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.

No abstract uploaded!

In this paper, we derive Li-Yau inequality for unbounded Laplacian on complete weighted graphs with the assumption of the curvature dimension inequality C D E(n, K), which can be regarded as a notion of curvature on graphs. Furthermore, we obtain some applications of Li-Yau inequality, including Harnack inequality, heat kernel bounds and Cheng's eigenvalue estimate. These are the first kind of results in this direction for unbounded Laplacian on graphs.

We describe a general geometrical construction of representations of fundamental groups of 3-manifolds into PU(2, 1) and eventually of spherical CR structures defined on those 3-manifolds. We construct branched spherical CR structures on the complement of the figure eight knot and the Whitehead link. They have discrete holonomies contained in PU(2, 1,Z[ω]) and PU(2, 1,Z[i]) respectively.

We prove the Zorich–Kontsevich conjecture that the non-trivial Lyapunov exponents of the Teichmüller ow on (any connected component of a stratum of) the moduli space of Abelian differentials on compact Riemann surfaces are all distinct. By previous work of Zorich and Kontsevich, this implies the existence of the complete asymptotic Lagrangian flag describing the behavior in homology of the vertical foliation in a typical translation surface.