The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Tools for visually exploring biological networks
Abstract
Many tools exist for visually exploring biological networks including well-known examples such as Cytoscape, VisANT, Pathway Studio and Patika. These systems play a key role in the development of integrative biology, systems biology and integrative bioinformatics. The trend in the development of these tools is to go beyond ‘static’ representations of cellular state, towards a more dynamic model of cellular processes through the incorporation of gene expression data, subcellular localization information and time-dependent behavior. We provide a comprehensive review of the relative advantages and disadvantages of existing systems with two goals in mind: to aid researchers in efficiently identifying the appropriate existing tools for data visualization; to describe the necessary and realistic goals for the next generation of visualization tools. In view of the first goal, we provide in the Supplementary Material a systematic comparison of more than 35 existing tools in terms of over 25 different features. Contact: msuder@mcb.mcgill.ca Supplementary information: Supplementary data are available at Bioinformatics online.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans
Fire, A., Xu, S., Montgomery, M. K., Kostas, S. A., Driver, S. E., & Mello, C. C. (1998) · Nature · doi:10.1038/35888 · Cited by 15,429
Network biology: understanding the cell's functional organization
Barabási, A.-L., & Oltvai, Z. N. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1272 · Cited by 7,903
Error and attack tolerance of complex networks
Albert, R., Jeong, H., & Barabási, A.-L. (2000) · Nature · doi:10.1038/35019019 · Cited by 7,534
Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants
Tong, A. H. Y., Evangelista, M., Parsons, A. B., Xu, H., Bader, G. D., Pagé, N., Robinson, M., Raghibizadeh, S., Hogue, C. W. V., Bussey, H., et al. (2001) · Science · doi:10.1126/science.1065810 · Cited by 2,138
Collins, S. R., Miller, K. M., Maas, N. L., Roguev, A., Fillingham, J., Chu, C. S., Schuldiner, M., Gebbia, M., Recht, J., Shales, M., et al. (2007) · Nature · doi:10.1038/nature05649 · Cited by 869
Karp, P. D., Paley, S., & Romero, P. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.suppl_1.s225 · Cited by 661
High-throughput RNAi screening in cultured cells: a user's guide
Echeverri, C. J., & Perrimon, N. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1836 · Cited by 380 · cited 2×
“…screens (e.g. [Rigaut et al., 1999, Fields and kyu Song, 1989, Selbach and Mann, 2006]), RNAi-based genetic interaction screens [Fire et al., 1998, Echeverri and Perrimon, 2006] gene expression [Lockhart et al., 1996], and ChIP-Chip arrays [Blat and Kleckner, 1999, Ren et al., 2000] are readily…”
BackgroundSystems biology markup language: Level 2 and beyond
Finney, A., & Hucka, M. (2003) · Biochemical Society Transactions · doi:10.1042/bst0311472 · Cited by 187
Barsky, A., Gardy, J. L., Hancock, R. E. W., & Munzner, T. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm057 · Cited by 175
Cited by
Statistical analysis strategies for association studies involving rare variants
Bansal, V., Libiger, O., Torkamani, A., & Schork, N. J. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2867 · Cited by 455
GPS-Prot: A web-based visualization platform for integrating host-pathogen interaction data
Fahey, M. E., Bennett, M. J., Mahon, C., Jäger, S., Pache, L., Kumar, D., Shapiro, A., Rao, K., Chanda, S. K., Craik, C. S., et al. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-298 · Cited by 87
Genome to Phenome: A Systems Biology Approach to PTSD Using an Animal Model
Chakraborty, N., Meyerhoff, J., Jett, M., & Hammamieh, R. (2017) · Methods in Molecular Biology · doi:10.1007/978-1-4939-6952-4_6 · Cited by 14
Metadata
- Authors
- Suderman, M., & Hallett, M.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-08-25
- Volume
- 23
- Issue
- 20
- Pages
- 2651-2659
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2140635350
- Cited by
- 237
- References
- 10
- FWCI
- 11.49
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Tools for visually exploring biological networks. https://app.cochat.ai/papers/10.1093/bioinformatics/btm401
- The paper
- Suderman, M., & Hallett, M. (2007). Tools for visually exploring biological networks. Bioinformatics. https://doi.org/10.1093/bioinformatics/btm401
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
