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Robust Method for Detecting Convergent Shifts in Evolutionary Rates

41/41 checkable references clean · checked 2026-07-22

Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.

2 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.

The 41 checked references that resolve

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Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals

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The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq

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GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

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Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis

resolves10.1038/nrg3074

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Convergent evolution of the genomes of marine mammals

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A “Forward Genomics” Approach Links Genotype to Phenotype using Independent Phenotypic Losses among Related Species

resolves10.1126/science.1253451

Whole-genome analyses resolve early branches in the tree of life of modern birds

resolves10.1093/molbev/msq244

A Phylogenetic Model for Investigating Correlated Evolution of Substitution Rates and Continuous Phenotypic Characters

resolves10.1186/gb-2014-15-2-r29

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

resolves10.1016/j.cell.2014.05.034

Expansion of Biological Pathways Based on Evolutionary Inference

resolves10.1038/nature08494

Finding the missing heritability of complex diseases

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“Reverse Genomics” Predicts Function of Human Conserved Noncoding Elements

resolves10.1126/science.1211028

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

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Ancient convergent losses of <i>Paraoxonase 1</i> yield potential risks for modern marine mammals

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Resolution of the Early Placental Mammal Radiation Using Bayesian Phylogenetics

resolves10.1101/gr.5918807

Using genomic data to unravel the root of the placental mammal phylogeny

resolves10.1038/nature12511

Genome-wide signatures of convergent evolution in echolocating mammals

resolves10.7554/eLife.25884

Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling

resolves10.1073/pnas.96.8.4285

Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

resolves10.1038/nrg3458

Enhancers: five essential questions

resolves10.1093/molbev/msw098

Controlling for Phylogenetic Relatedness and Evolutionary Rates Improves the Discovery of Associations Between Species’ Phenotypic and Genomic Differences

resolves10.1038/nature11247

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resolves10.1038/518314a

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resolves10.1038/s41467-018-07122-z

Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution

resolves10.1089/nat.2012.0414

Long Non-Coding RNAs: Challenges for Diagnosis and Therapies

resolves10.1093/bioinformatics/btq706

phangorn: phylogenetic analysis in R

resolves10.1038/nrg3682

Transcriptional enhancers: from properties to genome-wide predictions

resolves10.1038/nrg3483

The genetic causes of convergent evolution

resolves10.1073/pnas.0400782101

A gene atlas of the mouse and human protein-encoding transcriptomes

resolves10.1093/molbev/msv013

Determining the Null Model for Detecting Adaptive Convergence from Genomic Data: A Case Study using Echolocating Mammals

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No Genome-Wide Protein Sequence Convergence for Echolocation

The 2 references without a DOI — listed, not checked

no DOI — not checkedRERconverge: an R package for associating evolutionary rates with convergent traits

no DOI — not checkedThe delayed rise of present-day mammals

What this badge says. CiteStamped means the CHECKABLE references of this work were clean at the dated check: each resolved to a known work in a public registry, and none carried a retraction notice at that time. It says nothing about the quality, findings, or importance of the work itself, and nothing about references deposited without a DOI.

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