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

Analysis of Population Pharmacokinetic Data01:12

Analysis of Population Pharmacokinetic Data

733
Analysis of population pharmacokinetic data involves studying the behavior of drugs within diverse populations to understand their pharmacokinetic parameters. Traditional pharmacokinetic methods typically involve collecting samples from a few individuals and estimating these parameters. While these methods are commonly used, they have limitations in capturing the variability in drug response among individuals or heterogeneous populations. Population pharmacokinetics is employed to address these...
733
Recombinant DNA01:09

Recombinant DNA

102.5K
Overview
102.5K
Rate-Determining Steps03:08

Rate-Determining Steps

37.0K
Relating Reaction Mechanisms
In a multistep reaction mechanism, one of the elementary steps progresses significantly slower than the others. This slowest step is called the rate-limiting step (or rate-determining step). A reaction cannot proceed faster than its slowest step, and hence, the rate-determining step limits the overall reaction rate.
The concept of rate-determining step can be understood from the analogy of a 4-lane freeway with a short-stretch of traffic-bottleneck caused due to...
37.0K
Viral Recombination00:57

Viral Recombination

25.1K
Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.
25.1K
Overview of Microsoft Excel as a Data Analysis Tool01:13

Overview of Microsoft Excel as a Data Analysis Tool

1.5K
Microsoft Excel is a cornerstone tool for data analysis and statistical operations, offering a wide array of functionalities to manage, analyze, and visualize data efficiently. Recognized for its versatility, Excel facilitates the performance of basic to complex statistical operations, serving as an indispensable asset for analysts, researchers, and students alike. Excel's significance in data analysis emanates from its spreadsheet environment, where data can be organized in rows and...
1.5K
What are Estimates?01:06

What are Estimates?

8.8K
It isn't easy to measure a parameter such as the mean height or the mean weight of a population. So, we draw samples from the population and calculate the mean height or mean weight of the individuals in the sample. This sample data acts as a representative measure of the population parameter. These sample statistics are known as estimates. 
The estimate for the mean of a sample is denoted by ͞x, whereas the mean of the population is designated as μ. Further, parameters such...
8.8K

You might also read

Related Articles

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

Sort by
Same author

Provable cluster-preserving visualizations with curvature-based stochastic neighbor embeddings.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Cellstitch: 3D cellular anisotropic image segmentation via optimal transport.

BMC bioinformatics·2023
Same author

At-home sample collection is an effective strategy for diagnosis and management of symptomatic and asymptomatic SARS-CoV-2 carriers.

BMC infectious diseases·2022
Same author

Corrigendum to: Fast Estimation of Recombination Rates Using Topological Data Analysis.

Genetics·2022
Same author

A Random Matrix Theory Approach to Denoise Single-Cell Data.

Patterns (New York, N.Y.)·2020
Same author

Detecting Shared Genetic Architecture Among Multiple Phenotypes by Hierarchical Clustering of Gene-Level Association Statistics.

Genetics·2020

Related Experiment Video

Updated: Jan 28, 2026

Electrochemical Impedance Spectroscopy as a Tool for Electrochemical Rate Constant Estimation
08:41

Electrochemical Impedance Spectroscopy as a Tool for Electrochemical Rate Constant Estimation

Published on: October 10, 2018

25.8K

Fast Estimation of Recombination Rates Using Topological Data Analysis.

Devon P Humphreys1, Melissa R McGuirl2, Michael Miyagi3

  • 1Department of Integrative Biology, The University of Texas at Austin, Texas 78712.

Genetics
|February 22, 2019
PubMed
Summary

We developed a novel topological data analysis (TDA) method for estimating recombination rates in genome sequences. This approach, TREE, is faster and handles larger datasets than existing software, offering comparable accuracy.

Keywords:
coalescent theorypopulation geneticsrecombinationtopological data analysis

More Related Videos

Estimating Virus Production Rates in Aquatic Systems
10:49

Estimating Virus Production Rates in Aquatic Systems

Published on: September 22, 2010

13.1K
Estimating Sediment Denitrification Rates Using Cores and N2O Microsensors
07:59

Estimating Sediment Denitrification Rates Using Cores and N2O Microsensors

Published on: December 6, 2018

8.6K

Related Experiment Videos

Last Updated: Jan 28, 2026

Electrochemical Impedance Spectroscopy as a Tool for Electrochemical Rate Constant Estimation
08:41

Electrochemical Impedance Spectroscopy as a Tool for Electrochemical Rate Constant Estimation

Published on: October 10, 2018

25.8K
Estimating Virus Production Rates in Aquatic Systems
10:49

Estimating Virus Production Rates in Aquatic Systems

Published on: September 22, 2010

13.1K
Estimating Sediment Denitrification Rates Using Cores and N2O Microsensors
07:59

Estimating Sediment Denitrification Rates Using Cores and N2O Microsensors

Published on: December 6, 2018

8.6K

Area of Science:

  • Population genetics
  • Computational biology
  • Genomics

Background:

  • Estimating recombination rates is crucial for understanding genetic diversity.
  • Full evolutionary models for recombination inference are computationally intensive.
  • Existing topological data analysis (TDA) methods have limitations in biological interpretation.

Purpose of the Study:

  • To develop a computationally efficient and accurate method for estimating recombination rates using TDA.
  • To introduce a new topological feature with a clear connection to coalescent models.
  • To package the method as user-friendly software (TREE).

Main Methods:

  • Applied topological data analysis (TDA) to genome sequences.
  • Introduced a new topological feature, psi (ψ), linked to coalescent models.
  • Developed the Topological Recombination Estimator (TREE) software.

Main Results:

  • The TDA method (TREE) analyzes larger datasets than existing software.
  • TREE demonstrates accuracy comparable to model-based methods with reduced processing time.
  • The new topological feature (ψ) shows differential sensitivity to missing data compared to the first Betti number.

Conclusions:

  • TREE provides an efficient and accurate first-pass estimator for recombination rate heterogeneity.
  • Topological statistics are validated as effective summaries of genome sequences.
  • A novel link between topological features of sequence data and recombination footprints is established.