ArticleJournal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America2012
Computational Tools for Evaluating Phylogenetic and Hierarchical Clustering Trees.
Article in Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed.
- Functional group classification using consensus clustering.PLoS computational biology · 2026Article
- A PANoptosis-Based Signature for Survival and Immune Predication in Glioblastoma Multiforme.Annals of clinical and translational neurology · 2025Article
- Psychopathological Implications of Behavioral Patterns in Obsessive-Compulsive Rituals: A Hierarchical Analysis.Brain sciences · 2025Article
- Analyzing microbial evolution through gene and genome phylogenies.Biostatistics (Oxford, England) · 2024Article
- Statistical summaries of unlabelled evolutionary trees.Biometrika · 2024Article
- Testing for genetic mutation of seasonal influenza virus.Journal of applied statistics · 2023Article
- Robust Analysis of Phylogenetic Tree Space.Systematic biology · 2022Article
- Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes.Systematic biology · 2021Article
- Signature RNAS and related regulatory roles in type 1 diabetes mellitus based on competing endogenous RNA regulatory network analysis.BMC medical genomics · 2021Article
- Prognostic Biomarkers on a Competitive Endogenous RNA Network Reveals Overall Survival in Triple-Negative Breast Cancer.Frontiers in oncology · 2021Article
- Distance metrics for ranked evolutionary trees.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Estimating autoantibody signatures to detect autoimmune disease patient subsets.Biostatistics (Oxford, England) · 2019Article
- treespace: Statistical exploration of landscapes of phylogenetic trees.Molecular ecology resources · 2017Article
- Review Paper: The Shape of Phylogenetic Treespace.Systematic biology · 2017Review
- Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution.Molecular biology and evolution · 2016Article
- Advancing our understanding of the human microbiome using QIIME.Methods in enzymology · 2013Article
- Assessing parameter identifiability in phylogenetic models using data cloning.Systematic biology · 2012Article
- A support vector machine based test for incongruence between sets of trees in tree space.BMC bioinformatics · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Inferential summaries of tree estimates are useful in the setting of evolutionary biology, where phylogenetic trees have been built from DNA data since the 1960s. In bioinformatics, psychometrics, and data mining, hierarchical clustering techniques output the same mathematical objects, and practitioners have similar questions about the stability and "generalizability" of these summaries. This article describes the implementation of the geometric distance between trees developed by Billera, Holmes, and Vogtmann (2001) equally applicable to phylogenetic trees and hierarchical clustering trees, and shows some of the applications in evaluating tree estimates. In particular, since Billera et al. (2001) have shown that the space of trees is negatively curved (called a CAT(0) space), a collection of trees can naturally be represented as a tree. We compare this representation to the Euclidean approximations of treespace made available through both a classical multidimensional scaling and a Kernel multidimensional scaling of the matrix of the distances between trees. We also provide applications of the distances between trees to hierarchical clustering trees constructed from microarrays. Our method gives a new way of evaluating the influence of both certain columns (positions, variables, or genes) and certain rows (species, observations, or arrays) on the construction of such trees. It also can provide a way of detecting heterogeneous mixtures in the input data. Supplementary materials for this article are available online.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.