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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
Phylogeny01:23

Phylogeny

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.
Phylogenetic Trees03:21

Phylogenetic Trees

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.

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Related Experiment Video

Updated: May 16, 2026

Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM)
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Published on: May 8, 2020

Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining.

Kevin An1, Sebastian Prillo1, Wilson Wu1

  • 1Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California 94720, USA.

Genome Research
|May 14, 2026
PubMed
Summary

This study introduces a new algorithm for reconstructing cell lineages using CRISPR-Cas9 technology. The method provides theoretical guarantees for accurate phylogenetic tree reconstruction, even with missing data.

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Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM)
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Efficient Generation of hiPSC Neural Lineage Specific Knockin Reporters Using the CRISPR/Cas9 and Cas9 Double Nickase System
14:46

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Published on: May 28, 2015

Area of Science:

  • Computational Biology
  • Genomics
  • Evolutionary Biology

Background:

  • CRISPR-Cas9 based lineage tracing enables single-cell phylogeny reconstruction from transcriptional data.
  • Developing algorithms with theoretical guarantees for tree reconstruction in this context is challenging.

Purpose of the Study:

  • To derive a novel tree-reconstruction algorithm with theoretical guarantees for CRISPR-Cas9 lineage tracing.
  • To address the realistic scenarios of unknown parameters and missing data in evolutionary models.

Main Methods:

  • Utilized Neighbor-Joining (NJ) on moment-matched distances to estimate true tree distances.
  • Developed analytical tools to prove theoretical guarantees for the reconstruction algorithm.
  • Applied the method to simulated lineage tracing data and real mouse lung cancer data.

Main Results:

  • The algorithm achieves theoretical guarantees, aligning with established evolutionary models when parameters are known and data is complete.
  • New theory demonstrates reconstruction guarantees are still possible with unknown parameters and missing data.
  • Empirical results show improved performance compared to traditional NJ on both simulated and real datasets.

Conclusions:

  • The developed algorithm offers a robust approach for phylogenetic tree reconstruction in CRISPR-Cas9 lineage tracing.
  • The new theoretical framework extends reconstruction guarantees to realistic scenarios with missing data.
  • This work advances computational methods for analyzing complex biological systems and evolutionary processes.