Grant: Research Tools and Instruments

In the era of next-generation sequencing, can we reach a complete and comprehensive understanding of our genomes? Recent technological advances are key to this goal but so are the analytical methods used. Most methods rely on reference annotations that map functional elements within our genomes such as genes, transcripts, or coding regions. Hitherto the biological knowledge extracted from the data using these methods will suffer from any erroneous or lacking annotation. Recent discoveries have highlighted functional elements that have eluded genome annotations, from novel genes to non-coding transcripts evolution and functions. These elements have been missed because their study is complex: highly homologous sequences (e.g. pseudogenes or alternatively spliced transcripts), embedded elements (e.g. overlapping coding regions or small nucleolar RNAs, snoRNA), and lack of biological knowledge (e.g. pseudogenes, transcript evolution, snoRNA). There is an urgent need for innovative computational methods to better understand our genomes, transcriptomes, and proteomes. Our team regroups leaders in developing computational methods to better interrogate omics data. Together, we have created internationally recognized resources to help the scientific community mend this knowledge gap. We have notably created the OpenProt proteogenomics resource which facilitates the discovery of novel functional coding sequences and are the only Canadian researchers in the international consortium driving annotation of overlooked coding sequences in collaboration with Gencode and EMBL-EBI. We have also established state-of-the-art annotation and methods for the identification of non-coding transcripts, such as TranscriptDB and snoDB. In this application, we federate our expertise in computational biology, deep learning, and omics data to aim for a more comprehensive and exhaustive annotation of functional elements within our genomes. Each of our research programs are supported by funding from the Natural Sciences and Engineering Research Council of Canada (NSERC). However, we urgently need a high-performance computing platform to support and warrant sustainability of our research programs. This computational server has been designed to foster data transfer and collaboration between our groups, offer resources to the wider community when possible, and further training of highly qualified personnel (HQP). Our research programs are synergistic and complementary, aiming to develop the tools (engineering) and fundamental knowledge (natural sciences) to better understand our genomes, transcriptomes, and proteomes. Direct and undelayed access to a high-performance computing platform is crucial to (1) maintain our internationally recognized resources, (2) sustain our innovative research programs and (3) equip HQP with cutting-edge computational skills, still too rare in the workforce. This will ultimately help us maintain Canadian leadership in computational biology.