SSBSS 2018 – 5th International Synthetic & Systems Biology Summer School

24 Speakers, 4 Tutors for 100 Attendants

5th International
Synthetic & Systems Biology
Summer School

July 25-29, 2018

Certosa di Pontignano

Siena

Italy

Tuscany - Hills

Certosa di Pontignano - School Venue

Florence - Old Bridge

Pisa - Leaning Tower

Certosa di Pontignano - School Venue

About the School

Recent advances in DNA synthesis have increased our ability to build biological systems. Synthetic Biology aims at streamlining the design and synthesis of robust and predictable biological systems using engineering design principles. Designing biological systems requires a deep understanding of how genes and proteins are organized and interact in living cells: Systems Biology aims at elucidating the cellular organization at gene, protein and network level using computational and biochemical methods.

The Synthetic and Systems Biology Summer School (SSBSS) is a full-immersion five-day residential summer school at the Certosa di Pontignano (Siena – Tuscany, Italy) on cutting-edge advances in systems and synthetic biology with lectures delivered by world-renowned experts. The school provides a stimulating environment for students (from Master students to PhD students), Post-Docs, early career researches, academics and industry leaders. Participants will also have the chance to present their results, and to interact with their peers, in a friendly and constructive environment.

Given the rapidity with which this field moves, it is challenging for both newcomers and experts alike to stay updated with all of the latest advances. The goal of this summer school and workshop is to bring together scientists from academia and industry with diverse but relevant expertise in a setting conducive to discussion of new results and potential collaborative efforts. Invited talks will cover a wide range of topics ranging from fundamental basic science through to applications. Attendees of this workshop will have the opportunity to hear about the latest findings in this fast-paced field and to establish collaborations with scientists who have complementary expertise.

The Summer School will involve a total of 36-40 hours of lectures, according to the academic system the final achievement will be equivalent to 8 ECTS points for the PhD Students and the Master Students attending the summer school; during the summer school the students will tackle homeworks/projects.

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Topics

Sessions integrate the recent achievements made in the fields of synthetic biology, systems biology, control engineering for synthetic biology, biochemical engineering, synthetic enzyme, evolutionary engineering, integrated omics, tools and methods, and emerging techniques, healthcare, biofuels, chemicals and materials, biologics, microbial and mammalian systems, and other disciplines and applications.

Call for Abstract/Poster submissions should be related to the following areas of synthetic biology, systems biology, genome and genetic engineering:

Computational Synthetic Biology
Genetic Engineering
Metabolic Engineering
Reading and Writing Genomes
Synthetic Genomes
Synthetic Circuits and Cells
Artificial Tissues and Organs
Genomically Recoded Organisms
Genome Design
Pathway Design
Biological Design Automation and Biological CAD

Computational Systems Biology
Genome Engineering
Cellular Systems Biology
Experimental Synthetic Biology
Computational Synthetic Biology
Stochastic Gene Regulation
Gene Signaling
Quantitative Molecular Biology
High-throughput Techniques
Biological Engineering
Industrial Synthetic and Systems Biology

Registration Deadline: Thursday May 31, 2018
Oral/Poster Presentation Submission Deadline: Thursday May 31, 2018
Notification of Decision for Oral/Poster Presentation: June 15, 2018

Early Registration: Thursday May 31, 2018
Late Registration: From June 1, 2018

Keynote Speakers

Patrick Yizhi Cai

University of Manchester, UK

Andrea Califano

Columbia University, USA

Barbara Di Ventura

University of Freiburg, Germany

John Glass

J. Craig Venter Institute, USA

Philipp Holliger

MRC Laboratory of Molecular Biology, Cambridge, UK

Dagmar Iber

SIB & ETH Zurich, Switzerland

Jonathan Karr

Icahn School of Medicine at Mount Sinai, USA

Jens Nielsen

Chalmers University of Technology, Sweden

Laura Riva

Wellcome Trust Sanger Institute, Cambridge, UK

Kelly V. Ruggles

Department of Medicine, NYU, USA

Pamela Silver

Harvard Medical School, Dept of Systems Biology, Harvard University, USA

Harris Wang

Columbia University, USA

Ron Weiss

MIT, USA

Speakers

Matteo Barberis

University of Amsterdam, The Netherlands

Barbara Di Camillo

University of Padova, Italy

Cristina Di Primio

Scuola Normale Superiore, Pisa, Italy

Simone Furini

University of Siena, Italy

Emanuele Domenico Giordano

University of Bologna, Italy

Rodrigo Ledesma-Amaro

Imperial College London, UK

Simonetta Lisi

Scuola Normale Superiore, Pisa, Italy

Laura Marchetti

Italian Institute of Technology, Italy

Velia Siciliano

Italian Institute of Technology, Italy

Lectures

Day 1

25 Jul 2018

14:30 - 15:20

Andrea Califano

Lecture 1: Reverse Engineering and Interrogating Cellular Networks

Andrea Califano

15:20 - 16:10

Andrea Califano

Lecture 2: Systems Biology: the Bench to Bedside Travel Guide

Andrea Califano

Day 2

27 Jul 2018

09:00 - 09:50

Patrick Yizhi Cai

Lecture 1: Design and Construction of Synthetic Yeast Chromosomes

In this lecture, I will discuss the design principles of the synthetic yeast genome, and approaches to construct the synthetic chromosomes including methods to debug the design problems.

Patrick Yizhi Cai

12:00 - 12:50

Patrick Yizhi Cai

Lecture 2: SCRaMbLEing the Synthetic Yeast Genome

This lecture we will focus on the SCRaMbLE (Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution) method to evolve the synthetic yeast strains for novel phenotypes.

Patrick Yizhi Cai

09:50 - 10:40

Barbara Di Ventura

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...

Barbara Di Ventura

11:10 - 12:00

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...

Barbara Di Ventura

Day 3

28 Jul 2018

09:00 - 09:50

John Glass

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...

John Glass

12:00 - 12:50

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...

John Glass

Day 4

26 Jul 2018

09:50 - 10:40

Philipp Holliger

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...

Philipp Holliger

12:00 - 12:50

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...

Philipp Holliger

Day 5

29 Jul 2018

09:00 - 09:50

Dagmar Iber

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...

Dagmar Iber

09:50 - 10:40

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...

Dagmar Iber

Day 6

28 Jul 2018

09:50 - 10:40

Jonathan Karr

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....

Jonathan Karr

14:30 - 15:20

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...

Jonathan Karr

Day 7

25 Jul 2018

09:50 - 10:40

Jens Nielsen

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...

Jens Nielsen

11:10 - 12:00

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...

Jens Nielsen

Day 8

27 Jul 2018

14:30 - 15:20

Laura Riva

Lecture 1: The Search for Genetic Drivers of Cancer

The remarkable efforts recently carried out to fully understand the mutational landscape of various cancer types have motivated the development of many computational approaches to interpret cancer genomic data. This...

Laura Riva

15:20 - 16:10

Laura Riva

Lecture 2: Mutational Signatures in Environmental Carcinogen-Induced Tumours

By analysing the catalogue of the somatic mutations present in several cancer genomes it is possible to understand the mutational processes active in different tumours. This session will introduce some...

Laura Riva

Day 9

26 Jul 2018

14:30 - 15:20

Kelly V. Ruggles

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...

Kelly V. Ruggles

16:40 - 17:30

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...

Kelly V. Ruggles

09:00 - 09:50

Pamela Silver

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...

Pamela Silver

11:10 - 12:00

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...

Pamela Silver

Day 10

28 Jul 2018

11:10 - 12:00

Harris Wang

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...

Harris Wang

15:20 - 16:10

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...

Harris Wang

Day 11

25 Jul 2018

09:00 - 09:50

Ron Weiss

Lecture 1: Synthetic Biology: from Parts to Complex Systems

Ron Weiss

12:00 - 12:50

Ron Weiss

Lecture 2: Mammalian Synthetic Biology: Scientific and Therapeutic Perspectives

Ron Weiss

Talks

Day 1

26 Jul 2018

15:20 - 16:10

Matteo Barberis

Deciphering Yeast Physiology by a Multi‐Scale Framework Integrating Cell Cycle and Metabolism

Cell division 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 metabolism fluctuate periodically...

Matteo Barberis

Day 2

27 Jul 2018

17:30 - 18:20

Barbara Di Camillo

MAST: A Multi-Agent based Spatio-Temporal Model of the Interaction between Immune System and Tumor Growth Feeded with Single-Cell Data

In recent years, single-cell technologies, both at imaging and sequencing level, have given the possibility to observe how tissues and organs are spatially and temporally organized as a system of...

Barbara Di Camillo

Day 3

28 Jul 2018

16:40 - 17:30

Cristina Di Primio

Designing Biosensors to Monitor Protein Folding and Aggregation

A growing number of diseases seem to be associated with toxic deposition of protein aggregates. Some of these diseases — such as Alzheimer’s disease— have been recognized for a long...

Cristina Di Primio

17:30 - 18:20

Simone Furini

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,...

Simone Furini

Day 4

25 Jul 2018

17:30 - 18:20

Emanuele Domenico Giordano

(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...

Emanuele Domenico Giordano

Day 5

27 Jul 2018

16:40 - 17:30

Rodrigo Ledesma-Amaro

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...

Rodrigo Ledesma-Amaro

Day 6

29 Jul 2018

11:10 - 12:00

Simonetta Lisi

PISA Technology : a Novel Tool to Select Intrabodies to Target the Post-Translationally Modified Proteome in the Cell

The complexity of the proteome greatly outnumbers that of the genome and the diversity is mainly due to post-translational modifications (PTMs). Indeed, PTMs are fundamental regulators of many pathways and...

Simonetta Lisi

Day 7

26 Jul 2018

17:30 - 18:20

Laura Marchetti

Talk: TBA

Laura Marchetti

Day 8

25 Jul 2018

16:40 - 17:30

Velia Siciliano

Designing New Tools for Synthetic Biology in Mammalian Cells

Synthetic Biology aims at developing and applying engineering tools to sense and process endogenous information and to implement robust responses to intracellular conditions. Mammalian synthetic networks build on the conjugation...

Velia Siciliano