The pharmacogenomics cube Credit: graphic concept by Francesco Iorio, illustration by Spencer Phillips, EMBL - EBI 2016 Il cubo farmacogenomico Credito: concept grafico Francesco Iorio, illustrazione Spencer Phillips, EMBL-EBI 2016
Computational biology

Iorio Group

The Iorio Group works at the interface of biology, machine learning, statistics and information theory with the goal of understanding and predicting how genomic alterations and molecular traits from other omics contribute to pathological processes, biological circuits’ rewiring and have an impact on therapeutic response in human cancers and other diseases.

Our research aims at advancing human health by designing algorithms, computational tools and novel analytical methods for the integration and the analysis of pharmacogenomics and functional-genomics datasets, with the objective of identifying new therapeutic targets, biomarkers and drug repositioning opportunities.

With our experimental collaborators, we are contributing to the creation of a comprehensive map of all the genetic dependencies occurring in human cancers, and to the development of a computational infrastructure for translating this map into guidelines for early-stage drug development and precision medicine.

The Iorio Group designs, implements and maintains bioinformatics methods and original tools for the assessment of cancer pre-clinical models, the pre-processing, analysis and visualisation of genome-editing screening data, for the in-silico correction of new-technology-specific biases in such data, and for the optimization of single guide RNA libraries for pooled CRISPR-Cas9 screens and other experimental settings.

We are also interested in big-data analytics, the development of biomedical predictive models based on non-biomedical data, and computationally efficient constrained randomization strategies for testing combinatorial properties in large-scale genomic datasets and networks.

Group members

Publications

  • 03/2021 - Nature Communications

    Integrated cross-study datasets of genetic dependencies in cancer

    CRISPR-Cas9 viability screens are increasingly performed at a genome-wide scale across large panels of cell lines to identify new therapeutic targets for precision cancer therapy. Integrating the datasets resulting from these studies is necessary to adequately represent the heterogeneity of human cancers and to assemble a comprehensive map of cancer genetic vulnerabilities. Here, we integrated […]

  • 02/2021 - Nature Communications

    Combinatorial CRISPR screen identifies fitness effects of gene paralogues

    Genetic redundancy has evolved as a way for human cells to survive the loss of genes that are single copy and essential in other organisms, but also allows tumours to survive despite having highly rearranged genomes. In this study we CRISPR screen 1191 gene pairs, including paralogues and known and predicted synthetic lethal interactions to […]

  • 01/2021 - Nature

    Cancer research needs a better map

    It is time to move beyond tumour sequencing data to identify vulnerabilities in cancers.

  • 01/2021 - Genome Biology

    Minimal genome-wide human CRISPR-Cas9 library

    CRISPR guide RNA libraries have been iteratively improved to provide increasingly efficient reagents, although their large size is a barrier for many applications. We design an optimised minimal genome-wide human CRISPR-Cas9 library (MinLibCas9) by mining existing large-scale gene loss-of-function datasets, resulting in a greater than 42% reduction in size compared to other CRISPR-Cas9 libraries while […]

  • 01/2021 - Nature Computational Science

    Redefining false discoveries in cancer data analyses

    The nature of biological networks still brings challenges related to computational complexity, interpretable results and statistical signifcance. Recent work proposes a new method that paves the way for addressing these issues when analyzing cancer genomic data.