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Showing 1 to 9 of 9 entries
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NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data.

BMC genomics

Kim NK, Jayatillake RV, Spouge JL.
PMID: 23706083
BMC Genomics. 2013 May 25;14:349. doi: 10.1186/1471-2164-14-349.

BACKGROUND: Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) can locate transcription factor binding sites on genomic scale. Although many models and programs are available to call peaks, none has dominated its competition in comparison studies.RESULTS: We propose a rigorous...

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Kim NK, Jayatillake RV, Spouge JL. NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data. BMC Genomics. 2013;14:349doi: 10.1186/1471-2164-14-349.
Kim, N. K., Jayatillake, R. V., & Spouge, J. L. (2013). NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data. BMC genomics, 14349. https://doi.org/10.1186/1471-2164-14-349
Kim, Nak-Kyeong, et al. "NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data." BMC genomics vol. 14 (2013): 349. doi: https://doi.org/10.1186/1471-2164-14-349
Kim NK, Jayatillake RV, Spouge JL. NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data. BMC Genomics. 2013 May 25;14:349. doi: 10.1186/1471-2164-14-349. PMID: 23706083; PMCID: PMC3672025.
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Nanobody-based chromatin immunoprecipitation.

Methods in molecular biology (Clifton, N.J.)

Duc TN, Hassanzadeh-Ghassabeh G, Saerens D, Peeters E, Charlier D, Muyldermans S.
PMID: 22886272
Methods Mol Biol. 2012;911:491-505. doi: 10.1007/978-1-61779-968-6_31.

Chromatin immunoprecipitation (ChIP), followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq), is becoming a widely used powerful method for the analysis of the in vivo DNA-protein interactions at genomic scale.The success of ChIP largely depends on the quality...

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Duc TN, Hassanzadeh-Ghassabeh G, Saerens D, et al. Nanobody-based chromatin immunoprecipitation. Methods Mol Biol. 2012;911:491-505doi: 10.1007/978-1-61779-968-6_31.
Duc, T. N., Hassanzadeh-Ghassabeh, G., Saerens, D., Peeters, E., Charlier, D., & Muyldermans, S. (2012). Nanobody-based chromatin immunoprecipitation. Methods in molecular biology (Clifton, N.J.), 911491-505. https://doi.org/10.1007/978-1-61779-968-6_31
Duc, Trong Nguyen, et al. "Nanobody-based chromatin immunoprecipitation." Methods in molecular biology (Clifton, N.J.) vol. 911 (2012): 491-505. doi: https://doi.org/10.1007/978-1-61779-968-6_31
Duc TN, Hassanzadeh-Ghassabeh G, Saerens D, Peeters E, Charlier D, Muyldermans S. Nanobody-based chromatin immunoprecipitation. Methods Mol Biol. 2012;911:491-505. doi: 10.1007/978-1-61779-968-6_31. PMID: 22886272.
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Analyzing ChIP-chip data using bioconductor.

PLoS computational biology

Toedling J, Huber W.
PMID: 19043553
PLoS Comput Biol. 2008 Nov;4(11):e1000227. doi: 10.1371/journal.pcbi.1000227. Epub 2008 Nov 28.

No abstract available.

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Toedling J, Huber W. Analyzing ChIP-chip data using bioconductor. PLoS Comput Biol. 2008;4(11):e1000227doi: 10.1371/journal.pcbi.1000227.
Toedling, J., & Huber, W. (2008). Analyzing ChIP-chip data using bioconductor. PLoS computational biology, 4(11), e1000227. https://doi.org/10.1371/journal.pcbi.1000227
Toedling, Joern, and Huber, Wolfgang. "Analyzing ChIP-chip data using bioconductor." PLoS computational biology vol. 4,11 (2008): e1000227. doi: https://doi.org/10.1371/journal.pcbi.1000227
Toedling J, Huber W. Analyzing ChIP-chip data using bioconductor. PLoS Comput Biol. 2008 Nov;4(11):e1000227. doi: 10.1371/journal.pcbi.1000227. Epub 2008 Nov 28. PMID: 19043553; PMCID: PMC2582686.
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A statistical framework for power calculations in ChIP-seq experiments.

Bioinformatics (Oxford, England)

Zuo C, Keleş S.
PMID: 23665773
Bioinformatics. 2014 Mar 15;30(6):753-60. doi: 10.1093/bioinformatics/btt200. Epub 2013 May 10.

MOTIVATION: ChIP-seq technology enables investigators to study genome-wide binding of transcription factors and mapping of epigenomic marks. Although the availability of basic analysis tools for ChIP-seq data is rapidly increasing, there has not been much progress on the related...

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Zuo C, Keleş S. A statistical framework for power calculations in ChIP-seq experiments. Bioinformatics. 2013;30(6):753-60doi: 10.1093/bioinformatics/btt200.
Zuo, C., & Keleş, S. (2014). A statistical framework for power calculations in ChIP-seq experiments. Bioinformatics (Oxford, England), 30(6), 753-60. https://doi.org/10.1093/bioinformatics/btt200
Zuo, Chandler, and Keleş, Sündüz. "A statistical framework for power calculations in ChIP-seq experiments." Bioinformatics (Oxford, England) vol. 30,6 (2014): 753-60. doi: https://doi.org/10.1093/bioinformatics/btt200
Zuo C, Keleş S. A statistical framework for power calculations in ChIP-seq experiments. Bioinformatics. 2014 Mar 15;30(6):753-60. doi: 10.1093/bioinformatics/btt200. Epub 2013 May 10. PMID: 23665773; PMCID: PMC3957067.
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Chromatin immunoprecipitation assay.

BioTechniques

Das PM, Ramachandran K, vanWert J, Singal R.
PMID: 15597545
Biotechniques. 2004 Dec;37(6):961-9. doi: 10.2144/04376RV01.

Association between proteins and DNA is crucial for many vital cellular functions such as gene transcription, DNA replication and recombination, repair, segregation, chromosomal stability, cell cycle progression, and epigenetic silencing. It is important to know the genomic targets of...

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Das PM, Ramachandran K, vanWert J, et al. Chromatin immunoprecipitation assay. Biotechniques. 2004;37(6):961-9doi: 10.2144/04376RV01.
Das, P. M., Ramachandran, K., vanWert, J., & Singal, R. (2004). Chromatin immunoprecipitation assay. BioTechniques, 37(6), 961-9. https://doi.org/10.2144/04376RV01
Das, Partha M, et al. "Chromatin immunoprecipitation assay." BioTechniques vol. 37,6 (2004): 961-9. doi: https://doi.org/10.2144/04376RV01
Das PM, Ramachandran K, vanWert J, Singal R. Chromatin immunoprecipitation assay. Biotechniques. 2004 Dec;37(6):961-9. doi: 10.2144/04376RV01. PMID: 15597545.
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CoCAS: a ChIP-on-chip analysis suite.

Bioinformatics (Oxford, England)

Benoukraf T, Cauchy P, Fenouil R, Jeanniard A, Koch F, Jaeger S, Thieffry D, Imbert J, Andrau JC, Spicuglia S, Ferrier P.
PMID: 19193731
Bioinformatics. 2009 Apr 01;25(7):954-5. doi: 10.1093/bioinformatics/btp075. Epub 2009 Feb 04.

MOTIVATION: High-density tiling microarrays are increasingly used in combination with ChIP assays to study transcriptional regulation. To ease the analysis of the large amounts of data generated by this approach, we have developed ChIP-on-chip Analysis Suite (CoCAS), a standalone...

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Benoukraf T, Cauchy P, Fenouil R, et al. CoCAS: a ChIP-on-chip analysis suite. Bioinformatics. 2009;25(7):954-5doi: 10.1093/bioinformatics/btp075.
Benoukraf, T., Cauchy, P., Fenouil, R., Jeanniard, A., Koch, F., Jaeger, S., Thieffry, D., Imbert, J., Andrau, J. C., Spicuglia, S., & Ferrier, P. (2009). CoCAS: a ChIP-on-chip analysis suite. Bioinformatics (Oxford, England), 25(7), 954-5. https://doi.org/10.1093/bioinformatics/btp075
Benoukraf, Touati, et al. "CoCAS: a ChIP-on-chip analysis suite." Bioinformatics (Oxford, England) vol. 25,7 (2009): 954-5. doi: https://doi.org/10.1093/bioinformatics/btp075
Benoukraf T, Cauchy P, Fenouil R, Jeanniard A, Koch F, Jaeger S, Thieffry D, Imbert J, Andrau JC, Spicuglia S, Ferrier P. CoCAS: a ChIP-on-chip analysis suite. Bioinformatics. 2009 Apr 01;25(7):954-5. doi: 10.1093/bioinformatics/btp075. Epub 2009 Feb 04. PMID: 19193731; PMCID: PMC2660873.
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Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis.

BMC bioinformatics

Cormier N, Kolisnik T, Bieda M.
PMID: 27377783
BMC Bioinformatics. 2016 Jul 05;17(1):270. doi: 10.1186/s12859-016-1125-3.

BACKGROUND: There has been an enormous expansion of use of chromatin immunoprecipitation followed by sequencing (ChIP-seq) technologies. Analysis of large-scale ChIP-seq datasets involves a complex series of steps and production of several specialized graphical outputs. A number of systems...

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Cormier N, Kolisnik T, Bieda M. Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis. BMC Bioinformatics. 2016;17(1):270doi: 10.1186/s12859-016-1125-3.
Cormier, N., Kolisnik, T., & Bieda, M. (2016). Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis. BMC bioinformatics, 17(1), 270. https://doi.org/10.1186/s12859-016-1125-3
Cormier, Nathan, et al. "Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis." BMC bioinformatics vol. 17,1 (2016): 270. doi: https://doi.org/10.1186/s12859-016-1125-3
Cormier N, Kolisnik T, Bieda M. Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis. BMC Bioinformatics. 2016 Jul 05;17(1):270. doi: 10.1186/s12859-016-1125-3. PMID: 27377783; PMCID: PMC4932705.
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Microfluidics Technologies for Low Cell Number Chromatin Immunoprecipitation.

Cold Spring Harbor protocols

Wu AR, Quake SR.
PMID: 26700100
Cold Spring Harb Protoc. 2016 Apr 01;2016(4):pdb.prot084996. doi: 10.1101/pdb.prot084996.

Protein-DNA interactions are responsible for numerous critical cellular events: For example, gene expression and silencing are mediated by transcription factor protein binding and histone protein modifications, and DNA replication and repair rely on site-specific protein binding. Chromatin immunoprecipitation (ChIP)...

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Wu AR, Quake SR. Microfluidics Technologies for Low Cell Number Chromatin Immunoprecipitation. Cold Spring Harb Protoc. 2016;2016(4):pdb.prot084996doi: 10.1101/pdb.prot084996.
Wu, A. R., & Quake, S. R. (2016). Microfluidics Technologies for Low Cell Number Chromatin Immunoprecipitation. Cold Spring Harbor protocols, 2016(4), pdb.prot084996. https://doi.org/10.1101/pdb.prot084996
Wu, Angela R, and Quake, Stephen R. "Microfluidics Technologies for Low Cell Number Chromatin Immunoprecipitation." Cold Spring Harbor protocols vol. 2016,4 (2016): pdb.prot084996. doi: https://doi.org/10.1101/pdb.prot084996
Wu AR, Quake SR. Microfluidics Technologies for Low Cell Number Chromatin Immunoprecipitation. Cold Spring Harb Protoc. 2016 Apr 01;2016(4):pdb.prot084996. doi: 10.1101/pdb.prot084996. PMID: 26700100.
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Computational analysis of protein-DNA interactions from ChIP-seq data.

Methods in molecular biology (Clifton, N.J.)

Rougemont J, Naef F.
PMID: 21938632
Methods Mol Biol. 2012;786:263-73. doi: 10.1007/978-1-61779-292-2_16.

Chromatin immunoprecipitation experiments followed by ultra-high-throughput sequencing (ChIP-seq) is becoming the method of choice to identify transcription factor binding sites in prokaryotes and eukaryotes in vivo. Here, we review the computational steps that are necessary for analyzing the sequenced...

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Rougemont J, Naef F. Computational analysis of protein-DNA interactions from ChIP-seq data. Methods Mol Biol. 2012;786:263-73doi: 10.1007/978-1-61779-292-2_16.
Rougemont, J., & Naef, F. (2012). Computational analysis of protein-DNA interactions from ChIP-seq data. Methods in molecular biology (Clifton, N.J.), 786263-73. https://doi.org/10.1007/978-1-61779-292-2_16
Rougemont, Jacques, and Naef, Felix. "Computational analysis of protein-DNA interactions from ChIP-seq data." Methods in molecular biology (Clifton, N.J.) vol. 786 (2012): 263-73. doi: https://doi.org/10.1007/978-1-61779-292-2_16
Rougemont J, Naef F. Computational analysis of protein-DNA interactions from ChIP-seq data. Methods Mol Biol. 2012;786:263-73. doi: 10.1007/978-1-61779-292-2_16. PMID: 21938632.
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Showing 1 to 9 of 9 entries