Cargando…

Pathogen detection in RNA-seq data with Pathonoia

BACKGROUND: Bacterial and viral infections may cause or exacerbate various human diseases and to detect microbes in tissue, one method of choice is RNA sequencing. The detection of specific microbes using RNA sequencing offers good sensitivity and specificity, but untargeted approaches suffer from h...

Descripción completa

Detalles Bibliográficos
Autores principales:	Liebhoff, Anna-Maria, Menden, Kevin, Laschtowitz, Alena, Franke, Andre, Schramm, Christoph, Bonn, Stefan
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2023
Materias:	Research
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9938591/ https://www.ncbi.nlm.nih.gov/pubmed/36803415 http://dx.doi.org/10.1186/s12859-023-05144-z

Ejemplares similares

Realistic in silico generation and augmentation of single-cell RNA-seq data using generative adversarial networks
por: Marouf, Mohamed, et al.
Publicado: (2020)

Preoperative Immunotherapy in Hepatocellular Carcinoma: Current State of the Art
por: Laschtowitz, Alena, et al.
Publicado: (2023)

Histological activity despite normal ALT and IgG serum levels in patients with autoimmune hepatitis and cirrhosis
por: Laschtowitz, Alena, et al.
Publicado: (2021)

Serum CXCL5 Detects Early Hepatocellular Carcinoma and Indicates Tumor Progression
por: Laschtowitz, Alena, et al.
Publicado: (2023)

Oasis 2: improved online analysis of small RNA-seq data
por: Rahman, Raza-Ur, et al.
Publicado: (2018)

Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq
por: Hartley, Stephen W., et al.
Publicado: (2016)

RNA-Seq for Plant Pathogenic Bacteria
por: Kimbrel, Jeffrey A., et al.
Publicado: (2011)

Assessment of kinship detection using RNA-seq data
por: Blay, Natalia, et al.
Publicado: (2019)

Global and unbiased detection of splice junctions from RNA-seq data
por: Ameur, Adam, et al.
Publicado: (2010)

Detecting differential usage of exons from RNA-seq data
por: Anders, Simon, et al.
Publicado: (2012)

Clinker: visualizing fusion genes detected in RNA-seq data
por: Schmidt, Breon M, et al.
Publicado: (2018)

Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data
por: Coudray, Alexandre, et al.
Publicado: (2018)

SEAweb: the small RNA Expression Atlas web application
por: Rahman, Raza-Ur, et al.
Publicado: (2020)

An Efficient Algorithm for Sensitively Detecting Circular RNA from RNA-seq Data
por: Zhang, Xuanping, et al.
Publicado: (2018)

deltaTE: Detection of Translationally Regulated Genes by Integrative Analysis of Ribo‐seq and RNA‐seq Data
por: Chothani, Sonia, et al.
Publicado: (2019)

DELongSeq for efficient detection of differential isoform expression from long-read RNA-seq data
por: Hu, Yu, et al.
Publicado: (2023)

ProkSeq for complete analysis of RNA-Seq data from prokaryotes
por: Mahmud, A K M Firoj, et al.
Publicado: (2020)

Impact of RNA degradation on fusion detection by RNA-seq
por: Davila, Jaime I., et al.
Publicado: (2016)

IFNγ and CTLA-4 Drive Hepatic CD4 T-Cell Tolerance and Protection From Autoimmunity in Mice
por: Krzikalla, Daria, et al.
Publicado: (2023)

Statistical methods on detecting differentially expressed genes for RNA-seq data
por: Chen, Zhongxue, et al.
Publicado: (2011)

Detection and removal of barcode swapping in single-cell RNA-seq data
por: Griffiths, Jonathan A., et al.
Publicado: (2018)

Detection of aberrant splicing events in RNA-seq data using FRASER
por: Mertes, Christian, et al.
Publicado: (2021)

DSAVE: Detection of misclassified cells in single-cell RNA-Seq data
por: Gustafsson, Johan, et al.
Publicado: (2020)

AS-Quant: Detection and Visualization of Alternative Splicing Events with RNA-seq Data
por: Fahmi, Naima Ahmed, et al.
Publicado: (2021)

Resolving host–pathogen interactions by dual RNA-seq
por: Westermann, Alexander J., et al.
Publicado: (2017)

ARH-seq: identification of differential splicing in RNA-seq data
por: Rasche, Axel, et al.
Publicado: (2014)

APA-Scan: detection and visualization of 3′-UTR alternative polyadenylation with RNA-seq and 3′-end-seq data
por: Fahmi, Naima Ahmed, et al.
Publicado: (2022)

An Efficient and Flexible Method for Deconvoluting Bulk RNA-Seq Data with Single-Cell RNA-Seq Data
por: Sun, Xifang, et al.
Publicado: (2019)

Deep learning–based cell composition analysis from tissue expression profiles
por: Menden, Kevin, et al.
Publicado: (2020)

SCRABBLE: single-cell RNA-seq imputation constrained by bulk RNA-seq data
por: Peng, Tao, et al.
Publicado: (2019)

Transcript quantification with RNA-Seq data
por: Bohnert, Regina, et al.
Publicado: (2009)

An Iterative Leave-One-Out Approach to Outlier Detection in RNA-Seq Data
por: George, Nysia I., et al.
Publicado: (2015)

Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data
por: Kumar, Shailesh, et al.
Publicado: (2016)

A flexible Bayesian method for detecting allelic imbalance in RNA-seq data
por: León-Novelo, Luis G, et al.
Publicado: (2014)

Comparison of Alternative Splicing Junction Detection Tools Using RNA-Seq Data
por: Ding, Lizhong, et al.
Publicado: (2017)

Detection of condition-specific marker genes from RNA-seq data with MGFR
por: El Amrani, Khadija, et al.
Publicado: (2019)

Improved detection of tumor suppressor events in single-cell RNA-Seq data
por: Teschendorff, Andrew E., et al.
Publicado: (2020)

Obstacles to detecting isoforms using full-length scRNA-seq data
por: Westoby, Jennifer, et al.
Publicado: (2020)

Combining signal and sequence to detect RNA polymerase initiation in ATAC-seq data
por: Tripodi, Ignacio J., et al.
Publicado: (2020)

Statistical Issues in the Analysis of ChIP-Seq and RNA-Seq Data
por: Ghosh, Debashis, et al.
Publicado: (2010)

Cannot write session to /tmp/vufind_sessions/sess_pg7sskurn60rq8l0qi8ltoeif6