Profile
Abstract
Peter F Stadler, born in 1965, is full professor for bioinformatics at the University Leipzig since 2002. He did a doctorate in 1990 in Chemistry at the University of Vienna. After a postal doctorate with Prof. Manfred Eigen at the department for biochemical kinetics in the Max-Planck's institute of biophysical chemistry in Göttingen he went back to Vienna in 1991 and qualified as a professor in 1994 in Theoretical Chemistry. Since 1994 he is also member of the external faculty of the Santa Fe institute in New Mexico. Since 2009 he works as a foreign scientific member at the Max-Planck's Institute of Mathematics in the Sciences. Peter F Stadler is corresponding member of the Austrian Academy of Sciences since 2010 and Profesor Honoria at the Facultad de Ciencias in Bogota since 2018. Since 2023 he is the director of the Inderdisciplinary Center for Bioinformatics (IZBI) at Leipzig University.
Professional career
- 01/1990 - 01/1991
Postdoc at the Department for Biochemical Kinetics, Max Planck, Institute for Bio-Physical Chemistry, Göttingen, Germany - 01/1991 - 01/1994
Universitätsassistent at the Institute for Theoretical Chemistry and Radiation Chemistry, University of Vienna, Austria - 01/1997 - 01/2002
Außerordentlicher Universitätsprofessor, University of Vienna, Austria - since 01/2002
Full Professor of Bioinformatics, University Leipzig, Germany
Education
- 01/1984 - 01/1990
Studies at the University of Vienna:Undergraduate degrees (1. Diplom) in Chemistry 1986, Astronomy 1988, Physics 1989, Mathematics 1990MSc in Chemistry 1988 - 01/1988 - 01/1990
Dissertation at the Institute for Theoretical Chemistry, University of Vienna, Austria (PhD in Chemistry)
The general theme of my research interests is the search for a consistent understanding of biological processes (with an emphasis on (molecular) evolution) at the genotypic, phenotypic, and dynamical level. The techniques range from the analysis of the dynamical systems arising in chemical kinetics and population genetics, to large scale simulations of RNA evolution and the analysis of viral sequence data, to knowledge based protein potentials, and to algebraic combinatorics applied to the study of fitness landscapes. Major achievements in the area of bioinformatics cover multiple aspects of RNA bioinformatics, from the development of folding algorithms to the design of efficient RNA gene finders. Large scale comparative genomics studies in these areas have e.g. lead to the characterization of several of several ncRNA families.
My group is providing a variety of software tools for the research community. Most importantly, the group is a co-developer of the Vienna RNA Package, a widely used software package for RNA bioinformatics.
Other important tools include FRANz, a pedigree reconstruction package, tools to deal with circular alignments, alignment software such as code2aln aln3nn. The group furthermore maintains tRNAdb, the modernized version of Sprinzl's classical tRNA sequence database. The group is committed to providing newly developed tools as open source software to the scientific community.
- show detailsTraining Alliance for Computational Systems chemistryStadler, Peter FlorianDuration: 03/2023 – 02/2027Funded by: EU Europäische UnionInvolved organisational units of Leipzig University: Bioinformatik
- show detailsAlgorithms for Reconstructing Evolutionary Relationships between Phylogenies: The Multi-Valued CaseMiddendorf, MartinDuration: 03/2023 – 02/2026Funded by: DFG Deutsche ForschungsgemeinschaftInvolved organisational units of Leipzig University: Fakultät für Mathematik und Informatik
- show detailstRNA pools and translational control in melanoma development and treatmentMörl, MarioDuration: 01/2023 – 01/2026Funded by: Stiftungen InlandInvolved organisational units of Leipzig University: Biochemie/Molekularbiologie; Bioinformatik; Klinik und Poliklinik für Dermatologie, Venerologie und Allergologie
- show detailsSynteny-Based Identification of Genomic Innovations in InsectsStadler, Peter FlorianDuration: 10/2022 – 09/2025Funded by: DFG Deutsche ForschungsgemeinschaftInvolved organisational units of Leipzig University: Bioinformatik
- show detailsVirtual Drug Screening in the Chemical Space Accessible by Chemical SynthesisStadler, Peter FlorianDuration: 10/2022 – 09/2025Funded by: DFG Deutsche ForschungsgemeinschaftInvolved organisational units of Leipzig University: Bioinformatik; Medizinische Fakultät und Universitätsklinikum AöR
- show detailsBonidia, R. P.; Avila Santos, A. P.; de Almeida, B. L. S.; Stadler, P. F.; da Rocha, U. N.; Sanches, D. S.; de Carvalho, A. C. P. L. F.Information Theory for Biological Sequence Classification: A Novel Feature Extraction Technique Based on Tsallis EntropyEntropy. 2022. 24 (10).DOI: 10.3390/e24101398
- show detailsMüller, S. P.; Flamm, C.; Stadler, P. F.What makes a reaction network "chemical"?Journal of cheminformatics. 2022.
- show detailsYao, H.-T.; Lorenz, R.; Hofacker, I. L.; Stadler, P. F.Mono-valent salt corrections for RNA secondary structures in the ViennaRNA packageAlgorithms for molecular biology. 2023. 18 (1).
- show detailsWaldl, M.; Spicher, T.; Beckmann, I. K.; von Löhneysen, S.; Stadler, P. F.; Hofacker, I. L.; Lorenz, R.Local RNA folding revisitedJournal of bioinformatics and computational biology. 2023. 21 (04).
- show detailsAvila Santos, A. P.; Muhammad, K. N.; Kasmanas, J.; Bartholomäus, A.; Keller-Costa, T.; Jurburg, S.; Tal, T.; Camarinha-Silva, A.; Saraiva , J. P.; Ponce de Leon Ferreira de Carvalho, A. C.; Stadler, P. F.; Sipoli Sanches, D.; Rocha, U.The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomesAnimal Microbiome. 2023. 5 (1).
The courses offered by Prof. Stadler and his research group contribute to a large extent to the research-oriented consecutive Masters program in Bioinformatics. It builds upon a Bachelors degree (preferably in computer science or biology) and provides a scientifically sound education in several research areas at the interface between computer science and biology. The aim is to acquire in-depth specialist knowledge in selected areas of computer science, biology, mathematics and natural sciences combined with the ability to conduct independent basic or application-oriented research.
Furthermore, Prof. Stadler's group is teaching and organizing the basic modules Algorithms and Data Structures 1&2 from the Bachelors program in Computer Science.