ReviewProtoplasma2012
Phylogenetic footprinting: a boost for microbial regulatory genomics.
Review in Protoplasma, 2012. 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
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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.
- Snowprint: a predictive tool for genetic biosensor discovery.Communications biology · 2024Article
- A survey on algorithms to characterize transcription factor binding sites.Briefings in bioinformatics · 2023Review
- Integrating genome sequence and structural data for statistical learning to predict transcription factor binding sites.Nucleic acids research · 2020Article
- Genome-scale exploration of transcriptional regulation in the nisin Z producer Lactococcus lactis subsp. lactis IO-1.Scientific reports · 2020Article
- RECTA: Regulon Identification Based on Comparative Genomics and Transcriptomics Analysis.Genes · 2018Article
- Combining phylogenetic footprinting with motif models incorporating intra-motif dependencies.BMC bioinformatics · 2017Article
- An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes.BMC genomics · 2016Article
- Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses.Scientific reports · 2016Article
- Investigating Evolutionary Dynamics of RHA1 Operons.Evolutionary bioinformatics online · 2016Article
- Following the Footsteps of Chlamydial Gene Regulation.Molecular biology and evolution · 2015Article
- Evolutionary genomics of Borrelia burgdorferi sensu lato: findings, hypotheses, and the rise of hybrids.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2014Review
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
No grant is acknowledged in the PubMed record.
Abstract
Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of homologous regulatory regions, usually collected from multiple species. It does so by identifying the best conserved motifs in those homologous regions. There are two popular sets of methods-alignment-based and motif-based, which are generally employed for phylogenetic methods. However, serious efforts have lacked to develop a tool exclusively for phylogenetic footprinting, based on either of these methods. Nevertheless, a number of software and tools exist that can be applied for prediction of phylogenetic footprinting with variable degree of success. The output from these tools may get affected by a number of factors associated with current state of knowledge, techniques and other resources available. We here present a critical apprehension of various phylogenetic approaches with reference to prokaryotes outlining the available resources and also discussing various factors affecting footprinting in order to make a clear idea about the proper use of this approach on prokaryotes.
Indexed as
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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.