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Information theory improves genetic analysis of complex traits

Claim that applying information theoretic frameworks can better capture complex genetic phenomena such as dominance and gene interactions, compared to standard additive/independence models.

Confidence
90%
active

Evidence Quote

“An information theoretic framework for analyzing trait variation can better capture phenomena like allelic dominance and gene-gene interaction.”

Relationship

Information theoretic framework increases Explanatory power for complex trait variation

Arguments

Information theoretic frameworksubject
Explanatory power for complex trait variationobject

Connections (6)

Limitations of additive models motivate information theory in geneticsInferenceChain
Elo ratings updated using R package eloAssociation
Information theory enables tractable quantification of genetic interactionsInferenceChain
Kullback-Leibler divergence (relative entropy)Factor
Mutual informationFactor
Explaining the significance of epistasis in quantitative geneticsInferenceChain

Evidence

“Reference to a method for modeling microbial abundances using beta-binomial regression.”

(2020). Modeling microbial abundances and dysbiosis with beta-binomial regression doi:10.1214/19-aoas1283 ↗

“Citation for the phyloseq R package for microbiome data analysis.”

McMurdie PJ & Holmes S. (2013). phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data doi:10.1371/journal.pone.0061217 ↗

“Citation for the Metacoder R package for community taxonomic diversity analysis.”

Foster ZSL et al. (2017). Metacoder: An R package for visualization and manipulation of community taxonomic diversity data doi:10.1371/journal.pcbi.1005404 ↗

“Citation for the sourmash library used for MinHash sketching of DNA.”

Titus Brown C & Irber L. (2016). sourmash: a library for MinHash sketching of DNA doi:10.21105/joss.00027 ↗

“Reference for LINflow computational pipeline for prokaryotic genome similarity matrices.”

Tian L et al. (2021). LINflow: a computational pipeline that combines an alignment-free with an alignment-based method to accelerate generation of similarity matrices for prokaryotic genomes doi:10.7717/peerj.10906 ↗

“Reference to Steinegger and Söding 2018 about linear-time clustering of protein sequence sets”

(2018). Clustering huge protein sequence sets in linear time doi:10.1038/s41467-018-04964-5 ↗

“Reference to Buchfink, Reuter, Drost 2021 on DIAMOND for protein alignment”

Buchfink B et al. (2021). Sensitive protein alignments at tree-of-life scale using DIAMOND doi:10.1038/s41592-021-01101-x ↗

“Reference to Boratyn et al. 2013 describing improvements to BLAST”

Boratyn GM et al. (2013). BLAST: a more efficient report with usability improvements doi:10.1093/nar/gkt282 ↗

“Reference to Köster and Rahmann 2012 describing the Snakemake workflow engine”

Köster J & Rahmann S (2012). Snakemake—a scalable bioinformatics workflow engine doi:10.1093/bioinformatics/bts480 ↗

“Reference to csvtk toolkit by Shen W”

Shen W. csvtk - a cross-platform, efficient and practical CSV/TSV toolkit link ↗

“Reference to Shen W, Ren H. 2021 describing TaxonKit”

Shen W & Ren H (2021). TaxonKit: A practical and efficient NCBI taxonomy toolkit doi:10.1016/j.jgg.2021.03.006 ↗

“Reference to Foster ED, Deardorff A. 2017 on the Open Science Framework”

Foster ED & Deardorff A (2017). Open Science Framework (OSF) doi:10.5195/jmla.2017.88 ↗

“Review on selection decisions and breeding program futures”

Cole JB et al. (2021). Invited review: The future of selection decisions and breeding programs: What are we breeding for, and who decides? doi:10.3168/jds.2020-19777 ↗