The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Integrated genome browser: visual analytics platform for genomics
Open accessAbstract
Motivation: Genome browsers that support fast navigation through vast datasets and provide interactive visual analytics functions can help scientists achieve deeper insight into biological systems. Toward this end, we developed Integrated Genome Browser (IGB), a highly configurable, interactive and fast open source desktop genome browser. Results: Here we describe multiple updates to IGB, including all-new capabilities to display and interact with data from high-throughput sequencing experiments. To demonstrate, we describe example visualizations and analyses of datasets from RNA-Seq, ChIP-Seq and bisulfite sequencing experiments. Understanding results from genome-scale experiments requires viewing the data in the context of reference genome annotations and other related datasets. To facilitate this, we enhanced IGB’s ability to consume data from diverse sources, including Galaxy, Distributed Annotation and IGB-specific Quickload servers. To support future visualization needs as new genome-scale assays enter wide use, we transformed the IGB codebase into a modular, extensible platform for developers to create and deploy all-new visualizations of genomic data. Availability and implementation: IGB is open source and is freely available from http://bioviz.org/igb. Contact: aloraine@uncc.edu
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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
ChIP–seq: advantages and challenges of a maturing technology
Park, P. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2641 · Cited by 2,217
RNA sequencing: advances, challenges and opportunities
Ozsolak, F., & Milos, P. M. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2934 · Cited by 2,135 · cited 1×
“As ultra high-throughput sequencing of cDNA (RNA-Seq) has supplanted microarrays for surveying gene expression (Ozsolak and Milos, 2011), we added new features to IGB to support visualization of RNA-Seq data.”
Cited by
Kang, Y., Kim, Y. W., Kang, J., & Kim, A. (2021) · The FASEB Journal · doi:10.1096/fj.202100488r · Cited by 93
York, R. A., Patil, C., Abdilleh, K., Johnson, Z. V., Conte, M. A., Genner, M. J., McGrath, P. T., Fraser, H. B., Fernald, R. D., & Streelman, J. T. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1810140115 · Cited by 60
Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver
Dubois, V., Gheeraert, C., Vankrunkelsven, W., Dubois‐Chevalier, J., Dehondt, H., Bobowski‐Gerard, M., Vinod, M., Zummo, F. P., Güiza, F., Ploton, M., et al. (2020) · Molecular Systems Biology · doi:10.15252/msb.20199156 · Cited by 46
An extended transcription factor regulatory network controls hepatocyte identity
Dubois‐Chevalier, J., Gheeraert, C., Berthier, A., Boulet, C., Dubois, V., Guille, L., Fourcot, M., Marot, G., Gauthier, K., Dubuquoy, L., et al. (2023) · EMBO Reports · doi:10.15252/embr.202357020 · Cited by 6
Metadata
- Authors
- Freese, N. H., Norris, D. C., & Loraine, A. E.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-03-16
- Volume
- 32
- Issue
- 14
- Pages
- 2089-2095
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2334656801
- Cited by
- 371
- References
- 3
- FWCI
- 13.39
- Type
- journal article
- Language
- en
- Open access
- hybrid
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