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The prediction of regulatory elements is a problem where computational methods offer great hope. Over the past few years, numerous tools have become available for this task. The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark(More)
In this work, we explore video lecture interaction in Massive Open Online Courses (MOOCs), which is central to student learning experience on these educational platforms. As a research contribution , we operationalize video lecture click-streams of students into cognitively plausible higher level behaviors, and construct a quantitative information(More)
One of the key factors that affects automated tutoring systems in making instructional decisions is the quality of the student model built in the system. A student model is a model that can solve problems in various ways as human students. A good student model that matches with student behavior patterns often provides useful information on learning task(More)
Recently, we performed an assessment of 13 popular computational tools for discovery of transcription factor binding sites (M. Tompa, N. Li, et al., "Assessing Computational Tools for the Discovery of Transcription Factor Binding Sites", Nature Biotechnology, Jan. 2005). This paper contains follow-up analysis of the assessment results, and raises and(More)
With recent increased expectations for quality, and the growth of agile processes and test driven development, developers are expected to do more and more effective unit testing. Yet, our knowledge of when to use the various unit level test criteria is incomplete. The paper presents results from a comparison of four unit level software testing criteria.(More)
Online social networks, which have been expanding at a blistering speed recently, have emerged as a popular communication infrastructure for Internet users. Meanwhile, malware that specifically target these online social networks are also on the rise. In this work, we aim to investigate the characteristics of malware propagation in online social networks.(More)
MOTIVATION The next-generation high-throughput sequencing technologies, especially from Illumina, have been widely used in re-sequencing and de novo assembly studies. However, there is no existing software that can simulate Illumina reads with real error and quality distributions and coverage bias yet, which is very useful in relevant software development(More)
Bacteria associated with the onset of type 1 diabetes in a rat model system were identified. In two experiments, stool samples were collected at three time points after birth from bio-breeding diabetes-prone (BB-DP) and bio-breeding diabetes-resistant (BB-DR) rats. DNA was isolated from these samples and the 16S rRNA gene was amplified using universal(More)
  • Ricardo Valladares, Dhyana Sankar, Nan Li, Emily Williams, Kin-Kwan Lai, Asmaa Sayed Abdelgeliel +8 others
  • 2010
BACKGROUND The intestinal epithelium is a barrier that composes one of the most immunologically active surfaces of the body due to constant exposure to microorganisms as well as an infinite diversity of food antigens. Disruption of intestinal barrier function and aberrant mucosal immune activation have been implicated in a variety of diseases within and(More)
Paroxysmal kinesigenic dyskinesias is a paroxysmal movement disorder characterized by recurrent, brief attacks of abnormal involuntary movements induced by sudden voluntary movements. Although several loci, including the pericentromeric region of chromosome 16, have been linked to paroxysmal kinesigenic dyskinesias, the causative gene has not yet been(More)