EpiViral Summer School 2023

Deciphering the Epitranscriptome: analysis of tRNA and mRNA modifications

RNA is a central player in life and to fulfil its various functions it is heavily modified. Modifications in all RNAs, including mRNA and tRNA, have a substantial impact on cellular homeostasis and a modification imbalance is connected to a plethora of human diseases, called modopathies. 

The summer school will focus on RNA modifications found in human mRNA and tRNA. During this 3 day course, participants will have the opportunity to learn how to isolate RNA from stable isotope-labeled cells, purify tRNA isoacceptors and mRNA. Participants will also learn how to analyze LC-MS/MS data of RNA hydrolysates and NAIL-MS experiments for modification quantification.

This course will include hands-on practical classes on standard and state-of-the-art RNA biology techniques, lectures from internationally renowned scientists, discussions, workshops and social activities in the wonderful city of Aveiro, Portugal.


Stefanie Kaiser

Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Germany

Pascal Giehr

Department of Organic Chemistry, LMU Munich, Germany

Matthias Schäfer

Center for Anatomy & Cell Biology, Medical University of Vienna, Austri

Robert Schneider

Institute of Functional Epigenetics (IFE), Helmholtz Munich, Germany


Day 1 | Monday, 4th September 2023
NAIL-MS and tRNA isoacceptor isolation

09h00 – 09h30Registration
09h30 – 10h00Course Introduction
10h00 – 10h45Introduction to RNA modifications
Stefanie Kaiser
10h45 – 11h00Coffee Break
11h00 – 12h00Finding new RNA methyltransferases and their function
Robert Schneider
12h00 – 13h00Lunch
13h00 – 13h15Introduction Practical Session I
Gregor Ammann
13h15 – 15h45Practical Session I
15h45 – 16h00Coffee Break
16h00 – 18h30Practical Session I
18h30 – 20h30Get together

Day 2 | Tuesday, 5th September 2023
MS data analysis and harvesting of RNA

09h00 – 10h00Introduction to Nanopore sequencing
Pascal Giehr
10h00 – 10h15 Introduction
Practical Session II
Max Berg
10h15 – 11h15Practical Session II
11h15 – 11h30Coffee Break
11h30 – 12h30TBA
Pascal Giehr
12h30 – 13h30Lunch
13h30 – 14h30Introduction to MS of RNA modifications
Stefanie Kaiser
14h30 – 14h45Break
14h45 – 15h00Introduction Practical Session III
Nur Yesiltac
15h00 – 16h30Practical Session III
16h30 – 16h45Coffee Break
16h45 – 19h00Practical Session III
19h00 – 23h00Dinner & Pub Quiz

Day 3 | Wednesday, 6th September 2023
mRNA preparation

09h00 – 10h00Can a Biologist (Really) Fix a Radio?: a Persistent Problem Impacting RNA Modification Research
Matthias Schäfer
10h00 – 10h15Introduction
Practical Session IV
Alexandre Vicente
10h15 – 11h15Practical Session IV
11h15 – 11h30Coffee Break
11h30 – 12h30tRNA-Derived Small RNAs (tsRNAs): Numbers, Molecular Interactions and Use of a ‘Waste Product’
Matthias Schäfer
12h30 – 13h30Lunch
13h30 – 13h45Introduction
Practical Session V
Alexandre Vicente & Jannick Schicktanz
13h45 – 14h15Practical Session V
14h15 – 14h45Introduction
Practical Session VI
Hagen Wesseling
14h45 – 16h00Practical Session VI
16h00 – 16h15Coffee Break
16h15 – 18h30Practical Session V
18h30 – 19h30Final Discussion
19h30 – 21h30Dinner

Course Coordination

The course will be coordinated by Prof. Stefanie Kaiser from the Laboratory of Analytical Chemistry,  Institute of Pharmaceutical Chemistry of Goethe University Frankfurt (GUF) in Germany. Prof. Kaiser is an international renowned RNA mass spectrometrist working on the forefront of RNA modification discovery, charaterization and absolute quantification.

Scientific Organization

Stefanie Kaiser

Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Germany

Ana Soares

Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro

Organizing Committee

Max Berg 

Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Germany

Felix Dalwigk

Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Germany

Gregor Ammann

Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Germany

Nur Yesiltac

Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Germany

Daniela Ribeiro

Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro

Ana Rita Ferreira

Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro


Registration deadline: August 15th 2023

Participants requirements

This Summer School is directed to MSc or PhD students, as well as early stage post-doctoral scientists who are interested in the topic. Basic background in molecular biology, biochemistry, cell biology or related fields is required. Applicants should provide a CV, a background on the study or research they are (or intend to be) engaged in, a motivation letter and a letter of recommendation from their current/past supervisor. There is a maximum of 16 people accepted to enroll the hands-on practical course.  Additional participants can join the theoretical program in person (with a maximum of 30 participants in total)


*The fee includes coffee breaks, lunches, 2 dinners and course materials

  • Pratical and theoretical course: 85€
  • Pratical and theoretical course for UA student & ECIU members: 50€
  • Theoretical course (on-site): 50€
  • Theoretical course (on-site) for UA students & ECIU members: 25€


iBiMED – Institute of Biomedicine
Department of Medical Sciences
Campus Universitário de Santiago,
Agra do Crasto – Edifício 30
3810-193 Aveiro

The University of Aveiro was founded in 1973 and is one of the most innovative universities in Portugal, recognized by the quality of its teaching and research and its cooperation with regional and national business. Map of the University Campus

Travel Information

Flying to Portugal:

The closest airport is Francisco Sá Carneiro International Airport in Oporto, located some 80 km to the north of Aveiro. 

Travel to Aveiro from Oporto Airport:

  • Public transport
  • Hire a car (driving time to Aveiro 1 hour)
  • Taxi (~ 60€)

Oporto Airport to Aveiro by Public Transport

Airporto to train station:

At the airport you can catch a TAXI to the train station (Porto-Campanhã). It costs approximately 20€ and takes about 25 minutes.


At the airport, you can catch the METRO (subway) to the city centre (Line E – Trindade; Ticket Z4 ~2.60€). 

At Porto-Trindade, validate the same ticket and change to any of the following lines to reach the train station “Porto-CampanhãSubway Map and Timetables

Line A and B to “Estádio do Dragão”

Line C to “Campanhã”

Line F to “Fânzeres”

Exit at Campanhã stop and reach the Porto-Campanhã train station after a short walk (~5min).


More information can be found on Public Transportation | Porto Airport (aeroportoporto.pt)

Porto-Campanhã to Aveiro:

Trains to Aveiro run regularly throughout the day (one every hour). The ticket costs 3.55€ and the trip takes 50min to 1h10min. 

Faster trains (Alpha or Intercidades) are also available. 

Please consult the website www.cp.pt for more information.

Aveiro train station to University Campus

Aveiro railway station is located about 30 minutes walking distance.

The Aveiro Bus Line 11 departs from the bus terminal “Terminal Rodoviário“, which is located next to the train station and stops at the venue “Universidade – Crasto” (it is not listed in the schedule but it is the stop between Universidade – Santiago A and ISCAUA A).

The ride takes approximately 15 min and the ticket costs 2.05€ (you can buy the ticket in the bus). Schedule information – Aveiro Bus


Taxi or uber ride takes about 5 minutes (~3€ -6€).


Go by bike – Buga2


Scroll to top