5th International Synthetic & Systems Biology Summer School   |   Certosa di Pontignano - Siena - Tuscany - Italy   |  July 25-29, 2018

Lectures

Lectures

Day 1
23 Jun 2018

Lecture 1: Optogenetic Control of Protein Nuclear Trafficking

Intracellular processes are controlled in many ways. One way consists in placing proteins in the right place at the right time. For instance, transcription factors (TFs) are often kept cytoplasmic...
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Barbara Di Ventura

Lecture 2: Split Inteins as Synthetic Biology Tool to Control Biological Processes

Biological processes are carried out by complex networks of interacting proteins that continuously adapt to cellular environment and external stimuli with structural changes, which lead to new functional properties and...
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Barbara Di Ventura

Lecture 1: Design, Construction, and Analysis of a Synthetic Minimal Bacterial Cell

The minimal cell is the hydrogen atom of cellular biology. Such a cell, because of its simplicity and absence of redundancy would be a platform for investigating just what biological...
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John Glass

Lecture 2: Building and Grand Scale Engineering of Eukaryotic Viral Genomes and Chromosomes

Over the last 5 years, the JCVI Synthetic Biology team, which is best known for construction of bacterial cells programmed with synthetic genomes, has also taken on projects that required...
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John Glass

Lecture 1: Synthetic Genetics I: beyond DNA and RNA

Synthetic biology seeks to probe fundamental aspects of biological form and function by construction (i.e. resynthesis) rather than deconstruction (analysis). Synthesis thus complements reductionist and analytic studies of life, and...
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Philipp Holliger

Lecture 2: Synthetic Genetics II: Replicating RNA with RNA

A critical event in the origin of life is thought to have been the emergence of an RNA molecule capable of self-replication as well as mutation, and hence evolution towards...
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Philipp Holliger

Lecture 1: From Networks to Function – Computational Models of Organogenesis

One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the...
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Dagmar Iber

Lecture 2: Physical Driving Forces of Epithelial Organisation

In the second lecture, I will focus on epithelial organisation. Epithelial cells adhere tightly, forming a polygonal lattice. The resulting cell packing exhibits striking universal regularities, regardless of the organism...
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Dagmar Iber

Lecture 1: An Introduction to Whole-Cell Modeling

Whole-cell (WC) computational models that predict phenotype from genotype are needed to help bioengineers rationally design bacteria and other organisms. Despite their potential, numerous challenges remain to achieve WC models....
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Jonathan Karr

Lecture 2: Scalably Building, Simulating, Calibrating, and Validating Whole-Cell Models

Recently, we and others demonstrated the feasibility of WC models by developing the first model that captures the function of each individual gene. However, it took over 10 person-years to...
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Jonathan Karr

Lecture 1: Systems Biology of Yeast Metabolism: Big Data Generation

Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use a holistic approach for studying metabolism. With the advancement of different omics technologies...
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Jens Nielsen

Lecture 2: Systems Biology of Yeast Metabolism: Modeling

Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies, the use of mathematical models in biology is...
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Jens Nielsen

Lecture 1: Multiomics Integration

With the wealth of omics data that is rapidly and continuously being generated, new computational methods are required to interpret data-centric studies aiming to integrate multiple omics data types. This...
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Kelly V. Ruggles

Lecture 2: Informing Cancer Biology using Computational Proteogenomics

Cancer has been well established as a disease of the genome, with a subset of somatic mutations frequently acting as drivers of tumor progression, and thereby influencing diagnosis, prognosis and...
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Kelly V. Ruggles

Lecture 1: Designing Biology for Health

Here, I will present background on health-related problems that can be addressed by synthetic and systems biology. I will present a personal case study on development of a cancer therapeutic...
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Pamela Silver

Lecture 2: Designing Biology for Sustainability

One major thrust for synthetic biologists is to harness the ability natural chemical processes to create a more sustainable industry for chemicals, consumables, materials and energy. I will cover new...
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Pamela Silver

Lecture 1: Multiplex Genome Engineering: Methods and Applications

Recent advances in genome engineering have enabled an unprecedented scale, accuracy, and ease to manipulate bacterial and eukaryotic genomes. In this lecture, I will discuss key contemporary methods for genome...
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Harris Wang

Lecture 2: Cellular Recording and Memory: Approaches and Uses

Recording environmental and biological information across cell populations over time enables new systems for biosurveillance and cellular sentinels. In this lecture, I will discuss the framework to chronicle cellular events...
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Harris Wang

Talks

Day 1
23 Jun 2018

Deciphering Cell’s Robustness by a Multi-scale Framework Integrating Cell Cycle and Metabolism in Budding Yeast

Cell cycle and metabolism are coupled networks. Cell growth and division require synthesis of macromolecules which is dependent on metabolic cues. Conversely, metabolites involved in storage carbon-, lipid- and nucleotide...
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Matteo Barberis

Talk: TBA

Barbara Di Camillo

Talk: TBA

Cristina Di Primio

Modelling noise in the design of synthetic gene networks

Random variability in gene expression (noise) might severely impact on cellular behaviours. At odds with other engineering applications, where noise is usually associated with a deterioration of the functional properties,...
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Simone Furini

(Synthetic) gene circuit architecture control of microbial phenotypic variability

The application of synthetic biology tools to investigate phenotypic variability has provided insight into the regulatory mechanisms that tune biological noise in natural networks. The efficiency of these mechanisms has...
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Emanuele Domenico Giordano

Synergies between synthetic biology and metabolic engineering for improving bioproduction

Synthetic biology has emerged as a powerful discipline that facilitates the manipulation of cells in a more reliable, predictable and standardized manner. Metabolic engineering aims to modify metabolic pathways to...
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Rodrigo Ledesma-Amaro