Mathilde GRELON, Loïc LEPINIEC, Vincent SAUVEPLANE.

The course is mainly organized on a practical workshop and interactive teaching basis format, follow-up with exercise and presentation of the results obtained during the practical sessions. Total hours of practical work: 50 Total number of hours of tutorials: 25.

The objective is a refresher course (or the acquisition of new knowledge depending on their previous experience) in basic knowledge around two fundamental pillars:
“Basics in Molecular Biology and Genetics” – 2 weeks
“Basics in primary metabolism (Carbon & Nitrogen) - 1 week
At the end of the course, students will be able to:
- Strengthen their knowledge in basic knowledge of the proposed topics
- Present a scientific study: explain the process and summarise the main results and conclusions; know how to communicate a scientific message;
- Implement the basic approaches in Genetics and Molecular Biology and Physiology.

Christine DILLMANN, Judith LEGRAND, Elodie MARCHADIER.

Personal project work with oral presentation. Training through practice. Total hours of practical work: 25.

To acquire basic notions in statistics for the processing of data sets from biology experiments.
At the end of the course, students will be able to:
Understand the principles of statistical testing.
Know how to make graphical representations in R and choose the right statistical test(s) in R from simple data sets.
Know how to identify the complexity of a dataset.

Jean-Denis FAURE, Isabelle FUDAL, Christine LELANDAIS.

During this course, students will be given a data set to analyse in depth. The teaching is based on active pedagogy, accompanied by a scientific tutor who will have his or her own dataset to be analysed.

During this course, students will learn to :
• Exhaustively search and synthesise the information available in public databases
(bibliographic, genomic, transcriptomic, proteomic data, etc.)
• The use of certain software to analyse these data
• Identify a relevant biological question from their synthesis
• Design and present a mini research project to answer this biological question and to deepen
the knowledge about it.

Matthieu JULES, Vincent SAUVEPLANE, Wolfram LIEBERMEISTER.

The course module is organized in 15h of lectures and 10h of tutorials to introduce knowledge and methodological tools.

In recent years the dynamics of biological systems has been increasingly described using concepts
and terminology borrowed from economics: cells face trade-offs between different strategies for
survival; metabolism can be viewed as a resource allocation problem; biomolecules can be associated
with a “value” within the free energy “market” of the cell, etc. These concepts indicate the
emergence of a new way of thinking about problems in biology.
In this course, we will explore biological questions that can be addressed using concepts of resource
allocation, efficiency and optimality on (1) genome-scale cellular metabolism, (2) gene expression
and protein synthesis, (3) cellular fitness and (4) game theory in cellular and multicellular biology.
At the end of the course, students will be able to:
•Explain the principles of cellular economics and resource allocation in living systems
•Analyse simple growth strategies of living systems in a competitive environment
•Describe simple models and identify their advantages and limitations.

Matthieu JULES, Iona POPESCU, Cécile GASSE.

The course module is organized in 16h of lectures and 9h of tutorials to introduce knowledge and methodological too.

The aim of this module is to give students perspectives in Synthetic Biology, a field where novel
biological and biologically based parts, devices and systems are (re)designed and constructed to
perform new functions that do not exist in nature.
Explain the strategies employed in the field of metabolic engineering for the production of
sustainable biobased compounds
• Analyse simple synthetic regulatory circuits
• Explain the principles of genome engineering techniques and illustrate the synthetic genomics
approaches
• Describe several orthogonal systems and analyse their advantages and limitations
Thus, students will have a strategic vision on how to progress in the field of synthetic biology: from
the extraction of innovative knowledge from the available biological data to the transformation of
the data into new rational and useful knowledge.

Etienne DELANNOY, Véronique BRUNAUD, Marie-Laure MARTIN MAGNIETTE, Dario MONACHELLO, Jean BIGEARD, Florence GONNET.

25h of lectures and practicals tutorials.

Integrative approaches are key steps in the thorough exploitation of omics data and their translation
into knowledge. In this module, students will have courses on the architecture and the machinery of
the cell, and on the genome and epigenome organization. They will learn how to combine predictive
and experimental approaches to decode the genomic information through the structural and
functional annotation of genomes. The integration and the querying of heterogeneous data imply to
perfectly know their origin in order to take into consideration their quality, relevance and confidence
levels. The understanding of this approach is the basis of holistic analyses for systems biology.
Students will see different methods to produce transcriptome, ORFeome, proteome and interactome
resources and how to integrate them in modeling approaches to have new insights on cellular
processes.
On completion of the course, students will be able to :
have a good understanding of the challenges posed by integration of omics data. They should be
able to understand and summarize a scientific paper in the field.

Matthieu JULES, Vincent FROMION, Anne GOELZIER, Vincent SAUVEPLANE, Laurent TOURNIER.

The course module is organized in 16h of lectures and 9h of tutorials to introduce knowledge and methodological tools.

Global analyses (omics) currently generate large datasets that do not capture the complexity of living
systems. Systems Biology is an approach where omics data are integrated and exploited (compared)
through mathematical models of biological systems or sub-systems. The complexity of biological
systems and the diversity of issues to be considered require the use of different types of modelling.
In this course, students will explore a number of mathematical approaches to tackle biological issues
through the integration of "omics" data. The mathematical approaches include the methods known
as constraint-based modeling, i.e. flux balance analysis, resource balance analysis, but also tools
specific to the analysis of dynamic systems and Boolean systems.
On completion of the course, students will be able to :
• Understand and explain the challenges of using constraint-based modeling approaches to describe
cellular behaviors
• Summarize and present a scientific paper in the field.

Jean-Denis FAURE, Matthieu JULES, Vincent SAUVEPLANE.

This course adopts a reverse pedagogy approach in which the students themselves construct the course. In each session, students will evaluate each other. The “teacher” will be evaluated on the basis of his 2-hour lecture while the “students” will be evaluated through the 1-hour tutorial.

Systems biology (SB) is an attempt to understand cells (or other biological systems) as complex
systems by studying their basic building blocks and their interactions, and connecting this
reductionist view with a holistic, systemic perspective. To understand biological functions, it often
does not suffice to study single proteins, single genes, single cells, or single organism. Rather, the
ability of living matter to perform amazing tasks relies on an ensemble of actors acting collectively.
Those tasks, involving for example decision making or information processing, can thus be
understood only at the system level.
The Teach Systems Biology project has the ambition to train students in new concepts (at the
interface in life sciences) and teaching them how to communicate their knowledge (self-learning).
Briefly, following a short introduction lecture, students will have to prepare a 2-hour lecture and a 1-
hour tutorial on a sub-theme of SB for the whole class.
At the end of the course, students will be able to:
• Describe biological systems at the system level as a list of units and their interactions, or as a
combination of modules, and the resulting dynamics
• Self-evaluate their knowledge and ability to communicate on biological.

Christine LELANDAIS, Céline SORIN, Ioana POPESCU, Speakers (may change depending on the year).

The EU takes place over a period of 2 weeks. Lecture: Genome engineering technologies, synthetic biology and RNA interference: principles, underlying molecular mechanisms and applications. Excercices with examples of applications. An experimental and practical approach will be carried out on silenced transgenic plants.

The objectives of this course are:
1) to train students in genome engineering and editing methodologies, synthetic biology and
RNA-mediated technologies
2) to describe the molecular basis of the non-coding RNA-mediated gene regulation and DNA
repair/recombination mechanisms underlying these technologies
3) to present the envisaged developments and applications in the fields of plant production and
health
4) to reflect on the societal, environmental and ethical challenges associated with the development
of these biotechnologies.

Moussa BENHAMED, Marianne DELARUE, Yves DEVEAUX, David LATRASSE, Dao-Xiu ZHOU.

This course promotes an active and interactive pedagogical approach including hands-on experiments . - A reversed pedagogy approach where students will have to revise before the course the basic notions of plant development thanks to a bibliography and documentation that will be provided to them. - A practical laboratory approach where students will have all the equipment available to set up their own experiments in order to characterise developmental mutants.

The students will have to choose the most relevant workshops for the characterisation of a mutant that they have been given, on the basis of the information that the teaching team will provide them.
At the end of these workshops, they will have to make a presentation to the whole group.
The teaching team will be available to provide technical support to the students during the various workshops. The pedagogical objective of these workshops is to offer the students a scientific approach similar to that used in our laboratories, with the analysis of a genotype without preconceived ideas, the formulation of hypotheses, the implementation of various analysis methods, the synthesis and presentation of results, including, if possible, a statistical analysis, and the oral presentation of this work.
At the end of the course, students will be able to:
- To understand in a theoretical and practical way the development of plants and their adaptations
- To be able to formulate hypotheses and to set up an experimental approach to answer them
- To gain autonomy in learning recent methods of plant cellular and molecular analysis.

Benoît Alunni, Marie Dufresne, Martine Thomas, Axel de Zélicourt.

The course is mainly practical, organized on a research basis format. Additional teachings consist in tutorials, either connected with the research project (web based RNA-Seq data analysis - bioinformatics) or in round table format to interact on fundamentals of a scientific approach in plant research. Total hours of practical work: 42 Total number of hours of tutorials: 8 Total number of hours spent on personal projects: 10.

To provide students with a technical base and scientific reasoning enabling them to get into future laboratory internships with greater confidence, thanks to the conduct of a small research project involving various experimental approaches (plant pathology, plant culturing and phenotyping, molecular biology, cytology, manipulation of plant–associated microbes, bioinformatics). These approaches are based on model plants, under development or subjected to abiotic or biotic stresses.
At the end of the course, students will be able to:
- Design and implement a scientific approach to answer a biological question(s);
- Present a scientific study: explain the process and summarise the main results and conclusions; know how to communicate a scientific message;
- Implement the basic approaches in phytopathology;
- Exploit databases as well as bioinformatics tool platforms (reinforcement).

Marianne DELARUE , Matthieu JULES.

Owing to the plethora of excellent laboratories in plant and microbiological sciences, in the Saclay area, the students will have a large number of projects proposed by these teams. The Internship can be pursue either in the Saclay area, or elsewhere in France or abroad during at least 8 weeks.

At the end of the course, students will be able to:
- Putting into practice a research approach in the context of the study of plant and microbial systems.
- Experimenting and practicing under laboratory conditions and producing knowledge.
- Professional training activities.
- Analyse, inventory and interpret data and knowledge in order to produce a synthesis and explain it orally and/or in writing.
- Collaborate and intervene within a group.

Marianne DELARUE , Matthieu JULES.

Lab rotations consist of short stays of 1 or 2 weeks in a laboratory of our network to observe and integrate into an ongoing research project.

At the end of the course, students will be able to:
• Putting into practice a research approach in the context of the study of plant and microbial systems.
• Experiment and practice under laboratory conditions and produce knowledge.
• Professional training activities.

Marianne DELARUE , Matthieu JULES.

Owing to the plethora of excellent laboratories in plant and microbiological sciences, in the Saclay area, the students will have a large number of projects proposed by these teams for his or her Internship of 8 weeks..

At the end of the course, students will be able to:.