Johannes Söllner

• PhD
• founder at Sodatana e.U.

The strategies employed in vaccinology have improved since the seminal work of Edward Jenner in the eighteenth century. Stimulated by failure to develop vaccines for cancers and chronic infectious diseases as well as an emergence of a multitude of new technologies not available earlier, vaccinology has moved from a largely experimental art to a new...

Immunoinformatics focuses on modeling immune responses for better understanding of the immune system and in many cases for proposing agents able to modify the immune system. The most classical of these agents are vaccines derived from living organisms such as smallpox or polio. More modern vaccines comprise recombinant proteins, protein domains, an...

Systematic study of the effect of mycophenolate mofetil (MMF) on the molecular level in the context of other drugs and molecular disease profiles became possible due to the availability of large scale molecular profiles on both disease characterization and drug mode of action. Such analysis is of particular value in elucidating alternative drug use...

The simplicity and potential of minimally invasive testing using sera from patients makes auto-antibody based biomarkers a very promising tool for use in can-cer diagnostics. Protein microarrays have been used for the identification of such auto-antibody signatures. Because high throughput protein expression and purifi-cation is laborious, syntheti...

Omics profiling in translational clinical research has provided detailed molecular characterization of disease phenotypes. Integrating this molecular data space with clinical phenotype descriptors has triggered advancements regarding a systems view on disease, resulting in the concept of stratified medicine. We present a methodology for patient str...

Vaccine research has significantly changed face within the last decade. Newly developed vaccines usually comprise defined subunits and often next generation adjuvants. On the downside, as in many areas ultimately of interest to clinical development, basic research does only slowly translate to bedside therapy. Part of the reason can be found in reg...

For diseases with complex phenotype such as diabetic nephropathy (DN), integration of multiple Omics sources promises an improved description of the disease pathophysiology, being the basis for novel diagnostics and therapy, but equally important personalization aspects. Molecular features on DN were retrieved from public domain Omics studies and b...

The last years have seen a renaissance of the vaccine area, driven by clinical needs in infectious diseases but also chronic diseases such as cancer and autoimmune disorders. Equally important are technological improvements involving nano-scale delivery platforms as well as third generation adjuvants. In parallel immunoinformatics routines have rea...

The Herpesviridae are a large family of DNA viruses. Several members of this family are known to cause disease in animals and human. In particular there are several lines of evidence for involvement in human cancer and autoimmune conditions. Although this group of viruses has been investigated intensively for several decades molecular mechanisms an...

Based on integration site preferences, retroviruses can be placed into three groups. Viruses that comprise the first group, murine leukemia virus and foamy virus, integrate preferentially near transcription start sites. The second group, notably human immunodeficiency virus and simian immunodeficiency virus, preferentially targets transcription uni...

list of protein names for antigenicity validation. This is a text file listing all proteins from the Blythe et.al. dataset used for the validation of antigenicity.

protectivity validation data. This is a compressed FASTA file which can be viewed (after decompression) using any text editor. Relevant protective or functionally altering epitopes as listed by the IEDB or as determined by homology mapping are contained in the FASTA headers.

The application of peptide based diagnostics and therapeutics mimicking part of protein antigen is experiencing renewed interest. So far selection and design rationale for such peptides is usually driven by T-cell epitope prediction, available experimental and modelled 3D structure, B-cell epitope predictions such as hydrophilicity plots or experie...

A B-cell epitope is the three-dimensional structure within an antigen that can be bound to the variable region of an antibody. The prediction of B-cell epitopes is highly desirable for various immunological applications, but has presented a set of unique challenges to the bioinformatics and immunology communities. Improving the accuracy of B-cell e...

Recently, new machine learning classifiers for the prediction of linear B-cell epitopes were presented. Here we show the application of Receiver Operator Characteristics (ROC) convex hulls to select optimal classifiers as well as possibilities to improve the post test probability (PTP) to meet real world requirements such as high throughput epitope...

Identification and characterization of antigenic determinants on proteins has received considerable attention utilizing both, experimental as well as computational methods. For computational routines mostly structural as well as physicochemical parameters have been utilized for predicting the antigenic propensity of protein sites. However, the perf...

An in vitro protein selection method, ribosome display, has been applied to comprehensively identify and map the immunologically relevant proteins of the human pathogen Staphylococcus aureus. A library built up from genomic fragments of the virulent S. aureus COL strain (methicillin-resistant S. aureus) allowed us to screen all possible encoded pep...

For the design of potent subunit vaccines, it is of paramount importance to identify all antigens immunologically recognized by a patient population infected with a pathogen. We have developed a rapid and efficient procedure to identify such commonly recognized antigens, and here we provide a comprehensive in vivo antigenic profile of Staphylococcu...