Tamas Rujan

• Genedata

Background: Despite a myriad of attempts in the last three decades to diagnose ovarian cancer (OC) earlier, this clinical aim still remains a significant challenge. Aberrant methylation patterns of linked CpGs analyzed in DNA fragments shed by cancers into the bloodstream (i.e. cell-free DNA) can provide highly specific signals indicating cancer p...

Genedata ProfilerTM is a translational research software platform developed in collaboration with leading pharmaceutical companies to effectively process, manage, and analyze omic and phenotypic data to the highest standards of data quality and regulatory compliance. Genedata Profiler complements the knowledge management platform tranSMART by stand...

In this paper we review the regulatory landscape and its impact on translational research, and define the key attributes of an “ideal” system to overcome the challenges of conducting translational research while respecting patient privacy.

The integration and analysis of large datasets in translational research has become an increasingly challenging problem. We propose a collaborative approach to integrate established data management platforms with existing analytical systems to fill the hole in the value chain between data collection and data exploitation. Our proposal in particular...

Breast, ovarian and endometrial cancers cause significant morbidity and mortality. Despite the presence of existing screening, diagnostic and treatment modalities, they continue to pose considerable unsolved challenges. Overdiagnosis is a growing problem in breast cancer screening and neither screening nor early diagnosis of ovarian or endometrial...

Breast and ovarian cancers pose huge and unsolved challenges to the medical profession. Breast cancer is the most common cancer in women in the EU: more than 332,000 women are diagnosed with breast cancer each year and a woman dies every 6 minutes from this disease. Ovarian cancer, whilst far less common than breast cancer, is often diagnosed when...

Recently, the analysis and functional elucidation of CpG island methylation has become a focus area of genomic research. Deviations from the normal parental imprinting pattern have been shown to cause developmental defects associated with serious symptoms. Aberrant DNA methylation of tumor suppressor and other functional genes, especially when foun...

Immortalized human cancer cell lines are widely used as tools and model systems in cancer research but their authenticity with regard to primary tissues remains a matter of debate. We have used differential methylation hybridisation to obtain comparative methylation profiles from normal and tumour tissues of lung and colon, and permanent cancer cel...

Chloroplasts were once free-living cyanobacteria that became endosymbionts, but the genomes of contemporary plastids encode only approximately 5-10% as many genes as those of their free-living cousins, indicating that many genes were either lost from plastids or transferred to the nucleus during the course of plant evolution. Previous estimates hav...

It is well known that chloroplasts and mitochondria donated many genes to nuclear chromosomes during evolution - but how many is "many"? A sample of 3961 Arabidopsis nuclear protein-coding genes was compared with the complete set of proteins from yeast and 17 reference prokaryotic genomes, including one cyanobacterium (the lineage from which plasti...

Isopentenyl diphosphate (IPP) is the central intermediate in the biosynthesis of isoprenoids, the most ancient and diverse class of natural products. Two distinct routes of IPP biosynthesis occur in nature: the mevalonate pathway and the recently discovered deoxyxylulose 5-phosphate (DXP) pathway. The evolutionary history of the enzymes involved in...

The interrogation of genome, transcriptome, and epigenome information is key to understanding genetic regulatory networks in crop species. While applications such as RNA-seq, ChIP-seq, and bisulfite sequencing can yield valuable information about such networks, it can be challenging for a scientist, or even a biostatistician, to bring all of this i...