Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Phylogenetic Trees03:21

Phylogenetic Trees

49.3K
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.
49.3K
Longitudinal Research02:20

Longitudinal Research

13.1K
Sometimes we want to see how people change over time, as in studies of human development and lifespan. When we test the same group of individuals repeatedly over an extended period of time, we are conducting longitudinal research. Longitudinal research is a research design in which data-gathering is administered repeatedly over an extended period of time. For example, we may survey a group of individuals about their dietary habits at age 20, retest them a decade later at age 30, and then again...
13.1K
The Tree of Life - Bacteria, Archaea, Eukaryotes02:40

The Tree of Life - Bacteria, Archaea, Eukaryotes

38.0K
The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both...
38.0K
Survival Tree01:19

Survival Tree

393
Survival trees are a non-parametric method used in survival analysis to model the relationship between a set of covariates and the time until an event of interest occurs, often referred to as the "time-to-event" or "survival time." This method is particularly useful when dealing with censored data, where the event has not occurred for some individuals by the end of the study period, or when the exact time of the event is unknown.
 Building a Survival Tree
Constructing a...
393
The Bronchial Tree01:23

The Bronchial Tree

6.4K
The human bronchi and bronchial tree play a crucial role in the respiratory system, facilitating the exchange of oxygen and carbon dioxide. Let's delve into the intricate structure and functions of these respiratory components.
The trachea, commonly known as the windpipe, is a tube that connects the larynx (voice box) to the bronchi. At a point called the carina, it bifurcates into two primary bronchi. The right primary bronchus is wider, shorter, and more vertical than the left primary...
6.4K
Theory of Attribution I: Correspondent Inference Theory01:15

Theory of Attribution I: Correspondent Inference Theory

485
Correspondent inference theory, proposed by Jones and Davis in 1965, seeks to explain how individuals infer stable personality traits from observed behaviors. It suggests that people attribute actions to underlying dispositions rather than external circumstances, particularly when the behavior appears intentional and socially significant.Voluntary Behavior and Dispositional AttributionAccording to this theory, individuals are more likely to attribute behavior to personal traits when it appears...
485

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

LAML-Pro: joint maximum likelihood inference of cell genotypes and cell lineage trees.

Bioinformatics (Oxford, England)·2026
Same author

Riemannian metric learning for alignment of spatial multiomics.

Bioinformatics (Oxford, England)·2026
Same author

The tree labeling polytope: A unified approach to ancestral reconstruction problems.

Cell systems·2026
Same author

Spatial Mapping of the Precancer-to-Cancer Transition in Breast and Prostate.

Cancer discovery·2026
Same author

LAML-Pro: Joint Maximum Likelihood Inference of Cell Genotypes and Cell Lineage Trees.

bioRxiv : the preprint server for biology·2026
Same author

Multimodal spatial alignment and morphology mapping with MOSAICField.

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: Jan 23, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

36.0K

CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples.

Matthew A Myers1, Gryte Satas2, Benjamin J Raphael1

  • 1Department of Computer Science, Princeton University, Princeton, NJ 08540, USA.

Cell Systems
|June 24, 2019
PubMed
Summary

We developed CALDER, a new algorithm for analyzing cancer patient DNA. CALDER reconstructs tumor evolution from longitudinal data, reducing ambiguity and improving phylogenetic tree accuracy.

Keywords:
algorithmcancerlongitudinal samplingphylogeneticstumor heterogeneitytumor phylogeny

More Related Videos

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.5K
Longitudinal Morphological and Physiological Monitoring of Three-dimensional Tumor Spheroids Using Optical Coherence Tomography
08:50

Longitudinal Morphological and Physiological Monitoring of Three-dimensional Tumor Spheroids Using Optical Coherence Tomography

Published on: February 9, 2019

8.2K

Related Experiment Videos

Last Updated: Jan 23, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

36.0K
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.5K
Longitudinal Morphological and Physiological Monitoring of Three-dimensional Tumor Spheroids Using Optical Coherence Tomography
08:50

Longitudinal Morphological and Physiological Monitoring of Three-dimensional Tumor Spheroids Using Optical Coherence Tomography

Published on: February 9, 2019

8.2K

Area of Science:

  • Genomics
  • Computational Biology
  • Cancer Research

Background:

  • Longitudinal DNA sequencing aids understanding of tumor evolution.
  • Bulk tumor sequencing data present challenges in inferring clonal composition and ancestral relationships.

Purpose of the Study:

  • To introduce Cancer Analysis of Longitudinal Data through Evolutionary Reconstruction (CALDER), an algorithm for inferring phylogenetic trees from longitudinal bulk DNA sequencing data.
  • To leverage longitudinal sampling constraints for improved phylogeny reconstruction.

Main Methods:

  • CALDER explicitly models longitudinally observed phylogenies.
  • Incorporates constraints specific to longitudinal sampling in phylogeny reconstruction.

Main Results:

  • Longitudinal constraints significantly reduce ambiguity in phylogeny reconstruction on simulated data.
  • CALDER outperforms existing methods lacking longitudinal information.
  • CALDER reconstructs more plausible and parsimonious phylogenies on real data from leukemia patients, identifying fewer tumor clones per sample.

Conclusions:

  • CALDER effectively utilizes longitudinal information for more accurate tumor evolution inference.
  • The algorithm offers advantages for future studies on tumor heterogeneity and evolution.