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 Experiment Videos

Large scale genotype-phenotype correlation analysis based on phylogenetic trees.

Farhat Habib1, Andrew D Johnson, Ralf Bundschuh

  • 1Department of Physics, The Ohio State University, Columbus, OH 43210, USA. farhat@pacific.mps.ohio-state.edu

Bioinformatics (Oxford, England)
|February 3, 2007
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

DNA Methylation Variation in Blood Cells may Impact Platelet Function.

TH open : companion journal to thrombosis and haemostasis·2026
Same author

A genome-wide meta-analysis identifies a sex-specific genetic effect for platelet aggregation in response to agonists.

medRxiv : the preprint server for health sciences·2026
Same author

PvGAP: Development of a globally-applicable, highly-multiplexed microhaplotype amplicon panel for Plasmodium vivax.

The Journal of infectious diseases·2026
Same author

Co-occurring clonal hematopoiesis exhibits strong selection and high leukemia risk.

Nature communications·2026
Same author

Computational Structural Analysis Predicts Host-Range Promiscuity and Antiviral Resistance in North American H5N1 Lineages.

Computational and structural biotechnology journal·2026
Same author

Sixty years of research into ancestry differences in platelet function.

Platelets·2026
Same journal

Biomedical Concept Recognition with Error-aware Negative-enhanced Ranking Framework.

Bioinformatics (Oxford, England)·2026
Same journal

TEDLH: Domain HMMs for sensitive detection of remote homologues.

Bioinformatics (Oxford, England)·2026
Same journal

PLNFGL: Joint Estimation of Multi-Condition Gene Networks from Single-cell RNA-seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
Same journal

EDEL: Enhancing Dense Retrievers for Curation of Biomedical Knowledge Bases.

Bioinformatics (Oxford, England)·2026
See all related articles

We developed two methods, VENN and CCTSWEEP, to link genetic changes to phenotypic traits using phylogenetic trees. These methods identified single nucleotide polymorphisms (SNPs) associated with Bacillus anthracis resistance in mice.

Area of Science:

  • Evolutionary biology
  • Genetics
  • Bioinformatics

Background:

  • Phylogenetic trees are crucial for understanding evolutionary relationships.
  • Identifying genotype-phenotype correlations is essential for biological research.
  • Previous methods for correlating genotype and phenotype changes on phylogenetic trees have limitations.

Purpose of the Study:

  • To develop novel computational methods for identifying genotype changes correlated with phenotype changes on phylogenetic trees.
  • To apply these methods to discover genetic variants associated with Bacillus anthracis resistance in mice.

Main Methods:

  • VENN: Identifies genetic changes completely correlated with phenotype changes on trees with modest branch numbers.
  • CCTSWEEP: Uses Maddison's concentrated changes test for partial matching and scoring of genotype-phenotype correlations.

Related Experiment Videos

  • Application to inbred mouse strains to find single nucleotide polymorphisms (SNPs) linked to Bacillus anthracis resistance.

    • Main Results:

    • Successful identification of genotype-phenotype correlations using both VENN and CCTSWEEP.
    • Discovery of SNPs significantly correlated with Bacillus anthracis resistance in mouse models.
    • Findings align with existing biological literature on host-pathogen interactions.

    Conclusions:

    • The developed methods (VENN and CCTSWEEP) are effective tools for genotype-phenotype correlation analysis on phylogenetic trees.
    • The identified SNPs provide insights into the genetic basis of Bacillus anthracis resistance.
    • Potential novel candidate genes for further investigation were suggested.