ArticleBMC bioinformatics2013
A computational pipeline for identifying kinetic motifs to aid in the design and improvement of synthetic gene circuits.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 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
5 citing papers in PubMed.
- UNified FramewOrk for reguLatory Dynamics (UNFOLD): Dissecting robustness, plasticity, evolvability and canalisation of biological function.PLoS computational biology · 2026Article
- A Noise-Tolerating Gene Association Network Uncovering an Oncogenic Regulatory Motif in Lymphoma Transcriptomics.Life (Basel, Switzerland) · 2023Article
- Multi-objective optimization framework to obtain model-based guidelines for tuning biological synthetic devices: an adaptive network case.BMC systems biology · 2016Article
- Understanding system dynamics of an adaptive enzyme network from globally profiled kinetic parameters.BMC systems biology · 2014Article
- Synthetic biology outside the cell: linking computational tools to cell-free systems.Frontiers in bioengineering and biotechnology · 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
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAn increasing number of genetic components are available in several depositories of such components to facilitate synthetic biology research, but picking out those that will allow a designed circuit to achieve the specified function still requires multiple cycles of testing. Here, we addressed this problem by developing a computational pipeline to mathematically simulate a gene circuit for a comprehensive range and combination of the kinetic parameters of the biological components that constitute the gene circuit.
resultsWe showed that, using a well-studied transcriptional repression cascade as an example, the sets of kinetic parameters that could produce the specified system dynamics of the gene circuit formed clusters of recurrent combinations, referred to as kinetic motifs, which appear to be associated with both the specific topology and specified dynamics of the circuit. Furthermore, the use of the resulting "handbook" of performance-ranked kinetic motifs in finding suitable circuit components was illustrated in two application scenarios.
conclusionsThese results show that the computational pipeline developed here can provide a rational-based guide to aid in the design and improvement of synthetic gene circuits.
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.