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Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate

By Gabriel Krouk, Piotr Mirowski, Yann LeCun, Dennis E Shasha and Gloria M Coruzzi
Topics: Research
Publisher: BioMed Central
OAI identifier: oai:pubmedcentral.nih.gov:3046483
Provided by: PubMed Central

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  1. (2005). A Bayesian approach to reconstructing genetic regulatory networks with hidden factors. Bioinformatics
  2. (2010). A: Nitrate and auxin transport by NRT1.1 defines a mechanism for nutrient sensing in plants. Dev Cell
  3. (2009). A: The nodule inception-like protein 7 modulates nitrate sensing and metabolism in Arabidopsis. Plant J
  4. (2010). An integrated machine learning approach for predicting DosR-regulated genes in Mycobacterium tuberculosis.
  5. (2009). Coruzzi GM: A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive “biomodule”.
  6. (2010). Coruzzi GM: A systems view of responses to nutritional cues in Arabidopsis: toward a paradigm shift for predictive network modeling. Plant Physiol
  7. (2007). Coruzzi GM: Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol
  8. (2009). D: miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell
  9. (2006). Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses. Cell
  10. (2008). Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana. Plant Cell
  11. (2007). Emes MJ: The effect of Glc6P uptake and its subsequent oxidation within pea root plastids on nitrite reduction and glutamate synthesis.
  12. (1998). Forde BG: An Arabidopsis MADS box gene that controls nutrient-induced changes in root architecture. Science
  13. (2004). Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen. Plant Physiol
  14. (2008). Gojon A: Oxidative pentose phosphate pathway-dependent sugar sensing as a mechanism for regulation of root ion transporters by photosynthesis. Plant Physiol
  15. (2006). Gojon A: Regulation of the high-affinity NO3- uptake system by NRT1.1-mediated NO3- demand signaling in Arabidopsis. Plant Physiol
  16. (2006). Gojon A: The Arabidopsis NRT1.1 transporter participates in the signaling pathway triggering root colonization of nitrate-rich patches. Proc Natl Acad Sci USA
  17. (2004). Gojon A: Transcript profiling in the chl1-5 mutant of Arabidopsis reveals a role of the nitrate transporter NRT1.1 in the regulation of another nitrate transporter, NRT2.1. Plant Cell
  18. (2009). Grouped graphical Granger modeling for gene expression regulatory networks discovery. Bioinformatics
  19. Inferring transcriptional networks using prior biological knowledge and constrained state-space models.
  20. (2008). KD: Cell-specific nitrogen responses mediate developmental plasticity.
  21. (2006). L: Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics
  22. (2009). LeCun Y: Dynamical factor graphs for time series modeling.
  23. Mian S: Modelling Gene Expression Data using Dynamic Bayesian Networks.
  24. (2009). Miyano S: Recursive regularization for inferring gene networks from time-course gene expression profiles.
  25. (2001). Modeling genetic regulatory dynamic in neural development.
  26. (1995). Nitrate - nutrient and signal for plant-growth. Plant Cell
  27. (2009). NM: A genetic screen for nitrate regulatory mutants captures the nitrate transporter gene NRT1.1. Plant Physiol
  28. (2000). NM: Genomic analysis of a nutrient response in Arabidopsis reveals diverse expression patterns and novel metabolic and potential regulatory genes induced by nitrate. Plant Cell
  29. (2004). NM: Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis. Plant Physiol
  30. (2007). NM: Insights into the genomic nitrate response using genetics and the Sungear Software System. J Exp Bot
  31. (2003). NM: Microarray analysis of the nitrate response in Arabidopsis roots and shoots reveals over 1,000 rapidly responding genes and new linkages to glucose, trehalose-6-phosphate, iron, and sulfate metabolism. Plant Physiol
  32. (2007). NS: A predictive model for transcriptional control of physiology in a free living cell. Cell
  33. (2009). Plant hormones and nutrient signaling. Plant Mol Biol
  34. (2009). Poethig RS: The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell
  35. (2009). RA: A Systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis. PLoS Comput Biol
  36. (2008). RA: A systems view of nitrogen nutrient and metabolite responses in Arabidopsis. Curr Opin Plant Biol
  37. (2006). Regression shrinkage and selection via the lasso.
  38. (2005). Regularization and variable selection via the elastic net.
  39. (2010). Reverse engineering of gene regulatory networks.
  40. (2009). Scheible WR: Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs by comprehensive real-time polymerase chain reaction profiling and small RNA sequencing. Plant Physiol
  41. (2009). Scheible WR: Members of the LBD family of transcription factors repress anthocyanin synthesis and affect additional nitrogen responses in Arabidopsis. Plant Cell
  42. (2007). SJ: Genome-wide analysis of Arabidopsis responsive transcriptome to nitrogen limitation and its regulation by the ubiquitin ligase gene NLA. Plant Mol Biol
  43. (2008). Systemic signaling of the plant nitrogen status triggers specific transcriptome responses depending on the nitrogen source in Medicago truncatula. Plant Physiol
  44. (2008). The microRNA regulated SBP-box genes SPL9 and SPL15 control shoot maturation in Arabidopsis. Plant Mol Biol
  45. (2004). Tibshirani R: Least angle regression. Ann Stat
  46. (2009). TJ: Uncovering small RNA-mediated responses to phosphate-deficiency in Arabidopsis by deep sequencing. Plant Physiol
  47. (2009). Tsay YF: AtCIPK8, a CBL-interacting protein kinase, regulates the low-affinity phase of the primary nitrate response. Plant J
  48. (2009). Tsay YF: CHL1 functions as a nitrate sensor in plants. Cell
  49. (2010). Tsay YF: Nitrate signaling: adaptation to fluctuating environments. Curr Opin Plant Biol
  50. (2001). WL: Validating clustering for gene expression data. Bioinformatics