The outcome of high-throughput biological experiments is affected by many operational factors in the experimental and data-analytical procedures. Understanding how these factors affect the reproducibility of the outcome is critical for establishing workflows that produce replicable discoveries. In this article, we propose a regression framework, based on a novel cumulative link model, to assess...

Chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) has been successfully used for genome-wide profiling of transcription factor binding sites, histone modifications, and nucleosome occupancy in many model organisms and humans. Because the compact genomes of prokaryotes harbor many binding sites separated by only few base pairs, applications of ChIP-Seq in this domai...

PURPOSE The purpose of this study was to develop an instrument to measure the parenting behavior of primary caregivers of children in early childhood. METHODS An instrument was developed according to Devellis's instrument development process. The participants in this study who completed the main survey were 370 mothers and grandmothers. The survey was conducted from June 1 to July 30, 2014, a...

RNA-seq has been widely adopted as a gene-expression measurement tool due to the detail, resolution, and sensitivity of transcript characterization that the technique provides. Here we present two transposon-based methods that efficiently construct high-quality RNA-seq libraries. We first describe a method that creates RNA-seq libraries for Illumina sequencing from double-stranded cDNA with onl...

The GWIPS-viz browser (http://gwips.ucc.ie/) is an on-line genome browser which is tailored for exploring ribosome profiling (Ribo-seq) data. Since its publication in 2014, GWIPS-viz provides Ribo-seq data for an additional 14 genomes bringing the current total to 23. The integration of new Ribo-seq data has been automated thereby increasing the number of available tracks to 1792, a 10-fold inc...

We consider a multicommodity routing problem, where demands are released online and have to be routed in a network during specified time windows. The objective is to minimize a time and load dependent convex cost function of the aggregate arc flow. First, we study the fractional routing variant. We present two online algorithms, called Seq and Seq. Our first main result states that, for cost fu...

The vast majority of multi-exon genes in higher eukaryotes are alternatively spliced and changes in alternative splicing (AS) can impact gene function or cause disease. High-throughput RNA sequencing (RNA-seq) has become a powerful technology for transcriptome-wide analysis of AS, but RT-PCR still remains the gold-standard approach for quantifying and validating exon splicing levels. We have de...

An analysis of four regions in four countries suggests that the best way to mitigate disruption of the pharmaceutical industry is not to ignore or stem it but to sponsor initiatives that keep scientists engaged.

Merger Profitability and Trade Policy by Steffen Huck and Kai A. Konrad We study the profitability and welfare effects of merger in a strategic trade policy environment. Merger changes the strategic trade policy equilibrium. We show that merger can be profitable and welfare enhancing here, even though it is not profitable in a laissez-faire economy. A key element is the change in the government...