Open Positions
This is the list of the group leaders working in the institutes of the SEMM network, who have open positions.
Use the filter below to browse the different projects:
Surname Name | Research center/University | Research Areas | N. of positions | Proposed PhD Project |
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Bachi Angela More Info |
IFOM ETS - The AIRC Institute of Molecular Oncology | Cancer Metabolism, Molecular Oncology, Omics Sciences (genomics and other omics) | 1 |
BACE2 shapes tumor microenvironment
BACE2 shapes tumor microenvironmentWe have recently discovered that BACE2-dependent amyloid fibrils are new components of the tumor extracellular environment in metastatic melanoma where they promote cell proliferation through the activation of the transcriptional coactivator YAP, a master sensor of extracellular stiffness (Matafora V et al. Amyloid aggregates accumulate in melanoma metastasis modulating YAP activity. 2020, EMBO Rep). |
Bardelli Alberto More Info |
IFOM ETS - The AIRC Institute of Molecular Oncology | Computational Biology and Bioinformatics, Immunology, Molecular Oncology | 1 |
Targeting DNA repair pathways in colorectal cancers
Targeting DNA repair pathways in colorectal cancersThe project will exploit patients- derived models to define new therapeutic vulnerabilities in colorectal cancers (CRC). The candidate will use gene editing approaches to identify the DNA repair landscape of CRC and its impact on tumor cell growth and immune surveillance. |
Bienko Magda More Info |
Human Technopole (HT) | Computational Biology and Bioinformatics, Human Genetics and Genomics, Omics Sciences (genomics and other omics) | 1 |
Single-cell multi-omic profiling of structural variants, 3D genome conformation, and gene expression in colorectal cancer organoids
Single-cell multi-omic profiling of structural variants, 3D genome conformation, and gene expression in colorectal cancer organoidsGenome structural variants (SVs) are a hallmark of cancer genomes. SVs and complex chromosomal rearrangements are thought to disrupt the physiological three-dimensional (3D) architecture of the genome, in turn leading to rewiring of key gene regulatory networks that control cell identity and tissue homeostasis. A thorough understanding of how SVs reshape 3D genome organization and gene expression at the single-cell level is currently missing. |
Bodega Beatrice More Info |
National Institute of Molecular Genetics (INGM) | Computational Biology and Bioinformatics, Immunology, Omics Sciences (genomics and other omics) | 1 |
Defining LINE1 dynamics in tumor-infiltrating lymphocytes to unveil novel immunotherapeutic candidates
Defining LINE1 dynamics in tumor-infiltrating lymphocytes to unveil novel immunotherapeutic candidatesThe composition of tumour infiltrating lymphocytes (TILs) can be highly heterogeneous; in particular, a high percentage of exhausted TILs and immunosuppressive Tregs is associated with bad prognosis. The discovery of immune-checkpoint inhibitors actuated a paradigm shift in cancer therapy even though the percentage of refractory patients is still high. Therefore, there is a compelling need to find novel targets to increase responders. |
Bonaldi Tiziana More Info |
European Institute of Oncology (IEO) | Epigenetics, Molecular Oncology, Omics Sciences (genomics and other omics) | 1 |
Proteomic characterization of antigens involved in the anti-tumor response elicited by antigen-presenting cells (APCs) expressing allogeneic MHC
Proteomic characterization of antigens involved in the anti-tumor response elicited by antigen-presenting cells (APCs) expressing allogeneic MHCImmunotherapy has radically modified the natural history of many tumors, yet most patients are either resistant to treatment or relapse with resistant disease. Accumulating evidence suggests that the efficacy of cancer immunotherapy relies on antigen-specific activation of T-lymphocytes with anti-tumor activities. |
Carninci Piero More Info |
Human Technopole (HT) | Computational Biology and Bioinformatics, Omics Sciences (genomics and other omics), RNA | 1 |
Regulation of chromatin activity by RNA
Regulation of chromatin activity by RNAA broad number of lncRNAs interact with chromatin providing regulation, yet the function is unknown for the majority of RNAs. Using our RNA and DNA Ligated and Sequenced (RADICL-seq) technology and other complementary genomics / transcriptomics data, we will map and functionally characterize key RNA regulators of chromatin activity/epigenome in cell differentiation and will charaterize the function of top candidates. |
Carninci Piero More Info |
Human Technopole (HT) | Computational Biology and Bioinformatics, Omics Sciences (genomics and other omics), RNA | 1 |
Role of transcribed repeat elements in regulation of translation
Role of transcribed repeat elements in regulation of translationSINEUPs are a class of RNAs that enhance translation of the mRNAs that they pairs as antisense RNAs, through the action of a transcribed SINE RNA embedded in the antisense RNA. |
Carninci Piero More Info |
Human Technopole (HT) | Computational Biology and Bioinformatics, Omics Sciences (genomics and other omics), RNA | 1 |
Single cell transcriptome analysis
Single cell transcriptome analysisWe have developed approaches for profiling single cell transcriptomes centered on sequencing single cell RNAs from 5' ends, which allows simultaneous mapping of regulatory elements wlike promoters and enhancers. We will explore these in a set of brain organoids, including models of neuron infections with SARS-CoV-2. |
Casañal Ana More Info |
Human Technopole (HT) | Structural biology | 1 |
Molecular Mechanisms of RNA Editing Macromolecular Complexes
Molecular Mechanisms of RNA Editing Macromolecular ComplexesGene expression can be regulated at multiple levels. This allows organisms to respond fast to specific cellular stimuli while maintaining a stable internal environment. This regulation can be achieved through chemical marks on DNA, RNA and proteins. |
Cereda Matteo More Info |
University of Milan | Computational Biology and Bioinformatics, Omics Sciences (genomics and other omics), Machine learning | 1 |
Integration of DNA and RNA binding proteins binding models in multiple tissues and cell lines as a tool to evaluate genome-wide regulatory mutational burden
Integration of DNA and RNA binding proteins binding models in multiple tissues and cell lines as a tool to evaluate genome-wide regulatory mutational burdenTranscription factors (TFs) are DNA-Binding proteins which have a prominent role in controlling expression by binding to gene regulatory regions. TFs can also recruit or otherwise interact with RNA-binding proteins which controls the processing of RNA. The interplay among DNA and RNA binding proteins is a possible source of gene dysregulation and the functional role of cis- and trans-acting genetic alterations requires investigation in this light. Aim of the project (in collaboration between the Computational Biology Lab at IRCCS E. Medea and the Cancer Genomics and Bioinformatics lab at the University of Milan) is to disentangle the regulatory crosstalk between DNA and RNA proteins and provide the scientific community with a list of binding preference models for both these protein types. The models will be identified through the application of computational methods, including artificial intelligence approaches, developed in our labs to a collection of publicly available, as well as generated in house, short- and long-reads sequencing experiments in different healthy and pre-clinical models. |
Chiocca Susanna More Info |
European Institute of Oncology (IEO) | Epigenetics, Molecular Oncology, Viruses in cancer onset | 1 |
Profiling and Targeting Epigenetic Marks to Improve Diagnosis and Therapeutic Approaches in Head and Neck Cancer
Profiling and Targeting Epigenetic Marks to Improve Diagnosis and Therapeutic Approaches in Head and Neck CancerRationale: We have recently shown that epigenetic remodelling enzymes, such as HDAC inhibitors, are feasible drugs in HNC. Preliminary data are indicating some deregulated epigenetics marks suggesting the corresponding histone modifiers as possible targets for the treatment of HNC, providing an attractive and feasible option to build upon. Our overarching hypothesis is that unique histone marks distinguish HPV+ and HPV- HNC and that specific histone modifiers are novel mediators of HNC tumorigenesis in an HPV specific manner. |
Condorelli Gianluigi More Info |
Humanitas University | Epigenetics, Molecular and Cellular Biology, Molecular Cardiology | 1 |
Genetic and epigenetic mechanisms of heart failure: therapeutic approaches
Genetic and epigenetic mechanisms of heart failure: therapeutic approachesThe research will be based on the identification of the mechanisms underlying heart failure. In particular, the candidate will carry out research aimed at defining the phenotype of a humanised model of LMNA mutation causing cardiomyopathy and on gene editing studies aimed at normalising the phenotype through a Crisp/Cas9 approach. Other projects are available according to the CV of the candidate |
Coscia Francesca More Info |
Human Technopole (HT) | Structural biology | 1 |
Integrative structural biology of thyroid hormone regulation in health and disease
Integrative structural biology of thyroid hormone regulation in health and diseaseThyroid hormones are essential iodinated molecules produced by the thyroid gland and essential for the metabolism and growth of all vertebrates. In humans, thyroid hormone levels are finely tuned across life and development, and their unbalance is related to cancer, hypothyroidism, and autoimmune diseases. |
Costanzo Vincenzo More Info |
IFOM ETS - The AIRC Institute of Molecular Oncology | Molecular and Cellular Biology, Molecular Oncology, Structural biology | 2 |
Molecular determinants of DNA replication stress and their link to cancer cell chemo-resistance / Consequences of DNA damage in cancer and stem cells
Molecular determinants of DNA replication stress and their link to cancer cell chemo-resistance / Consequences of DNA damage in cancer and stem cellsReplication forks are constantly challenged by exogenous and endogenous threats inducing replication stress (RS), which has been linked to cell transformation. RS is monitored by DNA repair proteins, including tumor suppressors BRCA1/2. Unresolved RS and consequent DNA damage induce cell fate changes typical of tumors, as we have recently demonstrated (Elife 2020). Using biochemical and cancer cell-based assays, combined with DNA electron-microscopy, we discovered that BRCA1/2 prevent replicative DNA gaps and DNA degradation, the products of which induce innate immunity responses. Malfunction of BRCA1/2 activates low fidelity repair pathways that fuel genome instability, promoting cancer cell chemo-resistance. Among these, we have shown that POLQ-dependent ones prevent replication fork breakage. Inhibition of POLQ is a promising strategy to kill chemo-resistant cancer cells by synthetic lethality. Over the years our work has been published in several high impact papers in which PhD students figure as first authors (Mol Cell 2017, 2018, 2021 and 2022, Elife 2020 and Nature 2018). |
d'Adda di Fagagna Fabrizio More Info |
IFOM ETS - The AIRC Institute of Molecular Oncology | Biology of Ageing, Molecular and Cellular Biology, Molecular Oncology | 1 |
Impact of SARS-COV-2 infection on genome stability and cancer
Impact of SARS-COV-2 infection on genome stability and cancerWe recently reported that SARS-CoV2 infection leads to DNA damage generation, cellular senescence and inflammation (Gioia, Tavella et al Nature Cell Biology 2023). We now aim too pursue the following two distinct, but mutually supportive, research lines. The candidate will be part of an international team and will be supported by a number of established experimental systems, technologies and range of collaborators to rapidly advance along the above-described research cell lines. |
Davila-Velderrain Jose More Info |
Human Technopole (HT) | Computational Biology and Bioinformatics, Neurobiology, Omics Sciences (genomics and other omics) | 1 |
Modeling mulitiomic states of brain cells in evolution, development, and disease
Modeling mulitiomic states of brain cells in evolution, development, and diseaseThe human brain, formed by millions of diverse cells, is the most complex organ known. How these cells collectively mediate brain function and behavior and why they lead to dysfunction in disease is not understood. We will combine single-cell multi omic data analysis, comparative genomics, and mechanistic modeling to study brain cell behavior in evolution, development, and disease. Computational predictions will guide collaborative experiments to dissect the mechanistic basis and behavioral consequences of brain (dys)function, opening up opportunities for therapeutic intervention and control. |
De Maria Ruggero More Info |
Catholic University of the Sacred Heart | Computational Biology and Bioinformatics, Immunology, Molecular Oncology | 1 |
Mapping tumor microenvironment heterogeneity and plasticity through single-cell transcriptomics
Mapping tumor microenvironment heterogeneity and plasticity through single-cell transcriptomicsCancer is a dynamic disease. Oncogenesis and tumor progression require the integrated destabilization of several key cellular regulatory processes. This phenomenon creates the necessary substrate for heterogeneity, which is subsequently maintained by selective pressures, including immune and therapeutic pressures. Cancer heterogeneity might result in a non-uniform distribution of genetically distinct cancer-cell subpopulations across and within disease sites (spatial heterogeneity) or temporal variations in the molecular makeup of cancer cells (temporal heterogeneity). Cancer heterogeneity underlies site-specific responses, provides the seeds for the emergence of resistance and disease relapse, and also complicates the selection of globally effective therapeutic agents. Therefore, an accurate assessment of tumor heterogeneity is essential for the development of effective therapies. So far, efforts in understanding cancer heterogeneity were largely limited to cancer cells. These revealed a remarkably complex and diverse portrait of cancer cells, with evidence for genetic diversification and clonal selection. However, the complex ecosystem of stromal cells, infiltrating immune cells, endothelial cells that, together with non-cellular tissue components, constitute the tumor microenvironment (TME), are themselves as complex and heterogeneous as the cancer cell compartment. Indeed, the high-level complexity of the TME is accompanied by substantial heterogeneity at the intra-tumoral, inter-tumoral, and inter-individual levels. Therefore, a comprehensive characterization of the whole tumor ecosystem is increasingly recognized to hold the promise for improving the benefit of anticancer (immune)therapies. |
Derenzini Enrico |
European Institute of Oncology (IEO) | Drug discovery and design, Immunology, Molecular Oncology | 1 |
Cell therapy (CAR-T, CAR-Nk, NK based immunotherapy combinations), targeted therapies in lymphoma and leukemia
Cell therapy (CAR-T, CAR-Nk, NK based immunotherapy combinations), targeted therapies in lymphoma and leukemiaOur research is focused on the discovery of novel treatment strategies in difficult-to-treat hematologic malignancies such as Acute Leukemias and Aggressive Lymphomas. The main field of interest is the study of chemoresistant lymphoma and leukemia specific vulnerabilities for the implementation of novel therapies based on synthetic lethalities. We are especially interested in targeting synthetic lethalities in MYC-driven aggressive lymphomas and TP53 mutant leukemias, focusing on MYC, BCL-2, MCL-1, DNA repair and telomere dysfunction. On the other hand, we are implementing novel strategies to enhance the efficacy of current immunotherapies including chimeric antigen receptor (CAR) T and NK-cell therapy. For these aims we employ preclinical leukemia and lymphoma models, large scale multi-omics profiling and we interrogate publicly available annotated clinical datasets. The main goal of our lab is the rapid transition of preclinical findings in precision-therapy clinical trials. Another goal of our research is the identification of biomarkers allowing response prediction, which could useful for better selection of patients for precision-therapy approaches. |
Doksani Ylli More Info |
IFOM ETS - The AIRC Institute of Molecular Oncology | Biology of Ageing, Molecular and Cellular Biology, Molecular Oncology | 1 |
Investigating the mechanisms of eccDNA accumulation following DNA damage
Investigating the mechanisms of eccDNA accumulation following DNA damageSometimes fragments of our genome can form extrachromosomal circular DNA (eccDNA). These species accumulate in tumor cells where they promote intratumor heterogeneity and evolution. Despite their relevance, still little is known on the mechanisms of eccDNA biogenesis. We have found that eccDNA formation at telomeres and other tandem repeats is triggered by DNA damage, which induces the formation of DNA loops that can then be excised as extrachromosomal circles. |
Domínguez Conde Cecilia More Info |
Human Technopole (HT) | Computational Biology and Bioinformatics, Human Genetics and Genomics, Immunology | 1 |
Dissecting immune developmental trajectories with single-cell genomics
Dissecting immune developmental trajectories with single-cell genomicsImmune development is essential for human life as demonstrated by the fatal consequences of inborn errors of immunity. Exposure to pathogens, vaccines and other environmental antigens during childhood shape our immune system. These exposures lead to lasting effects, most notably, to the differentiation, expansion and maintenance of memory lymphocytes. Despite the key importance of these events, our knowledge of the dynamic characteristics of the human developing immune system remains limited. |
Erdmann Philipp Sebastian More Info |
Human Technopole (HT) | Molecular Oncology, Neurobiology, Structural biology | 1 |
Understanding Biomolecular Condensation in Neurodegenerative Disease Models from In Vitro to Tissue
Understanding Biomolecular Condensation in Neurodegenerative Disease Models from In Vitro to TissueWe have recently created a pipeline for imaging large samples by cryo-electron tomography using an improved lift-out procedure. We now seek to apply this technology to understanding the power and the limitation of investigating liquid liquid phase separation of proteins relevant to neurodegenerative disorders in vitro, in cells, and in tissue. |
Gauthier Nils More Info |
IFOM ETS - The AIRC Institute of Molecular Oncology | Molecular and Cellular Biology, Neurobiology, Mechanobiology | 1 |
Diversity in Glioblatoma mechanoproperties
Diversity in Glioblatoma mechanopropertiesGlioblastoma (GBM) are very aggressive tumors (14 months of life expectancy after diagnosis). They are non-curable because GBM cells are highly proliferative and exceedingly invasive, migrating on linear tracks like the abluminal walls of brain blood vessels. Glioblastoma transcriptomic and genomic analysis showed high inter- and intra-patient heterogeneity. We also showed high inter-patient heterogeneity in GBM motility modes and linked them to their mechanoproperties. We proved the value of gridded micropatterns as a mimicry of peri-vascular migration. At this stage, we want to investigate more deeply GBM heterogeneity in motility modes, mechanoproperties and molecular signatures at single patient level. Recent relevant contributions of the lab: Monzo et al. Dev Cell 2021, Ghisleni et al. Nature Com 2020, Barger et al. Nature com 2019. |
Giustacchini Alice More Info |
Human Technopole (HT) | Computational Biology and Bioinformatics, Developmental and Stem Cell Biology, Immunology, Molecular and Cellular Biology, Molecular Oncology, Omics Sciences (genomics and other omics) | 1 |
Deciphering the paediatric Leukaemia stem cells – Immune crosstalk: from mechanisms to therapy
Deciphering the paediatric Leukaemia stem cells – Immune crosstalk: from mechanisms to therapyAcute Myeloid Leukaemia (AML) is a rare disease in children and teenagers but a significant cause of childhood cancer mortality. Relapse is the primary cause of treatment failure. Outcomes have not improved over the last two decades and novel therapies are therefore urgently needed. The successful treatment AML has been hindered by the disease heterogeneity and complicated by the chemo-resistant and immune-evasive properties of AML leukaemia stem cells (LSCs). LSCs persist in a dormant state which limits their uptake of cytotoxic drugs and makes them selectively unresponsive to conventional chemotherapies. As a consequence, quiescent LSCs undergo a selective survival advantage during treatment and can eventually fuel disease relapse. Intrinsic properties of AML cells can lead to the accumulation of suppressive immune cell populations and impaired cytotoxic lymphocytes activity. In turn, an impaired immune system, can promote AML disease progression. Decoding how the crosstalk between LSCs and their immune microenvironment evolves across stages of the disease, promises to unravel intrinsic and extrinsic mechanisms of resistance and pinpoint a therapeutic windows therapeutic intervention. |
Iorio Francesco More Info |
Human Technopole (HT) | Computational Biology and Bioinformatics, Drug discovery and design, Omics Sciences (genomics and other omics) | 1 |
Computational Drug repurposing for NeuroCOVID
Computational Drug repurposing for NeuroCOVIDWe will focus on the development of novel computational tools and machine learning methods to identify drug repositioning opportunities for rescuing or preventing SARS-CoV-2-related neuropathologies. |
Iorio Francesco More Info |
Human Technopole (HT) | Computational Biology and Bioinformatics, Drug discovery and design, Omics Sciences (genomics and other omics) | 1 |
Elucidating the interplay between DNA damage and immune responses in cancer via multi-omics data integration
Elucidating the interplay between DNA damage and immune responses in cancer via multi-omics data integrationThe DNA damage response (DDR) and immune response are two pivotal processes in the development and progression of cancer, characterized by intricate molecular mechanisms that remain poorly understood. The DDR pathways are essential for maintaining genomic stability and preventing the onset of cancer. Simultaneously, the immune system plays a crucial role in identifying and eradicating cancerous cells, and disruptions in immune surveillance are associated with tumor progression. Interestingly, inhibiting DDR pathways can enhance the immunogenicity of cancer cells, rendering them more vulnerable to immune attacks, thereby transforming "cold" tumors into "hot" tumors. Designing and using novel computational methods, we will aim to elucidate the interplay between DDR and the immune response by leveraging publicly available cancer genomics databases integrated with recently assembled data from chemo/functional-genetic screens. Our ultimate goal will be to investigate how this can be utilised to develop effective combination therapies. This is a collaborative project with (and externally funded by) Nerviano Medical Sciences (NSM). The enrolled PhD student will focus on developing computational and machine learning methods to elucidate the crosstalk between DNA damage and immune responses. This will involve the analysis of publicly available genomics and functional genetics datasets, as well as experimental data generated in house. |
Jereczek Barbara More Info |
European Institute of Oncology (IEO) | Computational Biology and Bioinformatics, Radiotherapy | 1 |
Investigating the role of new oncological drugs in the high-precision radiotherapy era with a focus on proton therapy (the High-Rad Project)
Investigating the role of new oncological drugs in the high-precision radiotherapy era with a focus on proton therapy (the High-Rad Project)Background Aim Methods |
Jereczek Barbara More Info |
European Institute of Oncology (IEO) | Computational Biology and Bioinformatics, Radiotherapy | 1 |
APO - Advancing Precision Oncology: Leveraging Big Data for Patient Outcomes and Treatment Optimization with a Focus on Proton Therapy
APO - Advancing Precision Oncology: Leveraging Big Data for Patient Outcomes and Treatment Optimization with a Focus on Proton TherapyBackground: Aim: Methods: |
Legnini Ivano More Info |
Human Technopole (HT) | Developmental and Stem Cell Biology, Molecular and Cellular Biology, Omics Sciences (genomics and other omics) | 1 |
Regulation of spatial gene expression territories in neurodevelopment
Regulation of spatial gene expression territories in neurodevelopmentAcross animals, the key to generate complex body plans from a single cell resides in the capacity to generate asymmetries early in development, by establishing spatially distinct gene expression territories. To reproduce and study these events in a reductionist manner, we work with new organoid models of neurodevelopment where precise genetic control (e.g. by synthetic biology and optogenetics) enables to reconstitute in vitro complex signalling events such as morphogen gradients. |
Legnini Ivano More Info |
Human Technopole (HT) | Omics Sciences (genomics and other omics), Molecular and Cellular Biology, Neurobiology | 1 |
The role of RNA binding proteins in neuronal transcriptome plasticity
The role of RNA binding proteins in neuronal transcriptome plasticityNeurons are highly polarized cells which function by forming functional connections with each other and with other cells. They possess the unique ability of changing the nature and number of these connections (synaptic plasticity), which strongly depends on their capacity to tightly regulate gene expression at different levels, from transcription to turnover, subcellular localization of RNA and translation (transcriptome plasticity). Recently, transcriptomic technologies made a huge leap in terms of throughput and resolution: we can now measure transcription and turnover rates genome-wide, map protein-RNA interactions at nucleotide resolution, accurately quantify translation and polyadenylation and image hundreds of transcripts in parallel at submicron resolution. |
Manfrini Nicola |
National Institute of Molecular Genetics (INGM) | Molecular and Cellular Biology, Molecular Oncology | 1 |
Defining the role of the FAM46C/FNDC3A complex in breast cancer
Defining the role of the FAM46C/FNDC3A complex in breast cancerFAM46C is one of the most frequently mutated genes in Multiple Myeloma (MM) and its mutations are associated with poor prognosis (1,2,3). |
Mapelli Marina More Info |
European Institute of Oncology (IEO) | Developmental and Stem Cell Biology, Molecular and Cellular Biology, Structural biology | 2 |
Molecular basis of Wnt-dependent self-renewal
Molecular basis of Wnt-dependent self-renewalThe PhD project will address the molecular mechanisms of Wnt-dependent self-renewal in the regulation of stem cell activity, tissue homeostasis and oncogenesis, with emphasis on intestinal cancers. Colorectal cancer is a leading cause of death among industrialized nations. A major issue affecting treatment efficacy is the high relapse rate, which largely depends on the presence of deregulated cancer stem-like cells. The normal adult intestinal epithelium is a polarized monolayer constantly being renewed by intestinal stem cells residing at the base of invaginations called crypts, whose proliferation is governed by Wnt3-ligands secreted by Paneth cells acting as niche. Wnt-signalling leads to beta-catenin stabilization and transcriptional activity. Evidence from our lab revealed that upon Wnt3 stimulation the protein NuMA is found in complexes with beta-catenin and participate to Wnt response. |
Mazzarella Luca More Info |
European Institute of Oncology (IEO) | Immunology, Omics Sciences (genomics and other omics), Human Genetics and Genomics | 1 |
Impact of somatic NF1 mutations on metastasis and drug response across multiple tumors
Impact of somatic NF1 mutations on metastasis and drug response across multiple tumorsWe have recently demonstrated that the tumor suppressor NF1, widely investigated as a RAS repressor, participates in multiple RAS-independent functions and is associated with selective response to antibody-drug conjugates in HER2+ breast cancer. To further our understanding of NF1 biology and druggability, we will develop mouse models of somatically inactivated NF1 tumors using cre-lox technology and CRISPR. We will employ single cell RNA sequencing and multidimensional imaging to investigate NF1 role in metastasis, cytoskeletal dynamics and the tumor immune environment. |
Minucci Saverio More Info |
European Institute of Oncology (IEO) | Cancer Metabolism, Drug discovery and design, Epigenetics, Molecular Oncology | 1 |
Regulation of the PP2A signaling axis in tumor cells by environmental signals, and intersection with the epigenome
Regulation of the PP2A signaling axis in tumor cells by environmental signals, and intersection with the epigenomeThe altered epigenome shapes the behavior of tumor cells, imposing transcriptional programs driving progression and resistance to current anti-cancer therapies. Environmental changes represent a key driver of epigenetic changes, and tumor cell metabolism/signaling pathways regulated by nutrient availability affect the epigenome through different mechanisms. |
Nezi Luigi More Info |
European Institute of Oncology (IEO) | Cancer Metabolism, Immunology, Microbiology and Microbiome | 1 |
Microbiome-host metabolic interactions in cancer
Microbiome-host metabolic interactions in cancerDespite significant lymphocyte infiltration, responses to immune checkpoint inhibitors (ICI) are still heterogenous and largely restricted to a fraction of tumors. Seminal works from us and others have pointed at the microbiome as master regulator of ICI response and its therapeutic value has been recently confirmed by two independent clinical trials. In this propject we will test if therapeutic manipulation of the metabolic output of gut bacteria can improve the response of solid tumors to ICI. |
Nicassio Francesco More Info |
Center for Genomic Science of IIT | Epigenetics, RNA | 1 |
Transcriptional and Epigenetic mechanisms provided by Noncoding RNAs in human cancer
Transcriptional and Epigenetic mechanisms provided by Noncoding RNAs in human cancerOur scientific goal is to provide key insights into regulatory mechanisms that involves non-coding RNAs (short and long transcripts) and control gene expression at the transcriptional, post-transcriptional or epigenetic level. This goal will be achieved through the application of advanced genomics technologies, developed for the discovery of RNA-based molecular mechanisms. A key priority is identifying among all non-coding RNAs and DNA elements, those that can play a functional role in promoting cancer aggressive behaviors, which can be used as disease markers or potential targets for pharmacological intervention. Our approaches incorporate the most recent high-resolution technologies, including single-cell multi-omics and Nanopore single molecule sequencing, used to dissect tumor heterogeneity at the phenotypic and transcriptional level, and CRISPR-based genetic approaches (cas9-/cas13-, CRISPRi and CRISPRa) exploited at individual gene level and at group level for functional screenings (CRISPR-library, CROP-seq approaches). In order to investigate non-coding RNA biology also at preclinical level, we take advantage of cancer models established in the years and available through our clinical cancer network, including cancer cell lines, primary samples, primary cultures and 3D models, such as patient-derived xenografts (PDX) and organoids (PDOs). Hosting Lab: The Genomic-Science Lab consists of 12 people (1 technologist, 1 technician, 5 post docs, 4 PhD students, 1 research fellows) plus other affiliated senior researchers. The lab is part of a vibrant international scientific network of IIT, centered on RNA biology, which includes the RNA initiative (iRNA@IIT); the LONGTREC consortium (European Doctoral-Network) focused on long-read sequencing, the National Center for Gene Therapy and Drugs based on RNA Technology, and many collaborators form outstanding international research institutes, including the EMBL-EBI; the RIKEN Institute; Karolinska Institutet.
Links |
Pagani Massimiliano More Info |
IFOM ETS - The AIRC Institute of Molecular Oncology | Epigenetics, Immunology, Omics Sciences (genomics and other omics) | 1 |
Investigating the impact of tumor infiltrating Treg cell modulation on their crosstalk with the tumor microenvironment
Investigating the impact of tumor infiltrating Treg cell modulation on their crosstalk with the tumor microenvironment
New immunotherapeutic approaches aim at restoring the natural balance and increase immune response against cancer by different mechanisms. The heterogeneity of immune cell subpopulations and their complex interactions, though, represent a real challenge when trying to develop novel immunotherapies and evaluate or predict their efficacy in vivo. In our lab we are focusing on the immunosuppressive T cell compartment that promotes tumor growth by dampening specific antitumor immune responses. Toward a better understanding of the molecular basis underlying tumor regulatory T cells function, we generated a comprehensive epigenetic profile (by ChIPseq and ATAC-seq) of peripheral blood, normal tissue and tumor infiltrating Treg cells (tiTreg). Among regulatory elements we focused on enhancers that are key to coordinate gene expression programs in a tissue-specific manner. Assessment of transcription factor binding dynamics to these regions showed transcription factors with distinct binding activity profile across Treg populations that are clearly lost or gained specifically in tiTreg suggesting the presence of regulatory hubs underlying the acquisition of their specific identity at tumor sites. With this proposal we aim to provide insights on these regulatory hubs through the modulation of selected target by standard shRNA downmodulation or CRISPR/Cas9 based editing approaches towards specific reprogramming of regulatory T cells recruited at tumor sites. Moreover, to investigate the basis of tumor immune-suppression, we will leverage a human tumor explant model which incorporates both epithelial and stromal components into a collagen-based air liquid interface 3D culture system. This model recapitulates the physiology of the whole tumor microenvironment (TME) maintaining tumor cells with the associated immune populations for days in culture, allowing for modulation of potentially actionable targets and the concurrent assessment of the interplay among the different components of the TME by combined methodologies such as multiparametric flow cytometry (FACS) analysis and single-cell transcriptome sequencing. |
Pasini Diego More Info |
European Institute of Oncology (IEO) | Developmental and Stem Cell Biology, Epigenetics, Molecular and Cellular Biology, Molecular Oncology, Omics Sciences (genomics and other omics), Structural biology | 3 |
Decrypting the mechanisms of Polycomb-dependent control of transcriptional identity with integrative multi-omics approaches
Decrypting the mechanisms of Polycomb-dependent control of transcriptional identity with integrative multi-omics approachesEstablishing and maintaining cellular identities involves multiple signals that instruct the activity of transcription factors and chromatin-remodeling activities to define cellular transcriptional states. These mechanisms play crucial roles in human pathologies and are directly implicated in the development of cancer. Indeed, deregulation of chromatin remodeling activities are frequent causative events. The Polycomb machinery represents the major repressive system in facultative heterochromatin and plays a crucial role in organism development and differentiation. The machinery is composed by more than 50 distinct factors forming multiple ensembles with high biochemical and functional heterogeneity to sustain the complexity of transcriptional identities. Indeed, mutations of several of these factors are common driver events in human tumor making this machinery a major oncogenic player and a very attractive target for cancer therapy. The projects will be aimed at decrypting such functional complexity combining approaches of genetic engineering with integrative and multi-omics approaches to uncover molecular vulnerabilities that could pave the way to new cancer prevention and treatment strategies. |
Pelicci Pier Giuseppe More Info |
European Institute of Oncology (IEO) | Molecular Oncology, Omics Sciences (genomics and other omics) | 1 |
Multi-omic approaches for the identification of novel targeted treatments
Multi-omic approaches for the identification of novel targeted treatmentsPelicci's group current activities mainly focus on the characterization of intra-tumoral genetic and phenotypic heterogeneity as critical drivers of disease progression and therapy resistance through the exploitation of multi-omic approaches, reverse genetics, cutting-edge preclinical models and patient samples. The final goal is to identify novel targeted treatments. |
Pelicci Pier Giuseppe More Info |
European Institute of Oncology (IEO) | Computational Biology and Bioinformatics | 1 |
Single-cell mutational and transcriptional tracing during metastatic progression and acquisition of treatment resistance
Single-cell mutational and transcriptional tracing during metastatic progression and acquisition of treatment resistanceIntra-tumoral genetic and phenotypic heterogeneity is a constant trait of the transformed phenotype and thought to be critical for tumor growth, metastatization and drug resistance. |
Pelicci Giuliana More Info |
European Institute of Oncology (IEO) | Epigenetics, Molecular and Cellular Biology, Molecular Oncology | 1 |
Single-cell mutational and transcriptional tracing during metastatic progression and acquisition of treatment resistance
Single-cell mutational and transcriptional tracing during metastatic progression and acquisition of treatment resistanceGlioblastoma is the most aggressive and heterogeneous primary brain tumor with varying clinical presentation and poor prognosis. |
Pelizzola Mattia More Info |
Center for Genomic Science of IIT | Computational Biology and Bioinformatics, RNA, Omics Sciences (genomics and other omics) | 1 |
Decoding the functional role of RNA modifications in breast cancer through Nanopore single molecule RNA sequencing
Decoding the functional role of RNA modifications in breast cancer through Nanopore single molecule RNA sequencingRNA abundance and its variation arise from the combined action of transcriptional and post-transcriptional machineries responsible for the synthesis of novel transcripts, their processing into mature species, and the degradation of the latter, collectively setting the dynamics of the RNA life cycle. Epitranscriptional modifications, whose patterning is controlled by the action of writers and erasers and decoded by specific readers, are emerging as important determinants of RNA fate, impacting key biological processes in healthy and disease conditions. Yet, we still have a limited understanding on the consequences of the aberrant regulation of epitranscriptional modifications on specific steps of the RNA life cycle. |
Pesole Graziano More Info |
University of Bari | Computational Biology and Bioinformatics, Molecular and Cellular Biology, Omics Sciences (genomics and other omics) | 1 |
High-throughput assessment of the mammalian RNA editing repertoire
High-throughput assessment of the mammalian RNA editing repertoireRNA editing by adenosine deamination is the most prominent epitranscriptome modification occurring in mammalian RNAs. It is carried out by ADAR enzymes acting on double RNA strands and its deregulation has been linked to several human disorders including immunological, neurological, neurodegenerative diseases and cancer. To date, over 15 million events from healthy human tissues have been identified and collected in the specialized REDIportal database. More than 95% of known edited sites reside in non-coding regions consisting of inversely oriented repetitive elements (mostly Alu elements). While the detection of RNA editing in non-coding regions is trivial, unveiling the complete landscape of recoding events, altering the encoded protein, is challenging but of course functionally relevant. Indeed, RNA editing represents a precious source of neoantigens and may play a relevant function in shaping the alternative splicing repertoire. |
Pigino Gaia More Info |
Human Technopole (HT) | Structural biology, Molecular and Cellular Biology | 1 |
Cellular and structural biology of cilia assembly and maintenance
Cellular and structural biology of cilia assembly and maintenanceCilia ate ubiquitous organelles, found in most cells, tissues and organs of the human body. Defects of the ciliary structure causes numerous human pathologies, called ciliopathies. We will use cell biology (Crispr targeted mutagenesis, immunofluorescence expansion microscopy, single molecule fluorescence microscopy, etc.) and structural biology methods (in situ cryo-electron tomography, subtomogram averaging, structural proteomics, etc.) to investigate machineries required for the assembly and maintenance of cilia. |
Pinheiro Fernanda More Info |
Human Technopole (HT) | Computational Biology and Bioinformatics, Microbiology and Microbiome, Evolutionary Biology | 1 |
Predicting antibiotic resistance evolution
Predicting antibiotic resistance evolutionEcological and evolutionary processes of microbial pathogens are key to understanding antibiotic resistance and human health. Antibiotic treatment is a complex interplay of antibiotic chemistry, bacterial physiology, and ecology. Increasing evidence indicates that antibiotic resistance evolution cannot be decoupled from bacterial physiology and environmental conditions. In real-life situations, bacteria are rarely in isolation and often grow in the presence of other microbes and/or environmental conditions that are not constant. How can we predict antibiotic resistance evolution in such cases? In this project, we will interrogate the evolution of antibiotic resistance in complex scenarios, including changing environments and interactions between members in simple microbial communities. We will combine theory and experiments to develop computable models of drug action grounded on cell metabolism models and mechanistic models of evolutionary response for antibiotics targeting different cellular processes (e.g., translation, transcription, cell-wall inhibitors). By informing rational protocols for sustainable antibiotic use, methods developed in this program will help the fight against the growing and alarming problem of antibiotic resistance. |
Polo Simona More Info |
IFOM ETS - The AIRC Institute of Molecular Oncology | Structural biology | 1 |
Unleashing the Power of NEDD4: Insights into the Structural Basis and Mechanisms of Action
Unleashing the Power of NEDD4: Insights into the Structural Basis and Mechanisms of ActionThe HECT E3 ubiquitin ligase NEDD4 plays a crucial role in regulating the stability and trafficking of plasma membrane receptors and signaling proteins. Previous research from our lab identified a Ub exosite in HECT as essential for enzyme processivity, and we have developed selective inhibitors to confirm our model. |
Polo Simona More Info |
IFOM ETS - The AIRC Institute of Molecular Oncology | Molecular Oncology | 1 |
Investigating beta-catenin-dependent alternative splicing reprogramming in colon cancer
Investigating beta-catenin-dependent alternative splicing reprogramming in colon cancerTumor-specific alternative splicing (AS) events have been found to play a crucial role in cancer cell adaptation during tumorigenesis. Recent evidence from the lab suggests that beta-catenin has a significant impact on AS reprogramming during colorectal cancer (CRC) onset and progression, independent of its role in transcription. We are currently dissecting the molecular mechanism exploited by beta-catenin, using a combination of RNA seq/ RIP analysis, advanced imaging techniques, genetic and biochemical tools. In-depth molecular characterization of selected cancer-specific isoforms and their validation in cancer settings can aid in identifying novel molecular biomarkers during cancer progression or even new candidate targets. Indeed, AS can be therapeutically targeted by restoring the expression of non-oncogenic isoforms using antisense oligonucleotides (AONs), as we are currently doing for myosin VI. |
Pravettoni Gabriella More Info |
European Institute of Oncology (IEO) | Medical Humanities | 1 |
AI-driven decision-making in cancer care
AI-driven decision-making in cancer careWe are seeking for a highly motivated PhD candidate to join a European doctoral program focused on the study of decision-making processes, usability experience, utility, and trust in AI-driven clinical decision-making in cancer patients and healthcare professionals. The successful PhD candidate will be involved in the following activities: |
Pravettoni Gabriella More Info |
European Institute of Oncology (IEO) | Medical Humanities | 1 |
Determinants of shared decision making and implementation strategies in clinical practice
Determinants of shared decision making and implementation strategies in clinical practiceWe are seeking for a highly motivated PhD candidate to join a European doctoral program focused on the study of patients’ and health professionals’ shared decision-making processes during the cancer trajectory. The successful PhD candidate will be involved in the following activities: |
Scaffidi Paola More Info |
European Institute of Oncology (IEO) | Epigenetics, Molecular and Cellular Biology, Molecular Oncology | 1 |
CRISPR-based Saturation Gene Editing to dissect epigenetic mechanisms promoting cancer development
CRISPR-based Saturation Gene Editing to dissect epigenetic mechanisms promoting cancer developmentOur laboratory investigates how epigenetic mechanisms regulate basic cell function and how their dysregulation favors cancer development, with a particular focus on chromatin-based mechanisms. By combining experimental and computational approaches, we seek to understand: (i) the epigenetic basis of malignant cell phenotypes at various disease stages; (ii) associated vulnerabilities that can be exploited to interfere with the disease. |
Scaffidi Paola More Info |
European Institute of Oncology (IEO) | Epigenetics, Computational Biology and Bioinformatics, Molecular Oncology | 1 |
Understanding and predicting the response to epigenetic drugs: from a robust regulatory network to acquired vulnerabilities
Understanding and predicting the response to epigenetic drugs: from a robust regulatory network to acquired vulnerabilitiesOur laboratory investigates how epigenetic mechanisms regulate basic cell function and how their dysregulation favors cancer development, with a particular focus on chromatin-based mechanisms. By combining experimental and computational approaches, we seek to understand: (i) the epigenetic basis of malignant cell phenotypes at various disease stages; (ii) associated vulnerabilities that can be exploited to interfere with the disease. |
Scita Giorgio More Info |
IFOM ETS - The AIRC Institute of Molecular Oncology | Computational Biology and Bioinformatics, Molecular and Cellular Biology, Molecular Oncology | 1 |
Contact Percolation Promotes Collective Flocking Migration and a Pro-Inflammatory Cytosolic DNA Response in Epithelial Tissues
Contact Percolation Promotes Collective Flocking Migration and a Pro-Inflammatory Cytosolic DNA Response in Epithelial TissuesThe process in which locally confined epithelial malignancies progressively evolve to become invasive cancer cells is associated with the acquisition of cell motility, fostered by a tissue-level phase transition (PT) from a solid-like to a liquid-like state, known as unjamming. The biomolecular machinery behind unjamming and its pathophysiological relevance have only begun to be unraveled. We have shown how the dynamic changes associated with PT feature the coexistence of long-range coordinated motion and local cell re-arrangement and are sufficient to promote matrix remodeling, and local invasion and exert mechanical stress on individual cell nuclei. This is accompanied by profound transcriptional rewiring, with the unexpected activation of an inflammatory response, change in cell state, and the emergence of malignant traits. Noticeably, carcinoma is composed of a heterogeneous set of cells that differ not only in their genetic landscape but also in their mechano-phenotypes. The impact of mechano-heterogeneity on tissue-level jamming transition is poorly understood. Here, we will also discuss unpublished findings that suggest that contact percolation, a purely geometrical feature, can impact the collective migratory behavior of tissues and, strikingly, promote the activation of an inflammatory gene transcription program in normal and breast carcinoma models. |
Scita Giorgio More Info |
IFOM ETS - The AIRC Institute of Molecular Oncology | Computational Biology and Bioinformatics, Molecular and Cellular Biology, Molecular Oncology | 1 |
Controlled deformations impact cell fate in 3D model of breast cancer cell assemblies
Controlled deformations impact cell fate in 3D model of breast cancer cell assembliesCells are often depicted as irregular spherical objects - the shape they adopt in suspension. However, the packed environment of tissues alters this simple shape, causing large cell deformations. This occurs during normal tissue growth and is even more pronounced upon tissue overgrowth, as in the case of solid tumors. We have observed that changes in the shape of cells and organelle(s) induce reversible and irreversible modifications in their behaviour and function(s). We hypothesize that cells use such mechanisms to integrate the successive deformations of distinct amplitudes and durations that they experience during their lifetime. |
Segata Nicola More Info |
University of Trento | Computational Biology and Bioinformatics, Microbiology and Microbiome | 1 |
Computational metagenomics an cultivation approaches to study microbiome transmissibility and links with host diseases for the ERC-CoG microTOUCH project
Computational metagenomics an cultivation approaches to study microbiome transmissibility and links with host diseases for the ERC-CoG microTOUCH projectThe research activity is part of the project ERC-CoG microTOUCH to study person-to-person microbiome transmission (MT) and how MT shapes the microbiome in the context of non-communicable diseases. |
Segata Nicola More Info |
European Institute of Oncology (IEO) | Computational Biology and Bioinformatics, Microbiology and Microbiome, Omics Sciences (genomics and other omics) | 1 |
Modeling and evaluating microbiological engraftment of fecal microbiota transplantation
Modeling and evaluating microbiological engraftment of fecal microbiota transplantationThe project aims at investigating the microbiological basis of fecal microbiota transplantation and its associated clinical outcome. |
Sottoriva Andrea More Info |
Human Technopole (HT) | Computational Biology and Bioinformatics, Molecular Oncology, Omics Sciences (genomics and other omics), Machine learning | 1 |
Single cell multi-omics for cancer evolution
Single cell multi-omics for cancer evolutionIt has become recently possible to profile the molecular content of human cells at unprecedented resolution. Those multidimensional datasets from single cells are highly complex and hard to interpret in a biologically meaningful way. In our lab, we generate single cell multi-omic readouts from oncological patients and patient-derived model systems to study cancer progression and the emergence of treatment resistance. To be transformative for cancer medicine, single-cell multiomic requires cutting edge data analysis, as well as the development of novel machine learning algorithms for data integration that will allow extracting new biological and medical information. |
Taverna Elena More Info |
Human Technopole (HT) | Developmental and Stem Cell Biology, Molecular and Cellular Biology, Neurobiology | 1 |
Synapse Evolution
Synapse EvolutionWe study the dynamics of synapse formation in human and apes using iPSC-derived induced neurons. The PhD candidate will unravel the cell biological basis and functional consequences of the different synaptogenesis tempo. |
Taverna Elena More Info |
Human Technopole (HT) | Developmental and Stem Cell Biology, Molecular and Cellular Biology, Neurobiology | 1 |
Cell biology of Neural Stem Cells
Cell biology of Neural Stem CellsWe are a cell biology lab that studies how single neural stem cell identity influences brain development, focusing on intracellular traffic and protein glycosylation. Thanks to a collaboration with clinicians, we recently started working on Congenital Disorders of Glycosylation (CDGs), a class of rare diseases associated with neurological manifestations. By using brain organoids and induced neurons the PhD candidate will model CDGs in a dish to gain insight into the role of protein glycosylation in physiology and in neurodevelopmental disorders. |
Testa Giuseppe More Info |
European Institute of Oncology (IEO) | Epigenetics, Molecular Oncology, Omics Sciences (genomics and other omics) | 1 |
Epigenetic modifiers of the GTF2i axis in thymomas
Epigenetic modifiers of the GTF2i axis in thymomasGTF2I is a transcription factor involved in the pathogenesis/progression of several rare cancers, including thymic epithelial tumours (TETs), the most frequent adult mediastinal cancer, that poses a significant challenge in terms of patient’s care. TETs are caused mainly by a recurrent hotspot GTF2I driver mutation, known as p.L383H/L424H, found in up to 49% of patients. This specific mutation renders GTF2I unrecognisable by the proteasomal degradation machinery, due to the alteration of a noncanonical destruction box, and has been proven oncogenic in murine thymic epithelial cells (TECs). |
Testa Giuseppe More Info |
Human Technopole (HT) | Computational Biology and Bioinformatics, Neurobiology, Omics Sciences (genomics and other omics) | 1 |
NeuroCOVID: experimental disease modelling for tackling brain vulnerability in COVID19 at high resolution
NeuroCOVID: experimental disease modelling for tackling brain vulnerability in COVID19 at high resolutionLong-term neurological and neuropsychiatric complications of infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) accompany as many as one third of COVID-19 cases, with a major impact on individual and societal welfare. While neurological deficits and psychiatric complications are increasingly recognized in patients with COVID-19, symptoms are diverse, difficult to predict, and little is known about which central nervous system (CNS) cell types or neuronal subpopulations are permissive to infection by SARS-CoV-2 or affected by SARS-CoV-2 associated inflammation and/or immunological responses. |
Testa Giuseppe More Info |
Human Technopole (HT) | Developmental and Stem Cell Biology, Neurobiology, Omics Sciences (genomics and other omics) | 1 |
RE-MEND – BUILDING RESILIENCE AGAINST MENTAL ILLNESS DURING ENDOCRINE-SENSITIVE LIFE STAGES: Brain organoid-based modelling of gene-environment interactions
RE-MEND – BUILDING RESILIENCE AGAINST MENTAL ILLNESS DURING ENDOCRINE-SENSITIVE LIFE STAGES: Brain organoid-based modelling of gene-environment interactionsEndocrine disrupting chemicals (EDCs) are a widespread and hazardous class of substances that interfere with hormonal signaling causing a wide range of adverse health effects. The interplay of their impact with the diversity of human genetic backgrounds and predispositions remains however to be elucidated. |
Testa Giuseppe More Info |
Human Technopole (HT) | Computational Biology and Bioinformatics, Neurobiology, Omics Sciences (genomics and other omics) | 1 |
RE-MEND – BUILDING RESILIENCE AGAINST MENTAL ILLNESS DURING ENDOCRINE-SENSITIVE LIFE STAGES: Single cell omics deconvolution of gene-environment interplay
RE-MEND – BUILDING RESILIENCE AGAINST MENTAL ILLNESS DURING ENDOCRINE-SENSITIVE LIFE STAGES: Single cell omics deconvolution of gene-environment interplayEndocrine disrupting chemicals (EDCs) are a widespread and hazardous class of substances that interfere with hormonal signalling causing a wide range of adverse health effects. The interplay of their impact with the diversity of human genetic backgrounds and predispositions remains however to be elucidated. |
Vannini Alessandro More Info |
Human Technopole (HT) | Structural biology | 1 |
Integrative structural biology of genome structure and organization
Integrative structural biology of genome structure and organizationGenome structure and organisation is largely controlled by the activity of loop extruder complexes (SMC complexes) throughtout the cell cycle. Integrating different structural biology approaches (cryo-EM, single molecule studies and cross-link mass spectrometry) we aim to obtain a mechanistical understanding of this process and the paramount role of SMC complexes in genome folding and their association with auxiliary proteins to control chromosome compaction, such as transcription factors, topoisomerases, chromokinesins and chromatin remodellers. |
Various PIs at TIGEM |
Telethon Institute for Genetics and Medicine (TIGEM) | Human Genetics and Genomics, Computational Biology and Bioinformatics | 5 |
Projects will be identified among the ones available at TIGEM
Projects will be identified among the ones available at TIGEMThe actual research projects will be identified among the research lines offered at TIGEM. Check the website for details: |
Various PIs at CEINGE |
Center for Genetic Engineering (CEINGE) | Human Genetics and Genomics, Molecular Oncology | 2 |
Projects will be identified among the ones available at CEINGE
Projects will be identified among the ones available at CEINGEThe actual research projects will be identified among the research lines offered at CEINGE. Check the website for details: |
Vitale Ilio More Info |
Italian Institute for Genomic Medicine | Computational Biology and Bioinformatics | 1 |
Dissecting the intracellular response to replication and mitotic stress in colorectal cancer for the design of novel effective (immuno)therapies
Dissecting the intracellular response to replication and mitotic stress in colorectal cancer for the design of novel effective (immuno)therapiesColorectal cancers (CRC) often display chromosomal instability (CIN). CIN originates from pre-mitotic defects, including DNA replication stress (RS), or mitotic defects, including a dysfunctional mitotic checkpoint (SAC). The precise contribution of these defects to intratumoral heterogeneity (ITH) and whether they impact on antitumor immune response require further investigation. |
Zhan Yinxiu More Info |
European Institute of Oncology (IEO) | Computational Biology and Bioinformatics | 1 |
Integrative analysis of multi-omics data to extract novel predictive biomarkers
Integrative analysis of multi-omics data to extract novel predictive biomarkersIn this project the candidate will develop automated pipelines to analyse and extract novel biomarkers from sequencing data. The candidate will learn to use tools such as NextFlow to build reproducible and scalable data analysis and integration pipelines. In addition, the candidate will learn to apply machine learning tools to extract biomarkers from multi-dimensional genomics and transcriptomics data. |