PhD Position: Integromics (genomics, transcriptomics, epigenomics) data analysis & applied bioinformatics in rare genetic diseases like cardiac arrhythmias and neurodevelopmental disorders Location: Centre for Medical Genetics Vrije Universiteit Brussel (Faculty of Medicine and Pharmacy) Contact: Sonia Van Dooren (Sonia.VanDooren@uzbrussel.be) Starting date: as soon as possible Context: Doctoral research concerning the added value of integrated versus single multi-omics (whole genomics, transcriptomics, epigenomics) data analysis in the context of the Innoviris BRIDGE project IGenCare ‘Integrated Medical Genomics Care Solution for Patients with Rare Genetic Diseases’ in a collaboration between VUB, ULB, BRIGHTcore (http://www.brightcore.be/) and (IB)2 (http://ibsquare.be/). Some background: In the era of high-throughput massive parallel sequencing, genome-wide analyses have become standard in medical health care. Although this (r)evolutionary technology has been increasingly important in the improvement of the genetic diagnostic yield in patients with rare genetic diseases, scientists and health care providers still phase many challenges. Indeed from the laboratory point of view, scientists had to limit most of the diagnostic genomic analyses to partial analysis of the human genome for cost-effectiveness reasons. This has on the one hand led to a higher number of genetic diagnoses, but on the other hand also to a higher number of unsolved cases, due to lack of identification of potentially causal variants and/or due to uncertainty in interpretation of the data. The project: With the implementation of low cost whole human genome sequencing, transcriptomics and epigenomics we enter a novel time frame of functional genomics and integromics health care, further expanding the possibilities in identifying the cause of rare genetic diseases. Part of the IGenCare project focuses at the laboratory level, where we plan to extend the diagnostic yield of rare genetic diseases by a multi-omics / functional genomics / integromics approach through simultaneous analysis of the patient’s whole genome, gene expression and epigenetic regulation profile in an integrative way. The tasks: - Support in the massive parallel sequencing & array multi-omics data generation through NovaSeq6000, HiSeq1500 & Iscan in collaboration with the BRIGHTcore team - Analysis of the multi-omics data and genotype-phenotype correlation at the single omics level - Evaluation and validation of the multi-omics data interpretation bioinformatics tool and GUI in collaboration with the (IB)2 multi-omics data integrator team - Support in the optimization of multi-omics integrator pipelines, algorithms and annotation tools - Implementation and application of the multi-omics integrator tool Continuous communication in a constant feedback loop between the multi-omics integrator tool and GUI developers on the one hand and the omics data interpretation experts on the other hand You are a bioengineer or a master in computational, biomedical or life sciences, with a strong affinity for applied bioinformatics and multi-omics data analysis. Requirements: You have knowledge of: - Multi-omics (full genome, transcriptome & epigenome) technology - Bioinformatics in a next generation sequencing and array workbench environment (data assembly, analysis and annotation) You are competent in: - Computational aspects of genomics, transcriptomics and / or epigenomics - Scripting and / or programming (eg R, Perl, Linux, Python, C, ...) - Relational databases (MySQL, PostgreSQL) You have capacities in: - Problem-solving (thinking & acting) - Fluent communication (oral & written) - Multi-tasking - Taking initiative, working autonomously - Positive attitude and team work - Eagerness to learn and you are driven to contribute to innovative research and diagnostics You are fluent in languages: - Excellent knowledge of the English language (oral & written) - Some knowledge of Dutch is desirable but not essential