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Transcriptional regulatory code of a eukaryotic genome

Citations

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Cited by:

  1. 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.
  2. Yue Yuan & Qiang Huo & Ziru Zhang & Qun Wang & Juanxia Wang & Shuaikang Chang & Peng Cai & Karen M. Song & David W. Galbraith & Weixiao Zhang & Long Huang & Rentao Song & Zeyang Ma, 2024. "Decoding the gene regulatory network of endosperm differentiation in maize," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  3. 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.
  4. 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.
  5. 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.
  6. Anshul Kundaje & Xiantong Xin & Changgui Lan & Steve Lianoglou & Mei Zhou & Li Zhang & Christina Leslie, 2008. "A Predictive Model of the Oxygen and Heme Regulatory Network in Yeast," PLOS Computational Biology, Public Library of Science, vol. 4(11), pages 1-21, November.
  7. 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.
  8. 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.
  9. 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.
  10. Kyoung-Jae Won & Saurabh Agarwal & Li Shen & Robert Shoemaker & Bing Ren & Wei Wang, 2009. "An Integrated Approach to Identifying Cis-Regulatory Modules in the Human Genome," PLOS ONE, Public Library of Science, vol. 4(5), pages 1-8, May.
  11. 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.
  12. 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.
  13. Sourav Bandyopadhyay & Ryan Kelley & Nevan J Krogan & Trey Ideker, 2008. "Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data," PLOS Computational Biology, Public Library of Science, vol. 4(4), pages 1-8, April.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. Eilon Sharon & Shai Lubliner & Eran Segal, 2008. "A Feature-Based Approach to Modeling Protein–DNA Interactions," PLOS Computational Biology, Public Library of Science, vol. 4(8), pages 1-17, August.
  20. 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.
  21. Xiaoyu Tu & Sibo Ren & Wei Shen & Jianjian Li & Yuxiang Li & Chuanshun Li & Yangmeihui Li & Zhanxiang Zong & Weibo Xie & Donald Grierson & Zhangjun Fei & Jim Giovannoni & Pinghua Li & Silin Zhong, 2022. "Limited conservation in cross-species comparison of GLK transcription factor binding suggested wide-spread cistrome divergence," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  22. Phaedra Agius & Aaron Arvey & William Chang & William Stafford Noble & Christina Leslie, 2010. "High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions," PLOS Computational Biology, Public Library of Science, vol. 6(9), pages 1-12, September.
  23. Magali Prigent & Hélène Jean-Jacques & Delphine Naquin & Stéphane Chédin & Marie-Hélène Cuif & Renaud Legouis & Laurent Kuras, 2024. "Sulfur starvation-induced autophagy in Saccharomyces cerevisiae involves SAM-dependent signaling and transcription activator Met4," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  24. Xiaoke Ma & Long Gao & Georgios Karamanlidis & Peng Gao & Chi Fung Lee & Lorena Garcia-Menendez & Rong Tian & Kai Tan, 2015. "Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks," PLOS Computational Biology, Public Library of Science, vol. 11(6), pages 1-19, June.
  25. Shojaie Ali & Michailidis George, 2010. "Network Enrichment Analysis in Complex Experiments," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-36, May.
  26. Timothy E Reddy & Charles DeLisi & Boris E Shakhnovich, 2007. "Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites," PLOS Computational Biology, Public Library of Science, vol. 3(5), pages 1-11, May.
  27. 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.
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