Chair of Bioinformatics

    Program details_2019

    Program details

    Lectures and labs will be held daily from 9.00 a.m. to 5.15 p.m. The main meeting point is lecture theatre A102.

    Monday September 23rd

    8.00 - 9.00 a.m.: Registration (compulsory)

    Course Certificates

    Dear Course Members,
    here are the details on getting your course certificate:

    standard certificate (3 ECTS) you simply send a short summary on the course days regarding the scientific contents and what the key  messages to learn were for every day (a total of 1-2 pages is enough; but this is no course evaluation but a scientific summary of the course contents) to Dr. Rapp-Galmiche, she will then send out the course certificate subsequently.

    For a 5 ECTS certificate you send a summary of a particular topic (you can pick any lecture topic you like, please contact the lecturer of choice per e-mail and cc Dr. Rapp-Galmiche so that she knows from whom to expect the grading of the essay). Here the key point is to give a summary on the topic (about 4 pages, looking at current literature and giving proper references to current literature and of course just remember what has been taught in the course) and then write 3-4 pages about your own opinion and investigation on the topic. You may confirm the view presented in the lecture but you are also welcome to extend it by own suggestions or also point out the critical points, what is not yet clear, where more experiments etc. are warranted. Aim here to finish during December to send in the first draft. After corrections from the supervisor, the deadline for the revision is 9th of February. The summaries will be re-evaluated for completeness and content. After this the certificate for the course is sent to you.For this more demanding essay on a topic of the summer school in infection biology you can also get the course certificate with 5 ECTS and a grading (international A-E scale).


    Systems Biology of Infection

    Lecturer: Prof. Dr. Thomas Dandekar (Homepage)

    Chair, Bioinformatics

    Pseudomonas Syringae attacks the host -- how do you understand the host response?
    (A) Phenotype: Pst (104 CFU/ml) infection; red arrows indicate pathogen inoculation; black arrow indicates mock (10mM MgCl2) inoculation. Symptoms weare photographed three days post pathogen inoculation (DPPI). (B) Network: Topology of Pst- mediated hormone disease networks in Arabidopsis. Connectivity among nodes is based either on activation (->) or inhibition (-|). Node designation: blue, enzymes of hormone biosynthesis and degradation; yellow, active hormone molecules; green, host regulatory factors; red, Pst- originated pathogenicity factors responsible for triggering immunity in Arabidopsis; pink, “PR-1”, marker node for immunity against the infection of Pst in Arabidopsis. All nodes are denoted by abbreviations.
    More information on these questions is found in our plant cell paper: Naseem M, Philippi N, Hussain A, Wangorsch G, Ahmed N, Dandekar T. Integrated systems view on networking by hormones in Arabidopsis immunity reveals multiple crosstalk for cytokinin. Plant Cell. 2012 May;24(5):1793-814.
    However, the same techniques can also be applied (and are shown in the course) to study human infection defense against pathogens. 


    Location: lecture theatre A102 and CIP pool, You find that easily, if you are in the main hall or Foyer of the Biocentre of the University of Würzburg

    Equipment: computers – these are provided (CIP pool)

    09:00-10:00 Introduction: Prof. Thomas Dandekar, Department of Bioinformatics University of Würzburg (chair) and EMBL Heidelberg
    Title: "Systems biology of infection – bioinformatical approaches" (lecture theatre  A102)

    Including administration: attendance, insurance

    10:00-11:30 Part I Database and Interactomics (CIP pool in the basement, we will lead you to it if not yet known)

    • Dr. Chunguang Liang, Department of Bioinformatics University of Würzburg
      Title: "Databases in infection biology"

    11:30-14:15 Part II Getting into -omics: transcriptomics and proteomics (CIP pool in the basement and lecture theatre A102)

    12:30-13:30 Lunch break

    • 13:30-14:00 Dr. Elena Bencúrová,  Laboratory of Biomedicine, Microbiology and Immunology,
      University of Veterinary Medicine and Pharmacy in Kosice, Slovakia and University of Würzburg (lecture theatre A102)
      Title: "Proteomics in infection biology"
    • 14:00-14:15 Discussion

    14:15-14:30 Break

    14:30-16:00 Part III Current trends in systems biology (lecture theatre A102)

    • Prof. Alicia Ponte-Sucre, Humboldt professor, Insituto de Medicina Experimental, Universidad Central de Venezuela, Caracas
      Title 1: "Surveillance and prevention of Chagas in Latino America, how different countries have deal with the disease"
      Title 2: "Host-parasite interaction in Leishmania, neuropeptides and chemotaxis"

    16:00-16:30 Coffee break

    16:30-18:00 Part IV Drug design and signalling in infection biology (CIP pool)

    • Dr. Meik Kunz, Department of Bioinformatics University of Würzburg
      Title: "Drug target identification in infection biology"
    • Prof. Thomas Dandekar, Department of Bioinformatics University of Würzburg (chair) and EMBL Heidelberg
      Title: "Current trends of modelling in infection biology"

    Useful link:


    Systems Biology
    A Textbook
    Klipp, Edda / Liebermeister, Wolfram / Wierling, Christoph / Kowald, Axel

    Arthur Lesk "introduction to bioinformatics"

    For German speaking students the book by Andrea Hansen is fine

    as well as my own (with Meik Kunz)  


    19:00 Welcome Dinner  

    Tuesday September 24th

    Intracellular S. aureus

    Lecturer: Dr. M. Fraunholz (Homepage)

    Figure: Staphylococcus aureus (cyan) in phagolysosomes of human cells (yellow)

    Topic area: Microscopic analysis of intracellular bacterial host-pathogen interactions: Practical image analysis with Fiji/ImageJ (basics & motion tracking, feature counting)

    Upon infection Staphylococcus aureus is readily phagocytosed by macrophages and neutrophils but is also to invade epithelial and endothelial cells, fibroblast, osteoblasts, and keratinocytes. The uptake by latter so-called non-professional phagocytes has been proposed to play a role in evasion of the innate immune system. Further survival of phagolysosomal killing by S. aureus may also lead to disseminating infections within migrating phagocytes. We and others have shown that S. aureus is capable of escaping from host cell phagosomes. One of our methods is microscopy based and relies on the recruitment of a cytoplasmically expressed host cell marker that is recruited to the bacterial cell wall upon phagosomal membrane rupture.

    We will address theoretical and practical aspects of confocal laser scanning microscopy as well as the underlying fluorophores. We will analyze images of uninfected and infected human cells using Fiji/ImageJ, a tool which is handy for other image analysis aspects, too.

    Participants should bring a USB Thumb drive, if they want to keep their own personalized Fiji/ImageJ version.


    Location: lecture theatre A102 and CIP pool

    Equipment: computers – these are provided (CIP pool), USB pendrive (optional)

    09:00-10:00 Introduction: Martin Fraunholz, Chair of Microbiology, University of Würzburg
    (Location: lecture theatre  A102)

    10:00-12:30 Fiji/ImageJ to analyze biological data

    • „Installation“ and Basics of biological image acquisition

    12:30-13:30 Lunch break

    13:30-16:00 Fiji/ImageJ to analyze biological data

    • Image/Movie analysis in multiple dimension, Image quantification

    Wednesday September 25th

    Location: Lecture Theatre A102

    09:00-09:30     Report from Bio-EU students about their personal experience (networking, Dr. U. Rapp-Galmiche)
    09:30-10:30     Round table
                               discussion possibilities for young researchers, possibilities infection biology
                               (Prof. Ponte-Sucre, Prof. T. Dandekar, moderation: Dr. U. Rapp-Galmiche)

    please transfer then to the Röntgenring, main entrance of chair of tissue engineering:

    11:15                 Guided Tour with Dr. Sarah Nietzer to visit the 3D tissue models laboratory (TERM) at Röntgen-Ring 11.
                                What do we do with this in Infection Biology? Have a look: https://www.uni-wuerzburg.de/grk2157/startseite/

    Lunch and free time

    16:00 tour of residence 

    Thursday September 26th

    Trypanosomes (Lectures, practical: A102)

    Lecturer: Dr. S. Kramer (Homepage)

    Zoology I


    African trypanosomes cause African Sleeping Sickness as well as the related cattle disease Nagana, affecting people’s health both directly and indirectly in sub-saharan Africa. During the ‘Trypanosome-day’ of the summerschool we will look at the parasites from the point of view of a parasitologist, but also from the point of view of a cell biologist: you will see that trypanosomes are model organisms for many biological questions. Currently, we have 5 laboratories in Würzburg that do research mainly on the African trypanosome Trypanosoma brucei. Guest speakers will introduce the related human pathogens Trypanosoma cruzi (Chagas disease) and Leishmania (Leishmaniasis).

    Typical contents of this course (subject to change) are:

    1. Welcome and introduction lecture to Trypanosoma brucei
    2. Guest speakers:   - Dr. Claudia Moreira, Brazil (Trypanosoma cruzi)
                                      - Prof. Alicia Ponte-Sucre, Venezuela, (Leishmania)
    3. Movie on African Sleeping Sickness + discussion (Medicin Sans Frontiers)
    4. Insight into trypanosome research at Würzburg University (PhD students report)
    5. Tour the labs’ to see trypanosomes and tsetse flies
    6. Concluding remarks


    Friday September 27nd

    Parasitic Helminths

    Lecturer: Dr. M. Spiliotis (Homepage)

    Medical Parasitology

    Institute of Hygiene and Microbiology

    Figure: Echinokokkus

    On the last day of the workshop the labs and lectures will not be at the Biocentre but at the University Clinics Department Hygiene and Microbiology (Haus E1).

    Please find the written directions and maps below (© OpenStreetMap)


    You can reach the main area of the University Hospital with the streetcar routes 1 and 5. You get on the streetcar at the Hautpbahnhof Ost (Main Station East) in the direction of Grombühl and get off at stop “Uniklinikum Bereich D (University Hospital area D; Petrinistrasse)". You can reach the Institute of Hygiene and Microbiology by walk (5 min) as indicated on the map. (The walk from the Main Station takes about 20-25 minutes.)

    Parasitic Flatworms: A tale of mortality and immortality.

    Parasitic helminths are a major cause of so-called ‘Neglected Diseases’. And Neglected Diseases are called ‘neglected’ because nobody (or only very few) has/have an interest to study them. So, why are we doing it? This is something we’re going to figure out in the ‘Parasitic Helminth’-day of the summer school. We shall learn that the development of novel therapies is not the only motivation to do infectious disease research and that these parasites (like many others) are highly fascinating from the view-point of immunologists as well as cell-, developmental- and evolutionary biologists. Above all, we shall learn how molecular research can be done in a ‘non-mainstream’ setting and which strategies should be followed to establish an infectious disease model system from scratch.


    9:00-10:30 Introduction: Parasitic helminths and the spellbinding world of tapeworm infections (including tapeworm movie; demonstration of specimen; narration of the ultimate tapeworm joke)

    10:30-10:50 Coffee break

    10:50-12:00 Interactive Teaching: how to develop a research model system from scratch.

    12:00-13:00 Lunch break

    13:00-14:20 Würzburg’s current tapeworm research projects: PhD students report

    14:20-15:50 Practical aspects of tapeworm and larval tapeworm research (in small groups)

    15:50-16:10 Coffee break

    16:10-18:00 Final discussion (including Quiz Show ‚Who wants to be a Parasitonaire?‘)

    19:00 Farewell Dinner at Bürgerspital-Weinstuben Würzburg (Theaterstraße 19)