Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
Phylogenetic tools are fundamental to the studies of evolutionary relationships. In this paper, we present , a novel high-throughput tool for alignment-free phylogenetic analysis. computes the pairwise distance matrix between molecular sequences, using seven widely accepted -mer based distance measures. Based on the distance matrix, constructs the phylogenetic tree with standard algorithms. When benchmarked with a golden standard 16S rRNA dataset, was found to be the most accurate tool among all five tools compared and was 19% more accurate than , a high-accuracy multiple sequence aligner. Above all, was tens to hundreds of times faster than , which helps eliminate the computation limit currently encountered in large-scale multiple sequence alignment. is freely available at https://github.com/labxscut/ksak.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10098151 | PMC |
| http://dx.doi.org/10.3389/fmicb.2023.1050130 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Deciphering cellular heterogeneity: Breakthroughs and prospects of single-cell-level SERS analysis in precision medicine.
Methods
September 2025
Gynaecology and Obstetrics, The Second Affiliated Hospital of Harbin Medical University, Harbin Medical University, Heilongjiang 150081, PR China. Electronic address:
Single-cell surface-enhanced Raman scattering (SERS) has emerged as a powerful tool for precision medicine owing to its label-free detection, ultrasensitivity, and unique molecular fingerprinting. Unlike conventional bulk analysis, it enables detailed characterization of cellular heterogeneity, with particular promise in circulating tumor cell (CTC) identification, tumor microenvironment (TME) metabolic profiling, subcellular imaging, and drug sensitivity assessment. Coupled with microfluidic droplet systems, SERS supports high-throughput single-cell analysis and multiparametric screening, while integration with complementary modalities such as fluorescence microscopy and mass spectrometry enhances temporal and spatial resolution for monitoring live cells.
View Article and Find Full Text PDFIntracellular lymphocyte protein biomarkers for early radiological triage in the human population.
PLoS One
September 2025
Center for Radiological Research, Columbia University Irving Medical Center, New York, New York, United States of America.
In the event of a large-scale radiological or nuclear emergency, a rapid, high-throughput screening tool will be essential for efficient triage of potentially exposed individuals, optimizing scarce medical resources and ensuring timely care. The objective of this work was to characterize the effects of age and sex on two intracellular lymphocyte protein biomarkers, BAX and p53, for early radiation exposure classification in the human population, using an imaging flow cytometry-based platform for rapid biomarker quantification in whole blood samples. Peripheral blood samples from male and female donors, across three adult age groups (young adult, middle-aged, senior) and a juvenile cohort, were X-irradiated (0-5 Gy), and biomarker expression was quantified at two- and three-days post-exposure.
View Article and Find Full Text PDFSmall-scale in situ Hi-C protocol for early embryos to resolve the three-dimensional genome structure.
STAR Protoc
September 2025
College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling 712100, China. Electronic address:
High-throughput chromosome conformation capture (Hi-C) provides genome-wide insights into chromatin interactions within the three-dimensional structure of the nucleus, making it a powerful tool for studying genome architecture. Here, we provide a modified in situ Hi-C protocol for small cell numbers, utilizing 50-100 embryonic cells at the 8-cell stage to investigate chromatin organization during bovine early embryonic development. This protocol overcomes the challenges of limited sample availability and offers valuable insights into chromatin dynamics during bovine early embryogenesis.
View Article and Find Full Text PDFExosomal Proteome from Hepatocellular Carcinoma Patient-Derived Xenograft Mice Serves as Identity of Liver Cancer.
J Proteome Res
September 2025
State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China.
Hepatocellular carcinoma (HCC) constitutes approximately 90% of liver cancers, yet its early detection remains challenging due to the low sensitivity of current diagnostic methods and the difficulty in identifying minimal cancer cells within the body. This study employed a patient-derived xenograft (PDX) mouse model to screen for biomarkers, leveraging its advantage of low background interference compared to human serum exosome studies. Using a novel microextraction technique, exosomes were isolated from just one microliter of serum from HCC PDX mice, followed by proteomic profiling.
View Article and Find Full Text PDFNext Generation Sequencing Improves Diagnostic 16S rRNA Amplicon-Based Microbiota Analyses of Clinical Samples Compared to Sanger Sequencing.
APMIS
September 2025
The Regional Department of Clinical Microbiology, Zealand University Hospital-Koege, Køge, Denmark.
Sequencing of the 16S ribosomal RNA (rRNA) gene is an important tool in addition to conventional methods for the identification of bacterial pathogens in human infections. In polymicrobial samples, Sanger sequencing can produce uninterpretable chromatograms. This limitation can be overcome by Next Generation Sequencing (NGS) of the 16S rRNA gene.
View Article and Find Full Text PDF