INTRODUCTION AND OBJECTIVES
INTRODUCTION AND OBJECTIVES
Two cost-efficient genome-scale methodologies to assess DNA-methylation are MethylCap-seq and Illumina's Infinium HumanMethylation450 BeadChips (HM450). Objective information regarding the best-suited methodology for a specific research question is scant. Therefore, we performed a large-scale evaluation on a set of 70 brain tissue samples, i.e. 65 glioblastoma and 5 non-tumoral tissues. As MethylCap-seq coverages were limited, we focused on the inherent capacity of the methodology to detect methylated loci rather than a quantitative analysis.
Genome engineering experiments used to be lengthy, inefficient and often expensive, preventing a widespread adoption of such experiments for the full assessment of endogenous protein functions. With the revolutionary CRISPR/Cas9 technology, genome engineering became accessible to the broad life sciences community and is now implemented in several research areas. One particular field that can benefit significantly from this evolution is proteomics where a substantial impact on experimental design and general proteome biology can be expected.
• A NGS workflow is developed to analyse GMOs.
• Transgene inserts are detected, proven to be integrated, and identified.
• A statistical framework is developed to support the NGS workflow.
• The framework is experimentally validated and influential factors are assessed.
• Samples encountered in routine analysis are investigated for NGS feasibility.
The Belgian State Secretary for Science Policy signed the ELIXIR Consortium Agreement. Belgium in now a voting participant in ELIXIR.
What is ELIXIR? Building a sustainable European infrastructure for biological information, supporting life science research and its translation to medicine, agriculture, bioindustries and society.
ELIXIR unites Europe’s leading life science organisations in managing and safeguarding the massive amounts of data being generated every day by publicly funded research. It is a pan-European research infrastructure for biological information.
Scientists from the team of Yvan Saeys (VIB Inflammation Research Center, UGent) have developed novel computational tools to automate the analysis of flow cytometry data. Using their algorithms, they were able to obtain the best performance in the FlowCAP IV challenge.
After performing de novo transcript assembly of >1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies) tissues that were not surface sterilized, we found that assembled sequences captured a mix of plant, lichen, and fungal transcripts. The latter were likely expressed by endophytic and epiphytic symbionts, indicating that these organisms were present, alive, and metabolically active.
Clonal populations accumulate mutations over time, resulting in different haplotypes. Deep sequencing of such a population in principle provides information to reconstruct these haplotypes and the frequency at which the haplotypes occur. However, this reconstruction is technically not trivial, especially not in clonal systems with a relatively low mutation frequency. The low number of segregating sites in those systems adds ambiguity to the haplotype phasing and thus obviates the reconstruction of genome-wide haplotypes based on sequence overlap information.
One of the initiatives of BIG N2N is to organize a seminar series where we invite excellent speakers that have made important and interesting contributions to the wider field of Bioinformatics and/or Systems Biology. For the academic year of 2015-2016 we can present to you Marek Mutwil, Roderic Guigo, Amos Bairoch, Eugene Meyers and many more.
Jump to http://www.bign2n.ugent.be/node/232 and be welcome!