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Summary: KNIME (Konstanz Information Miner) is a user-friendly and comprehensive open-source data integration, processing, analysis and exploration platform. We present here new functionality and workflows that open the door to performing next-generation sequencing analysis using the KNIME framework.
Availability: All sources and compiled code are available via the KNIME update mechanism. Example workflows and descriptions are available through http://tech.knime.org/community/next-generation-sequencing.
Contact: bernd.jagla@pasteur.fr
Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btr478 | DOI Listing |
Genome Biol
September 2025
Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Biology, Plön, Germany.
Background: Most RNA-seq datasets harbor genes with extreme expression levels in some samples. Such extreme outliers are usually treated as technical errors and are removed from the data before further statistical analysis. Here we focus on the patterns of such outlier gene expression to investigate whether they provide insights into the underlying biology.
View Article and Find Full Text PDFNPJ Biofilms Microbiomes
September 2025
Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, 24105 Kiel University, Kiel, Schleswig-Holstein, Germany.
Urinary tract infections (UTIs) are among the most common bacterial infections and are increasingly complicated by multidrug resistance (MDR). While Escherichia coli is frequently implicated, the contribution of broader microbial communities remains less understood. Here, we integrate metatranscriptomic sequencing with genome-scale metabolic modeling to characterize active metabolic functions of patient-specific urinary microbiomes during acute UTI.
View Article and Find Full Text PDFZhonghua Jie He He Hu Xi Za Zhi
September 2025
Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210009, China.
Severe pneumonia, as a critical and prevalent condition of the respiratory system, poses a significant threat to patient survival and health outcomes. This article focuses on the similarities and differences between community-acquired pneumonia (CAP) and hospital-acquired pneumonia (HAP)/ventilator-associated pneumonia (VAP). There is significant divergence in the predominant pathogens between severe community-acquired pneumonia (SCAP) and HAP/VAP.
View Article and Find Full Text PDFInt Immunopharmacol
September 2025
School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India.
Over the past few decades, the scientific perspective on gut microbiota has undergone a profound transformation, particularly with the emergence and advancement of microbiome research. Next-generation sequencing technologies have emerged as a foundational tool in microbiome research, facilitating comprehensive characterization of microbial communities across diverse sample types and ecological niches. Significant alterations in gut microbiota composition have been observed in disease states compared to healthy individuals, suggesting a direct association between gut dysbiosis and host health status.
View Article and Find Full Text PDFDiagn Microbiol Infect Dis
September 2025
Department of Infectious Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China. Electronic address:
Objectives: This study aimed to evaluate the prognostic value of metagenomic next-generation sequencing(mNGS) using Nanopore sequencing technology (NST) versus traditional culture methods in infectious disease cases.
Methods: We conducted a retrospective, single-center observational study comparing clinical outcomes between patients and specimen types in NST group and those in culture-based control group. Cox Proportional Hazards regression and Kaplan-Meier survival analysis were conducted to evaluate the association between diagnostic strategy and 28-day mortality.