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Many statistical potentials were developed in last two decades for protein folding and protein structure recognition. The major difference of these potentials is on the selection of reference states to offset sampling bias. However, since these potentials used different databases and parameter cutoffs, it is difficult to judge what the best reference states(More)
MOTIVATION Computationally generated non-native protein structure conformations (or decoys) are often used for designing protein folding simulation methods and force fields. However, almost all the decoy sets currently used in literature suffer from uneven root mean square deviation (RMSD) distribution with bias to non-protein like hydrogen-bonding and(More)
Robustness is a fundamental characteristic of biological systems since all living systems need to adapt to internal or external perturbations, unpredictable environments, stochastic events and unreliable components, and so on. A long-term challenge in systems biology is to reveal the origin of robustness underlying molecular regulator network. In this(More)
MicroRNAs are a predominant type of small non-coding RNAs approximately 21 nucleotides in length that play an essential role at the post-transcriptional level by either RNA degradation, translational repression or both through an RNA-induced silencing complex. Identification of these molecules can aid the dissecting of their regulatory functions. The(More)
Coherent feed-forward loops exist extensively in realistic biological regulatory systems, and are common signaling motifs. Here, we study the characteristics and the propagation mechanism of the output noise in a coherent feed-forward transcriptional regulatory loop that can be divided into a main road and branch. Using the linear noise approximation, we(More)
Motivation: Computationally generated non-native protein structure conformations (or decoys) are often used for designing protein folding simulation methods and force fields. However, almost all the decoy sets currently used in literature suffer from uneven root mean square deviation (RMSD) distribution with bias to non-protein like hydrogen-bonding and(More)
Spiral waves are observed in the chemical, physical and biological systems, and the emergence of spiral waves in cardiac tissue is linked to some diseases such as heart ventricular fibrillation and epilepsy; thus it has importance in theoretical studies and potential medical applications. Noise is inevitable in neuronal systems and can change the electrical(More)
Spiral waves in the neocortex may provide a spatial framework to organize cortical oscillations, thus help signal communication. However, noise influences spiral wave. Many previous theoretical studies about noise mainly focus on unbounded Gaussian noise, which contradicts that a real physical quantity is always bounded. Furthermore, non-Gaussian noise is(More)
Recently, a new type of small interfering RNAs (qiRNAs) of typically 20~21 nucleotides was found in Neurospora crassa and rice and has been shown to regulate gene silencing in the DNA damage response. Identification of qiRNAs is fundamental for dissecting regulatory functions and molecular mechanisms. In contrast to other expensive and time-consuming(More)
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