cdev: a ground-truth based measure to evaluate RNA-seq normalization performance.

Normalization of RNA-seq data has been an active area of research since the problem was first recognized a decade ago. Despite the active development of new normalizers, their performance measures have been given little attention. To evaluate normalizers, researchers have been relying on measures, most of which are either qualitative, potentially biased, or easily confounded by parametric choices of downstream analysis.

A graph-based algorithm for RNA-seq data normalization.

The use of RNA-sequencing has garnered much attention in recent years for characterizing and understanding various biological systems. However, it remains a major challenge to gain insights from a large number of RNA-seq experiments collectively, due to the normalization problem. Normalization has been challenging due to an inherent circularity, requiring that RNA-seq data be normalized before any pattern of differential (or non-differential) expression can be ascertained; meanwhile, the prior knowledge of non-differential transcripts is crucial to the normalization process.

Cardioinformatics: the nexus of bioinformatics and precision cardiology.

Cardiovascular disease (CVD) is the leading cause of death worldwide, causing over 17 million deaths per year, which outpaces global cancer mortality rates. Despite these sobering statistics, most bioinformatics and computational biology research and funding to date has been concentrated predominantly on cancer research, with a relatively modest footprint in CVD. In this paper, we review the existing literary landscape and critically assess the unmet need to further develop an emerging field at the multidisciplinary interface of bioinformatics and precision cardiovascular medicine, which we refer to as 'cardioinformatics'.

On the mechanism of colloidal silica action to improve flow properties of pharmaceutical excipients.

The mechanism of colloidal silica action to improve flow properties of pharmaceutical powders is known to be based on inter-particle force disruption by silica particles adhered to the particle surface. In the present article, the kinetic aspects of this action are investigated, focusing on non-spherical particles of different size. Blends comprising microcrystalline cellulose or calcium hydrogen phosphate dihydrate and colloidal silica were examined using powder rheometer.

anexVis: visual analytics framework for analysis of RNA expression.

Summary: Although RNA expression data are accumulating at a remarkable speed, gaining insights from them still requires laborious analyses, which hinder many biological and biomedical researchers. This report introduces a visual analytics framework that applies several well-known visualization techniques to leverage understanding of an RNA expression dataset. Our analyses on glycosaminoglycan-related genes have demonstrated the broad application of this tool, anexVis (analysis of RNA expression), to advance the understanding of tissue-specific glycosaminoglycan regulation and functions, and potentially other biological pathways.

Discover binding pathways using the sliding binding-box docking approach: application to binding pathways of oseltamivir to avian influenza H5N1 neuraminidase.

Drug binding and unbinding are transient processes which are hardly observed by experiment and difficult to analyze by computational techniques. In this paper, we employed a cost-effective method called "pathway docking" in which molecular docking was used to screen ligand-receptor binding free energy surface to reveal possible paths of ligand approaching protein binding pocket. A case study was applied on oseltamivir, the key drug against influenza a virus.