Angela Bachi

Born in Genoa where she graduated in Pharmaceutical Chemistry & Technology in 1990 and in Pharmacy in 1991. She got her PhD in analytical biochemistry at the Mario Negri Institute in Milan where she studied arachidonic acid metabolism and in vivo biosynthesis of prostacyclin and thromboxane to identify new metabolites indicators of free radical mediated lipid peroxidation in vivo. During her PhD studies she got interested in new mass spectrometry-based analytical methods applied to biology. For this reason she decided to move, for her post-doctoral studies, to Heidelberg in the group of Matthias Mann at the EMBL where the first proteomics techniques were developed. She then decided to return to Italy to bring back her expertise in biomolecular mass spectrometry in 2000 and became Group Leader and then Head of Unit at the San Raffaele scientific Institute. She has more than 100 publications in international scientific journals. Since May 2013 Angela Bachi is principal investigator at IFOM where she will apply and expand modern quantitative proteomics to cancer research.

Alberto Bardelli

Alberto Bardelli, a molecular geneticist and expert in the field of personalized therapies, directs the IFOM Genomics of Cancer and Targeted Therapies program at the Institute for Cancer Research and Treatment in Candiolo, near Turin. Born in Turin in 1967, Bardelli studied Biological Sciences at the University of Turin, graduating cum laude in 1991 and an honourable mention. After graduation he moved to the Ludwig Institute for Cancer Research in London were he obtained a Ph.D. in Biochemistry and Molecular biology from the University College London (UCL), in 1996. He returned briefly to Turin to conduct research at the Institute for Cancer Research and Treatment, before moving to the United States in 1999 for a post-doctoral fellowship in the laboratory directed by Bert Vogelstein at the Howard Hughes Medical Institute at the Johns Hopkins University in Baltimore. Here Bardelli began studying the genetics of cancer. From a molecular point of view, cancer is a genetic disease, i.e., the result of the sequential accumulation of mutations in the genomes of tumor cells, which acquire subversive characteristics and extraordinary proliferative advantages with respect to normal cells. The complete sequence of the human genome was unveiled while Bardelli was in Baltimore. This landmark scientific achievement and advances in DNA sequencing technologies made another ambitious project possible: deciphering the genomes of tumors to hunt for mutations in cancer genes. The research that Volgelstein was conducting was heading in this direction and had just started to reveal the genetic profiles of colorectal cancer and tracing the molecular patterns of tumor progression. Bardelli was involved from the beginning in this ambitious project. One of his most significant publications from that period identified for the first time mutations in kinase genes (the kinome) that are associated with colorectal cancer. Next he discovered mutations in the lipid kinase PIK3CA, the most commonly mutated kinase gene. Kinases act as central regulators of the neoplastic process and are amenable to pharmacological inhibition. Accordinlgly,this and other discoveries, to which the scientist has contributed, have had profound implications for the diagnosis and treatment of the disease. During his postdoctoral training at the Johns Hopkins, Bardelli published multiple papers in high profile journals such as Nature, Science and PNAS. In 2004 he decided to return to Italy. The opportunity to create a research unit dedicated to the study of tumor genomes and to transfer the findings to clinical practice came in two different centers at once: The Institute for Cancer Research and Treatment in Candiolo and the IFOM in Milan. The IFOM Genomics of Cancer and Targeted Therapies research program at the Institute for the Cancer Research and Treatment in Candiolo was established through an agreement between these two institutions. Since 2005 Bardelli has also held an Associate Professorship at the Dept. of Oncology, Medical School, University of Turin. He has authored more than 140 scientific articles of which 100 as an independent investigator. Discoveries from his group led the development of diagnostic tests, currently in clinical use, which are based on the genetic profiles of individual tumors. These discoveries represent the first example of personalized therapies for colorectal cancer patients, as was recently reported by the Bardelli's laboratory in Nature, JAMA, and Lancet Oncology.

Elena Battaglioli

Elena Battaglioli is an associate professor at the Department of Medical Biotechnology and Translational Medicine in the University of Milan. She received her Ph.D. in Cellular and Molecular Biology from the University of Milan in 1997, after receiving her B.A. in Biology. EB did her postdoctoral training in the lab of Gail Mandel at the HHMI Medical Institute, SUNY Stony Brook (NY). Her main scientific interest is understand how the environment and experiences shape our behavior by affecting gene expression. Her laboratory participated to the discovery of LSD1/KDM1A, the first and unique flavin-dependent histone demethylase (Forneris et al., 2005) and was the first one to identify how LSD1/KDM1A activity is regulated in the brain thanks to alternative splicing mechanism generating demethylase-null, dominant-negative neuroLSD1. She showed that in response to stimuli, such as behavioral stress and epilepsy, LSD1 can transduce environmental inputs into changes in chromatin structure and gene transcription of a peculiar class of target genes, the Immediate Early Genes (IEGs). Recently her laboratory has developed a novel murine model in which the neurospecific alternatively spliced exon (exon E8a) is deleted (neuroLSD1KO). This mouse model, characterized by altered emotional and cognitive behavior is used to model mood and anxiety-related disorders in preclinical research (Rusconi et al., 2015 and Rusconi et al., 2016). For all these reasons LSD1 can now be considered a unique epigenetic factor able to shape mammalian behavior in an adaptive but also maladaptive manner. Her group is now studying LSD1 in the context of epilepsy, and stress-related mental illness such as anxiety and post-traumatic stress disorder.
The alternative-splicing pathway regulating the correct balance between LSD1 and neuroLSD1 is also altered in rodent models of neurodevelopmental disorder characterized by seizures, cognitive impairment, autism spectrum disorder (ASD) such as the Rett Syndrome (RTT; Rusconi et al., 2015) and the Epileptic Encephalopathy 9 (DEE9; Gerosa et al., 2022). Thanks to the use of antisense oligonucleotides, EB’s lab is now developing an exon skipping-based therapy to normalize the fine LSD1/neuroLSD1 balance in neurons in rodent models of the disease (Longaretti et al., 2020). A further significant contribution of her work is the implication of de novo loss of function hLSD1/KDM1A mutations in a new form of developmental disorder with intellectual disability, Cleft Palate, Psychomotor Retardation, and Distinctive Facial Features (CPRF) OMIM#616728.

Silvio Bicciato

I started my first independent, bioinformatics lab at the University of Padova in 2004. In 2007, I moved to Modena where I created the Bioinformatics Core at the Center for Genome Research, an interdisciplinary group that includes computer scientists, molecular biologists, statisticians, biotechnologists, and engineers who cooperate in the generation and application of bioinformatics tools for the analysis of high-throughput molecular data. Currently, the team consists of 1 associate professor, 3 postdocs, 2 PhD students, and 4 MS students. In the last 16 years, I raised more than 2.7M € in research funds from national and international competitive grants. Within my group, I trained more than 25 undergraduate students, 15 PhD students, and 12 postdocs. The principal research interest of my group is the design and application of computational biology and bioinformatics methods to organize, analyze, compare, interpret, and visualize -omics data. From a methodological standpoint, our current research lines comprise the development of methods, resources and tools for i) integrative analysis of multi -omics and phenotypic data; ii) epigenomics and 3D genome; iii) computational systems biology; and iv) single cell genomics. From an applicative perspective, my group support wet biologists in national and international research institutions in investigating the genomic bases of complex biological systems, with particular emphasis on onco-genomics, immunogenomics, and neurosciences. With some of these groups, we are operating like one extended laboratory, where we provide key support to bioinformatics analyses of -omics data.

Marie Claude Blatter

Marie Claude Blatter works in the Swiss-Prot group (SIB Swiss Institute of Bioinformatics). She was involved in the biocuration, documentation and user support of the UniProtKB protein knowledgebase (www.uniprot.org) for many years. She coordinates and participates in the bioinformatics teaching program of the University of Geneva at the bachelor and master levels. She has been taking part in EU-funded outreach activities for several years with special expertise in the fields of biological data & knowledgebases.

Raoul JP Bonnal

Raoul Jean Pierre Bonnal is a Senior Staff Bioinformatician at IFOM ETS - THE AIRC INSTITUTE OF MOLECULAR ONCOLOGY, Milan, Italy. He is interested in applying bioinformatics techniques and analyses to characterize the human T lymphocytes and their regulatory networks that shape T cells identity and functional plasticity, even in tumoral microenvironments. He has extensive experience in analysing a broad range of Next Generation Sequencing, bulk and Single-Cell. He is interested on building scalable pipelines leveraging the cloud and using containerization technologies, to guarantee reproducible bioinformatics analyses. He trains graduate and PhD students on bioinformatics. He is a lecturer and oversees the organization of the second level master in “Bioinformatics and Functional Genomics” organized by the University of Milan.

Raffaele Calogero

Raffaele Calogero is the PI of the Bioinformatics and Genomics core lab (BGcore) at Molecular Biotechnology Center in Torino. Between 2000 and 2010 he was deeply involved in transcriptomics data analysis and mining (microarray technology). In 2010 he moved his interest on Next Generation Sequencing (NGS) data analysis (RNA-seq, miRNA-seq, Exome-seq, single-cell-seq).
He is the co-founder of the Reproducible Bioinformatics Project, a community of scientists devoted to the development of reproducible bioinformatics workflows in genomics. The actual main research focus of Prof. Calogero is single-cell data analysis workflow development for single cell and spatial transcriptomics. He is part of the Elixir Italy management committee, and of the Elixir Single Cell Omics Community team. He is the president of the Italian Society of Bioinformatics (BITS) and member of the Scientific Committee of the Infolife CINI laboratory.

Arianna Carbone

Arianna Carbone is a physicist who spent over ten years doing research in theoretical nuclear physics before she pivoted her career to information and communication technologies (ICTs). She holds a PhD in Physics from the University of Barcelona. Thereafter, she worked as a postdoctoral researcher, first at the Technical University of Darmstadt (Germany), and then at the European Centre for Theoretical Studies in Nuclear Physics and Related Areas within the Bruno Kessler Foundation, in Trento (Italy). While in Darmstadt, she won the Humboldt Fellowship for Postdoctoral Researchers and received full funding to develop her own scientific project. Her focus was in the theoretical study of nuclear many-body systems, developing mathematical and computational models to perform and analyze complex data.
After a career as an academic researcher in nuclear theoretical physics, she wanted to switch to disciplines more connected to information and communication technology. She then pursued a Master in ICT for Development and Social Good at the University of Turin. Her thesis focused on the ethical employment of data mining and machine learning in international development projects.
She later joined the computing center of the Italian National Institute for Nuclear Physics (INFN) as a research assistant, working on projects related to cloud computing and blockchain technologies. She then worked as a machine learning and data engineer for a non-profit organization building a machine learning platform to improve the usage of health applications for underserved countries. Subsequently she joined IFOM as a data engineer to devise methods to manage clinical trials data and develop a data repository to access and query such data.
In addition, she has spoken multiple times at research conferences and also published over 15 journal articles, as well as a chapter in a book about computational nuclear physics.

Stefano Casola

Stefano Casola is a molecular immunologist and cancer biologist interested in identifying mechanisms and molecular determinants controlling B-lymphocyte differentiation and malignant transformation, and to exploit such knowledge to improve treatment of B cell disorders including lymphomas, immunodeficiencies and autoimmune diseases.
After receiving his MD and PhD degree from the University Federico II of Naples, he joined the Institute of Genetics at the University of Cologne in Germany as post-doctoral fellow, working in the group of immunologist K. Rajewsky. Here, he developed genetically engineered mouse models ensuring in vivo conditional gene targeting in germinal center B cells, to functionally dissect the molecular bases of B cell adaptive immunity and lymphomagenesis.
In 2001, Casola was recruited to the Harvard Medical School in Boston becoming Junior Investigator at the CBR Institute for Biomedical Research and Instructor in the Department of Pathology, Harvard Medical School. In 2006, he was awarded the Armenise Harvard Career Development Award and with support from the Italian Foundation for Cancer Research (FIRC), he established the “Genetics of B cells and lymphoma” unit at the IFOM-ETS- The AIRC Institute of Molecular Oncology in Milan.
The Casola laboratory applies in vivo and ex vivo functional genomics approaches to mouse and human normal and cancerous B cells, to unveil key genetic and epigenetic determinants controlling B cell differentiation and malignant transformation, and to define their role in lymphoma therapy resistance, or as cancer vulnerability targets.

Cristina Cheroni

After her PhD in the laboratory of Molecular Neurobiology at Mario Negri Institute for Pharmacological Research, Cristina Cheroni moved to Istituto Nazionale di Genetica Molecolare as Post-doc and continued there as Bioinformatician. In 2017 she joined as Senior Computational Biologist Prof. Testa Research Group. From October 2022 she is manager of CEll REference BRain Atlas (CEREBRA) scientific support unit in Human Technopole Neurogenomics Research Centre.

Davide Cittaro

Davide Cittaro graduated in 2002 at the University of Milan and obtained a Master's degree in Bioinformatics in 2003. Soon after, he started his path in bioinformatics at the FIRC Institute for Molecular Oncology in the proteomics group. He received a PhD in Complex Systems for Life Sciences in 2010 at University of Turin while working in the NGS core lab at the European Institute for Oncology.
He moved to the Center for Omics Sciences in 2011 as coordinator of the Bioinformatics unit. He has been the leading computational biologist at the Innovation Lab since 2017.

Piero Conca

Piero Conca got his PhD in “electronic engineering” from the University of York. After graduating, he worked in the academy and in the industry, for companies such as Fujitsu and Nuritas, mostly on knowledge graphs and natural Language processing. He is now part of the Cogentech team building machine learning models for tumor detection based on genetic signatures of tissues and liquid biopsies, as well as models for classifying histopathologic images.

Francesca Corderdo

Francesca Cordero is an associate professor in the Computer Science Department.
She is a bioinformatician working at the intersection of computer science, genomic and transcriptomic biology, and systems to develop approaches to solve research questions and to model the cancer progression and response to treatment.
The strong multidisciplinary background obtained from a master degree in Biological Sciences and a Ph.D. degree in Computer Science gives to Dr. Cordero the possibility to easily and efficiently work on both biological/clinical areas and computer science.
She has worked in different fields of bioinformatics, from analysis of sequences to biological modeling to developing specific algorithms and computational solutions tailored to bio-medical requests. The broad range of research themes followed by Dr. Cordero demonstrates her ability to master different research fields both successfully ad productively. Dr. Cordero is specialized in implementing algorithms to analyze genome-wide data obtained by high-throughput technologies. For deep sequencing techniques, she is interested in the definition of new algorithms and workflow with different purposes: deconvolution for assembly of new genomes, mapping, analysis of RNA-seq, microRNA, ChIP-seq, structural genomics variations detection, etc. For what concerns the systems biology topic, she works in the analysis of biological systems by applying computational and mathematical formalisms. She has focused on the use of in-silico models to investigate the different stages of cancer development and progression as well as the simulation of specific therapies.
Dr. Cordero is the founder and responsible for the Quantitative Biology (q-Bio) group at Dept. of Computer Science at the University of Turin (http://beta.di.unito.it/index.php/english/research/groups/computational-and-mathematical- methodologies-modelling-multi-omics-systems/about).

Giovanni Crisafulli

I'm a bioinformatics manager and computational researcher at IFOM ETS – The AIRC Institute of Molecular Oncology and my fields of research are Genetics, Bioinformatics, Oncology, Molecular Genetics and Precision Medicine. I have worked in the private and public sectors. I gathered excellent skills in Bioinformatics, Systems Biology, Oncology, Molecular Genetics and analysis of NGS data. I contributed to different projects: 1) Monitoring clonal evolution dynamics and the emerging of new resistant clone to therapy using liquid biopsy in CRC (Crisafulli et al., ESMO open 2019, Siravegna G, Lazzari L, Crisafulli G -- co-first author -- et al., Cancer Cell. 2018, Van Emburgh BO et al, Nat Commun. 2016), glioma (Orzan et al. Clin. Cancer Res. 2022) and breast cancer (Siravegna et al., ESMO open 2017), translating discoveries in clinics (Sartore-Bianchi et al. Nature Med 2022); 2) Understanding genetic processes such as adaptive mutability. Using NGS data of samples and cell models from CRC, we understood that cancer cells can adapt to therapeutic pressures by enhancing their mutability (Russo et al., Science 2019, Russo et al. Nat Genetics 2022); 3) Discovering a new biomarker to use in precision medicine: the number of mutations/neoantigens, linked to Tumor Load, can guide the therapy in colorectal cancer. High Tumor Load tumors can improve immune surveillance and are required for effective immunotherapy response (Germano et al. Nature 2017, Pinocchino, Crisafulli et al. Cancers 2021, Merlini et al. Frontiers in Oncology 2022) and these results could be translated in clinics as shown in ARETHUSA clinical trial (Crisafulli et al. Cancer Discovery 2022).

Silvestro Di Pietro

My name is Silvestro Di Pietro, but anyone know me as Pino. I was born in Rome on the 10 of February 1961. I’m married with two sons and a grandchild.
I'm on professional computing since 1983. I spent 10 years on the financial market as financial analyst because my economist formation. In 1991 I developed a fully automatic AI trader and this before AI become a buzz word.
In 1997 I decided to commit myself to help bioscience in computing starting as ITC manager at IEO (European Institute of Oncology) designing the network architecture and the system integration. At that time I met the first computational challenges in protein alignment and some advanced and faster c algorithms where developed in order to make it possible with the computer resources available in 2000 building a cluster of linux workstations and a integrated pipeline with the sequencing machines.
After spent 3 year as firmware videogame designer, I moved to IFOM in late 2004 where I'm trying to develop recipes that can still be tasty in a world leading research institution with weekly transformation and challenges coming from the data lake of deep sequencing, advanced imaging, computer clusters, cloud and brilliant minds ideas.

Michaela Fakiola

Michaela Fakiola studied Biology at the Aristotle University of Thessaloniki, Greece, obtained an MSc in Environmental Technology at Imperial College London, UK and received a PhD in Human Genetics from the University of Cambridge, UK.
During her postdoctoral studies in the group of Jenefer M Blackwell at the Cambridge Institute of Medical Research (CIMR), she developed expertise in human genetic susceptibility and participated in international collaborative projects (funded by the Wellcome Trust, UK and the National Institutes of Health, USA) that identified clinically relevant genes, and common and rare genetic risk variants for infectious diseases, metabolic disorders and immune-related diseases. Some of this work involved placements in the US and Australia, as well as field work in India. Her early postdoctoral research, conducted as part of the Wellcome Trust Case-Control Consortium (WTCCC), provided strong evidence for the specific risk and protective HLA-DRB1 alleles that determine susceptibility to the parasitic infection of visceral leishmaniasis (VL). This led to molecular and experimental studies to understand VL pathogenesis which she continued pursuing, after a short post-doc with Jim Kaufman, as an independent research fellow at the Department of Pathology, University of Cambridge.
In recent years, she joined the group of Massimiliano Pagani and received funding from the Umberto Veronesi Foundation to reorient her interests towards cancer research. Her work seeks to understand how the transcriptional and epigenetic reprogramming of lymphocyte populations and cancer cells leads to the impairment of immune responses and tumor growth. She has broad experience in omics-based data, including analyses of RNA-seq, ChIP-seq, ATAC-seq, whole-exome sequencing, single-cell RNA-seq, and chromosome conformation capture approaches (capture HiC). She is currently based at IFOM ETS - the AIRC Institute of Molecular Oncology and her research focuses on the following areas:
- Tracing the roots of T lymphocyte-mediated immune suppression and dysfunction in cancer through the integration of epigenomics and single-cell multiomics.
- Molecular characterization of metastatic tissues to decipher their distinct and shared epigenomic patterns compared to the primary tumors from which they originate.
- Dissecting the molecular complexity of colorectal cancer by analyzing the transcriptional and epigenomic landscape of genetically heterogeneous patient-derived tumor organoids (PDOs), and identifying the key trans regulators and chromosomal interactions of the tumor-specific enhancerome.

Francesco Ferrari

Francesco Ferrari joined IFOM in 2015 and here he coordinates a new research group focusing on computational genomics.
Francesco Ferrari graduated with honors in Medical Biotechnology at the University of Modena in 2004, with a thesis on microarray-based gene expression profiling of melanocytes from melanoma patients. From the beginning of his activity he experienced the need to develop novel informatics tools to answer biological questions using genome-wide data.
During his doctoral studies in Biotechnology and Molecular Medicine he shifted the focus of his research activity to bioinformatics to identify chromatin domains with co-regulated expression, and to characterize their role in myeloid cells differentiation. He obtained his doctoral degree in 2008, working in the laboratory of Sergio Ferrari at the University of Modena and ReggiFerrariFrancescoo Emilia.
As a post-doc, he worked with Silvio Bicciato and Stefania Bortoluzzi at the University of Padova, where he extended his previous work to discover co-expressed, co-regulated and co-localized gene modules. The finding that distant genomic regions can share coordinated expression patterns led to the interest in the role of epigenetics modifications and chromatin three-dimensional architecture in regulating genome functionality.
He had the opportunity to explore these topics while working as a post-doc in Peter J. Park group at Harvard Medical School from 2010, where he focused on novel methods for next generation sequencing data in epigenetics and gene expression studies. In particular he studied the genome-wide chromatin architecture rearrangements occurring around a key pluripotency gene (Nanog) during reprogramming of somatic cells to induced pluripotent stem cells. This work identified a pluripotency-specific interactome for Nanog, which is lost upon differentiation, and re-established during reprogramming. These genomic rearrangements precede gene expression changes associated to pluripotency, thus being pivotal for cell identity change.
He also investigated again coordinated regulation of gene expression over large chromatin domains in an extreme case, as it is dosage compensation of sex chromosomes. Epigenetic regulation of transcription is the key to compensate copy number differences between sexes. In Drosophila melanogaster, by using data from several next generation sequencing-based techniques to study transcription dynamics, he was able to prove the key role of enhanced pausing release and transcription elongation to achieve increased chromosome X expression.
In 2015 he joined IFOM as group leader of the computational genomics laboratory. His group is particularly focused on understanding the role of chromatin organization and epigenetics in regulating gene expression, and how these mechanisms are altered in cancer.

Maxime Garcia

Maxime U Garcia did his PhD in Bioinformatics and Genomics at the Cancer Research Center of Marseille, France.
He developed Nextflow pipelines, at the Swedish Childhood Tumor Bionbank from Karolinska Institutet, in collaboration with Scilifelab's platforms National Genomics Infrastructure and National Bioinformatics Infrastructure Sweden.
Involved in nf-core since its inception, he is also a member of the core team that manages the community.
Now working for Seqera Labs, he continues to develop pipelines within the nf-core community.

Nancy George

Dr Nancy George (PhD) is a senior scientific curator in the Gene Expression team at the EBI. Within the team we maintain and develop resources for functional genomics submissions, archival and reanalysis in our knowledgebases Expression Atlas and its newer counterpart Single Cell Expression Atlas. This involves designing ways to represent and store latest sequencing technology alongside best practices for curation and FAIR guidelines to ensure data storage and reusability for the scientific community.

Gabriele Giachin

Gabriele Giachin graduated in Biotechnology at the University of Udine in 2008. He then obtained a PhD in 2012 at the International School of Advanced Studies (SISSA) in Trieste where he studied the structural characteristics of prions, proteins involved in human neurodegenerative diseases. He spent a period as Visiting Scientist at the Nuclear Magnetic Resonance Center in Ljubljana (Ljubljana) until 2014 and then moved to Grenoble (France) where he began working at the European Synchrotron Radiation Facility, ESRF, one of the most important synchrotrons currently in function in the world. At ESRF, he specializes in synchrotron light applications aimed at studying the atomic characteristics of proteins. In particular, he studies some mitochondrial proteins responsible for the correct functioning of the respiratory chain. In 2018 he returned to Italy thanks to the award of a Marie Skłodowska-Curie Action (MSCA) postdoctoral fellowship at the Department of Cellular, Computational and Integrated Biology (CIBio) of the University of Trento. In 2020 he obtained the funding to start his independent research line as a junior PI thanks to the STARS @ UniPD project promoted by the University of Padua. Since 2022 he has been a researcher (rtd-b) and professor of Organic Chemistry at the Department of Chemical Sciences (DiSC) of the University of Padua. He is currently developing a research project aimed at characterizing some mitochondrial protein complexes through the use of multidisciplinary techniques, including cryo-electron microscopy.

Elisabeth Gasteiger

Elisabeth Gasteiger joined the Swiss-Prot group in 1995 as a software developer and later became software development coordinator. She was in charge of the Expasy website which was one of the first websites in molecular biology and served as the main access point for Swiss-Prot and many proteomics tools. In the UniProt group, she now works at the interface between users and developers, as a senior user experience and support manager. Elisabeth is also involved in teaching and other outreach activities.

Fabio Iannelli

Fabio Iannelli is Head of Bioinformatics unit at IFOM, The AIRC Institute of Molecular Oncology. He is a senior bioinformatician with more than 15 years of experience in genomics, transcriptomics, high-throughput data analysis and solid skills in management of a bioinformatics unit, training of PhD students and teaching of bioinformatics and programming at the European School of Molecular Medicine (SEMM).
He graduated from the University of Milan with a PhD in Molecular Biology of the Cell.
As a PhD student and then postdoc, he worked in the group of Graziano Pesole, where he studied the evolutionary dynamics of the mitochondrial genome in terms of base composition variability, gene order rearrangements and rate of gene loss/gain.
He then moved as a postdoc to IEO (European Institute of Oncology) in the group of Francesca Ciccarelli (now at The Francis Crick Institute). In these years (i) he showed that inflammation promotes liver cancer in human and mouse through massive copy number variations and structural variations, (ii) he contributed to a study proving L1-mediated retrotransposition as an important etiological factor in liver cancer, and (iii) he contributed to three studies on colorectal cancer rebuilding their proliferation history by deep sequencing of the somatic mutation landscape, demonstrating the presence of genomic instability in non-neoplastic tissues in hereditary colorectal cancer patients, and showing an environmental field effect that promotes synchronous colorectal cancers in the background of inflammation.
He then worked as a senior postdoc in the group of Fabrizio d'Adda di Fagagna at IFOM, where his research has been focused primarily on the impact of DNA double-strand breaks (DSBs) on transcription. In this lab he co-authored a paper as a first and co-corresponding author where he has consistently demonstrated the repression of pre-existing transcription in proximity to DSBs using a novel technique (namely BLISS) for single-nucleotide in situ detection of DSBs together with four independent approaches monitoring transcriptome alterations upon DSB induction at steady-state RNA levels, rates of RNA synthesis, transcription initiation and elongation events. He also contributed to show that DNA damage induces the transcription of long and small non-coding RNAs termed dilncRNAs and DDRNAs.
As of today, in the Bioinformatics Unit, he is collaborating with 20 IFOM groups and 5 external groups on projects spanning a variety of technologies and approaches e.g., next generation sequencing (WGS, WES, ChIP-seq, RNA-seq bulk or single-cell, CAGE, NET-CAGE, BLISS, Cut-and Tag, DRIP-seq, ATAC-seq), and third-generation sequencing (Oxford Nanopore). Examples of projects he is involved in: (i) in collaboration with the group of Giorgio Scita he has contributed in demonstrating how a solid-to-fluid phase transition promotes a pro-inflammatory transcriptional rewiring in invasive breast carcinoma. (ii) He collaborated in studies conducted with the group of Valter Longo and with the group of Claudio Vernieri, where he contributed to demonstrate how calorie restriction is able to activate specific metabolic responses in cancer cells, which may represent new pharmacological targets, and to modulate the immune response of patients leading to the activation of antitumor responses. (iii) He contributed with the group of Fabrizio d'Adda di Fagagna to explain the role of telomere shortening - already associated with cancer and aging - in susceptibility to SARS-CoV-2 infection.
The results of his research have been published on international journals such as Cell, Cancer Discovery, Nature Materials, Nature Cell Biology, Nature Communications, Nature Protocols.

Elisa Mariella

Dr Mariella graduated in Molecular Biotechnology at the University of Torino where she subsequently got her PhD in Biomedical Sciences and Oncology. Her training has been focused on computational biology. In detail, she has always been fascinated by mechanisms of gene expression regulation and she initially contributed to the development of an algorithm for the quantitative study of alternative polyadenylation based on standard RNA-seq data (Grassi et al., BMC Bioinformatics 2016). Then, she has been active in the field of human population genetics, working on different projects that have investigated the effect of human genetic variants on intermediate molecular phenotypes such as gene expression (Grassi, Mariella, Forneris et al., Hum Genet 2017; Mariella et al., Front Genet 2019). She joined Prof. Bardelli's lab in 2019 as a postdoc and thanks to her expertise in omics-data analysis she has contributed to different works exploring different aspects of colorectal cancer (Durinikova et al., Clin Cancer Res 2022; Pergolizzi et al., J Exp Clin Cancer Res; Flanagan et al., Nat Commun 2022). Furthermore she recently found that mapping extreme and transcriptome-wide positive and negative gene expression outliers in CRC cell lines is an effective strategy to identify putative drug targets and biomarkers, independently from the underlying genetic or epigenetic alterations (manuscript submitted for publication). Her research activity is currently supported by the FIRC-AIRC "Michele e Carlo Ardizzone" fellowship for Italy.

Vittoria Matafora

Staff scientist at IFOM ETS - The AIRC Institute of Molecular Oncology (Milan, Italy). She got her PhD in “Nephrological Science” at University of Campania “Luigi Vanvitelli”, (Naples, Italy); at present, she works in Angela Bachi’s group. She has strong expertise in mass spectrometry-based proteomics and lipidomics applied to biological research. Currently, she is studying tumor microenvironment in melanoma, setting up a new method, named Secret3D, for the analysis of secreted proteins. She has also recently developed a new method, named Opti-nQL, for lipidomic analysis with nano-LC/MSMS approach.
She had teaching experiences as temporary Professor at Medical school, Vita-Salute San Raffaele University, Milan Italy. She belongs to the editorial board of Journal of Integrated Omics. Vittoria has received Awards for Best Poster Prize at Italian Proteomic Association, ITPA.
Author or co-author over 37 research articles, 3-chapter books.

Luca Mollica

Massimiliano Pagani

I am a 50 years old PhD currently responsible for the Molecular Oncology and Immunology lab at the IFOM - the FIRC Institute for Molecular Oncology in Milan and Full Professor of Molecular Biology at the University of Milan (Italy). After the PhD (1996-2000, in the lab of R. Sitia, at the San Raffaele Research Centre in Milan), my research career is clearly divided in two parts: I spent eight years (2000-2008) in an Italian Biotech company, PRIMM (Milan, Italy) where I have combined my research activities with growing managerial responsibilities from Staff Scientist to Head of R&D.
In June 2008, I have been offered the challenging task of establishing a new translational research group in the area of human immunology (Integrative Biology Program) at the National Institute of Molecular Genetics (INGM).
In 2013 I have been awarded a Consolidator Grant by the ERC to investigate the role of Long non-coding RNAs of tumor infiltrating lymphocytes as novel anti-cancer therapeutic targets; I have been appointed as Associate (January 1st 2015) and then as Full Professor (April 1st 2018) of Molecular Biology in the Department of Medical Biotechnology and Translational Medicine at the Università degli Studi di Milano.
A start-up company (CheckMab?) has been created in 2018 stemming from my research activities on the identification of cell surface molecules selectively present on tumour infiltrating lymphocytes that could be novel therapeutic targets for cancer.
Since 2018 I am coordinating the Master in Bioinformatics and Functional Genomics at the Università degli Studi di Milano that is intended for students who are interested in the application of advanced bioinformatics and computational approaches to complex biological questions.
In 2019, following the growing interest for the exploitation of organoids technology for disease modeling, I have promoted the creation of the Human Organoid Models Integrative Center “Homic” with the generous support of Fondazione “Romeo ed Enrica Invernizzi” and Università degli Studi di Milano.

Giovanni Palla

Giovanni Palla is a PhD student in Fabian Theis' group, at the Computational Health Center, Helmholtz Munich, Germany and the Munich School for Data Science. He studied Biotechnology and Bioinformatics in Trento, Italy, and Utrecht, The Netherlands.

Dario Parazzoli

Born in Milano, Dario Parazzoli has shown very early his interest in the interplay of physics and biology. Graduated in Physics from the University in Milan, Dario's career has followed a path at the intersection of technology and the biological effects of radiations. Pursuing this passion, in 1997 he joined a leading industrial company in the field of microscopy where he had the opportunity to work as project manager at the forefront of confocal technology and high-end solutions for life science microscopy. In 2004, after almost a decade in the industry where he also refined his managerial abilities, Dario decided to deepen his interests in biomedical research by joining the research arm of the European Institute of Oncology in Milano where he was a key figure in setting up an advanced configuration of a Total Internal Fluorescence Microscope making it suitable for long time living cell applications. In 2008 he briefly joined the National Institute of Molecular Genetics where he established the imaging facility but in 2009 he was back in cancer research at IFOM where he now leads the Imaging Technological Development Unit (TDU).

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Grazisa Rossetti

Giorgio Scita

A cell biologist and expert on the dynamics of cell movement, Giorgio Scita directs the Mechanisms of Tumor Cell Migration research unit at IFOM.
Born in 1963 near Parma, Scita enrolled in the Faculty of Biology at the University of Parma in 1982 with a precise intention: to study animal behavior alongside the famous Italian ethologist Danilo Mainardi.
However, this was the time of the great explosion of molecular biology: "They began to identify and clone genes, to move from genes to proteins, to study their functions. It was impossible not to be fascinated."
Therefore, Scita focused on the behavior of proteins, graduating in 1986 with a thesis on the biochemistry of the metabolism of one of the most powerful antioxidants that protect cells from damage induced by free radicals: vitamin A.
In 1989, at the same University, he specialized in Chemistry and Food Technology and then left for the United States. There, in the laboratories of the Department of Nutritional Sciences at the University of California at Berkeley, he continued his studies on the effects of vitamin A and its derivatives - particularly beta-carotene and retinoic acid - on cell adhesion.
It was becoming increasingly apparent at the time that retinoic acid functions as a powerful molecular signal capable of influencing gene expression. Scita discovered that the cellular response to this signal could be altered following the activation of genes that promote tumor transformation.
To study these issues further, he left California in 1994 for Maryland to work in the Laboratory of Cellular Carcinogenesis and Tumor Promotion at the National Cancer Institute in Bethesda.
Meanwhile, in Milan, Italy a project to create a new organization was taking shape: a Department of Experimental Oncology at the European Institute of Oncology (IEO). Two scientists, in particular, were advocates: Pier Giuseppe Pelicci and Pier Paolo Di Fiore.
Attracted by the idea of studying beside them, Scita returned to Italy in 1995 to work on the staff of Pier Paolo Di Fiore.
In 2001, he left the IEO, accepting the offer by IFOM to develop his own line of research there. He established a new group to investigate how cancer cells acquire mobility, a feature essential for the spread of cancer in the body. This gave rise to the Mechanisms of Tumor Cell Migration research program at IFOM.
In 2006, after five years of significant contributions to the advancement of scientific knowledge, making important discoveries in his field, was confirmed as director of research at IFOM.
In the same year, he became Associate Professor of General Pathology in the Faculty of Medicine at the University of Milan.
He is also associated with various studies that deepen our understanding of the mechanisms by which cells perceive their external environments and transduce signals, in response to which they change their behavior, especially that of migration.
In particular, he was responsible for the discovery that highlighted the fundamental connection between tumor cell mobility and the cellular process of endocytosis, traditionally considered to act in quite different cellular events.
Author of around 100 publications, Scita is among the more productive and cited Italian scientists, he is ERC awardee (2011) and EMBO member since 2014.

Andrea Spitaleri

Computational scientist working at the intersection of basic and applied research. Principal Investigator Italian Association Cancer Research (3y, AIRC). Co-founder of a start-up BiKi Technologies srl in which novel algorithms molecular dynamics based provide pharmaceutical and biotech companies innovative computational solutions. Bioinformatician working at the Emerging Bacterial Pathogen Unit to study antimicrobial resistance. Involved in WHO infection control consortiums. Researcher assistant in the neurogenomics unit at Human Technopole.

Alessandro Vitriolo

After a brief career in theoretical chemistry, studying protein dynamics and molecular mechanics, he moved to European Institute of Oncology in Milan, to earn a PhD in Systems Medicine, by studying epigenetic convergences across neurodevelopmental disorders. He then joined Human Technopole Neurogenomics Department, to study the role of evolution in shaping the development of modern humans brain and face. He has also been appointed Adjunct Professor for the Master in Bioinformatics for Functional Genomics (2019-2023), teaching Data Integration in Neurogenomics. He studies chromatin structure-function relationships, using omics- approaches, to reconstruct chromatin regulation, its dysregulation in disease, and evolutionary relevant chromatin structural changes.

Chris Wyatt

Christopher D.R. Wyatt is a bioinformation at Seqera Labs and based in Barcelona, Spain. He did his PhD in Biomedicine at the Centre for Genomic Regulation (Pompeu Fabra University, Barcelona), working on evolutionary development and splicing. He has also worked at University College London, developing Nextflow workflows for evolutionary and synteny analysis. His current work entails helping building Nextflow pipelines for clients and developing the training material at Seqera (https://training.seqera.io/) to help share the best practices in Nextflow pipeline development.