Estimating drivers of cell state transitions using gene regulatory network models
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Summary
MONSTER, MOdeling Network State Transitions from Expression and Regulatory data, a regression-based method for inferring transcription factor drivers of cell state conditions at the gene regulatory network level is described.
- Type
- article
- Published
- 2016-11-21
- Cited by
- 19
- References
- 66
- Access
- Open access
- OpenAlex
- https://openalex.org/W2949927938
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:21196367
Keywords
Gene regulatory network, Systems biology, Computational biology, State (computer science), Regulatory state
References
- Airway mucus function and dysfunction.
- Transcription factors of the Sp1 family: interaction with E2F and regulation of the murine thymidine kinase promoter.
- Wisdom of crowds for robust gene network inference
- An atlas of combinatorial transcriptional regulation in mouse and man
- Interaction of Sp1 with the growth- and cell cycle-regulated transcription factor E2F
- OligoSpawn: a software tool for the design of overgo probes from large unigene datasets
- JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles
- WGCNA: an R package for weighted correlation network analysis
- Perturbation Biology: Inferring Signaling Networks in Cellular Systems
- Intraflagellar Transport Gene Expression Associated with Short Cilia in Smoking and COPD
- Analysis of chromatin-state plasticity identifies cell-type–specific regulators of H3K27me3 patterns
- Structure, Expression, and Chromosomal Assignment of the Human Gene Encoding Nuclear Respiratory Factor 1 (*)
- Altered Gene Expression in Blood and Sputum in COPD Frequent Exacerbators in the ECLIPSE Cohort
- Semi-supervised prediction of protein subcellular localization using abstraction augmented Markov models
- A Genome-Wide Association Study in Chronic Obstructive Pulmonary Disease (COPD): Identification of Two Major Susceptibility Loci
- Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
- Hierarchical Organization of Modularity in Metabolic Networks
- Passing Messages between Biological Networks to Refine Predicted Interactions
- A network model for angiogenesis in ovarian cancer
- Detection of gene pathways with predictive power for breast cancer prognosis
Cited by
- Estimating Sample-Specific Regulatory Networks
- Predicting growth rate from gene expression
- Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations
- Genetic Modulation of Neurocognitive Development in Cancer Patients throughout the Lifespan: a Systematic Review
- Gene networks with transcriptional bursting recapitulate rare transient coordinated expression states in cancer
- Methods for Estimating Hidden Structure and Network Transitions in Genomics
- A paradigm shift in medicine: A comprehensive review of network-based approaches.
- Towards Reliable Gene Regulatory Network Inference
- Gene networks with transcriptional bursting recapitulate rare transient coordinated high expression states in cancer
- Logic-based Analysis of Gene Expression Data Predicts Association Between TNF, TGFB1 and EGF Pathways in Basal-like Breast Cancer.
- Allelic correlation is a marker of tradeoffs between barriers to transmission of expression variability and signal responsiveness in genetic networks
- The Network Zoo: a multilingual package for the inference and analysis of biological networks
- Altered transcription factor targeting is associated with differential peripheral blood mononuclear cell proportions in sarcoidosis
- The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks
- Predicting anti-cancer drug combination responses with a temporal cell state network model
- Higher-order correction of persistent batch effects in correlation networks
- Estimating drivers of breast tissue transitions from normal to tumor state
- Additional file 2 of The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks
- Additional file 1 of The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks
- Insights into respiratory disease through bioinformatics
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