Nodulation gene networks in legumes

[1]  Judith F. Thomas,et al.  Overlapping plant signal transduction pathways induced by a parasitic nematode and a rhizobial endosymbiont. , 2001, Molecular plant-microbe interactions : MPMI.

[2]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[3]  Jason A. Corwin,et al.  Combining Genome-Wide Association Mapping and Transcriptional Networks to Identify Novel Genes Controlling Glucosinolates in Arabidopsis thaliana , 2011, PLoS biology.

[4]  Fernando González-Ladrón-de-Guevara,et al.  Towards an integrated crowdsourcing definition , 2012, J. Inf. Sci..

[5]  J. Besag.  Spatial Interaction and the Statistical Analysis of Lattice Systems , 1974 .

[6]  Halil Kilicoglu,et al.  Augmenting Microarray Data with Literature-Based Knowledge to Enhance Gene Regulatory Network Inference , 2014, PLoS Comput. Biol..

[7]  David Z. Chen,et al.  Architecture of the human regulatory network derived from ENCODE data , 2012, Nature.

[8]  K. Tang,et al.  Identification of Gene Modules Associated with Drought Response in Rice by Network-Based Analysis , 2012, PloS one.

[9]  J. F. Marsh,et al.  Nodulation Signaling in Legumes Requires NSP2, a Member of the GRAS Family of Transcriptional Regulators , 2005, Science.

[10]  M. Vidal,et al.  Selecting causal genes from genome-wide association studies via functionally coherent subnetworks , 2014, Nature Methods.

[11]  Constantin F. Aliferis,et al.  A Novel Algorithm for Scalable and Accurate Bayesian Network Learning , 2004, MedInfo.

[12]  E. R. Morrissey,et al.  Inferring the time-invariant topology of a nonlinear sparse gene regulatory network using fully Bayesian spline autoregression. , 2011, Biostatistics.

[13]  M. Luckow,et al.  The Rest of the Iceberg. Legume Diversity and Evolution in a Phylogenetic Context1 , 2003, Plant Physiology.

[14]  Christian von Mering,et al.  STRING: known and predicted protein–protein associations, integrated and transferred across organisms , 2004, Nucleic Acids Res..

[15]  Julia Frugoli,et al.  The Medicago truncatula SUNN Gene Encodes a CLV1-like Leucine-rich Repeat Receptor Kinase that Regulates Nodule Number and Root Length , 2005, Plant Molecular Biology.

[16]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[17]  Yibo Wu,et al.  GOSemSim: an R package for measuring semantic similarity among GO terms and gene products , 2010, Bioinform..

[18]  B. Roe,et al.  Medicago truncatula DMI1 Required for Bacterial and Fungal Symbioses in Legumes , 2004, Science.

[19]  Constantin F. Aliferis,et al.  The max-min hill-climbing Bayesian network structure learning algorithm , 2006, Machine Learning.

[20]  M. Kawaguchi,et al.  Common symbiosis genes CERBERUS and NSP1 provide additional insight into the establishment of arbuscular mycorrhizal and root nodule symbioses in Lotus japonicus , 2014, Plant signaling & behavior.

[21]  T. Bisseling,et al.  A Putative Ca2+ and Calmodulin-Dependent Protein Kinase Required for Bacterial and Fungal Symbioses , 2004, Science.

[22]  George M. Church,et al.  Multiplex and homologous recombination–mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9 , 2013, Nature Biotechnology.

[23]  S. Tabata,et al.  A Gain-of-Function Mutation in a Cytokinin Receptor Triggers Spontaneous Root Nodule Organogenesis , 2007, Science.

[24]  Jon W. Huss,et al.  A Gene Wiki for Community Annotation of Gene Function , 2008, PLoS biology.

[25]  R. Gentleman,et al.  Independent filtering increases detection power for high-throughput experiments , 2010, Proceedings of the National Academy of Sciences.

[26]  Junichi Tsujii,et al.  Event extraction for systems biology by text mining the literature. , 2010, Trends in biotechnology.

[27]  S. Tabata,et al.  A plant receptor-like kinase required for both bacterial and fungal symbiosis , 2002, Nature.

[28]  L. Brill,et al.  Plant lectins: the ties that bind in root symbiosis and plant defense , 2009, Molecular Genetics and Genomics.

[29]  R. Tibshirani,et al.  Sparse inverse covariance estimation with the graphical lasso. , 2008, Biostatistics.

[30]  Jun Yu,et al.  LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs , 2014, Nucleic Acids Res..

[31]  J. Davis.  Bioinformatics and Computational Biology Solutions Using R and Bioconductor , 2007 .

[32]  Yin Liu,et al.  Incorporating prior knowledge into Gene Network Study , 2013, Bioinform..

[33]  R. Sharan,et al.  Network-based prediction of protein function , 2007, Molecular systems biology.

[34]  Alessandro Vespignani,et al.  Global protein function prediction from protein-protein interaction networks , 2003, Nature Biotechnology.

[35]  Leif Schauser,et al.  A plant regulator controlling development of symbiotic root nodules , 1999, Nature.

[36]  Chris Wiggins,et al.  ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context , 2004, BMC Bioinformatics.

[37]  Nicholas M. Pajewski,et al.  Six Degrees of Epistasis: Statistical Network Models for GWAS , 2011, Front. Gene..

[38]  Jean-Philippe Vert,et al.  TIGRESS: Trustful Inference of Gene REgulation using Stability Selection , 2012, BMC Systems Biology.

[39]  Tao Chen,et al.  A MAP Kinase Kinase Interacts with SymRK and Regulates Nodule Organogenesis in Lotus japonicus[C][W] , 2012, Plant Cell.

[40]  Satoshi Tabata,et al.  Deregulation of a Ca2+/calmodulin-dependent kinase leads to spontaneous nodule development , 2006, Nature.

[41]  Anne-Laure Boulesteix,et al.  Regularized estimation of large-scale gene association networks using graphical Gaussian models , 2009, BMC Bioinformatics.

[42]  Yang Xie,et al.  Ensemble-Based Network Aggregation Improves the Accuracy of Gene Network Reconstruction , 2014, PloS one.

[43]  G. Weiller,et al.  A gene expression atlas of the model legume Medicago truncatula. , 2008, The Plant journal : for cell and molecular biology.

[44]  David Tritchler,et al.  BMC Bioinformatics BioMed Central Methodology article Filtering Genes for Cluster and Network Analysis , 2009 .

[45]  Christophe Ambroise,et al.  Statistical Applications in Genetics and Molecular Biology Weighted-LASSO for Structured Network Inference from Time Course Data , 2011 .

[46]  M. Guerinot,et al.  GmZIP1 Encodes a Symbiosis-specific Zinc Transporter in Soybean* , 2002, The Journal of Biological Chemistry.

[47]  R. Tibshirani.  Regression Shrinkage and Selection via the Lasso , 1996 .

[48]  Jeffry D. Sander,et al.  CRISPR-Cas systems for editing, regulating and targeting genomes , 2014, Nature Biotechnology.

[49]  Alberto de la Fuente,et al.  Discovery of meaningful associations in genomic data using partial correlation coefficients , 2004, Bioinform..

[50]  A. Kereszt,et al.  A receptor kinase gene regulating symbiotic nodule development , 2002, Nature.

[51]  M E J Newman,et al.  Community structure in social and biological networks , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[52]  Zi Wang,et al.  Network-guided regression for detecting associations between DNA methylation and gene expression , 2014, Bioinform..

[53]  Maria L. Rizzo,et al.  Measuring and testing dependence by correlation of distances , 2007, 0803.4101.

[54]  M. Crespi,et al.  The Medicago truncatula CRE1 Cytokinin Receptor Regulates Lateral Root Development and Early Symbiotic Interaction with Sinorhizobium meliloti[W] , 2006, The Plant Cell Online.

[55]  Alexander R. Pico,et al.  WikiPathways: Pathway Editing for the People , 2008, PLoS biology.

[56]  E. Wingender,et al.  Integration of gene expression data with prior knowledge for network analysis and validation , 2011, BMC Research Notes.

[57]  Djordje Djordjevic,et al.  How Difficult Is Inference of Mammalian Causal Gene Regulatory Networks? , 2014, PloS one.

[58]  M. Parniske,et al.  Evolution of root endosymbiosis with bacteria: How novel are nodules? , 2009, Trends in plant science.

[59]  Jungwon Yoon,et al.  The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community , 2003, Nucleic Acids Res..

[60]  J. Giles.  Internet encyclopaedias go head to head , 2005, Nature.

[61]  Jean-Michel Ané,et al.  Tracing Nonlegume Orthologs of Legume Genes Required for Nodulation and Arbuscular Mycorrhizal Symbioses , 2006, Genetics.

[62]  D. Pe’er,et al.  Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data , 2003, Nature Genetics.

[63]  Arnaud Doucet,et al.  A boosting approach to structure learning of graphs with and without prior knowledge , 2009, Bioinform..

[64]  E. Schadt,et al.  Unifying immunology with informatics and multiscale biology , 2014, Nature Immunology.

[65]  R. Wrangham,et al.  Legume nodulation , 2014, Current Biology.

[66]  R. Albert.  Scale-free networks in cell biology , 2005, Journal of Cell Science.

[67]  Kathleen Marchal,et al.  Module networks revisited: computational assessment and prioritization of model predictions , 2009, Bioinform..

[68]  N. J. Brewin,et al.  Legume lectins and nodulation by Rhizobium , 1997 .

[69]  S. Horvath,et al.  Statistical Applications in Genetics and Molecular Biology , 2011 .

[70]  Anton Crombach,et al.  Evolution of Evolvability in Gene Regulatory Networks , 2008, PLoS Comput. Biol..

[71]  Kun Xu,et al.  The Medicago truncatula ortholog of Arabidopsis EIN2, sickle, is a negative regulator of symbiotic and pathogenic microbial associations. , 2008, The Plant journal : for cell and molecular biology.

[72]  Alvaro J. González,et al.  The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses , 2011, Nature.

[73]  M. Sussman,et al.  Symbiosis and the social network of higher plants. , 2013, Current opinion in plant biology.

[74]  Yukiko Matsuoka,et al.  PathText: a text mining integrator for biological pathway visualizations , 2010, Bioinform..

[75]  Leo Breiman,et al.  Bagging Predictors , 1996, Machine Learning.

[76]  A. Brazma,et al.  Reuse of public genome-wide gene expression data , 2012, Nature Reviews Genetics.

[77]  A. Barabasi,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

[78]  P. Poole,et al.  The rules of engagement in the legume-rhizobial symbiosis. , 2011, Annual review of genetics.

[79]  E. Marcotte,et al.  Genetic dissection of the biotic stress response using a genome-scale gene network for rice , 2011, Proceedings of the National Academy of Sciences.

[80]  J. B. Reid,et al.  Relationship between gibberellin, ethylene and nodulation in Pisum sativum. , 2011, The New phytologist.

[81]  Guy Karlebach,et al.  Modelling and analysis of gene regulatory networks , 2008, Nature Reviews Molecular Cell Biology.

[82]  Ming Yuan,et al.  High Dimensional Inverse Covariance Matrix Estimation via Linear Programming , 2010, J. Mach. Learn. Res..

[83]  B. Matthews.  Comparison of the predicted and observed secondary structure of T4 phage lysozyme. , 1975, Biochimica et biophysica acta.

[84]  Tomasz Arodz,et al.  ENNET: inferring large gene regulatory networks from expression data using gradient boosting , 2013, BMC Systems Biology.

[85]  N. J. Brewin.  Development of the legume root nodule. , 1991, Annual review of cell biology.

[86]  Arthur E. Hoerl,et al.  Ridge Regression: Biased Estimation for Nonorthogonal Problems , 2000, Technometrics.

[87]  Martin Crespi,et al.  MicroRNA166 controls root and nodule development in Medicago truncatula. , 2008, The Plant journal : for cell and molecular biology.

[88]  R. Tibshirani,et al.  Least angle regression , 2004, math/0406456.

[89]  B. Usadel,et al.  PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species[W][OA] , 2011, Plant Cell.

[90]  Rafael A Irizarry,et al.  Exploration, normalization, and summaries of high density oligonucleotide array probe level data. , 2003, Biostatistics.

[91]  Su-Shing Chen,et al.  Text mining biomedical literature for constructing gene regulatory networks , 2009, Interdisciplinary Sciences: Computational Life Sciences.

[92]  Sandrine Dudoit,et al.  Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments , 2010, BMC Bioinformatics.

[93]  G. Altay,et al.  Empirically determining the sample size for large-scale gene network inference algorithms. , 2012, IET systems biology.

[94]  R. Hoffmann.  A wiki for the life sciences where authorship matters , 2008, Nature Genetics.

[95]  Julie A. Dickerson,et al.  Arabidopsis gene co-expression network and its functional modules , 2009, BMC Bioinformatics.

[96]  J. Nap,et al.  Developmental Biology of a Plant-Prokaryote Symbiosis: The Legume Root Nodule , 1990, Science.

[97]  Qiang Liu,et al.  Learning Scale Free Networks by Reweighted L1 regularization , 2011, AISTATS.

[98]  Nori Kurata,et al.  OryzaExpress: An Integrated Database of Gene Expression Networks and Omics Annotations in Rice , 2010, Plant & cell physiology.

[99]  R. Heller,et al.  A consistent multivariate test of association based on ranks of distances , 2012, 1201.3522.

[100]  Satoru Miyano,et al.  Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data , 2003, CMSB.

[101]  D. Weston,et al.  Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max. , 2011, Plant, cell & environment.

[102]  Diogo M. Camacho,et al.  Wisdom of crowds for robust gene network inference , 2012, Nature Methods.

[103]  B. Palsson,et al.  The model organism as a system: integrating 'omics' data sets , 2006, Nature Reviews Molecular Cell Biology.

[104]  S. Tabata,et al.  A nucleoporin is required for induction of Ca2+ spiking in legume nodule development and essential for rhizobial and fungal symbiosis. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[105]  J. F. Marsh,et al.  Medicago truncatula NIN Is Essential for Rhizobial-Independent Nodule Organogenesis Induced by Autoactive Calcium/Calmodulin-Dependent Protein Kinase1 , 2007, Plant Physiology.

[106]  A. Bonner,et al.  Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions , 2011, Proceedings of the National Academy of Sciences.

[107]  Dennis B. Troup,et al.  NCBI GEO: mining millions of expression profiles—database and tools , 2004, Nucleic Acids Res..

[108]  M. Kawaguchi,et al.  Genetic basis of cytokinin and auxin functions during root nodule development , 2013, Front. Plant Sci..

[109]  S. Tabata,et al.  NUCLEOPORIN85 Is Required for Calcium Spiking, Fungal and Bacterial Symbioses, and Seed Production in Lotus japonicus , 2007, The Plant Cell Online.

[110]  W. Cleveland,et al.  Locally Weighted Regression: An Approach to Regression Analysis by Local Fitting , 1988 .

[111]  Salma Jamoussi,et al.  Weighted ensemble learning of Bayesian network for gene regulatory networks , 2015, Neurocomputing.

[112]  Christian von Mering,et al.  STRING 8—a global view on proteins and their functional interactions in 630 organisms , 2008, Nucleic Acids Res..

[113]  C. Li,et al.  Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[114]  Kai Wang,et al.  Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks , 2007, ISMB/ECCB.

[115]  M. Crespi,et al.  Nodule Initiation Involves the Creation of a New Symplasmic Field in Specific Root Cells of Medicago Species Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.017020. , 2003, The Plant Cell Online.

[116]  Thomas Schiex,et al.  Gene Regulatory Network Reconstruction Using Bayesian Networks, the Dantzig Selector, the Lasso and Their Meta-Analysis , 2011, PloS one.

[117]  Bin Yu,et al.  High-dimensional covariance estimation by minimizing ℓ1-penalized log-determinant divergence , 2008, 0811.3628.

[118]  Ann M. Hess,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Filtering for increased power for microarray data analysis , 2008 .

[119]  Klaas Vandepoele,et al.  Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice1[W] , 2011, Plant Physiology.

[120]  Kengo Kinoshita,et al.  ATTED-II in 2014: Evaluation of Gene Coexpression in Agriculturally Important Plants , 2014, Plant & cell physiology.

[121]  J. Slovin,et al.  Floral Transcriptomes in Woodland Strawberry Uncover Developing Receptacle and Anther Gene Networks1[W][OPEN] , 2014, Plant Physiology.

[122]  Ralf Zimmer,et al.  Inferring gene regulatory networks by ANOVA , 2012, Bioinform..

[123]  Naoya Takeda,et al.  Plastid proteins crucial for symbiotic fungal and bacterial entry into plant roots , 2005, Nature.

[124]  J. B. Reid,et al.  Nodulation Phenotypes of Gibberellin and Brassinosteroid Mutants of Pea1 , 2005, Plant Physiology.

[125]  Jianbing Yan,et al.  Dissecting meiotic recombination based on tetrad analysis by single-microspore sequencing in maize , 2015, Nature Communications.

[126]  Martin Vingron,et al.  Improved detection of overrepresentation of Gene-Ontology annotations with parent-child analysis , 2007, Bioinform..

[127]  Kevin L. Childs,et al.  Gene Coexpression Network Analysis as a Source of Functional Annotation for Rice Genes , 2011, PloS one.

[128]  H. Ryu,et al.  Plant hormonal regulation of nitrogen-fixing nodule organogenesis , 2012, Molecules and cells.

[129]  T. Bisseling,et al.  NSP1 of the GRAS Protein Family Is Essential for Rhizobial Nod Factor-Induced Transcription , 2005, Science.

[130]  Gary Stacey,et al.  MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. , 2011, Genes & development.

[131]  Larry A. Wasserman,et al.  The huge Package for High-dimensional Undirected Graph Estimation in R , 2012, J. Mach. Learn. Res..

[132]  Sergei Maslov,et al.  Automatic Pathway Building in Biological Association Networks , 2006 .

[133]  Piet Demeester,et al.  NIMEFI: Gene Regulatory Network Inference using Multiple Ensemble Feature Importance Algorithms , 2014, PloS one.

[134]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[135]  P. Geurts,et al.  Inferring Regulatory Networks from Expression Data Using Tree-Based Methods , 2010, PloS one.

[136]  Xia Li,et al.  A network-based, integrative approach to identify genes with aberrant co-methylation in colorectal cancer. , 2014, Molecular bioSystems.

[137]  Bogumil J. Karas,et al.  A Cytokinin Perception Mutant Colonized by Rhizobium in the Absence of Nodule Organogenesis , 2007, Science.

[138]  Michael Schroeder,et al.  Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies? , 2008, Briefings Bioinform..

[139]  Xiangfeng Wang,et al.  Application of the Gini Correlation Coefficient to Infer Regulatory Relationships in Transcriptome Analysis[W][OA] , 2012, Plant Physiology.

[140]  Laurent Laplaze,et al.  SymRK defines a common genetic basis for plant root endosymbioses with arbuscular mycorrhiza fungi, rhizobia, and Frankiabacteria , 2008, Proceedings of the National Academy of Sciences.

[141]  Joshua M. Stuart,et al.  A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules , 2003, Science.

[142]  P. Bühlmann,et al.  Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis thaliana , 2004, Genome Biology.

[143]  Qing Nie,et al.  Incorporating Existing Network Information into Gene Network Inference , 2009, PloS one.

[144]  M. Lynch.  The evolution of genetic networks by non-adaptive processes , 2007, Nature Reviews Genetics.

[145]  Neville E. Sanjana,et al.  Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells , 2014, Science.

[146]  J. Young,et al.  The evolution of specificity in the legume-rhizobium symbiosis. , 1989, Trends in ecology & evolution.

[147]  Jens Kattge,et al.  A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms , 2014, Nature Communications.

[148]  Barbara J. Wold,et al.  A ratiometric-based measure of gene co-expression , 2014, BMC Bioinformatics.

[149]  T. Maekawa,et al.  Gibberellin controls the nodulation signaling pathway in Lotus japonicus. , 2009, The Plant journal : for cell and molecular biology.

[150]  O. Voinnet,et al.  Two MicroRNAs Linked to Nodule Infection and Nitrogen-Fixing Ability in the Legume Lotus japonicus1[W] , 2012, Plant Physiology.

[151]  Anthony Ralston,et al.  Mathematical Methods for Digital Computers , 1960 .

[152]  F. Ariel,et al.  Two Direct Targets of Cytokinin Signaling Regulate Symbiotic Nodulation in Medicago truncatula[W][OA] , 2012, Plant Cell.

[153]  R. Schapire.  The Strength of Weak Learnability , 1990, Machine Learning.

[154]  T. Bisseling,et al.  Medicago LYK3, an Entry Receptor in Rhizobial Nodulation Factor Signaling1[W] , 2007, Plant Physiology.

[155]  Larry A. Wasserman,et al.  Stability Approach to Regularization Selection (StARS) for High Dimensional Graphical Models , 2010, NIPS.

[156]  K. Strimmer,et al.  Statistical Applications in Genetics and Molecular Biology A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics , 2011 .

[157]  Nicolas Servant,et al.  A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis , 2013, Briefings Bioinform..

[158]  Staffan Persson,et al.  Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. , 2009, Plant, cell & environment.

[159]  M. Crespi,et al.  Complexity of miRNA-dependent regulation in root symbiosis , 2012, Philosophical Transactions of the Royal Society B: Biological Sciences.

[160]  Gary Stacey,et al.  Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data , 2013, BMC Bioinformatics.

[161]  W. Hoeffding.  A Non-Parametric Test of Independence , 1948 .

[162]  T. Cai,et al.  A Constrained ℓ1 Minimization Approach to Sparse Precision Matrix Estimation , 2011, 1102.2233.

[163]  Rafael A. Irizarry,et al.  A Model-Based Background Adjustment for Oligonucleotide Expression Arrays , 2004 .

[164]  T. Soyano,et al.  Transcriptional networks leading to symbiotic nodule organogenesis. , 2014, Current opinion in plant biology.

[165]  David Warde-Farley,et al.  GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function , 2008, Genome Biology.

[166]  Jinyuan Liu,et al.  Fungal Symbiosis in Rice Requires an Ortholog of a Legume Common Symbiosis Gene Encoding a Ca2+/Calmodulin-Dependent Protein Kinase1[OA] , 2007, Plant Physiology.

[167]  Yudi Pawitan,et al.  Filtering genes to improve sensitivity in oligonucleotide microarray data analysis. , 2007, Nucleic acids research.

[168]  Wei-Min Liu,et al.  Robust estimators for expression analysis , 2002, Bioinform..

[169]  Mingyi Wang,et al.  The Medicago truncatula gene expression atlas web server , 2009, BMC Bioinformatics.

[170]  A. Edwards,et al.  The Medicago truncatula DMI1 Protein Modulates Cytosolic Calcium Signaling1[W][OA] , 2007, Plant Physiology.

[171]  Rina Foygel,et al.  Extended Bayesian Information Criteria for Gaussian Graphical Models , 2010, NIPS.

[172]  Martin Vingron,et al.  Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana , 2014, Front. Plant Sci..

[173]  Jonathan D. G. Jones,et al.  Evidence for Network Evolution in an Arabidopsis Interactome Map , 2011, Science.

[174]  M. Parniske,et al.  Cleavage of the SYMBIOSIS RECEPTOR-LIKE KINASE Ectodomain Promotes Complex Formation with Nod Factor Receptor 5 , 2014, Current Biology.

[175]  E. Marcotte,et al.  Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana , 2010, Nature Biotechnology.

[176]  Julie A. Dickerson,et al.  PLEXdb: gene expression resources for plants and plant pathogens , 2011, Nucleic Acids Res..

[177]  Angelica Lindlöf,et al.  Simulations of simple artificial genetic networks reveal features in the use of Relevance Networks , 2005, Silico Biol..

[178]  Jens Stougaard,et al.  The molecular network governing nodule organogenesis and infection in the model legume Lotus japonicus , 2010, Nature communications.

[179]  N. Meinshausen,et al.  High-dimensional graphs and variable selection with the Lasso , 2006, math/0608017.

[180]  Colby G Starker,et al.  Conservation in function of a SCAR/WAVE component during infection thread and root hair growth in Medicago truncatula. , 2010, Molecular plant-microbe interactions : MPMI.

[181]  Suzana de Siqueira Santos,et al.  A comparative study of statistical methods used to identify dependencies between gene expression signals , 2014, Briefings Bioinform..

[182]  Alfred O. Hero,et al.  High Throughput Screening of Co-Expressed Gene Pairs with Controlled False Discovery Rate (FDR) and Minimum Acceptable Strength (MAS) , 2005, J. Comput. Biol..

[183]  P. Rougé,et al.  The Medicago truncatula Lysine Motif-Receptor-Like Kinase Gene Family Includes NFP and New Nodule-Expressed Genes1[W] , 2006, Plant Physiology.

[184]  S. Tabata,et al.  A Novel Ankyrin-Repeat Membrane Protein, IGN1, Is Required for Persistence of Nitrogen-Fixing Symbiosis in Root Nodules of Lotus japonicus1[OA] , 2007, Plant Physiology.

[185]  S. Tabata,et al.  Plant recognition of symbiotic bacteria requires two LysM receptor-like kinases , 2003, Nature.

[186]  B. Schwikowski,et al.  A network of protein–protein interactions in yeast , 2000, Nature Biotechnology.

[187]  David Milward,et al.  Mining protein-protein interactions from published literature using Linguamatics I2E. , 2009, Methods in molecular biology.

[188]  P. Bushel,et al.  Principal component analysis-based filtering improves detection for Affymetrix gene expression arrays , 2011, Nucleic acids research.

[189]  M. Parniske,et al.  CYCLOPS, a DNA-binding transcriptional activator, orchestrates symbiotic root nodule development. , 2014, Cell host & microbe.

[190]  J. E. García,et al.  A non-parametric test of independence ∗ , 2011 .

[191]  Atul J. Butte,et al.  Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks , 2005, BMC Bioinformatics.

[192]  Yoshiyuki Ogata,et al.  Approaches for extracting practical information from gene co-expression networks in plant biology. , 2007, Plant & cell physiology.

[193]  Edward I. George,et al.  Variable selection for BART: An application to gene regulation , 2013, 1310.4887.

[194]  Martin Krallinger,et al.  Analysis of biological processes and diseases using text mining approaches. , 2010, Methods in molecular biology.

[195]  M. Holsters,et al.  Nodule numbers are governed by interaction between CLE peptides and cytokinin signaling. , 2012, The Plant journal : for cell and molecular biology.

[196]  G. Hon,et al.  Next-generation genomics: an integrative approach , 2010, Nature Reviews Genetics.

[197]  Michael Mitzenmacher,et al.  Detecting Novel Associations in Large Data Sets , 2011, Science.

[198]  Nir Friedman,et al.  Inferring Cellular Networks Using Probabilistic Graphical Models , 2004, Science.

[199]  Satoru Miyano,et al.  Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks , 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

[200]  S. Schornack,et al.  A novel nuclear protein interacts with the symbiotic DMI3 calcium- and calmodulin-dependent protein kinase of Medicago truncatula. , 2007, Molecular plant-microbe interactions : MPMI.

[201]  S. Tabata,et al.  CYCLOPS, a mediator of symbiotic intracellular accommodation , 2008, Proceedings of the National Academy of Sciences.

[202]  T. Yamanaka,et al.  Gene Interaction Network Suggests Dioxin Induces a Significant Linkage between Aryl Hydrocarbon Receptor and Retinoic Acid Receptor Beta , 2004, Environmental health perspectives.