Wednesday, 28 July 2021

Thursday, 29 July 2021

Friday, 30 July 2021

Francesca Ciccarelli, PhD

Professor of Cancer Genomics at King’s College London, U.K.
Head of Cancer Systems Biology at the Francis Crick Institute, London, U.K.

Gene deregulations driving cancer at single patient resolution

A major challenge in cancer biology is the identification of gene alterations that promote cancer. Current methods tackle this issue by detecting signs of positive selection, i.e. identifying genes whose mutations recur across cancer samples because they confer selective growth advantages to the mutated cancer cells. However, in cancers where the recurrence of mutations across sample is low and the mutational landscape is highly variable but mostly flat, these approaches are clearly insufficient. We have developed a novel approach that allows a comprehensive characterisation of genes contributing to cancer one patient at a time. Our approach applies machine learning to identify aberrations in the individual patients based on their similarity to known cancer-driver alterations rather than how frequently they occur across patients. In my talk, I will explain how this approach works and will describe how we have validated experimentally some of these predictions to confirm their role in cancer. I will give examples of how a better knowledge of the completer repertoire of drive genes at the single-patient resolution contribute to enhance our understanding of carcinogenesis.

About the speake: Francesca Ciccarelli is Professor of Cancer Genomics at King’s College London and Group Leader at the Francis Crick Institute. Francesca graduated in Pharmaceutical Chemistry at the University of Bologna and received a PhD in Natural Sciences from the University of Heidelberg where she worked under the supervision of Peer Bork at the EMBL. There she studied the evolution of genomes using comparative genomics and phylogenetics. In 2005, Francesca started her independent research group at the European Institute of Oncology in Milan where she applied genomics and systems biology to study the evolution of gastrointestinal cancer. In 2014, she moved to King’s College London and since 2017 her group is seconded to the Francis Crick Institute. Francesca is co-lead of the patient stratification theme of the Cancer Research UK KHP Centre and of the cancer evolution theme of the CRUK City of London Cancer Centre. Francesca works with a multidisciplinary team of biologists, mathematicians, oncologists, engineers and computer scientists who apply molecular genetics, data analysis and theoretical modelling to study cancer biology and evolution. The work in her lab is supported by Cancer Research UK, King’s Health Partners and the European Union.

Nikos C Kyrpides, PhD

Head of Prokaryotic Super Program and the Microbiome Data Science Group, DOE Joint Genome Institute, Walnut Creek, U.S.A.

Microbiome Data Science: from the Earth microbiome to the Global virom

Microbiome research is rapidly transitioning into Data Science. The unprecedented volume of microbiome data being generated pose significant challenges with respect to standards and management strategies, but also bear great new opportunities that can fuel discovery. Computational analysis of microbiome samples involving previously uncultured organisms, is currently advancing our understanding of the structure and function of entire microbial communities and expanding our knowledge of genetic and functional diversity of individual micro-organisms. I will describe some of our computational approaches and will emphasize the value of data processing integration in enabling the exploration of large metagenomic datasets and the discovery of novelty. I will discuss current approaches and success stories for the discovery of novel phylogenetic lineages as well as the exploration of the viral dark matter.

About the speaker: Dr. Kyrpides joined the DOE Joint Genome Institute in 2004 to lead the Genome Biology Program and the development of the data management and comparative analysis platforms for microbial genomes and metagenomes (IMG). He became the Metagenomics Program head in 2010 and leads the Prokaryotic Super Program and the Microbiome Data Science Group since 2011. Prior to joining the DOE Joint Genome Institute, Dr. Kyrpides led the development of the genome analysis and Bioinformatics core at Integrated Genomics Inc. in Chicago, IL. He did his postdoctoral studies with Carl Woese at the University of Illinois at Urbana-Champaign and with Ross Overbeek at the Argonne National Laboratory. On twitter @kyrpides