Estimating drivers of cell state transitions using gene regulatory network models

[1]  H. Bussemaker,et al.  Network-based approaches that exploit inferred transcription factor activity to analyze the impact of genetic variation on gene expression. , 2017, Current opinion in systems biology.

[2]  Thomas Thorne,et al.  NetDiff – Bayesian model selection for differential gene regulatory network inference , 2016, Scientific Reports.

[3]  Quanquan Gu,et al.  Identifying gene regulatory network rewiring using latent differential graphical models , 2016, Nucleic acids research.

[4]  John Quackenbush,et al.  PyPanda: a Python package for gene regulatory network reconstruction , 2016, Bioinform..

[5]  F. Maltais,et al.  Bridging Lung Development with Chronic Obstructive Pulmonary Disease. Relevance of Developmental Pathways in Chronic Obstructive Pulmonary Disease Pathogenesis. , 2016, American journal of respiratory and critical care medicine.

[6]  John Quackenbush,et al.  Mitochondrial iron chelation ameliorates cigarette-smoke induced bronchitis and emphysema in mice , 2015, Nature Medicine.

[7]  Benjamin Haibe-Kains,et al.  A network model for angiogenesis in ovarian cancer , 2015, BMC Bioinformatics.

[8]  John Quackenbush,et al.  Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring , 2015, Genome Medicine.

[9]  Daphne Koller,et al.  Sharing and Specificity of Co-expression Networks across 35 Human Tissues , 2014, PLoS Comput. Biol..

[10]  John Quackenbush,et al.  Sexually-dimorphic targeting of functionally-related genes in COPD , 2014, BMC Systems Biology.

[11]  Bartolome Celli,et al.  Altered Gene Expression in Blood and Sputum in COPD Frequent Exacerbators in the ECLIPSE Cohort , 2014, PloS one.

[12]  Sudipto Roy,et al.  Switching on cilia: transcriptional networks regulating ciliogenesis , 2014, Development.

[13]  Christopher S. Stevenson,et al.  Intraflagellar Transport Gene Expression Associated with Short Cilia in Smoking and COPD , 2014, PloS one.

[14]  S. Orkin,et al.  Analysis of chromatin-state plasticity identifies cell-type–specific regulators of H3K27me3 patterns , 2014, Proceedings of the National Academy of Sciences.

[15]  David J. Arenillas,et al.  JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles , 2013, Nucleic Acids Res..

[16]  Weiqing Wang,et al.  Perturbation Biology: Inferring Signaling Networks in Cellular Systems , 2013, PLoS Comput. Biol..

[17]  Nichole Reisdorph,et al.  Peripheral blood mononuclear cell gene expression in chronic obstructive pulmonary disease. , 2013, American journal of respiratory cell and molecular biology.

[18]  C. Huttenhower,et al.  Passing Messages between Biological Networks to Refine Predicted Interactions , 2013, PloS one.

[19]  Terence P. Speed,et al.  Bayesian Inference of Signaling Network Topology in a Cancer Cell Line , 2012, Bioinform..

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

[21]  Julio Saez-Rodriguez,et al.  Integrating literature-constrained and data-driven inference of signalling networks , 2012, Bioinform..

[22]  Edwin K Silverman,et al.  Identification of a chronic obstructive pulmonary disease genetic determinant that regulates HHIP. , 2012, Human molecular genetics.

[23]  Peter Langfelder,et al.  Fast R Functions for Robust Correlations and Hierarchical Clustering. , 2012, Journal of statistical software.

[24]  Mingsheng Zhang,et al.  Comparing signaling networks between normal and transformed hepatocytes using discrete logical models. , 2011, Cancer research.

[25]  Andrew Brenner,et al.  Abstract 5400: Antiangiogenic gene therapy with VB111 is active in glioblastoma xenografts , 2011 .

[26]  Douglas C Johnson,et al.  Airway mucus function and dysfunction. , 2011, The New England journal of medicine.

[27]  E. Regan,et al.  Genetic Epidemiology of COPD (COPDGene) Study Design , 2011, COPD.

[28]  Vasant Honavar,et al.  Semi-supervised prediction of protein subcellular localization using abstraction augmented Markov models , 2010, BMC Bioinformatics.

[29]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[30]  Ariel S. Schwartz,et al.  An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man , 2010, Cell.

[31]  Alina Sîrbu,et al.  Comparison of evolutionary algorithms in gene regulatory network model inference , 2010, BMC Bioinformatics.

[32]  Michael R. Kosorok,et al.  Detection of gene pathways with predictive power for breast cancer prognosis , 2010, BMC Bioinformatics.

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

[34]  K. Shianna,et al.  A Genome-Wide Association Study in Chronic Obstructive Pulmonary Disease (COPD): Identification of Two Major Susceptibility Loci , 2009, PLoS genetics.

[35]  D. Lauffenburger,et al.  Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data , 2009, Molecular systems biology.

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

[37]  Janet S. Lee,et al.  Egr-1 Regulates Autophagy in Cigarette Smoke-Induced Chronic Obstructive Pulmonary Disease , 2008, PloS one.

[38]  W. MacNee,et al.  Evaluation of COPD Longitudinally to Identify Predictive Surrogate End-points (ECLIPSE) , 2008, European Respiratory Journal.

[39]  Kathleen Marchal,et al.  Evaluation of time profile reconstruction from complex two-color microarray designs , 2008, BMC Bioinformatics.

[40]  R. Bronson,et al.  E2f4 is required for normal development of the airway epithelium. , 2007, Developmental biology.

[41]  Delbert Dueck,et al.  Clustering by Passing Messages Between Data Points , 2007, Science.

[42]  J. Collins,et al.  Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles , 2007, PLoS biology.

[43]  Cheng Li,et al.  Adjusting batch effects in microarray expression data using empirical Bayes methods. , 2007, Biostatistics.

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

[45]  Tao Jiang,et al.  OligoSpawn: a software tool for the design of overgo probes from large unigene datasets , 2006, BMC Bioinformatics.

[46]  R. Myers,et al.  Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data , 2005, Nucleic acids research.

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

[48]  J. Hogg,et al.  Pathophysiology of airflow limitation in chronic obstructive pulmonary disease , 2004, The Lancet.

[49]  Benjamin M. Bolstad,et al.  affy - analysis of Affymetrix GeneChip data at the probe level , 2004, Bioinform..

[50]  Mark Gerstein,et al.  Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data , 2003, Bioinform..

[51]  M. Gerstein,et al.  Genomic analysis of gene expression relationships in transcriptional regulatory networks. , 2003, Trends in genetics : TIG.

[52]  R. Tjian,et al.  Transcription regulation and animal diversity , 2003, Nature.

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

[54]  A. Barabasi,et al.  Hierarchical Organization of Modularity in Metabolic Networks , 2002, Science.

[55]  S. Oliviero,et al.  Sp1 and Sp3 physically interact and co-operate with GABP for the activation of the utrophin promoter. , 2001, Journal of molecular biology.

[56]  H Rotheneder,et al.  Transcription factors of the Sp1 family: interaction with E2F and regulation of the murine thymidine kinase promoter. , 1999, Journal of molecular biology.

[57]  E. Wintersberger,et al.  Interaction of Sp1 with the growth- and cell cycle-regulated transcription factor E2F , 1996, Molecular and cellular biology.

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

[59]  R. Scarpulla,et al.  Structure, Expression, and Chromosomal Assignment of the Human Gene Encoding Nuclear Respiratory Factor 1 (*) , 1995, The Journal of Biological Chemistry.