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Seiðr: Efficient Calculation of Robust Ensemble Gene Networks
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Overexpression of AtBBX29 Improves Drought Tolerance by Maintaining Photosynthesis and Enhancing the Antioxidant and Osmolyte Capacity of Sugarcane Plants
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A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain
inferredcites →https://doi.org/10.1016/j.cels.2017.08.014openalex-snapshot
Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures
inferredcites →https://doi.org/10.1016/j.copbio.2019.12.002openalex-snapshot
Network inference in systems biology: recent developments, challenges, and applications
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Laplacian centrality: A new centrality measure for weighted networks
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The anatomy of a large-scale hypertextual Web search engine
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Gene Ontology: tool for the unification of biology
inferredcites →https://doi.org/10.1038/nature12211openalex-snapshot
The Norway spruce genome sequence and conifer genome evolution
inferredcites →https://doi.org/10.1038/nmeth.2016openalex-snapshot
Wisdom of crowds for robust gene network inference
inferredcites →https://doi.org/10.1038/nmeth.3773openalex-snapshot
Inferring causal molecular networks: empirical assessment through a community-based effort
inferredcites →https://doi.org/10.1038/nmeth.4463openalex-snapshot
SCENIC: single-cell regulatory network inference and clustering
inferredcites →https://doi.org/10.1080/07352689.2011.615706openalex-snapshot
Cell Wall Modifying Proteins Mediate Plant Acclimatization to Biotic and Abiotic Stresses
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Co-expression networks for plant biology: why and how
inferredcites →https://doi.org/10.1093/bioinformatics/btm440openalex-snapshot
Improved detection of overrepresentation of Gene-Ontology annotations with parent–child analysis
inferredcites →https://doi.org/10.1093/bioinformatics/bts619openalex-snapshot
NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference
inferredcites →https://doi.org/10.1093/nar/28.1.27openalex-snapshot
KEGG: Kyoto Encyclopedia of Genes and Genomes
inferredcites →https://doi.org/10.1093/nar/gkaa1113openalex-snapshot
The Gene Ontology resource: enriching a GOld mine
inferredcites →https://doi.org/10.1093/nar/gkj013openalex-snapshot
The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae
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The BioGRID interaction database: 2019 update
inferredcites →https://doi.org/10.1093/treephys/tpaa178openalex-snapshot
Candidate regulators and target genes of drought stress in needles and roots of Norway spruce
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Intracellular Redox Compartmentation and ROS-Related Communication in Regulation and Signaling
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Network Backboning with Noisy Data
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mapman : a user‐driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
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The Photolyase/Cryptochrome Family of Proteins as DNA Repair Enzymes and Transcriptional Repressors
inferredcites →https://doi.org/10.1128/msystems.00884-20openalex-snapshot
Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce
inferredcites →https://doi.org/10.1186/1471-2105-5-118openalex-snapshot
Estimating mutual information using B-spline functions – an improved similarity measure for analysing gene expression data
inferredcites →https://doi.org/10.1186/1471-2105-7-s1-s7openalex-snapshot
ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context
inferredcites →https://doi.org/10.1186/1471-2105-9-559openalex-snapshot
WGCNA: an R package for weighted correlation network analysis
inferredcites →https://doi.org/10.1186/1752-0509-6-145openalex-snapshot
TIGRESS: Trustful Inference of Gene REgulation using Stability Selection
inferredcites →https://doi.org/10.1186/s12859-016-1398-6openalex-snapshot
Gene regulatory network inference using PLS-based methods
inferredcites →https://doi.org/10.1186/s12859-018-2217-zopenalex-snapshot
Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data
inferredcites →https://doi.org/10.1186/s12859-021-03987-yopenalex-snapshot
ComHub: Community predictions of hubs in gene regulatory networks
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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.12688/f1000research.7563.1openalex-snapshot
Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences
inferredcites →https://doi.org/10.1371/journal.pbio.0050008openalex-snapshot
Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles
inferredcites →https://doi.org/10.1371/journal.pone.0012776openalex-snapshot
Inferring Regulatory Networks from Expression Data Using Tree-Based Methods
inferredcites →https://doi.org/10.1371/journal.pone.0067434openalex-snapshot
LegumeGRN: A Gene Regulatory Network Prediction Server for Functional and Comparative Studies
inferredcites →https://doi.org/10.1371/journal.pone.0092709openalex-snapshot
NIMEFI: Gene Regulatory Network Inference using Multiple Ensemble Feature Importance Algorithms
inferredcites →https://doi.org/10.1371/journal.pone.0106319openalex-snapshot
Ensemble-Based Network Aggregation Improves the Accuracy of Gene Network Reconstruction
inferredcites →https://doi.org/10.2202/1544-6115.1175openalex-snapshot
A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics
inferredcites →https://doi.org/10.3389/fpls.2019.00653openalex-snapshot
The Plant DNA Damage Response: Signaling Pathways Leading to Growth Inhibition and Putative Role in Response to Stress Conditions
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Mitogen-activated protein kinase signaling in plants under abiotic stress
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/9781119312994.apr0688openalex-snapshot
High Spatial Resolution Profiling in Tree Species
inferred← citeshttps://doi.org/10.1002/ece3.6691openalex-snapshot
Leaf shape in Populus tremula is a complex, omnigenic trait
inferred← citeshttps://doi.org/10.1016/j.pbi.2018.10.005openalex-snapshot
Computational prediction of gene regulatory networks in plant growth and development
inferred← citeshttps://doi.org/10.1038/s41598-020-61758-wopenalex-snapshot
Specific functions for Mediator complex subunits from different modules in the transcriptional response of Arabidopsis thaliana to abiotic stress
inferred← citeshttps://doi.org/10.1073/pnas.2118852119openalex-snapshot
Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests
inferred← citeshttps://doi.org/10.1093/treephys/tpaa178openalex-snapshot
Candidate regulators and target genes of drought stress in needles and roots of Norway spruce
inferred← citeshttps://doi.org/10.1101/2023.08.24.554647openalex-snapshot
The genome of the Wollemi pine, a critically endangered “living fossil” unchanged since the Cretaceous, reveals extensive ancient transposon activity
inferred← citeshttps://doi.org/10.1111/tpj.15990openalex-snapshot
Integrative analysis in Pinus revealed long‐term heat stress splicing memory
inferred← citeshttps://doi.org/10.1186/s12864-020-07338-8openalex-snapshot
Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria
inferred← citeshttps://doi.org/10.1186/s12864-021-07659-2openalex-snapshot
Inferring and analyzing gene regulatory networks from multi-factorial expression data: a complete and interactive suite
inferred← citeshttps://doi.org/10.3389/fpls.2019.00775openalex-snapshot
Systems and Synthetic Biology of Forest Trees: A Bioengineering Paradigm for Woody Biomass Feedstocks
inferred← citeshttps://doi.org/10.3389/fpls.2019.00813openalex-snapshot
Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment
inferred← citeshttps://doi.org/10.62773/jcocs.v2i2.74openalex-snapshot
Recent approaches of Systems Biology and Omics in Plant Research
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