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List of works by Francesco Iorio

A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia.

scientific article

A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions

scientific article

A landscape of pharmacogenomic interactions in cancer.

scientific article published on 05 July 2016

A screen for combination therapies in BRAF/NRAS wild type melanoma identifies nilotinib plus MEK inhibitor as a synergistic combination

A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches

scientific article

Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets

scientific article published on 20 December 2019

Analysis of CRISPR-Cas9 screens identify genetic dependencies in melanoma

scientific article published on 07 August 2020

Artificial neural network analysis of circulating tumor cells in metastatic breast cancer patients

scientific article

BRAF inhibitor resistance mediated by the AKT pathway in an oncogenic BRAF mouse melanoma model

scientific article

Blood transcriptomics of drug-naïve sporadic Parkinson's disease patients

scientific article published on 28 October 2015

CELLector: Genomics Guided Selection of Cancer in vitro Models

article

Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network

scientific article

CoRe: a robustly benchmarked R package for identifying core-fitness genes in genome-wide pooled CRISPR-Cas9 screens

scientific article published on 17 November 2021

Comprehensive Pharmacogenomic Profiling of Malignant Pleural Mesothelioma Identifies a Subgroup Sensitive to FGFR Inhibition

scientific article

Discovery of drug mode of action and drug repositioning from transcriptional responses ⬇️

scientific article published on August 2, 2010

Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens

scientific article published on 01 July 2020

Drug repurposing: progress, challenges and recommendations

scholarly article by Sudeep Pushpakom et al published 12 October 2018 in Nature Reviews Drug Discovery

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.

scientific article

Efficient randomization of biological networks while preserving functional characterization of individual nodes

scientific article

Exploiting combinatorial patterns in cancer genomic data for personalized therapy and new target discovery

scientific article

Fast randomization of large genomic datasets while preserving alteration counts

scientific article published on September 2014

Functional Impact of Genomic Complexity on the Transcriptome of Multiple Myeloma

scientific article published on 15 September 2021

Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening

article

GDSCTools for Mining Pharmacogenomic Interactions in Cancer

scientific article published on 24 November 2017

Gene ontology fuzzy-enrichment analysis to investigate drug mode-of-action

article

Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations

scientific article published on 8 February 2017

Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts.

scientific article published on 08 September 2016

Heterogeneity of genomic evolution and mutational profiles in multiple myeloma

scientific article published on January 2014

Identification of Intrinsic Drug Resistance and Its Biomarkers in High-Throughput Pharmacogenomic and CRISPR Screens

scientific article published on 02 July 2020

Identification of drug-specific pathways based on gene expression data: application to drug induced lung injury

scientific article

Identification of small molecules enhancing autophagic function from drug network analysis

scientific article

Identification of small molecules enhancing autophagic function from drug network analysis

article

Identifying network of drug mode of action by gene expression profiling

scientific article

Integrated cross-study datasets of genetic dependencies in cancer

scientific article published in 2021

Integrated transcriptomic and proteomic analysis identifies protein kinase CK2 as a key signaling node in an inflammatory cytokine network in ovarian cancer cells

scientific article published on 08 February 2016

Interactive data analysis and clustering of genomic data

scientific article published on 31 December 2007

JACKS: joint analysis of CRISPR/Cas9 knockout screens

article published in 2019

Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy

scientific article

Loss of functional BAP1 augments sensitivity to TRAIL in cancer cells

scientific article published on 18 January 2018

Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties

scientific article

Minimal genome-wide human CRISPR-Cas9 library

scientific article published on 21 January 2021

Multilevel models improve precision and speed of IC50 estimates.

scientific article published on 16 May 2016

NIRest: a tool for gene network and mode of action inference

scientific article published in March 2009

Network based elucidation of drug response: from modulators to targets

scientific article

Pathway-based dissection of the genomic heterogeneity of cancer hallmarks' acquisition with SLAPenrich.

scientific article published on 30 April 2018

Phenotypic plasticity and genetic control in colorectal cancer evolution

scientific article published in 2022

Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors

scientific article

Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens

scientific article published on 10 April 2019

Prospective derivation of a living organoid biobank of colorectal cancer patients.

scientific article published on May 2015

Stem cell-like transcriptional reprogramming mediates metastatic resistance to mTOR inhibition.

scientific article

Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects

article

The germline genetic component of drug sensitivity in cancer cell lines

scientific article published in Nature Communications

Transcription factor activities enhance markers of drug sensitivity in cancer.

scientific article published on 11 December 2017

Transcriptional data: a new gateway to drug repositioning?

scientific article

Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function.

scientific article published on 23 July 2011

Transcriptional response networks for elucidating mechanisms of action of multitargeted agents

scientific article published on 11 March 2016

Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting

scientific article published on 13 August 2018

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