The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing
Abstract
SUMMARY: Manual processing of DNA methylation data from bisulfite sequencing is a tedious and error-prone task. Here we present an interactive software tool that provides start-to-end support for this process. In an easy-to-use manner, the tool helps the user to import the sequence files from the sequencer, to align them, to exclude or correct critical sequences, to document the experiment, to perform basic statistics and to produce publication-quality diagrams. Emphasis is put on quality control: The program automatically assesses data quality and provides warnings and suggestions for dealing with critical sequences. The BiQ Analyzer program is implemented in the Java programming language and runs on any platform for which a recent Java virtual machine is available. AVAILABILITY: The program is available without charge for non-commercial users and can be downloaded from http://biq-analyzer.bioinf.mpi-inf.mpg.de/
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Citations
Cites
1 retracted
Induction of DNA methylation and gene silencing by short interfering RNAs in human cells
Kawasaki, H., & Taira, K. (2004) · Nature · doi:10.1038/nature02889 · Cited by 367
RetractedThompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4673 · Cited by 64,617
Frommer, M., McDonald, L. E., Millar, D. S., Collis, C. M., Watt, F., Grigg, G. W., Molloy, P. L., & Paul, C. L. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.5.1827 · Cited by 3,238
MethPrimer: designing primers for methylation PCRs
Li, L.-C., & Dahiya, R. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.11.1427 · Cited by 2,729
The history of cancer epigenetics
Feinberg, A. P., & Tycko, B. (2004) · Nature Reviews Cancer · doi:10.1038/nrc1279 · Cited by 2,344
BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes
Tusn dy, G. B. E. (2005) · Nucleic Acids Research · doi:10.1093/nar/gni012 · Cited by 197
Age-related epigenetic changes and the immune system
Issa, J.-P. (2003) · Clinical Immunology · doi:10.1016/s1521-6616(03)00203-1 · Cited by 182
Walter, J., & Paulsen, M. (2003) · Seminars in Cell and Developmental Biology · doi:10.1016/s1084-9521(02)00142-8 · Cited by 112
Self-citationMammalian epigenomics: reprogramming the genome for development and therapy
Reik, W., Santos, F., & Dean, W. (2002) · Theriogenology · doi:10.1016/s0093-691x(02)01269-4 · Cited by 112
DNA-Methylation Analysis by the Bisulfite-Assisted Genomic Sequencing Method
Hájková, P., El‐Maarri, O., Engemann, S., Oswald, J., Olek, A., & Walter, J. (2003) · Humana Press eBooks · doi:10.1385/1-59259-182-5:143 · Cited by 111
Self-citation
Cited by
Bock, C., Kiskinis, E., Verstappen, G., Gu, H., Boulting, G., Smith, Z. D., Ziller, M., Croft, G. F., Amoroso, M. W., Oakley, D. H., et al. (2011) · Cell · doi:10.1016/j.cell.2010.12.032 · Cited by 1,009
Self-citationHo, S.-M., Tang, W.-Y., Belmonte de Frausto, J., & Prins, G. S. (2006) · Cancer Research · doi:10.1158/0008-5472.can-06-0516 · Cited by 796
QUMA: quantification tool for methylation analysis
Kumaki, Y., Oda, M., & Okano, M. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn294 · Cited by 606
Quantitative comparison of genome-wide DNA methylation mapping technologies
Bock, C., Tomazou, E. M., Brinkman, A. B., Müller, F., Simmer, F., Gu, H., Jäger, N., Gnirke, A., Stunnenberg, H. G., & Meissner, A. (2010) · Nature Biotechnology · doi:10.1038/nbt.1681 · Cited by 593
Self-citationBoyko, A., Blevins, T., Yao, Y., Golubov, A., Bilichak, A., Ilnytskyy, Y., Hollander, J., Meins, F., & Kovalchuk, I. (2010) · Zurich Open Repository and Archive (University of Zurich) · doi:10.5167/uzh-44099 · Cited by 462
Metadata
- Authors
- Bock, C., Reither, S., Mikeska, T., Paulsen, M., Walter, J., & Lengauer, T.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2005-09-01
- Volume
- 21
- Issue
- 21
- Pages
- 4067-4068
- ISSN
- 0266-7061 (ISSN-L)
- 1367-4803
- 1460-2059
- OpenAlex
- W2161584400
- Cited by
- 621
- References
- 11
- FWCI
- 5.53
- Type
- journal article
- Language
- en
- Open access
- closed
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