Incorporating the Rate of Transcriptional Change Improves Construction of Gene Regulatory Networks
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Lovely Mae Lawas | Jigar Desai | Ryan C. Sartor | S.V. Krishna Jagadish | Colleen J. Doherty | S. Jagadish | Jigar S. Desai | L. M. Lawas
[1] J. Darnell. STATs and gene regulation. , 1997, Science.
[2] Colleen J Doherty,et al. Circadian control of global gene expression patterns. , 2010, Annual review of genetics.
[3] E. M. Farré,et al. Direct regulation of abiotic responses by the Arabidopsis circadian clock component PRR7. , 2013, The Plant journal : for cell and molecular biology.
[4] Chris Wiggins,et al. ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context , 2004, BMC Bioinformatics.
[5] I. Simon,et al. Studying and modelling dynamic biological processes using time-series gene expression data , 2012, Nature Reviews Genetics.
[6] Vân Anh Huynh-Thu,et al. Machine learning-based feature ranking: Statistical interpretation and gene network inference , 2012 .
[7] Tao Zhang,et al. Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis[C][W][OA] , 2012, Plant Cell.
[8] J. Darnell,et al. The JAK-STAT pathway at twenty. , 2012, Immunity.
[9] Paul Theodor Pyl,et al. HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.
[10] Cole Trapnell,et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.
[11] A. Ridley,et al. Regulators and effectors of Small Gtpases: Rho Family , 2006 .
[12] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[13] J. Takahashi,et al. ChIP-seq and RNA-seq methods to study circadian control of transcription in mammals. , 2015, Methods in enzymology.
[14] Diogo M. Camacho,et al. Wisdom of crowds for robust gene network inference , 2012, Nature Methods.
[15] Hung-Chung Huang,et al. Nobuya Koike Circadian Clock in Mammals Transcriptional Architecture and Chromatin Landscape of the Core , 2013 .
[16] J. Darnell,et al. Jak-STAT pathways and transcriptional activation in response to IFNs and other extracellular signaling proteins. , 1994, Science.
[17] P. Geurts,et al. Inferring Regulatory Networks from Expression Data Using Tree-Based Methods , 2010, PloS one.
[18] A. Oudenaarden,et al. Cellular Decision Making and Biological Noise: From Microbes to Mammals , 2011, Cell.
[19] Angel D. Pizarro,et al. CircaDB: a database of mammalian circadian gene expression profiles , 2012, Nucleic Acids Res..
[20] Kun He,et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors , 2015, Molecular biology and evolution.
[21] Daniel E. Newburger,et al. High-resolution DNA-binding specificity analysis of yeast transcription factors. , 2009, Genome research.
[22] Mark Gerstein,et al. Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data , 2003, Bioinform..
[23] Alfred O. Hero,et al. An individualized predictor of health and disease using paired reference and target samples , 2016, BMC Bioinformatics.
[24] Dawn H. Nagel,et al. Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis , 2015, Proceedings of the National Academy of Sciences.
[25] Richard Bonneau,et al. EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments[OPEN] , 2016, Plant Cell.
[26] Christopher A. Penfold,et al. Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks , 2012, Bioinform..
[27] M. Goldsmith,et al. JAK/STAT signaling by cytokine receptors. , 1998, Current opinion in immunology.
[28] D. Botstein,et al. Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[29] Hui Liu,et al. AnimalTFDB: a comprehensive animal transcription factor database , 2011, Nucleic Acids Res..
[30] Richard Bonneau,et al. Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks , 2013, Bioinform..
[31] Hongyu Zhao,et al. Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of Development[W] , 2007, The Plant Cell Online.
[32] P. Park. ChIP–seq: advantages and challenges of a maturing technology , 2009, Nature Reviews Genetics.
[33] M. Bansal,et al. Running Title : OsMADS 1 DNA binding and floret gene regulation , 2016 .
[34] C. Horvath,et al. STAT proteins and transcriptional responses to extracellular signals. , 2000, Trends in biochemical sciences.
[35] Aviv Regev,et al. Comparative analysis of gene regulatory networks: from network reconstruction to evolution. , 2015, Annual review of cell and developmental biology.
[36] J. Collins,et al. Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles , 2007, PLoS biology.
[37] Christopher A. Penfold,et al. CSI: a nonparametric Bayesian approach to network inference from multiple perturbed time series gene expression data , 2015, Statistical applications in genetics and molecular biology.
[38] Tao Liu,et al. CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human , 2012, Bioinform..
[39] Zheng Li,et al. Large-scale dynamic gene regulatory network inference combining differential equation models with local dynamic Bayesian network analysis , 2011, Bioinform..
[40] Thomas Lengauer,et al. ROCR: visualizing classifier performance in R , 2005, Bioinform..
[41] Connor W. McEntee,et al. Network Discovery Pipeline Elucidates Conserved Time-of-Day–Specific cis-Regulatory Modules , 2007, PLoS genetics.
[42] Xing Wang Deng. Faculty Opinions recommendation of Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules. , 2008 .
[43] Mathew G. Lewsey,et al. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape , 2016, Cell.
[44] Takuji Sasaki,et al. The map-based sequence of the rice genome , 2005, Nature.
[45] Ziv Bar-Joseph,et al. Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis , 2013, eLife.
[46] Xuemei Chen,et al. Orchestration of the Floral Transition and Floral Development in Arabidopsis by the Bifunctional Transcription Factor APETALA2[W][OA] , 2010, Plant Cell.
[47] I. Amit,et al. Sequential feedback induction stabilizes the phosphate starvation response in budding yeast. , 2014, Cell reports.
[48] Andy Liaw,et al. Classification and Regression by randomForest , 2007 .
[49] J. Bromberg,et al. STAT proteins: signal tranducers and activators of transcription. , 2001, Methods in enzymology.
[50] Shane J. Neph,et al. Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana. , 2014, Cell reports.
[51] Richard Bonneau,et al. The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo , 2006, Genome Biology.
[52] Clifford A. Meyer,et al. Cistrome: an integrative platform for transcriptional regulation studies , 2011, Genome Biology.