ArticleBioinformatics (Oxford, England)2016
ChemTreeMap: an interactive map of biochemical similarity in molecular datasets.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 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
10 citing papers in PubMed.
- Visualising lead optimisation series using reduced graphs.Journal of cheminformatics · 2025Article
- Molecular similarity: Theory, applications, and perspectives.Artificial intelligence chemistry · 2024Article
- The iPhylo suite: an interactive platform for building and annotating biological and chemical taxonomic trees.Briefings in bioinformatics · 2024Article
- Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review.International journal of molecular sciences · 2021Review
- A machine-learning-based alloy design platform that enables both forward and inverse predictions for thermo-mechanically controlled processed (TMCP) steel alloys.Scientific reports · 2021Article
- Visualization of very large high-dimensional data sets as minimum spanning trees.Journal of cheminformatics · 2020Article
- Learning Drug Functions from Chemical Structures with Convolutional Neural Networks and Random Forests.Journal of chemical information and modeling · 2019Article
- Are there physicochemical differences between allosteric and competitive ligands?PLoS computational biology · 2017Article
- C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms.Nucleic acids research · 2017Article
- From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics.GigaScience · 2017Review
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
motivationWhat if you could explain complex chemistry in a simple tree and share that data online with your collaborators? Computational biology often incorporates diverse chemical data to probe a biological question, but the existing tools for chemical data are ill-suited for the very large datasets inherent to bioinformatics. Furthermore, existing visualization methods often require an expert chemist to interpret the patterns. Biologists need an interactive tool for visualizing chemical information in an intuitive, accessible way that facilitates its integration into today's team-based biological research.
resultsChemTreeMap is an interactive, bioinformatics tool designed to explore chemical space and mine the relationships between chemical structure, molecular properties, and biological activity. ChemTreeMap synergistically combines extended connectivity fingerprints and a neighbor-joining algorithm to produce a hierarchical tree with branch lengths proportional to molecular similarity. Compound properties are shown by leaf color, size and outline to yield a user-defined visualization of the tree. Two representative analyses are included to demonstrate ChemTreeMap's capabilities and utility: assessing dataset overlap and mining structure-activity relationships. AVAILABILITY AND IMPLEMENTATION: The examples from this paper may be accessed at http://ajing.github.io/ChemTreeMap/ Code for the server and client are available in the Supplementary Information, at the aforementioned github site, and on Docker Hub (https://hub.docker.com) with the nametag ajing/chemtreemap. CONTACT: carlsonh@umich.eduSupplementary information: Supplementary data are available at Bioinformatics online.
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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.