Related Experiment Video
Updated: Sep 25, 2025
09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
3.5K
Interactive, integrated analysis of single-cell transcriptomic and phylogenetic data with PhyloVision.
Matthew G Jones1,2,3,4, Yanay Rosen1, Nir Yosef1,2,5,6
1Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA 94720 USA.
Cell Reports Methods
|May 2, 2022
Summary
PhyloVision is a new open-source software tool that integrates single-cell transcriptomic and phylogenetic data. It helps researchers identify gene modules linked to cell lineage, aiding cancer research and other single-cell analyses.
Area of Science:
- Genomics
- Computational Biology
- Bioinformatics
Background:
- Simultaneous measurement of single-cell transcriptomic and phylogenetic profiles is now possible.
- Limited computational tools exist for integrating and analyzing these dual-modality datasets.
Purpose of the Study:
- To introduce PhyloVision, an open-source software for joint analysis of transcriptomic and phylogenetic data.
- To enable interactive exploration and identification of heritable gene modules associated with phylogenetic relationships.
Main Methods:
- Development of PhyloVision, an interactive, web-based software.
- Utilizing CRISPR-Cas9 lineage tracing for phylogenetic profiling.
- Applying the tool to a metastatic lung adenocarcinoma dataset.
Main Results:
- PhyloVision facilitates interactive exploration of integrated single-cell data.
- The software identifies and interprets heritable gene modules linked to phylogeny.
- Demonstrated utility on a lung adenocarcinoma dataset.
Conclusions:
- PhyloVision provides a scalable and intuitive resource for analyzing assays measuring cell state and lineage.
- The tool supports interactive data exploration and identification of gene modules.
- It is applicable to various single-cell assays combining expression and lineage information.
Related Concept Videos
02:54Evolutionary Relationships through Genome Comparisons
6.2K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.2K
01:23Phylogeny
52.6K
Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
52.6K
01:20Applications of Molecular Taxonomy
140
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
140
03:21Phylogenetic Trees
47.6K
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
47.6K
01:29Modern Molecular Taxonomy
186
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
186
02:16Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
14.3K
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
14.3K