Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites
Author
Abstract
Suggested Citation
DOI: 10.1371/journal.pcbi.0030090
Download full text from publisher
References listed on IDEAS
- Rahul Siddharthan & Eric D Siggia & Erik van Nimwegen, 2005. "PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny," PLOS Computational Biology, Public Library of Science, vol. 1(7), pages 1-23, December.
- Christopher T. Harbison & D. Benjamin Gordon & Tong Ihn Lee & Nicola J. Rinaldi & Kenzie D. Macisaac & Timothy W. Danford & Nancy M. Hannett & Jean-Bosco Tagne & David B. Reynolds & Jane Yoo & Ezra G., 2004. "Transcriptional regulatory code of a eukaryotic genome," Nature, Nature, vol. 431(7004), pages 99-104, September.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Harri Lähdesmäki & Alistair G Rust & Ilya Shmulevich, 2008. "Probabilistic Inference of Transcription Factor Binding from Multiple Data Sources," PLOS ONE, Public Library of Science, vol. 3(3), pages 1-24, March.
- Kenzie D MacIsaac & Ernest Fraenkel, 2006. "Practical Strategies for Discovering Regulatory DNA Sequence Motifs," PLOS Computational Biology, Public Library of Science, vol. 2(4), pages 1-10, April.
- Ivan Dotu & Scott I Adamson & Benjamin Coleman & Cyril Fournier & Emma Ricart-Altimiras & Eduardo Eyras & Jeffrey H Chuang, 2018. "SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data," PLOS Computational Biology, Public Library of Science, vol. 14(3), pages 1-25, March.
- Matvei Khoroshkin & Andrey Buyan & Martin Dodel & Albertas Navickas & Johnny Yu & Fathima Trejo & Anthony Doty & Rithvik Baratam & Shaopu Zhou & Sean B. Lee & Tanvi Joshi & Kristle Garcia & Benedict C, 2024. "Systematic identification of post-transcriptional regulatory modules," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
- Zing Tsung-Yeh Tsai & Shin-Han Shiu & Huai-Kuang Tsai, 2015. "Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast," PLOS Computational Biology, Public Library of Science, vol. 11(8), pages 1-22, August.
- Gross, Eitan, 2015. "Effect of environmental stress on regulation of gene expression in the yeast," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 430(C), pages 224-235.
- Armita Nourmohammad & Michael Lässig, 2011. "Formation of Regulatory Modules by Local Sequence Duplication," PLOS Computational Biology, Public Library of Science, vol. 7(10), pages 1-12, October.
- Wei-Sheng Wu & Fu-Jou Lai, 2016. "Detecting Cooperativity between Transcription Factors Based on Functional Coherence and Similarity of Their Target Gene Sets," PLOS ONE, Public Library of Science, vol. 11(9), pages 1-12, September.
- Rahul Siddharthan & Eric D Siggia & Erik van Nimwegen, 2005. "PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny," PLOS Computational Biology, Public Library of Science, vol. 1(7), pages 1-23, December.
- Jens Keilwagen & Jan Grau & Ivan A Paponov & Stefan Posch & Marc Strickert & Ivo Grosse, 2011. "De-Novo Discovery of Differentially Abundant Transcription Factor Binding Sites Including Their Positional Preference," PLOS Computational Biology, Public Library of Science, vol. 7(2), pages 1-13, February.
- Guo-Cheng Yuan & Jun S Liu, 2008. "Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion," PLOS Computational Biology, Public Library of Science, vol. 4(1), pages 1-11, January.
- Jia Lu & Xiaoyi Cao & Sheng Zhong, 2018. "A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome," PLOS Computational Biology, Public Library of Science, vol. 14(12), pages 1-28, December.
- Saket Navlakha & Anthony Gitter & Ziv Bar-Joseph, 2012. "A Network-based Approach for Predicting Missing Pathway Interactions," PLOS Computational Biology, Public Library of Science, vol. 8(8), pages 1-13, August.
- Leelavati Narlikar & Raluca Gordân & Alexander J Hartemink, 2007. "A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast," PLOS Computational Biology, Public Library of Science, vol. 3(11), pages 1-10, November.
- Jeremiah J Faith & Boris Hayete & Joshua T Thaden & Ilaria Mogno & Jamey Wierzbowski & Guillaume Cottarel & Simon Kasif & James J Collins & Timothy S Gardner, 2007. "Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles," PLOS Biology, Public Library of Science, vol. 5(1), pages 1-13, January.
- Joshua S Weitz & Philip N Benfey & Ned S Wingreen, 2007. "Evolution, Interactions, and Biological Networks," PLOS Biology, Public Library of Science, vol. 5(1), pages 1-3, January.
- Saeed Omidi & Mihaela Zavolan & Mikhail Pachkov & Jeremie Breda & Severin Berger & Erik van Nimwegen, 2017. "Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors," PLOS Computational Biology, Public Library of Science, vol. 13(7), pages 1-22, July.
- Aqil M Azmi & Abdulrakeeb Al-Ssulami, 2014. "Encoded Expansion: An Efficient Algorithm to Discover Identical String Motifs," PLOS ONE, Public Library of Science, vol. 9(5), pages 1-9, May.
- Dana S F Homsi & Vineet Gupta & Gary D Stormo, 2009. "Modeling the Quantitative Specificity of DNA-Binding Proteins from Example Binding Sites," PLOS ONE, Public Library of Science, vol. 4(8), pages 1-9, August.
- Manikandan Narayanan & Adrian Vetta & Eric E Schadt & Jun Zhu, 2010. "Simultaneous Clustering of Multiple Gene Expression and Physical Interaction Datasets," PLOS Computational Biology, Public Library of Science, vol. 6(4), pages 1-13, April.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pcbi00:0030090. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.