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

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...

Multiple Allele Traits

Multiple Allele Traits

The Concept of Multiple Allelism

Multiple Allele Traits

Multiple Allele Traits

The Concept of Multiple Allelism

Evolutionary Relationships through Genome Comparisons

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...

Modern Molecular Taxonomy

Modern Molecular Taxonomy

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...

Methods of Medium Optimization

Methods of Medium Optimization

Optimizing growth media enhances microbial proliferation and maximizes product yield. Statistical experimental design methodologies provide structured and reproducible approaches, offering progressively higher levels of robustness and efficiency.The One-Factor-at-a-Time (OFAT) MethodThe One-Factor-at-a-Time (OFAT) method involves adjusting a single variable while keeping all others constant. However, it cannot detect interactions between variables, often leading to suboptimal outcomes when...

You might also read

Related Articles

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

Sort by

Same author

A Flexible Computational Framework Using R and Map-Reduce for Permutation Tests of Massive Genetic Analysis of Complex Traits.

IEEE/ACM transactions on computational biology and bioinformatics·2016

Same author

MAPfastR: quantitative trait loci mapping in outbred line crosses.

G3 (Bethesda, Md.)·2013

Same author

Fast and accurate detection of multiple quantitative trait Loci.

Journal of computational biology : a journal of computational molecular cell biology·2013

Same author

An adaptive pseudospectral method for wave packet dynamics.

The Journal of chemical physics·2012

Same author

Assessing a multiple QTL search using the variance component model.

Computational biology and chemistry·2010

Same author

Accurate time propagation for the Schrodinger equation with an explicitly time-dependent Hamiltonian.

The Journal of chemical physics·2008

Same journal

Network Pharmacology of Natural Polyphenols for Stroke: A Bioinformatic Approach to Drug Design.

Advances and applications in bioinformatics and chemistry : AABC·2025

Same journal

LAMP5, One of Four Genes Related to Oxidative Stress That Predict Biochemical Recurrence-Free Survival, Promotes Proliferation and Invasion in Prostate Cancer [Retraction].

Advances and applications in bioinformatics and chemistry : AABC·2025

Same journal

Virtual Screening, Toxicity Evaluation and Pharmacokinetics of Erythrina Alkaloids as Acetylcholinesterase Inhibitor Candidates from Natural Products.

Advances and applications in bioinformatics and chemistry : AABC·2025

Same journal

Non-Invasive Cancer Detection Using Blood Test and Predictive Modeling Approach.

Advances and applications in bioinformatics and chemistry : AABC·2025

Same journal

Recent Applications of Artificial Intelligence in Discovery of New Antibacterial Agents.

Advances and applications in bioinformatics and chemistry : AABC·2024

Same journal

LAMP5, One of Four Genes Related to Oxidative Stress That Predict Biochemical Recurrence-Free Survival, Promotes Proliferation and Invasion in Prostate Cancer.

Advances and applications in bioinformatics and chemistry : AABC·2024

See all related articles

Search research articles

Related Experiment Video

Updated: May 29, 2026

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Published on: October 11, 2018

Efficient algorithms for multidimensional global optimization in genetic mapping of complex traits.

Kajsa Ljungberg¹, Kateryna Mishchenko, Sverker Holmgren

¹Division of Scientific Computing, Department of Information Technology, Uppsala University, Uppsala, Sweden.

Advances and Applications in Bioinformatics and Chemistry : AABC

|September 16, 2011

Summary

This summary is machine-generated.

We developed a new two-phase optimization strategy for genetic mapping of quantitative traits. This method accurately identifies quantitative trait loci (QTL) in high dimensions, significantly improving speed and accuracy over existing algorithms.

Keywords:

DIRECT QTL mapping global optimization

More Related Videos

Large-Scale Multi-Omics Genome-Wide Association Studies (Mo-GWAS): Guidelines for Sample Preparation and Normalization

Large-Scale Multi-Omics Genome-Wide Association Studies (Mo-GWAS): Guidelines for Sample Preparation and Normalization

Published on: July 27, 2021

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

Related Experiment Videos

Last Updated: May 29, 2026

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Published on: October 11, 2018

Large-Scale Multi-Omics Genome-Wide Association Studies (Mo-GWAS): Guidelines for Sample Preparation and Normalization

Large-Scale Multi-Omics Genome-Wide Association Studies (Mo-GWAS): Guidelines for Sample Preparation and Normalization

Published on: July 27, 2021

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

Area of Science:

Genetics
Computational Biology
Optimization

Background:

Genetic mapping of quantitative traits involves complex, multidimensional optimization problems.
Identifying multiple quantitative trait loci (QTL) leads to high-dimensional search spaces with numerous local optima.

Purpose of the Study:

To present an efficient and accurate two-phase optimization strategy for quantitative trait loci (QTL) mapping.
To improve the computational performance and precision of genetic mapping algorithms.

Main Methods:

Combined the global optimization algorithm DIRECT with local optimization methods.
Adapted algorithms to exploit problem-specific features and optimize the objective function evaluation.
Developed a two-phase strategy for multidimensional, nonconvex function optimization.

Main Results:

The proposed two-phase method demonstrates accuracy in at least six dimensions.
Achieved up to a tenfold increase in speed compared to current QTL mapping algorithms.
Improved objective function evaluation by exploiting optimization landscape smoothness.

Conclusions:

The presented two-phase optimization strategy offers a significant advancement in quantitative trait loci (QTL) mapping.
This approach enhances both the speed and accuracy of genetic analysis for complex traits.
The method is robust and effective for high-dimensional genetic mapping problems.