ArticleGenome biology and evolution2013
On the need for mechanistic models in computational genomics and metagenomics.
Article in Genome biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Teaching bioinformatics with generative AI: judgment, uncertainty, and responsibility.Journal of microbiology & biology education · 2026Article
- When Complex Models Fit the Wrong Mechanistic Complexity in Phylogenomic Analysis.Journal of molecular evolution · 2026Article
- Exploring the role of intestinal microbiota in mitigating acute radiation-induced intestinal injury through high-energy X-ray FLASH radiotherapy via metagenomic analysis.Frontiers in microbiology · 2025Article
- Detecting Selection on Segregating Gene Duplicates in a Population.Journal of molecular evolution · 2021Article
- Characterizing Amino Acid Substitution with Complete Linkage of Sites on a Lineage.Genome biology and evolution · 2021Article
- Protein Evolution in the Flaviviruses.Journal of molecular evolution · 2020Article
- Relative Model Fit Does Not Predict Topological Accuracy in Single-Gene Protein Phylogenetics.Molecular biology and evolution · 2020Article
- A New Editorial Beginning at Journal of Molecular Evolution.Journal of molecular evolution · 2019Article
- Improved inference of site-specific positive selection under a generalized parametric codon model when there are multinucleotide mutations and multiple nonsynonymous rates.BMC evolutionary biology · 2019Article
- Properties of Samples With Segregating Polymerase Chain Reaction (PCR) Dropout Mutations Within a Species.Evolutionary bioinformatics online · 2019Article
- Review
- Differential strengths of molecular determinants guide environment specific mutational fates.PLoS genetics · 2018Article
- Protein evolution depends on multiple distinct population size parameters.BMC evolutionary biology · 2018Review
- A new parameter-rich structure-aware mechanistic model for amino acid substitution during evolution.Proteins · 2018Article
- Introgression and repeated co-option facilitated the recurrent emergence of CEvolution; international journal of organic evolution · 2017Article
- Analysis of a mechanistic Markov model for gene duplicates evolving under subfunctionalization.BMC evolutionary biology · 2017Article
- A Comparison of One-Rate and Two-Rate Inference Frameworks for Site-Specific dN/dS Estimation.Genetics · 2016Article
- Making sense of big data in health research: Towards an EU action plan.Genome medicine · 2016Article
- Causes of evolutionary rate variation among protein sites.Nature reviews. Genetics · 2016Review
- What Fraction of Duplicates Observed in Recently Sequenced Genomes Is Segregating and Destined to Fail to Fix?Genome biology and evolution · 2015Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Computational genomics is now generating very large volumes of data that have the potential to be used to address important questions in both basic biology and biomedicine. Addressing these important biological questions becomes possible when mechanistic models rooted in biochemistry and evolutionary/population genetic processes are developed, instead of fitting data to off-the-shelf statistical distributions that do not enable mechanistic inference. Three examples are presented, the first involving ecological processes inferred from metagenomic data, the second involving mechanisms of gene regulation rooted in protein-DNA interactions with consideration of DNA structure, and the third involving existing models for the retention of duplicate genes that enables prediction of evolutionary mechanisms. This description of mechanistic models is generalized toward future developments in computational genomics and the need for biological mechanisms and processes in biological models.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.