Bioinformatics

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The Interuniversity Messerli Research Institute, Vienna, Austria
Cancer Research Center (DKFZ), Heidelberg, Germany
Paracelsus Medical University, Salzburg
Medical University of Vienna, Vienna
Children's Cancer Research Institute, Vienna, Austria
University of Cambridge, UK
University of Navarra, Pamplona, Spain

Cooperative Hedgehog/GLI and JAK/STAT signaling drives immunosuppressive tryptophan/kynurenine metabolism via synergistic induction of IDO1 in skin cancer.
2025
Elmer, D.P., Stockmaier, G., Grund-Gröschke, S. et al.
Cell Communication and Signaling
https://biosignaling.biomedcentral.com/articles/10.1186/s12964-025-02101-6

Mould allergen Alt a 1 spiked with the micronutrient retinoic acid reduces Th2 response and ameliorates Alternaria allergy in BALB/c mice.
2024
Fakhimahmadi, A., Roth‐Walter, F., Hofstetter, G. et al.
Allergy
https://onlinelibrary.wiley.com/doi/10.1111/all.16181

In Vivo Screening Characterizes Chromatin Factor Functions during Normal and Malignant Hematopoiesis
2023
Lara-Astiaso, D., Goñi-Salaverri, A., Mendieta-Esteban, J., Narayan, N., Valle, C. D., Gross, T., Giotopoulos, G. et al.
Nature Genetics
https://doi.org/10.1038/s41588-023-01471-2

Single-cell transcriptomics and epigenomics unravel the role of monocytes in neuroblastoma bone marrow metastasis
2023
Fetahu, I., Esser-Skala, W., Dnyansagar, R. Sindelar, S., Rifatbegovic, F., Bileck, A., Skos, L. et al.
Nature Communications
https://doi.org/10.1038/s41467-023-39210-0

Systematic functional screening of chromatin factors identifies strong lineage and disease dependencies in normal and malignant haematopoiesis.
2022
Lara-Astiaso, D., Goñi-Salaverri, A., Mendieta-Esteban, J., Narayan, N., Valle, C. D., Gross, T., Giotopoulos, G., Navarro-Alonso, M., Zazpe, J., Marchese, F., Torrea, N., Calvo, I. A., Lopez, C., Alignani, D., Lopez, A., Saez, B., Taylor-King, J. P., Prosper, F., Fortelny, N. & Huntly, B. J. P.
BioRxiv
https://doi.org/10.1101/2022.08.11.503571

Backbone distortions in lactam-bridged helical peptides
2022
Moazzam, A., Stanojlovic, V., Hinterholzer, A., Holzner, C., Roschger, C., Zierer, A. et al.
Journal of Peptide Science
https://doi.org/10.1002/psc.3400

Bet v 1 from birch pollen is a hypoallergen with vitamin D3 in the pocket
2021
Hufnagl K, Kromp L, Bianchini R, Afify SM, Wiederstein M, Redegeld FA et al.
Allergy
https://doi.org/10.1111/all.15052

Disease-related blood-based differential methylation in cystic fibrosis and its representation in lung cancer revealed a regulatory locus in PKP3 in lung epithelial cells
2021
Schamschula E., Lahnsteiner A., Assenov Y., Hagmann W., Zaborsky N., Wiederstein M. et al.
Epigenetics
https://doi.org/10.1080/15592294.2021.1959976

MHCII3D-Robust Structure Based Prediction of MHC II Binding Peptides
2021
Laimer, J., & Lackner, P.
International Journal of Molecular Sciences
https://doi.org/10.3390/ijms22010012

In silico Design of Phl p 6 Variants With Altered Fold-Stability Significantly Impacts Antigen Processing, Immunogenicity and Immune Polarization
2020
Winter P., Stubenvoll S., Scheiblhofer S., Joubert I.A., Strasser L., Briganser C et al.
Frontiers in Immunology
https://doi.org/10.3389/fimmu.2020.01824

TopMatch-web: pairwise matching of large assemblies of protein and nucleic acid chains in 3D
2020
Wiederstein M. & Sippl M.J.
Nucleic Acids Research
https://doi.org/10.1093/nar/gkaa366

Synergistic cross-talk of hedgehog and interleukin-6 signaling drives growth of basal cell carcinoma
2018
Sternberg, C., Gruber W., et al.
International Journal of Cancer
https://doi.org/10.1002/ijc.31724

MAESTROweb: a web server for structure based protein stability prediction
2016
Laimer J., Hiebl-Flach J., Lengauer D., Lackner P.
Bioinformatics
http://bioinformatics.oxfordjournals.org/content/early/2016/01/27/bioinformatics.btv769.abstract

Structure-Based Characterization of Multiprotein Complexes
2014
Wiederstein M., Gruber M., Frank K., Melo F., Sippl M.J.
Structure
http://dx.doi.org/10.1016/j.str.2014.05.005

D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements
2013
Laimer J., Zuzan C.J., Ehrenberger T., Freudenberger M., Gschwandtner S., Lebherz C., Lackner P.
BMC Bioinformatics
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-140

Detection of spatial correlations in protein structures and molecular complexes
2012
Sippl M.J., Wiederstein M.
Structure
http://dx.doi.org/10.1016/j.str.2012.01.024

Real space refinement of crystal structures with canonical distributions of electrons
2011
Ginzinger S., Gruber M., Brandstetter H., Sippl M.J.
Structure
http://dx.doi.org/10.1016/j.str.2011.10.011

High-performance signal peptide prediction based on sequence alignment techniques
2008
Frank K., Sippl M.J.
Bioinformatics
http://dx.doi.org/10.1093/bioinformatics/btn422

ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
2007
Wiederstein M., Sippl M.J.
Nucleic Acids Research
http://dx.doi.org/10.1093/nar/gkm290

NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures
2007
Weichenberger C.X., Sippl M.J.
Nucleic Acids Research
http://dx.doi.org/10.1093/nar/gkm263