A novel framework for inferring condition-specific TF and miRNA co-regulation of protein-protein interactions.

[1]  L. Dailey,et al.  High throughput technologies for the functional discovery of mammalian enhancers: new approaches for understanding transcriptional regulatory network dynamics. , 2015, Genomics.

[2]  R. Gregory,et al.  MicroRNA biogenesis pathways in cancer , 2015, Nature Reviews Cancer.

[3]  Volkhard Helms,et al.  TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks , 2015, Nucleic Acids Res..

[4]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[5]  Julian Mintseris,et al.  Transcription factor networks in Drosophila melanogaster. , 2014, Cell reports.

[6]  Hsuan-Cheng Huang,et al.  Mirin: identifying microRNA regulatory modules in protein-protein interaction networks , 2014, Bioinform..

[7]  Ting Wang,et al.  OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs , 2014, Bioinform..

[8]  Lili Xiong,et al.  Genome-wide survey of tissue-specific microRNA and transcription factor regulatory networks in 12 tissues , 2014, Scientific Reports.

[9]  D. Greenbaum,et al.  Genome-Wide Survey , 2014 .

[10]  Yi-Ping Phoebe Chen,et al.  Computational developments in microRNA-regulated protein-protein interactions , 2014, BMC Systems Biology.

[11]  Aihua Wang,et al.  Exploring and exploiting the fundamental role of microRNAs in tumor pathogenesis , 2013, OncoTargets and therapy.

[12]  Joshua M. Stuart,et al.  The Cancer Genome Atlas Pan-Cancer analysis project , 2013, Nature Genetics.

[13]  Jiuyong Li,et al.  Inferring microRNA and transcription factor regulatory networks in heterogeneous data , 2013, BMC Bioinformatics.

[14]  Hongjing Han,et al.  miRCancer: a microRNA-cancer association database constructed by text mining on literature , 2013, Bioinform..

[15]  Tom Michoel,et al.  Context-specific transcriptional regulatory network inference from global gene expression maps using double two-way t-tests , 2012, Bioinform..

[16]  Holger Fröhlich,et al.  Joint Bayesian inference of condition-specific miRNA and transcription factor activities from combined gene and microRNA expression data , 2012, Bioinform..

[17]  Yen-Jen Oyang,et al.  Crosstalk between transcription factors and microRNAs in human protein interaction network , 2012, BMC Systems Biology.

[18]  R. Sanz-Pamplona,et al.  Tools for protein-protein interaction network analysis in cancer research , 2012, Clinical and Translational Oncology.

[19]  Damian Roqueiro,et al.  Identifying transcription factors and microRNAs as key regulators of pathways using Bayesian inference on known pathway structures , 2011, Proteome Science.

[20]  Fabian J. Theis,et al.  MicroRNAs coordinately regulate protein complexes , 2011, BMC Systems Biology.

[21]  Hei-Chia Wang,et al.  Inference of transcriptional regulatory network by bootstrapping patterns , 2011, Bioinform..

[22]  David J. Arenillas,et al.  MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model , 2011, BMC Bioinformatics.

[23]  W. Filipowicz,et al.  The widespread regulation of microRNA biogenesis, function and decay , 2010, Nature Reviews Genetics.

[24]  Ivan Merelli,et al.  A multilevel data integration resource for breast cancer study , 2010, BMC Systems Biology.

[25]  Robi Tacutu,et al.  MicroRNA-regulated protein-protein interaction networks: how could they help in searching for pro-longevity targets? , 2010, Rejuvenation research.

[26]  Fabian J Theis,et al.  PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes , 2010, Genome Biology.

[27]  Shuli Kang,et al.  Clustered microRNAs' coordination in regulating protein-protein interaction network , 2009, BMC Systems Biology.

[28]  Juan M. Vaquerizas,et al.  A census of human transcription factors: function, expression and evolution , 2009, Nature Reviews Genetics.

[29]  D. Bartel MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.

[30]  Yadong Wang,et al.  miR2Disease: a manually curated database for microRNA deregulation in human disease , 2008, Nucleic Acids Res..

[31]  Q. Cui,et al.  An Analysis of Human MicroRNA and Disease Associations , 2008, PloS one.

[32]  Chun-Wei Hsu,et al.  Characterization of microRNA‐regulated protein‐protein interaction network , 2008, Proteomics.

[33]  Fidel Ramírez,et al.  Computing topological parameters of biological networks , 2008, Bioinform..

[34]  Simo V. Zhang,et al.  A map of human cancer signaling , 2007, Molecular systems biology.

[35]  Wen-Hsiung Li,et al.  MicroRNA regulation of human protein protein interaction network. , 2007, RNA.

[36]  Phillip D Zamore,et al.  Beginning to understand microRNA function , 2007, Cell Research.

[37]  Yitzhak Pilpel,et al.  Global and Local Architecture of the Mammalian microRNA–Transcription Factor Regulatory Network , 2007, PLoS Comput. Biol..

[38]  Gary D Bader,et al.  NetMatch: a Cytoscape plugin for searching biological networks , 2007, Bioinform..

[39]  Edwin Wang,et al.  MicroRNAs preferentially target the genes with high transcriptional regulation complexity. , 2006, Biochemical and biophysical research communications.

[40]  Sarka Pospisilova,et al.  MicroRNA biogenesis, functionality and cancer relevance. , 2006, Biomedical papers of the Medical Faculty of the University Palacky, Olomouc, Czechoslovakia.

[41]  M. Gerstein,et al.  Genomic analysis of the hierarchical structure of regulatory networks , 2006, Proceedings of the National Academy of Sciences.

[42]  Q. Cui,et al.  Principles of microRNA regulation of a human cellular signaling network , 2006, Molecular systems biology.

[43]  Wen-Shyen E. Chen,et al.  CRSD: a comprehensive web server for composite regulatory signature discovery , 2006, Nucleic Acids Res..

[44]  N. Rajewsky microRNA target predictions in animals , 2006, Nature Genetics.

[45]  K. S. Deshpande,et al.  Human protein reference database—2006 update , 2005, Nucleic Acids Res..

[46]  C. Burge,et al.  Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.

[47]  Alan F. Scott,et al.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2004, Nucleic Acids Res..

[48]  Zhiping Weng,et al.  PromoSer: improvements to the algorithm, visualization and accessibility , 2004, Nucleic Acids Res..

[49]  K. Becker,et al.  The Genetic Association Database , 2004, Nature Genetics.

[50]  T. Hubbard,et al.  A census of human cancer genes , 2004, Nature Reviews Cancer.

[51]  Z. Oltvai,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

[52]  D. Bartel MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[53]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[54]  E. Nimwegen Scaling Laws in the Functional Content of Genomes , 2003, physics/0307001.

[55]  V. Ambros MicroRNA Pathways in Flies and Worms Growth, Death, Fat, Stress, and Timing , 2003, Cell.

[56]  S. Shen-Orr,et al.  Network motifs in the transcriptional regulation network of Escherichia coli , 2002, Nature Genetics.

[57]  V. Ambros microRNAs Tiny Regulators with Great Potential , 2001, Cell.

[58]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[59]  David L. Steffen,et al.  The Breast Cancer Gene Database: a collaborative information resource , 1999, Oncogene.

[60]  Michael R. Green,et al.  Transcription Factors and Human Disease , 1999, Nature Medicine.

[61]  Shigeru Takasaki Roles of microRNAs in cancers and development. , 2015, Methods in molecular biology.

[62]  Hong-Mei Zhang,et al.  Transcription factor and microRNA co-regulatory loops: important regulatory motifs in biological processes and diseases , 2015, Briefings Bioinform..

[63]  S. Barik,et al.  MicroRNAs: Processing, Maturation, Target Recognition and Regulatory Functions. , 2011, Molecular and cellular pharmacology.

[64]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[65]  Liu Cc,et al.  (Nucleic Acids Res., 34:W571-W577)CRSD: a comprehensive web server for composite regulatory signature discovery , 2006 .

[66]  E. Wingender,et al.  TRANSFAC®: transcriptional regulation, from patterns to profiles , 2003, Nucleic Acids Res..

[67]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[68]  P. Atadja,et al.  Regulation of transcription factor activity during cellular aging. , 1996, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[69]  T. Pawson,et al.  Signal transduction--a conserved pathway from the membrane to the nucleus. , 1993, Developmental genetics.

[70]  C. Lobe,et al.  Transcription factors and mammalian development. , 1992, Current topics in developmental biology.