Causal Network References

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• Aten JE, Fuller TF, Lusis AJ, Horvath S (2008) Using genetic markers to orient the edges in quantitative trait networks: the NEO software. BMC systems biology 2: 34. [doi:10.1186/1752-0509-2-34]

• Bernard A, Hartemink AJ (2005) Informative structure priors: joint learning of dynamic regulatory networks from multiple types of data. [http://psb.stanford.edu/psb-online/proceedings/psb05/abstracts/p459.html]
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• Castelo R, Siebes A (2000) Priors on network structures. Biasing the search for Bayesian networks. International Journal of Approximate Reasoning 24: 39-57. [doi:10.1016/S0888-613X(99)00041-9]
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• Das D, Pellegrini M, Gray JW (2009) A primer on regression methods for decoding cis-regulatory logic. PLoS Computational Biology 5: e1000269. [doi:10.1371/journal.pcbi.1000269]
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• Imoto S, Higuchi T, Goto T, Tashiro K, Kuhara S, Miyano S (2004) ombining microarrays and biological knowledge for estimating gene networks via Bayesian networks . Journal of Bioinformatics and Computational Biology 2: 77. [doi:10.1142/S021972000400048X | http://dnagarden.ims.u-tokyo.ac.jp/en/doku.php]

• Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M (2003) A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302: 449-453. [doi:10.1126/science.1087361]

• Keurentjes JJB, Fu J, Terpstra IR, Garcia JM, van den Ackerveken G, Snoek LB, Peeters AJM, Vreugdenhil D, Koornneef M, Jansen RC (2007) Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. Proceedings of the National Academy of Sciences 104: 1708-1713. [doi:10.1073/pnas.0610429104]
• Kulp DC, Jagalur M (2006) Causal inference of regulator-target pairs by gene mapping of expression phenotypes. BMC genomics 7: 125. [doi:10.1186/1471-2164-7-125]

• Lee SI, Dudley AM, Drubin D, Silver PA, Krogan NJ, Pe'er D, Koller D (2009) Learning a prior on regulatory potential from eQTL data. PLoS Genetics 5: e1000358. [doi:10.1371/journal.pgen.1000358 | http://dags.stanford.edu/lirnet]
• Li J, Li X, Su H, Chen H, Galbraith DW (2006) A framework of integrating gene relations from heterogeneous data sources: an experiment on Arabidopsis thaliana. Bioinformatics (Oxford, England) 22: 2037-2043. [doi:10.1093/bioinformatics/btl345]
• Li R, Tsaih SW, Shockley K, Stylianou IM, Wergedal J, Paigen B, Churchill GA (2006) Structural model analysis of multiple quantitative traits. PLoS Genetics 2: e114. [doi:10.1371/journal.pgen.0020114]
• Liu B, de la Fuente A, Hoeschele I (2008) Gene Network Inference via Structural Equation Modeling in Genetical Genomics Experiments. Genetics 178: 1763-1776. [doi:10.1534/genetics.107.080069]
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• Markowetz F, Spang R (2007) Inferring cellular networks--a review. BMC bioinformatics 8 Suppl 6: S5. [doi:10.1186/1471-2105-8-S6-S5]
• Millstein J, Zhang B, Zhu J, Schadt EE (2009) Disentangling molecular relationships with a causal inference test. BMC genetics 10: 23. [doi:10.1186/1471-2156-10-23]
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• Pearl J (2009) Causality: Models, Reasoning and Inference . Cambridge University Press. ISBN . [http://bayes.cs.ucla.edu/BOOK-2K | http://www3.cambridge.org/us/catalogue/catalogue.asp?isbn=0521773628]

• Schadt EE, Lamb J, Yang X, Zhu J, Edwards S, Guhathakurta D, Sieberts SK, Monks S, Reitman M, Zhang C, Lum PY, Leonardson A, Thieringer R, Metzger JM, Yang L, Castle J, Zhu H, Kash SF, Drake TA, Sachs A, Lusis AJ (2005) An integrative genomics approach to infer causal associations between gene expression and disease. Nature Genetics 37: 710-717. [doi:10.1038/ng1589]
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• Sun W, Yu T, Li KC (2007) Detection of eQTL modules mediated by activity levels of transcription factors. Bioinformatics 23: 2290-2297. [doi:10.1093/bioinformatics/btm327]

• Thomas R, Gohlke JM, Stopper GF, Parham FM, Portier CJ (2009) Choosing the right path: enhancement of biologically-relevant sets of genes or proteins using pathway structure. Genome biology 10: R44. [doi:10.1186/gb-2009-10-4-r44 | http://genomebiology.com/]
• Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D (2003) A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proceedings of the National Academy of Sciences of the United States of America 100: 8348-8353. [doi:10.1073/pnas.0832373100]

• von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399-403. [doi:10.1038/nature750]
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• Wang K, Saito M, Bisikirska BC, Alvarez MJ, Lim WK, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin AA, Klein U, Dalla-Favera R, Califano A (2009) Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nature Biotechnology 27: 829-837. [doi:10.1038/nbt.1563]
• Werhli AV, Husmeier D (2007) Reconstructing gene regulatory networks with bayesian networks by combining expression data with multiple sources of prior knowledge. Statistical applications in genetics and molecular biology 6: Article15. [doi:10.2202/1544-6115.1282]
• Winrow CJ, Williams DL, Kasarskis A, Millstein Joshua L, Yang HS, Mrazek K, Zhou L, Owens JR, Radzicki D, Preuss F, Schadt EE, Shimomura K, Vitaterna MH, Zhang C, Koblan KS, Renger JJ, Ture FW (2009) Uncovering the genetic landscape for multiple sleep-wake traits. PLoS ONE 4: e5161. [doi:10.1371/journal.pone.0005161]
• Wu MC, Zhang L, Wang Z, Christiani DC, Lin X (2009) Sparse linear discriminant analysis for simultaneous testing for the significance of a gene set/pathway and gene selection. Bioinformatics 25: 1145-1151. [doi:10.1093/bioinformatics/btp019]

• Yeang CH, Ideker T, Jaakkola T (2004) Physical Network Models. Journal of Computational Biology 11: 243-262. [doi:10.1089/1066527041410382]

• Zheng W, Zhao H, Mancera E, Steinmetz LM, Snyder M (2010) Genetic analysis of variation in transcription factor binding in yeast. Nature 00: 000. [doi:10.1038/nature08934 | http://www.nature.com/nature/current_issue/]
• Zhu J, Wiener MC, Zhang C, Fridman A, Minch E, Lum PY, Sachs JR, Schadt EE (2007) Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations. PLoS Computational Biology 3: e69. [doi:10.1371/journal.pcbi.0030069]
• Zhu J, Zhang B, Smith EN, Drees B, Brem RB, Kruglyak L, Bumgarner RE, Schadt EE (2008) Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nature Genetics 40: 854-861. [doi:10.1038/ng.167]

Last modified: Tue Mar 30 15:40:50 2010 by Brian S. Yandell