Chair of Bioinformatics

    Program details 2023

    Lectures and labs will be held daily from 9.00 a.m. to 5.15 p.m.

    The main meeting point on Monday is lecture hall A103, Tuesday, Thursday and Friday: lecture hall A102.

    Monday October 9th

    8.00 - 8.30 a.m.: Registration (compulsory) office Bioinformatics

    8.30 a.m. Welcome by Prof. Dandekar (including administration: attendance, insurance)


    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).

    Monday October 9th 

    lecture hall A103 and CIP Pool (ck 02-05)

    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.


    08:30-09:15 Introduction: Prof. Thomas Dandekar, Department of Bioinformatics University of Würzburg (chair) and EMBL Heidelberg
    Title: "Systems biology of infection – bioinformatical approaches"

    09:15-09:30  Coffee Break

    09:30-10:30 Part I Database and Interactomics

    • Dr. Shishir Gupta, University of Würzburg (CIP Pool ck02-05)
      Title: "Networks in infection biology"

    10:30-12:30 Part II Designing novel chemoinformatics algorithms to boost rational drug discovery in infection biology

    • 10:30-11:30 Prof. Sergey Shityakov, ITMO University St. Petersburg

    11:30-12:00  Coffee Break

    • 12:00-12:30 Prof. Sergey Shityakov, ITMO University St. Petersburg

    12:30-13:30 Lunch break

    • 13:30-14:15 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"

    14:15-16:00 Part III Current trends in parasitology

    • Prof. Alicia Ponte-Sucre, Humboldt professor, Insituto de Medicina Experimental, Universidad Central de Venezuela, Caracas
      Title 1: "TICS, surveillance and prevention in neglected diseases Relation with the sustainable and millenium goals"
      Title 2: "Betulinic acid derivates activity in L.braziliensis. Statisitcal methods to evaluate the IC50"

    16:15-18:00 Part IV Drug design and current trends in infection biology

    • 16:15-17:00 Dr. Meik Kunz, University of Erlangen (ZOOM Meeting! A102)
    • 17:00-18:00 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  October 10th

    lecture hall A102 and CIP Pool (ck 02-05)

    Intracellular S. aureus

    Lecturer: Dr. Martin 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 hall A101 and CIP Pool

    09:00-10:00 Introduction: Martin Fraunholz, Chair of Microbiology, University of Würzburg

    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 October 11th

    Location: Seminar Room Bioinformatics

    09:15-10:00     Career Day: Talk Ass. Prof. Mauld Lamarque (University of Montpellier)
    10:00-10:30     Round table
                               Discussion about BIPs, CharmEU and student exchange opportunities
    11:00                 Visit to the Chair of Tissue Engineering and Regenerative Medicine

    from 2:00         Visit your prospective collaboration partners or
                               visit the Würzburg castle (Festung Marienberg) and/or the Residence.

    Thursday October 12th

    lecture hall A102 and CIP Pool (ck 02-05)

    Trypanosomes and Leishmania

    Location: Location: lecture hall A102

    Lecturer: Dr. Susanne Kramer (Homepage)

    Zoology I

    Session 1: 09:00-13:00 Trypanosoma brucei and Sleeping Sickness

    09:00-9:10    Welcome and Safety instructions

    09:10-10:15  Trypanosoma brucei: introduction to the parasite and disease
                           Lecture (Susanne Kramer)

    10:15-10:30  Coffee-Break

    10:30-11:00  Methods in Infection Biology (10 min talks)
                           - Expansion microscopy (Bernardo Gabiatti)
                           - Tokuyasu microscopy (Fabian Link)
                           - Breeding Tsetse Flies (Movie, Carina Praisler)   

    11:00-13:00 Practical part (in 2 groups, switch at 12:00)
                           - Tsetse-Dissection (Carina Praisler)
                           - Cell culture, determining cell densities of BSF and PCF trypanosomes (Susanne Kramer and Silke Braune)

    LUNCH BREAK: 13:00-14:00

    Session 2: 14:00-16:00 Leishmaniasis and Chagas

    14:00-14:45 Chagas disease: Surveillance and prevention in Latin America. Different countries and ways of approaches.
                          Lecture with discussion (Alicia Ponte-Sucre)

    14:45-15:00 Coffee-Break

    15:00-15:45 Leishmania, concepts and challenges, diagnosis, chemotherapy and drug resistance
                          Lecture with discussion (Alicia Ponte-Sucre)

    15:00-16:00 Concluding remarks


    Friday October 13th

    lecture hall A102 and CIP Pool (ck 02-05)

    Parasitic Helminths

    Lecturer: Prof. Klaus Brehm (Homepage)

    Medical Parasitology

    Institute of Hygiene and Microbiology

    Figure: Echinokokkus


    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.


    09:00-12:00 Self-preparation on the topic (using materials provided in WueCampus)

    13:00-15:30 Lecture and practical in the Hygiene Institute of the University Hospital (Prof. Klaus Brehm)

    15:30-16:00 Conclusions, final discussion (all)


    19:00 Farewell dinner