ReviewNature biotechnology2007
Towards zoomable multidimensional maps of the cell.
Review in Nature biotechnology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers, 1 of them a synthesis that pooled it.
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
43 citing papers in PubMed, 1 synthesis or guideline pooled it, 89 citations in OpenAlex.
- The evolving transcriptome of head and neck squamous cell carcinoma: a systematic review.PloS one · 2008Pooled it
- Heuristic shortest hyperpaths in cell signaling hypergraphs.Algorithms for molecular biology : AMB · 2022Article
- Graphery: interactive tutorials for biological network algorithms.Nucleic acids research · 2021Article
- Mapping the multiscale structure of biological systems.Cell systems · 2021Review
- We need to keep a reproducible trace of facts, predictions, and hypotheses from gene to function in the era of big data.PLoS biology · 2020Article
- Hypergraph-based connectivity measures for signaling pathway topologies.PLoS computational biology · 2019Article
- Towards Building a Plant Cell Atlas.Trends in plant science · 2019Review
- Dark Proteome Database: Studies on Dark Proteins.High-throughput · 2019Article
- Article
- Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.PLoS computational biology · 2016Article
- Xtalk: a path-based approach for identifying crosstalk between signaling pathways.Bioinformatics (Oxford, England) · 2016Article
- xiNET: cross-link network maps with residue resolution.Molecular & cellular proteomics : MCP · 2015Article
- Mimoza: web-based semantic zooming and navigation in metabolic networks.BMC systems biology · 2015Article
- Extended LineSets: a visualization technique for the interactive inspection of biological pathways.BMC proceedings · 2015Article
- Functional characterization of breast cancer using pathway profiles.BMC medical genomics · 2014Article
- Signaling hypergraphs.Trends in biotechnology · 2014Article
- Using VisANT to Analyze Networks.Current protocols in bioinformatics · 2014Article
- NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps.BMC systems biology · 2013Article
- VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies.Nucleic acids research · 2013Article
- The BioIntelligence Framework: a new computational platform for biomedical knowledge computing.Journal of the American Medical Informatics Association : JAMIA · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
The detailed structure of molecular networks, including their dependence on conditions and time, are now routinely assayed by various experimental techniques. Visualization is a vital aid in integrating and interpreting such data. We describe emerging approaches for representing and visualizing systems data and for achieving semantic zooming, or changes in information density concordant with scale. A central challenge is to move beyond the display of a static network to visualizations of networks as a function of time, space and cell state, which capture the adaptability of the cell. We consider approaches for representing the role of protein complexes in the cell cycle, displaying modules of metabolism in a hierarchical format, integrating experimental interaction data with structured vocabularies such as Gene Ontology categories and representing conserved interactions among orthologous groups of genes.
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.