, Inbred C57BL

Advances in nanopore direct RNA sequencing and its impact on biological research.

Autoren: Sun K Li J Chen C et al.

Quelle: Biotechnology advances [Biotechnol Adv] 2025 Dec; Vol. 85, pp. 108710. Date of Electronic Publication: 2025 Sep 08.

Publikationsart: Journal Article; Review

Info zur Zeitschrift: Publisher: Elsevier Science Country of Publication: England NLM ID: 8403708 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-1899 (Electronic) Linking ISSN: 07349750 NLM ISO Abbreviation: Biotechnol Adv Subsets: MEDLINE

MeSH-Schlagworte: Sequence Analysis, RNA*/methods , Nanopore Sequencing*/methods , Nanopores* , RNA*/genetics, Humans ; Animals ; Transcriptome

The offonome reveals on and off states of gene expression near the detection limit of RNA-seq.

Autoren: Choi WY Zhao X Holt J et al.

Quelle: Scientific reports [Sci Rep] 2025 Nov 28; Vol. 15 (1), pp. 43141. Date of Electronic Publication: 2025 Nov 28.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

MeSH-Schlagworte: RNA-Seq*/methods , Gene Expression Profiling*/methods , Neoplasms*/genetics , Gene Expression Regulation, Neoplastic* , Sequence Analysis, RNA*/methods, Humans ; Single-Cell Analysis ; Transcriptome

Direct RNA sequencing enables improved transcriptome assessment and tracking of RNA modifications for medical applications.

Autoren: Hewel C Wierczeiko A Miedema J et al.

Quelle: Nucleic acids research [Nucleic Acids Res] 2025 Nov 26; Vol. 53 (22).

Publikationsart: Journal Article

Info zur Zeitschrift: 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-Schlagworte: Sequence Analysis, RNA*/methods , Transcriptome*/genetics , RNA*/genetics , RNA*/chemistry , RNA*/metabolism , RNA Processing, Post-Transcriptional*, Humans ; Adenosine/analogs & derivatives ; Pseudouridine/genetics ; Methyltransferases/genetics ; High-Throughput Nucleotide Sequencing/methods ; Methylation