The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology
Open accessAbstract
Summary: Next-generation sequencing can provide insight into protein–DNA association events on a genome-wide scale, and is being applied in an increasing number of applications in genomics and meta-genomics research. However, few software applications are available for interpreting these experiments. We present here an efficient application for use with chromatin-immunoprecipitation (ChIP-Seq) experimental data that includes novel functionality for identifying areas of gene enrichment and transcription factor binding site locations, as well as for estimating DNA fragment size distributions in enriched areas. The FindPeaks application can generate UCSC compatible custom ‘WIG’ track files from aligned-read files for short-read sequencing technology. The software application can be executed on any platform capable of running a Java Runtime Environment. Memory requirements are proportional to the number of sequencing reads analyzed; typically 4 GB permits processing of up to 40 million reads. Availability: The FindPeaks 3.1 package and manual, containing algorithm descriptions, usage instructions and examples, are available at http://www.bcgsc.ca/platform/bioinfo/software/findpeaks Source files for FindPeaks 3.1 are available for academic use. Contact: afejes@bcgsc.ca
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“The data sets were limited by applying thresholds as defined by an FDR cutoff of 0.01 and by trimming at 20% of maximal height to remove flanks and separate composite regions (Fejes et al., 2008).”
From Hippo Signaling Influences HNF4A and FOXA2 Enhancer Switching during Hepatocyte Differentiation (2014) · cites this paper as Fejes et al., 2008
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High-Resolution Profiling of Histone Methylations in the Human Genome
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845
Automated generation of heuristics for biological sequence comparison
Slater, G., & Birney, E. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-31 · Cited by 2,959
Genome-Wide Mapping of in Vivo Protein-DNA Interactions
Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007) · Science · doi:10.1126/science.1141319 · Cited by 2,927
Dynamic Regulation of Nucleosome Positioning in the Human Genome
Schones, D. E., Cui, K., Cuddapah, S., Roh, T., Barski, A., Wang, Z., Wei, G., & Zhao, K. (2008) · Cell · doi:10.1016/j.cell.2008.02.022 · Cited by 1,473
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Self-citationMorin, R. D., O’Connor, M. D., Griffith, M., Kuchenbauer, F., Delaney, A., Prabhu, A.-L., Zhao, Y., McDonald, H., Zeng, T., Hirst, M., et al. (2008) · Genome Research · doi:10.1101/gr.7179508 · Cited by 1,110
Genomic mapping by fingerprinting random clones: A mathematical analysis
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Integrative analysis of 111 reference human epigenomes
Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368
Self-citationChIP–seq: advantages and challenges of a maturing technology
Park, P. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2641 · Cited by 2,217
Identifying ChIP-seq enrichment using MACS
Feng, J., Liu, T., Qin, B., Zhang, Y., & Liu, X. S. (2012) · Nature Protocols · doi:10.1038/nprot.2012.101 · Cited by 1,848
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
Zhu, L. J., Gazin, C., Lawson, N. D., Pagès, H., Lin, S. M., Lapointe, D. S., & Green, M. R. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-237 · Cited by 1,159
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
Zang, C., Schones, D. E., Zeng, C., Cui, K., Zhao, K., & Peng, W. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp340 · Cited by 1,072
Metadata
- Authors
- Fejes, A. P., Robertson, G., Bilenky, M., Varhol, R., Bainbridge, M., & Jones, S. J. M.
- Affiliations
- BC Cancer Agency (CA)
- Corresponding author
- Fejes, Anthony P.
- Jones, Steven J. M.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-07-03
- Volume
- 24
- Issue
- 15
- Pages
- 1729-1730
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC2638869
- OpenAlex
- W2141222038
- Cited by
- 272
- References
- 8
- Citations by year
- 2026: 1 · 2025: 2 · 2023: 6 · 2022: 2 · 2021: 4 · 2020: 2 · 2019: 4 · 2018: 1 · 2017: 9 · 2016: 12 · 2015: 16 · 2014: 23 · 2013: 34 · 2012: 36
- FWCI
- 16.47
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- eSpace (Curtin University) (submittedVersion)
- Funders
- Genome Canada
- Michael Smith Health Research BC
- Genome British Columbia
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- ChIP-seq, peak calling, gene enrichment, transcription factor binding sites, DNA fragment size distribution, short-read sequencing, protein-DNA interactions, UCSC Genome Browser
- MeSH terms
- Algorithms, Binding Sites, Chromosome Mapping, Pattern Recognition, Automated, Software, Transcription Factors, Sequence Analysis, DNA, Chromatin Immunoprecipitation
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