The incidence of renal cell carcinoma (RCC) is increasing worldwide, and its prevalence is particularly high in some parts of Central Europe. Here we undertake whole-genome and transcriptome sequencing of clear cell RCC (ccRCC), the most common form of the disease, in patients from four different European countries with contrasting disease incidence to explore the underlying genomic architecture of RCC. Our findings support previous reports on frequent aberrations in the epigenetic machinery and PI3K/mTOR signalling, and uncover novel pathways and genes affected by recurrent mutations and abnormal transcriptome patterns including focal adhesion, components of extracellular matrix (ECM) and genes encoding FAT cadherins. Furthermore, a large majority of patients from Romania have an unexpected high frequency of A:T4T:A transversions, consistent with exposure to aristolochic acid (AA). These results show that the processes underlying ccRCC tumorigenesis may vary in different populations and suggest that AA may be an important ccRCC carcinogen in Romania, a finding with major public health implications.

Abstract. The paper describes a new graphical model transformation language MOLA. The basic idea of MOLA is to merge traditional structured programming as a control structure with pattern-based transformation rules. The key language element is a graphical loop concept. The main goal of MOLA is to describe model transformations in a natural and easy readable way.

We present the results of a systematic literature review that examines the main paradigms and properties of programming languages developed for and used in High Performance Computing for Big Data processing. The systematic literature review is based on a combination of automated keyword-based search in the Elsevier Science Direct database and further digital databases for articles published in international peer-reviewed journals and conferences, leading to an initial sample of 420 articles, which was then narrowed down in a second phase to 152 articles found relevant and published 2006-2018. The manual analysis of these articles allowed us to identify 26 languages used in 33 of these articles for HPC for Big Data processing. We analyzed the languages and their usage in these articles by 22 criteria and summarize the results in this article. We evaluate the outcomes of the literature review by comparing them with opinions of domain experts. Our results indicate that, for instance, the majority of the used HPC languages in the context of Big Data are text-based general-purpose programming languages and target the end-user community.

Mass spectrometry (MS)-based quantitative proteomics experiments typically assay a subset of up to 60% of the ≈20 000 human protein coding genes. Computational methods for imputing the missing values using RNA expression data usually allow only for imputations of proteins measured in at least some of the samples. In silico methods for comprehensively estimating abundances across all proteins are still missing. Here, a novel method is proposed using deep learning to extrapolate the observed protein expression values in label-free MS experiments to all proteins, leveraging gene functional annotations and RNA measurements as key predictive attributes. This method is tested on four datasets, including human cell lines and human and mouse tissues. This method predicts the protein expression values with average R 2 scores between 0.46 and 0.54, which is significantly better than predictions based on correlations using the RNA expression data alone. Moreover, it is demonstrated that the derived models can be "transferred" across experiments and species. For instance, the model derived from human tissues gave a R 2 = 0.51 when applied to mouse tissue data. It is concluded that protein abundances generated in label-free MS experiments can be computationally predicted using functional annotated attributes and can be used to highlight aberrant protein abundance values.

Background: One of the crucial aspects of day-to-day laboratory information management is collection, storage and retrieval of information about research subjects and biomedical samples. An efficient link between sample data and experiment results is absolutely imperative for a successful outcome of a biomedical study. Currently available software solutions are largely limited to largescale, expensive commercial Laboratory Information Management Systems (LIMS). Acquiring such LIMS indeed can bring laboratory information management to a higher level, but often implies sufficient investment of time, effort and funds, which are not always available. There is a clear need for lightweight open source systems for patient and sample information management.