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This paper is focused on the derivation of some universal properties of capacity-approaching low-density parity-check (LDPC) code ensembles whose transmission takes place over memoryless binary-input output-symmetric (MBIOS) channels. Properties of the degree distributions, graphical complexity, and the number of fundamental cycles in the bipartite graphs are considered via the derivation of information-theoretic bounds. These bounds are expressed in terms of the target block/bit error probability and the gap (in rate) to capacity. Most of the bounds are general for any decoding algorithm, and some others are proved under belief propagation (BP) decoding. Proving these bounds under a certain decoding algorithm, validates them automatically also under any suboptimal decoding algorithm. A proper modification of these bounds makes them universal for the set of all MBIOS channels which exhibit a given capacity. Bounds on the degree distributions and graphical complexity apply to finite-length LDPC codes and to the asymptotic case of an infinite block length. The bounds are compared with capacity-approaching LDPC code ensembles under BP decoding, and they are shown to be informative and are easy to calculate. Finally, some interesting open problems are considered. [ABSTRACT FROM AUTHOR]

Identification of rhythmic gene expression from metabolic cycles to circadian rhythms is crucial for understanding the gene regulatory networks and functions of these biological processes. Recently, two algorithms, JTK_CYCLE and ARSER, have been developed to estimate periodicity of rhythmic gene expression. JTK_CYCLE performs well for long or less noisy time series, while ARSER performs well for detecting a single rhythmic category. However, observing gene expression at high temporal resolution is not always feasible, and many scientists are interested in exploring both ultradian and circadian rhythmic categories simultaneously. In this paper, a new algorithm, named autoregressive Bayesian spectral regression (ABSR), is proposed. It estimates the period of time-course experimental data and classifies gene expression profiles into multiple rhythmic categories simultaneously. Through the simulation studies, it is shown that ABSR substantially improves the accuracy of periodicity estimation and clustering of rhythmic categories as compared to JTK_CYCLE and ARSER for the data with low temporal resolution. Moreover, ABSR is insensitive to rhythmic patterns. This new scheme is applied to existing time-course mouse liver data to estimate period of rhythms and classify the genes into ultradian, circadian, and arrhythmic categories. It is observed that 49.2% of the circadian profiles detected by JTK_CYCLE with 1-hour resolution are also detected by ABSR with only 4-hour resolution. [ABSTRACT FROM AUTHOR]