Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Woodward–Hoffmann Selection Rules and Microscopic Reversibility

Woodward–Hoffmann Selection Rules and Microscopic Reversibility

Electrocyclic reactions, cycloadditions, and sigmatropic rearrangements are concerted pericyclic reactions that proceed via a cyclic transition state. These reactions are stereospecific and regioselective. The stereochemistry of the products depends on the symmetry characteristics of the interacting orbitals and the reaction conditions. Accordingly, pericyclic reactions are classified as either symmetry-allowed or symmetry-forbidden. Woodward and Hoffmann presented the selection criteria for...

Reversible and Irreversible Processes

Reversible and Irreversible Processes

The thermodynamic processes can be classified into reversible and irreversible processes. The processes that can be restored to their initial state are called reversible processes. It is only possible if the process is in quasi-static equilibrium, i.e., it takes place in infinitesimally small steps, and the system remains at equilibrium However, these are ideal processes and do not occur naturally. An ideal system undergoing a reversible process is always in thermodynamic equilibrium within...

Reynolds Transport Theorem

Reynolds Transport Theorem

The Reynolds transport theorem provides a framework to relate the time rate of change of an extensive property within a system to that in a control volume, which is crucial for analyzing fluid dynamics. Extensive properties, such as mass, velocity, acceleration, temperature, and momentum, can be expressed in terms of the mass of a fluid portion. These properties are called extensive because they depend on the system's size, while intensive properties are their corresponding values per unit mass.

Rationalizing Substitutions

Rationalizing Substitutions

Integrals involving non-rational functions are often difficult to evaluate using standard techniques, especially when radicals appear in the integrand. Rationalizing substitution provides a systematic method for simplifying such integrals by converting them into rational forms that are easier to handle.Consider a rod whose linear mass density depends on a constant linear density, a characteristic length, and the distance from the left end of the rod. Determining the total mass requires...

Area Computation by the Alternative Coordinate Method

Area Computation by the Alternative Coordinate Method

The alternative coordinate method, also known as the Shoelace Formula, is a technique for determining the area of a traverse using Cartesian coordinates. This method relies on the sequential arrangement of x and y coordinates for each point of the shape, ensuring accuracy and ease of application.In this approach, each corner's x and y coordinates are listed as fractions, with the x-coordinate as the numerator and the y-coordinate as the denominator. These coordinates are arranged sequentially...

Median

Median

Besides mean, the median is a widely used measure of central tendency. Typically, median is defined as the central or middle value of a data set, measured by arranging the data elements in an increasing or decreasing order. Since this middle value is not affected by the precise numerical values of the outliers or fluctuations, it is insensitive to them. Hence, in cases where a data set may have outliers or the extreme values are not known, the median is a better measure of the central tendency...

You might also read

Related Articles

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

Sort by

Same author

An Interpretable Deep Learning Framework Leveraging RNA Foundation Model and Capsule Networks for Accurate Prediction of RNA 2'-O-Methylation Sites.

Journal of chemical information and modeling·2026

Same author

A sequence knowledge-guided deep learning method for single-cell multi-omics translation.

Genome biology·2026

Same author

MultiPert: An adversarial alignment and dual attention framework for single-cell multi-omics perturbation prediction.

PLoS computational biology·2026

Same author

Containment of antimicrobial resistance for strengthening global public health security: Biorisk management perspectives.

Biosafety and health·2026

Same author

scGACL: a generative adversarial network with multi-scale contrastive learning for accurate single-cell RNA sequencing imputation.

Briefings in bioinformatics·2026

Same author

Synergistic adsorption-photocatalysis of In₂S₃/Bi₂₄Fe₂O₃₉ based on oxygen vacancy for efficient tetracycline removal.

Nanotechnology·2025

Search research articles

Related Experiment Video

Updated: Jul 2, 2026

Evaluation of an Exclusive Spur Dike U-Turn Design with Radar-Collected Data and Simulation

Evaluation of an Exclusive Spur Dike U-Turn Design with Radar-Collected Data and Simulation

Published on: February 1, 2020

Improving reversal median computation using commuting reversals and cycle information.

William Arndt¹, Jijun Tang

¹Department of Computer Science and Engineering, University of South Carolina, Columbia, SC 29208, USA.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology

|September 9, 2008

Summary

A new genome rearrangement heuristic significantly speeds up phylogenetic analysis. This method improves the efficiency of direct optimization techniques for reconstructing evolutionary histories from genomic data.

More Related Videos

Operation of the Collaborative Composite Manufacturing (CCM) System

Operation of the Collaborative Composite Manufacturing (CCM) System

Published on: October 1, 2019

Optimization of the Longa Middle Cerebral Artery Occlusion Method for Complete Reperfusion

Optimization of the Longa Middle Cerebral Artery Occlusion Method for Complete Reperfusion

Published on: November 22, 2024

Related Experiment Videos

Last Updated: Jul 2, 2026

Evaluation of an Exclusive Spur Dike U-Turn Design with Radar-Collected Data and Simulation

Evaluation of an Exclusive Spur Dike U-Turn Design with Radar-Collected Data and Simulation

Published on: February 1, 2020

Operation of the Collaborative Composite Manufacturing (CCM) System

Operation of the Collaborative Composite Manufacturing (CCM) System

Published on: October 1, 2019

Optimization of the Longa Middle Cerebral Artery Occlusion Method for Complete Reperfusion

Optimization of the Longa Middle Cerebral Artery Occlusion Method for Complete Reperfusion

Published on: November 22, 2024

Area of Science:

Computational Biology
Bioinformatics
Evolutionary Biology

Background:

Genome rearrangements are increasingly used for phylogenetic analysis.
Direct optimization methods offer high accuracy but are computationally intensive.
The reversal median problem is a key bottleneck in direct optimization.

Purpose of the Study:

To develop a faster heuristic for the reversal median problem.
To enhance the efficiency of direct optimization methods for phylogenetic reconstruction.
To expand the applicability of these methods to diverse genomic datasets.

Main Methods:

A novel batch-based reversal median heuristic for unichromosomal genomes.
The heuristic applies commuting reversals that do not disrupt cycles.
Testing on simulated datasets compared performance against existing solvers.

Main Results:

The new heuristic is significantly faster than leading solvers on difficult datasets.
It achieves comparable accuracy to faster heuristics and better accuracy than others.
The method supports searching for multiple medians, enhancing flexibility.

Conclusions:

This heuristic dramatically accelerates direct optimization methods.
It extends the applicability of accurate phylogenetic reconstruction to organellar and small nuclear genomes.
The approach offers a practical solution for analyzing genomes with numerous rearrangements.