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EMBO Practical Course

Computational analysis of protein-protein interactions: Sequences, networks and diseases

05 – 10 November 2018 | Rome, Italy

  • Registration Deadline
  • 27 August 2018
  • Abstract Submission Deadline
  • 27 August 2018
  • Chosen Participants Will Be Notified By
  • 07 September 2018
  • Payment Deadline
  • 17 September 2018

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About the Practical Course

Recent growth in protein-protein interaction (PPI) data provides massive opportunities for gaining biological insights, including the characterization of protein complexes and pathways. Many tools and resources exist to analyse and disseminate these data, but often bench scientists are not trained in them. In particular, they need to learn how to explore, manage, and interconnect these datasets.

Given the importance of such techniques in several biomedical science disciplines, there is a major need for training in relevant tools without which bench scientists risk missing important insights from their own data. This EMBO Practical Course aims to train participants in bioinformatics techniques for gaining a network perspective on PPIs, predicting and analysing them, highlighting differences between globular (protein "domains") and non-globular (intrinsically disordered peptide) modules, and working with large datasets. Ideal participants for this course are bench scientists who are working to obtain data related to protein-protein interactions, or already have such data they want to analyse. One of the focuses of this course will be teaching the importance of PPIs in biological systems, and how bioinformatics tools can be harnessed for understanding and controlling physiological states and when these states are perturbed by disease. Keeping these aspects into consideration, disease datasets are integrated into the training materials.

We will teach state-of-the-art bioinformatics tools, including Cytoscape, STRING, ELM, IUPRED and Chimera2. We will focus on integrating experimental interaction data (XL-MS, Bio-ID) into PPI networks. Many of the publicly available tools are highly interconnected and we will show participants how to take advantage of this integration. This course has been offered with different focuses since 2014, through which we have pioneered training in bioinformatics tools associated with the diversity and importance of PPIs involving various protein modules. The content of the course will be similar to that of an EMBO Practical Course taught in Budapest in May 2016. These pages contain all the material taught during the course, you may find it useful to look at this when deciding whether to apply for the course.

We initially focus on predicting PPI modules from protein sequences, highlighting differences (structure, function, and bioinformatics) between globular protein "domains" and non-globular intrinsically-disordered peptide regions, the latter being rich in short protein-binding regions involved in signal transduction and other functions. Understanding the differing roles these modules play in PPIs is key to unravelling the dynamism and complexity of cellular systems. The course ends by focusing on large PPI datasets, emphasizing a network perspective.

The overall impact of the course is enhanced by giving the trainees opportunities to analyse their own data in the presence of expert trainers, who are also the developers of aforementioned tools. Significant time is allocated for trainees to apply the skills learnt in the course to their own data with the trainers in attendance.

 

Speakers

 

Programme

 

Registration

  • Registration Deadline
  • 27 August 2018
  • Abstract Submission Deadline
  • 27 August 2018
  • Chosen Participants Will Be Notified By
  • 07 September 2018
  • Payment Deadline
  • 17 September 2018

 

  • LOCAL EUR 150
  • STUDENT/POSTDOCS EUR 400
  • ACADEMIC EUR 550
  • INDUSTRY EUR 1000

Registration includes:

  • Accommodation (seven nights)
  • Course materials
  • Meals, coffee breaks
  • Social events, excursion

NOTE: Local registration does not include accommodation and evening meals apart from the social events.

Payment

Payment instructions will be sent to successful applicants once the selection procedure is complete.

Selection criteria

We expect that students will be actively conducting research in a field involving some or all aspects of the materials taught in the course. Thus, our selection criteria will focus on estimating the degree to which the students can use what is taught in the course, to be applied to their current research projects.

We will also look at the previous exposure students have had to bioinformatics and computational approaches to biology. We will select those most likely to understand the material presented bearing in mind that it is unlikely that students will have advanced bioinformatics experience.

We will provide a limited number of grants to cover travel expense and/or registration fee for a few eligible participants. Please tick the appropriate fields under the ‘registration’ section.

We will seek equity during the selection process by considering participants from diverse background, nationality and gender.

Abstract guidelines

We expect an abstract no more than 250 words explaining the current research work of the participants.

In addition, please attach a short CV and motivation letter (maximum 1 page each) with information on your previous and current research experiences and the relevance of computational biology in your work. The abstract will be evaluated both for the participation in the course and eligibility for the financial support of the candidates.

Poster specifications

We expect all course participants to present a poster (A0 size portrait format) describing their project at the course.

Travel grants

A limited number of travel grants are available for participants. Applicants do not need to apply separately for travel grants for this event but should indicate on the registration form if they wish to be considered for a travel grant. Selection of awardees is handled directly by the organizers who will notify all eligible participants. More information is available at EMBO Travel Grants' page.

Additional information

Trainees not resident in Rome will be provided double occupancy hotel accommodation in the vicinity of the main venue.

Please contact the organizers if you have any special need or queries regarding the logistics.

 

Contact

For all kinds of queries, please contact the organizers here: embo.ppi.2018@gmail.com

 

 

Venue

The National Research Council (CNR)

Piazzale Aldo Moro, 7

00185 Rome, Italy

Sapienza University,

Piazzale Aldo Moro, 5

00185 Rome, Italy

Accommodation

The accommodation is located at a walkable distance from the venue. It will be made sure that the double occupancy rooms have an individual bed for each participant.

Participants with special needs will be provided with the taxi/required service.

Transport

Rome can be reached easily and cheaply from neighbouring countries by train and air. The course venue - National Research Council (CNR) is approximately 30 km from the International airports and 2 km from the main train stations (Termini and Tiburtina). The venue is located close to the Sapienza university campus and is easily reachable by public transportation.

About the Area

Besides being one of the preferred tourist attractions, Rome is an international city that harbours several excellent life-science research centres. Running the course at this location will increase the opportunities for the young scientists to participate in the course in a new (for this course) region of Europe.

Our reasons for selecting CNR as a venue are its state-of-the-art facilities, excellent logistical and IT-support, and its accessibility that makes it suitable to hold seminars and workshops.

Supporters

Molecular Systems Biology