7th International Synthetic & Systems Biology Summer School   |   Scuola Normale Superiore - Pisa - Tuscany - Italy   |   June 8-12, 2020

Lecturers

Our Valuable Speakers

Keynote Speakers

Topics
Cancer, Systems Biology, Synthetic Biology, Synthetic Chromosomes, Genome-wide association studies

Biography

Joel S. Bader, Ph.D., Professor in the Department of Biomedical Engineering, uses engineering-based mathematical, computational, and high-throughput methods to study biomedical systems. Bader is Interim Director of the High-Throughput Biology Center at the School of Medicine, has a secondary appointment in the Department of Computer Science, and is a member of the Institute of Computational Medicine (School of Engineering) and the Institute of Genetic Medicine (School of Medicine).

Bader’s research interest is the relationship between genotype, the DNA sequence that encodes life’s information, and phenotype, a living system’s observable properties. Applications are to human disease, primarily complex genetic disorders and cancer, and to designed synthetic systems. The Human Genome Project, which provided a reference sequence of the 3 billion DNA letters that are the instructions for human life, also identified heritable genetic variants that influence disease risk. Mutations that arise in individual cells similarly can lead to cancer and other diseases. Bader develops new computational methods and joint wet-lab approaches to define how inborn genetic variants and acquired mutations lead to disease, with the goal of developing new therapies.

Bader leads the Johns Hopkins Cancer Target Discovery and Development (CTD2) Center, which was funded by the National Cancer Institute to identify new targets for metastatic breast cancer. His study is recruiting women receiving breast cancer treatment at Johns Hopkins Hospital to donate biological specimens that will help reveal the molecular drivers of tumor invasion and metastasis. These phenotypes, rather than cell proliferation in the primary tumor, are the main cause of breast cancer mortality.

In synthetic biology, Bader’s lab develops methods for designing, building, testing, and analyzing DNA sequences that encode genes, pathways, chromosomes, and entire genomes. He is the computational leader of the international Saccharomyces cerevisiae 2.0 (Sc2.0) project, whose aim is to create a yeast cell with a synthetic genome. The milestone of synthesizing 6 of the 16 yeast chromosomes was highlighted in a series of 7 papers in the March 10, 2017, issue of the journal Science.Bader’s lab also develops technologies for biosafety and biosecurity, preventing escape of engineered life and identifying evidence of genetic engineering in genetic sequence data.

Bader developed and teaches a core course in systems biology in the BME undergraduate program and has also been faculty for courses in the Department of Applied Math and Statistics and the Department of Biology. He is a faculty advisor to the Tau Beta Pi Maryland Alpha Chapter at Johns Hopkins. Bader is a member of the Climate, Culture, and Campus Experience Subcommittee of the Homewood Council on Inclusive Excellence and has served on the University-wide Library Advisory Council. He is a Fellow of the American Institute for Medical and Biological Engineering (AIMBE); a member of the NIH Genomics, Computational Biology and Technology (GCAT) study section; and Deputy Editor of PLOS Computational Biology.

Prior to joining Johns Hopkins, Bader was Director of Bioinformatics at CuraGen Corp., where he worked from 1995-2003 and co-invented the 454 Genome Sequencer, the first next-generation DNA sequencer to reach the market.

Bader received a B.S. in Biochemistry from Lehigh University, where he was elected to Phi Beta Kappa and Tau Beta Pi, and a Ph.D. in Chemistry from the University of California, Berkeley, where he was an NSF Pre-Doctoral Fellow. He did postdoctoral research at Columbia University. He joined the faculty of the Whiting School of Engineering as an assistant professor in 2003, which has been his academic home ever after.

Topics
Humane Genome Project - Write, Genomics, Genetics, Retrotransposons, Synthetic Biology

Biography

Jef D. Boeke is an American geneticist who is currently the founding director of The Institute for Systems Genetics at NYU Langone Medical Center. From 1986 to 2014 he was on the faculty of The Johns Hopkins University School of Medicine, where he was the founding director of the High Throughput (HiT) Center. He is a member of the American Academy of Arts and Sciences as well as the National Academy of Sciences.

Boeke received a Bachelor’s degree summa cum laude in Biochemistry in 1976 from Bowdoin College. He is a member of the Phi Beta Kappa chapter at Bowdoin. He then received a PhD in Molecular Biology from Rockefeller University in 1982, where he worked with Peter Model and Norton Zinder on the genetics of the filamentous phage. He did his postdoctoral work at The Whitehead Institute of MIT as a Helen Hay Whitney Postdoctoral Fellow with Gerald Fink.

Boeke is primarily known for his pioneering fundamental genetic and biochemical work on understanding the mechanisms of DNA transposition. He along with Gerald Fink discovered the mechanism by which yeast Ty1 transposable elements move via an RNA intermediate. He coined the term “retrotransposon” to describe transposable elements that move via this process.These retrotransposons are distantly related to retroviruses such as HIV.

Boeke is currently leading an international team of collaborators in an effort to construct a synthetic version of the entire genome of Baker’s Yeast, Saccharomyces cerevisiae. It was reported in March 2014, that Boeke along with this team had synthesized the third smallest chromosome, chromosome III. The synthetic chromosome was designed to be shorter and more stable than the original. The effort to complete all 16 chromosomes of S. cerevisae is currently underway and is reportedly half complete.

Topics
Systems Biology, Functional Genomics, Transcriptomics, Biostatistics, Computational Biology, Integrative Genomics & Metabolism

Biography

After a Masters Degree in Theoretical Physics from the University of Turin, Francesca completed her PhD in Physics and Mathematical Modelling at the Institute of Cancer Research within the University of London. She then undertook a postdoctoral research fellowship in Mathematical Modelling and Biostatistics at the Gray Cancer Institute, London, before joining the Molecular Oncology Laboratories at the Weatherall Institute of Molecular Medicine, University of Oxford, first as a postdoctoral research fellow in Bioinformatics / Biostatistics then as a Group Leader. She is the recipient of a Cancer Research UK programme and a European Research Council consolidator award.

In addition to her research programme, she teaches at national and international Masters Courses and Advanced Schools, is a member of national and international panels, and acts as bioinformatics / biostatistics advisor for genomics clinical research studies.

She has been invited to present her work at national and international conferences, and authored or co-authored over 100 publications, several in high impact journals.

Antonino Cattaneo

Scuola Normale Superiore, Pisa, Italy

Biography

After obtaining a Degree in Physics at the University of Rome La Sapienza (1976), Antonino Cattaneo undertook research in Neurobiology at Scuola Normale Superiore with Lamberto Maffei, working on the encoding of visual information by cells of the the visual cortex (1977-1980). He then worked at the CNR Institute of Cell Biology with Rita Levi Montalcini and Pietro Calissano on the molecular mechanisms of neuronal differentiation by Nerve Growth Factor (1981-1984) and at the MRC Laboratory of Molecular Biology (Cambridge UK) (1985-1989) with Cesar Milstein and Michael Neuberger, where he demonstrated the experimental strategy of ectopical antibody expression targeted to different subcellular compartments, for protein interference in the nervous system and other biological systems. From 1991 he was Full Professor of Biophysics at the International School for Advanced Studies (SISSA) in Trieste, where as Head of the Biophysics Sector and Deputy Director he was involved in setting up from scratch SISSA Neuroscience Program. From 2004 he assisted Rita Levi-Montalcini in launching the European Brain Research Institute, for which he served as the Scientific Director, before joyning Scuola Normale Superiore in 2009. He is a member of the European Molecular Biology Organization (EMBO) and of the Accademia delle Scienze dei XL, has been a Visiting Fellow at Trinity College (University of Cambridge, UK) and has received many international awards for his research. He is the author of over 180 peer reviewed pubblications in international scientific journals and an inventor on several biotechnology patents, based on his research, all of which have been industrially exploited.
His research led to i) the development of the intrabody protein silencing technology, ii) the discovery of proNGF/NGF imbalance as an unpstream driver mechanism for Alzheimer’s neurodegeneration, iii) the development of innovative neurotrophic factor based therapies for neurodegenerative diseases. Two humanized recombinant antibodies developed in his laboratory are currently under clinical testing in man.
His current research aims at deciphering the molecular and cellular mechanisms that lead to neurodegeneration, at studying protein misfolding in living cells and at identifying new targets for the development of new therapies for neurodegenerative diseases (most notably Alzheimer’s disease), based on these mechanisms. A strong interest in his research is dedicated to the development of new technologies and experimental strategies for intefering with protein function in living neurons in a spatially and temporally precise fashion (intrabodies). More details in BioSNS Laboratory.

Topics
Mammalian Synthetic Biology, Cell-based therapies for intractable diseases, chimeric antigen receptor (CAR)-T cells.

Biography

Dr. Yvonne Chen is an Associate Professor of Microbiology, Immunology, and Molecular Genetics at the University of California, Los Angeles. Prior to joining UCLA in 2013, Dr. Chen was a Junior Fellow in the Harvard Society of Fellows. She received her B.S. in Chemical Engineering from Stanford University and her Ph.D. in Chemical Engineering from the California Institute of Technology.  She performed postdoctoral research at the Seattle Children’s Research Institute and the Department of Systems Biology at Harvard Medical School. The Chen lab’s work on engineering next-generation T-cell therapies for cancer has been recognized by the NIH Director’s Early Independence Award, the NSF CAREER Award, the Hellman Fellowship, the ACGT Young Investigator Award in Cell and Gene Therapy for Cancer, the Mark Foundation Emerging Leader Award, and the Cancer Research Institute Lloyd J. Old STAR Award. Dr. Chen is also a Member Researcher in the Parker Institute for Cancer Immunotherapy.

Topics
Synthetic Biology, Chemical Complementation & Ribosome Chemistry

Biography

Virginia W. Cornish graduated summa cum laude from Columbia University with a B.A. in Biochemistry in 1991, where she did undergraduate research with Professor Ronald Breslow. She earned her Ph.D. in Chemistry with Professor Peter Schultz at the University of California at Berkeley and then was a Postdoctoral Fellow in the Biology Department at M.I.T. under the guidance of Professor Robert Sauer. Virginia joined the faculty of the Chemistry Department at Columbia in 1999, where she carries out research at the interface of chemistry and biology, and was promoted to Associate Professor with tenure in 2004 and then Professor in 2007. Her laboratory brings together modern methods in synthetic chemistry and DNA technology to expand the synthetic capabilities of living cells. Her research has resulted in 59 research publications and several patents and currently is supported by multiple grants from the NIH and NSF. Virginia has been recognized for her research by awards including an NSF Career Award (2000), a Sloan Foundation Fellowship (2003), the Protein Society Irving Sigal Young Investigator Award (2009), and the American Chemical Society Pfizer Award in Enzyme Chemistry (2009)

All Talks by Virginia Cornish

Lecture 1: Expanding the Synthetic Capabilities of Yeast

In vitro directed evolution allows biomolecules with new and useful properties to be engineered—mimicking natural evolution on an experimentally accessible time scale by creating large libraries of DNA mutants using PCR and then carrying out a high-throughput assay for variants with improved function. To provide a breakthrough in the complexity of libraries that can be readily searched experimentally for synthetic biology and to allow systems to be directly engineered in the cell, my laboratory is engineering S. cerevisiaeso that both the mutagenesis and selection steps of directed evolution can be carried out entirely in vivo, under conditions of sexual reproduction. We have built a modular chemical complementation assay, which provides a selection for diverse chemistry beyond that natural to the cell using themes and variations on the yeast two-hybrid assay. In addition, we devised a heritable recombination system, for simultaneous mutagenesis and selection in vivounder conditions of sexual reproduction. Finally, we have begun to utilize these mutagenesis and selection technologies to engineer yeast to carry out new functions themselves ranging from being a biosensor, to a therapeutic, to a self-organizing community.

Lecture 2: TMP-Tag: A Chemical Surrogate to the Fluorescent Proteins for Live Cell Imaging

The fluorescent proteins revolutionized our ability to study protein function directly in the cell by enabling individual proteins to be selectively labeled through genetic encoding of a fluorescent tag.  As researchers seek to make increasingly sophisticated dynamic measurements of protein function in the cell to unravel molecular mechanism, we designed a chemical tag to combine the advantages of genetic encoding with a modular organic fluorophore.  With TMP-tag, the protein of interest is tagged with E. coli dihydrofolate reductase, which can subsequently be labeled with a cell permeable trimethoprim-fluorophore conjugate.  Here we demonstrate that TMP-tag is a robust cellular reagent.  We present recent results exploiting the modular nature of the chemical tag to generate TMP-tags for specific applications in single-molecule, super-resolution, and multi-color imaging.  We look forward to innovations at the interface of chemical tag technology and spectroscopy for biological imaging.

Topics
Human cancer genetics, microRNA

Biography

Prof. Carlo M. Croce is an Italian-American molecular geneticist and professor of medicine at Ohio State University. He is the director of Human Cancer Genetics, Chairman of Molecular Virology, Immunology and Medical Genetics, and director of the Institute of Genetics at The Ohio State University Comprehensive Cancer Center. He is also professor of medical oncology at the University of Ferrara School of Medicine.

Prof. Croce has made major contributions to the understanding of the specific genetic bases of specific cancers. He is a pioneer in the unraveling of the molecular basis of a number of lymphoma and leukemia cancers. Mastering both cytogenetics and molecular biology, he identified the role of major oncogenes as drivers of cancer development, progression and resistance to therapy. His studies also demonstrated the role of micro RNAs in tumor pathogenesis. His numerous findings in cancer enable precise cancer diagnosis, individualized targeting of therapy and the development of novel rationally designed anti-cancer drugs.
Among his many awards he received, the Charles S. Mott Prize from the General Motors Cancer Research Foundation (1993,) the Scientific Excellence in Medicine Award from the American-Italian Cancer Foundation (1997), the Chauncey D. and Elizabeth W. Leake Speaker Award in 2014 and in 2015 the Outstanding Investigator Award from the National Cancer Institute. He was awarded by the American Association for Cancer Research both the G.H.A. Clowes Memorial Award in 2006, and the Margaret Foti Award in 2017.

In 1999, Prof. Croce received the Raymond Bourgine Award and Gold Medal of Paris, and in 2000, the Honor of Merit of the Italian Republic. He was honored with The Henry M. Stratton Medal by the American Society of Hematology in 2007.

Prof. Croce is a member of The National Academy of Sciences, USA, the National Academy of Medicine, the Institute of Medicine of the National Academies, and the National Academy of Inventors. He is a Fellow of the American Academy of Arts and Sciences, and the American Association for the Advancement of Science.

Filippo Drago

University of Catania, Italy

Biography

Filippo Drago is Full Professor of Pharmacology and Chairman of the Biomedical and Biotechnological Sciences at the University of Catania. He is Chairman of the Master in Regulatory Disciplines and President of the Research and Consultancy Activity Centre for HTA and Drug Regulatory Affairs at the University of Catania. He was Member of the Scientific Committee and of the Committee for Prices and Reimbursement of the Italian Agency of Medicines.

His basic research activity has been directed to different fields of Pharmacology ranging from Neuropsychopharmacology to Ocular Pharmacology and has focused on several topics such as endocannabinoids, neuropeptides, and the pharmacological treatment of neuropsychiatric diseases such as schizophrenia, major depression and Alzheimer’s disease.

He introduced the “success fee” as a managed entry agreement in the negotiation procedures of the Italian Agency of Medicine. In the field of Clinical Pharmacology, he studied the value-based pricing of anti-cancer drugs and the management of pain therapy.

Topics
Synthetic Genomics, Synthetic Biology, Genome Engineering, Biotechnology

Biography

Tom Ellis is Professor in the Department of Bioengineering at Imperial College London researching on synthetic biology and synthetic genomes. Before joining Imperial in 2010, he was a PhD at Cambridge and postdoc at Boston University, USA, in one of the field’s founding groups under Prof James J. Collins. Dr Ellis is leader of the UK-funded project to build a synthetic yeast chromosome for the international synthetic yeast project (Sc2.0). He co-leads the teaching of Imperial’s synthetic biology undergraduate module and has supervised 4 of the UK’s most successful iGEM teams. His research focuses on developing the foundational tools for accelerating and automating design-led synthetic biology, focusing on research projects in yeast (S. cerevisiae) and E. coli model organisms, as well as industrially-relevant interesting microbes such as Acetobacter, Geobacillus and Bacillus.

Rodrigo Ledesma-Amaro

Department of Bioengineering, Imperial College London, UK
Topics
Metabolic Engineering

Biography

Rodrigo Ledesma-Amaro obtained his PhD at the University of Salamanca under the supervision of Prof. Jose Luis Revuelta, the head of the metabolic engineering group. The PhD thesis is about systems metabolic engineering of A. gossypii for the production of vitamins, nucleosides and lipids. It combines modeling, synthetic biology, systems biology and metabolic engineering techniques and it produced numerous research papers and industrial patents (being currently used by BASF). Before that, Rodrigo coursed an MSc in Microbial Biotechnology at the Universidad Autonoma de Madrid and two undergraduate degrees (Biotechnology and Chemical Engineering) at the University of Salamanca. During his PhD, Rodrigo was a visiting researcher at Prof. Jens Nielsen’s group at Chalmers University of Technology (Sweden), at Prof. Jean-Marc Nicaud at INRA (France) and at Prof. Kamisaka’s group at AIST (Japan).

After the PhD, he moved to France thanks to an Agreenskills Marie Curie Fellowship and he performed his postdoc in the group of Jean-Marc Nicaud. Most of his postdoctoral research work was done in the oleaginous yeast Yarrowia lipolytica. During those years, Rodrigo engineered this organism to 1) produce different compounds (lipids, lipid-derived chemicals, carotenoids, etc), 2) to be able to use low-cost carbon sources such as lignocellulosic materials or starch and 3) to facilitate the recovery of the products by engineering lipid secretion. During the postdoc, Rodrigo has been teaching synthetic biology related subjects at SUP biotech.

Rodrigo Ledesma-Amaro is leading a research group at the interface of synthetic biology and metabolic engineering. His research lab is based in the Department of Bioengineering and the Center for Synthetic Biology and Innovation at Imperial College London.

All Talks by Rodrigo Ledesma-Amaro

Lecture 1: Engineering microbial metabolism for a bio-based economy

Synthetic biology has emerged as a novel discipline that tries to engineer biology in a more controllable, predictable and standardize manner. Bringing such characteristics to microbial systems allow us to expand the tools available to engineering metabolism in a more powerful way. This talk will present through some examples, how cutting-edge synthetic biology tools such as combinatorial assembly methods or CRISPR can be used to improve microbial bioproduction.

Lecture 2: Synthetic microbial communities for biotechnology and biomedicine

After several decades of engineering microbes for biotechnological applications, we have realized that overengineer strains often present undesirable features that limit the improvement of current production systems. Moreover, natural systems evolve as ecosystems and not as an individual to allow better performance in the environment. The use of microbial communities in the food and feed industry is clearly effective and it is responsible the most of our fermentable products. Now, thanks to synthetic biology we can engineer microbial communities in a way not possible in single organisms. In this talk, the concepts and tools to create synthetic communities will be discussed and applications of engineered communities will be presented.

Topics
Synthetic Biology, Engineering Plant Biology, Recoding Regulation, Recoding Plant Metabolism

Biography

Nicola Patron is a molecular and synthetic biologist interested in the natural and engineered transfer of genetic material between genomes of different species. Her lab is focused on engineering photosynthetic organisms for industrial biotechnology and crops that are healthier to consume and less environmentally damaging to cultivate.

Nicola obtained her PhD in plant molecular biology studying recombination between viruses and viral transgenes inserted into plant genomes. In post-doctoral research at The John Innes Centre, U.K. and The University of British Columbia, Canada she studied the impact that genes transferred from endosymbionts have on cellular metabolism and function, and evolution of endosymbiont genomes. From 2009-2013 Nicola was based in Melbourne, Australia leading a plant molecular biology group working with industry. Achievements included precision genome editing and targeted gene transfer with programmable nucleases. In 2013, Nicola returned to the UK to head a new Synthetic Biology venture at The Sainsbury Laboratory in Norwich before moving to EI.

As recipient of a 2015 SynbioLEAP fellowship, Nicola was recognised as an emerging leader in synthetic biology with a vision and aspiration to shape biotechnology for the public good. She is particularly interested the societal impacts of synthetic biology and the complex intellectual property issues that surround genetic sequences, DNA and natural products. Nicola is an advocate of responsible and ethical innovation and of open-source tools for biotechnology. She is also active in promoting diversity and inclusivity in science.

Topics
Systems Biology, Biomedical Artificial Intelligence, Probabilistic Modeling of Biological systems.

Biography

Guido Sanguinetti is a Reader in Machine Learning in the Institute for Adaptive and Neural Computation at the School of Informatics, University of Edinburgh. My interests focus on probabilistic modelling of biological systems, with particular emphasis on inference in dynamical systems. For more details of my research interests, including live projects and possible PhD projects, please see the research projects page. I’m also a potential supervisor on the newly funded EPSRC Centre for Doctoral Training in Data Science, see Data Science Ph.D. programme.

Speakers

Cristina Di Primio

Scuola Normale Superiore, Pisa, Italy

Simonetta Lisi

Scuola Normale Superiore, Pisa, Italy

Laura Marchetti

Italian Institute of Technology, Italy