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Previous ncRNA annotation efforts have generated datasets of negatives by shuffling actual genome alignments [40] rather than simulating the evolutionary process.
Using numerical models simulating the evolutionary changes in the gene regulation network required to achieve a particular expression pattern, we first confirmed that gene expression dynamics robust to mutation evolved in the presence of a sufficient level of transcriptional noise.
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In the first simulation method, starting from a randomly generated root sequence, we simulated the evolutionary process to obtain leaf node sequences based on a tree and a rate matrix.
In our study, we built a computer model to simulate the evolutionary process.
To address the problem, a multi-species coexistence dynamical model under habitat restoration is set up to simulate the evolutionary trait of different species in different communities.
He also developed software to simulate the evolutionary game under different conditions and to visualize the results.
Early analogies between the mechanism of natural selection and learning or optimization process have been led to development of so-called evolutionary algorithms whose main goal is to simulate the evolutionary process on a computer (Coello Coello and Lamont 2004).
For a population with more than two types, we simulate the evolutionary dynamics numerically.
Fregene simulates the evolutionary process of genetic sequencing data in a population following the Fisher Wright model (a monoecious, diploid, randomly mating population that evolves across nonoverlapping generations).
To show how many patients are necessary to reveal the ground truth, we simulate the evolutionary and sampling process by an artificial example.
We use a degree-dependent model (DDM) to simulate the evolutionary path from a putative ancestral network to its extant state.
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