ArticleProceedings of the National Academy of Sciences of the United States of America2005
Subtree power analysis and species selection for comparative genomics.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed.
- Article
- A phylogenetic approach for weighting genetic sequences.BMC bioinformatics · 2021Article
- Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution.PLoS genetics · 2020Article
- Statistical approaches to use a model organism for regulatory sequences annotation of newly sequenced species.PloS one · 2012Article
- Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data.Nature reviews. Genetics · 2011Review
- Greedy selection of species for ancestral state reconstruction on phylogenies: elimination is better than insertion.PloS one · 2010Article
- Detection of nonneutral substitution rates on mammalian phylogenies.Genome research · 2010Article
- Statistical power of phylo-HMM for evolutionarily conserved element detection.BMC bioinformatics · 2007Article
- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.Nature · 2007Article
- ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements.Genome research · 2006Article
- Species choice for comparative genomics: being greedy works.PLoS genetics · 2005Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Sequence comparison across multiple organisms aids in the detection of regions under selection. However, resource limitations require a prioritization of genomes to be sequenced. This prioritization should be grounded in two considerations: the lineal scope encompassing the biological phenomena of interest, and the optimal species within that scope for detecting functional elements. We introduce a statistical framework for optimal species subset selection, based on maximizing power to detect conserved sites. Analysis of a phylogenetic star topology shows theoretically that the optimal species subset is not in general the most evolutionarily diverged subset. We then demonstrate this finding empirically in a study of vertebrate species. Our results suggest that marsupials are prime sequencing candidates.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.