Ewa A. Bergmann

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As the second most common type of variation in the human genome, insertions and deletions (indels) have been linked to many diseases, but the discovery of indels of more than a few bases in size from short-read sequencing data remains challenging. Scalpel (http://scalpel.sourceforge.net) is an open-source software for reliable indel detection based on the(More)
Investments in renewable energy, such as new wind farms and hydro schemes, are being promoted as a new means of diversifying rural employment in Scotland*. However, such investments are associated with a range of environmental impacts which might be detrimental to other economic activities, such as those based on nature tourism. When designing policy(More)
In this paper, we investigate whether people's knowledge of the past influences their preferences and values towards future landscape change. "Knowledge of the past" is one aspect of the information set held by individuals, and a well-established finding in economics is that changes in information can change preferences and values. The particular aspects of(More)
OBJECTIVE To analyze a glioblastoma tumor specimen with 3 different platforms and compare potentially actionable calls from each. METHODS Tumor DNA was analyzed by a commercial targeted panel. In addition, tumor-normal DNA was analyzed by whole-genome sequencing (WGS) and tumor RNA was analyzed by RNA sequencing (RNA-seq). The WGS and RNA-seq data were(More)
MOTIVATION Sequencing of matched tumor and normal samples is the standard study design for reliable detection of somatic alterations. However, even very low levels of cross-sample contamination significantly impact calling of somatic mutations, because contaminant germline variants can be incorrectly interpreted as somatic. There are currently no(More)
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