High-throughput biological technologies (e.g. ChIPseq, RNA-seq and single-cell RNA-seq) rapidly accelerate the accumulation of genome-wide omics data in diverse interrelated biological scenarios (e.g. cells, tissues and conditions). Integration and differential analysis are two common paradigms for exploring and analyzing such data. However, current integrative methods usually ignore the differential part, and typical differential analysis methods either fail to identify combinatorial patterns of difference or require matched dimensions of the data. Here, we propose a flexible framework CSMF to combine them into one paradigm to simultaneously reveal Common and Specific patterns via Matrix Factorization from data generated under interrelated biological scenarios. We demonstrate the effectiveness of CSMF with four representative applications including pairwise ChIP-seq data describing the chromatin modification map between K562 and Huvec cell lines; pairwise RNA-seq data representing the expression profiles of two different cancers; RNA-seq data of three breast cancer subtypes; and single-cell RNA-seq data of human embryonic stem cell differentiation at six time points. Extensive analysis yields novel insights into hidden combinatorial patterns in these multi-modal data. Results demonstrate that CSMF is a powerful tool to uncover common and specific patterns with significant biological implications from data of interrelated biological scenarios.

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In this paper we present an error estimate for the explicit Runge-Kutta discontinuous Galerkin method to solve a linear hyperbolic equation in one dimension with discontinuous but piecewise smooth initial data. The discontinuous finite element space is made up of piecewise polynomials of arbitrary degree $k\geq1$, and time is advanced by the third order explicit total variation diminishing Runge-Kutta method under the standard CFL temporal-spatial condition. The $L^2(\mathbb{R}\backslash\mathcal{R}_T)$-norm error at the final time $T$ is optimal in both space and time, where $\mathcal{R}_T$ is the pollution region due to the initial discontinuity with the width $\mathcal{O}(\sqrt{T\beta}h^{1/2}\log(1/h))$. Here $h$ is the maximum cell length and $\beta$ is the flowing speed. These results are independent of the time step and hold also for the semi-discrete discontinuous Galerkin method.

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This paper studies a special class of population-size-dependent branching processes, in which the offspring distribution is supercritical when the population size does not exceed a given threshold 𝐾𝐾, and is subcritical or critical when the population size exceeds 𝐾𝐾. Up to now, the author has found no paper concerning continuous time threshold processes, and study of the discrete case is also limited to the extinction time 𝑇𝑇 and 𝔼𝔼𝑇𝑇. In this paper, both of the two cases were studied more thoroughly: for the discrete case, a limit theorem of the process has been proved; for the continuous case, the existence of Markovian threshold processes has been proved, and an equivalent condition for the process to extinct almost surely was also given. This paper also further generalized discrete time threshold processes by giving a random delay to the threshold’s influence of offspring distribution. The properties of these delayed threshold processes were studied, and a limit theorem was obtained.