Research Seminar: Bioinformatics and Machine Learning

This month the research seminar will feature talks from members of the Bioinformatics and Machine Learning Community. This month's talks are listed below:

Pan-cancer discovery of driver mutations in long noncoding RNAs reveals widespread functional rewiring of RNA regulatory elements

• Background: While fitness altering somatic 'driver' mutations are conventionally thought to impact protein coding genes, the 100kGP dataset contains extensive tumour mutations in regulatory long noncoding RNAs, which appear to act by rewiring secondary structures and binding sites for proteins.
• Presentation focus: The speaker will present the accelerated, versatile driver discovery tool "ExInAtor-PS" and show how we can use 100kGP's deep mutational data to probe RNA regulatory elements at high resolution and discover new therapeutic vulnerabilities.
• Main take: The non-protein-coding genome is targeted by an extensive, undiscovered universe of somatic driver mutations that shape tumour cell evolution and might soon be targeted by new therapies.

-Rory Johnson, Associate Professor, University College Dublin

Transcriptional specificity disruption as a non-coding axis of rare disease risk

• Background: Machine-learning models reveal cross-tissue dysregulatory variants with pathogenic potential in rare disease patients.
• Presentation focus: The speaker will focus on using sequence-to-transcriptome models to predict changes in transcriptional specificity, validate these effects experimentally and in population data, and prioritise candidate non-coding variants in unresolved rare disease genomes.
• Main take: Pathogenic regulatory variants may act not only by changing how much a gene is expressed, but also where and when it is expressed, providing a new functional axis for prioritizing non-coding variants in rare disease.

-Miquel Anglada-Girotto, Postdoctoral Researcher, Centre for Genomic Regulation (CRG)

About the speakers:

Rory Johnson, Associate Professor, University College Dublin

Rory Johnson is an Associate Professor at University College Dublin, where he leads the Laboratory for Genomics of Long Noncoding RNAs (GOLD Lab). His research goal is to understand the roles of long noncoding RNAs (lncRNAs) in cancer and to harness them as therapeutic targets. To achieve this, his team develops genome editing and bioinformatic tools to identify and characterise disease-driving lncRNAs at scale. This approach recently produced the first catalogue of somatically mutated cancer driver lncRNAs. He holds an MSc in Physics from Imperial College London and completed a Wellcome Trust PhD at the University of Leeds on microRNAs in neurodegenerative disease (2007). After postdoctoral work at the Genome Institute of Singapore, he received Spain's Ramón y Cajal fellowship to join Roderic Guigó's group at the Centre for Genomic Regulation, Barcelona. There, as part of the GENCODE consortium, he contributed to the systematic annotation of the human lncRNA gene catalogue and developed CRISPR-based and computational tools for lncRNA functional discovery. He founded the GOLD Lab in 2016. The group, now comprising 15 experimental and computational biologists, actively collaborates with international consortia including Genomics England and FANTOM.

Miquel Anglada-Girotto, Postdoctoral Researcher, Centre for Genomic Regulation (CRG)

Miquel Anglada-Girotto is a Postdoctoral Researcher in the Probabilistic Machine Learning and Genomics laboratory at the Centre for Genomic Regulation (CRG), Barcelona. His doctoral research centred on developing statistical methods to characterise the role of alternative splicing in cancer. His current work applies probabilistic machine learning to model transcriptional regulation, with the dual aim of improving rare disease diagnosis through the interpretation of non-coding regulatory variants and informing the design of next-generation RNA-based treatments.

About the research seminars:

The Genomics England Research Seminar series is a season of events held to demonstrate the best research from Genomics England and our partners. They started in October 2018, and are monthly, free-to-attend talks presented by Research Network members on the latest research being performed using data from the National Genomic Research Library.

The seminars will be held on the last Tuesday of each month at 2 to 3pm. These will be online sessions open to everyone and free to attend, we hope to have representation from across the Research Network and 100,000 Genomes Project participants as well as anyone else who would be interested in joining.

For updates on the seminars including announcements and speakers please follow the Genomics England twitter page. You can watch all previous Research Seminars on the Genomics England YouTube channel.

If you would like to present your research from the Genomics England Research Environment at one of these events please get in touch with the Research Management team at [email protected] and if you intend to publish on this research please include this so that we can publicise your paper on our Publications page.