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Professor, Principal Investigator

Laboratory of Phylogenetic Combinatorics

Email: stefan@picb.ac.cn

Research interests 

  1. Phylogenetics 

  2. Developing methods to reconstruct phylogenetic networks 

  3. Combinatorics and graph theory 

  4. Applications of phylogenetic methods within and outside phylogenetics  

The main research area of the group is phylogenetics. We develop methods to reconstruct phylogenetic trees or networks, with an emphasis on displaying ambiguity in the data and reticulate evolution. The structures that we would like to construct from biological data can often be described in combinatorial terms. For example, an unrooted phylogenetic network can be considered as a collection of bipartitions (splits) of the taxa set and a rooted phylogenetic network is an acyclic directed graph. Compared with the combinatorics of trees, there are many open problems for more general networks. We work on those combinatorial problems and the results are published in mathematical journals. They often have algorithmic consequences and give rise to new methods or insights in the performance or limitations of existing methods. We implement our new algorithms and collaborate with biologists to analyze their data, comparing the results of different phylogenetic methods. 

There are many more problems in molecular biology where phylogenetic methods or similar combinatorial techniques can be applied. Thus, in addition to working on "proper" phylogenetic analysis, we have worked on the analysis and alignment of biological networks such as protein-protein interaction networks or gene regulatory networks, and our current work on the quartet distance between phylogenetic trees gives rise to a new measure of dependence between random variables or data sets. 


Brief Biography : 

Professional Experience 

2006.09 –Present: Professor ,Principal Investigator, CAS-MPG Partner institute for Computational Biology(PICB),CAS 

2005.09 – 2006.08: Combined Postdoc, Linnaeus Center for Bioinformatics, Uppsala University in Uppsala, Sweden, and the University of Canterbury in Christchurch, New Zealand.  

2001.04 – 2003.03: Postdoc, Graduate College “Bioinformatics” and Department of Mathematics,  

University of Bielefeld, Bielefeld, Germany.   


1998.04 – 2001.02: Ph.D. in Mathematics, Department of Mathematics, University of Bielefeld 

1994.02 – 1998.03: Diploma in Mathematics, Department of Mathematics, University of Bielefeld  

1991.10 – 1994.01, Vordiplom (B.Sc. equivalent) in Mathematics ,Department of Mathematics, University of Bielefeld  


Selected Publications:*Corresponding Author 

1. Wolf, S. & Gruenewald, S. Sequence, Structure and Ligand Binding Evolution of Rhodopsin-Like G Protein-Coupled Receptors: A Crystal Structure-Based Phylogenetic Analysis. Plos One 10, e0123533 (2015).
2. Jialiang Yang, Stefan Gruenewald, Yifei Xu, Xiu-Feng Wan: Quartet-based methods to reconstruct phylogenetic networks. BMC Systems Biology
 8: 21 (2014)
3. Jialiang Yang, Jun Li, Stefan Gruenewald, Xiu-Feng Wan. BinAligner: a heuristic method to align biological networks. BMC Bioinformatics
. 2013, 14(Suppl 14):S8
4. Jialiang Yang, Stefan Gruenewald, Xiu-Feng Wan. Quartet-Net: A quartet-based method to reconstruct phylogenetic networks. Mol Biol Evol
. 2013, 30(5): 1206-1217.
5. Grunewald S, Spillner A, Bastkowski S, Bogershausen A, Moulton V. SuperQ: Computing Supernetworks from Quartets. IEEE/ACM Trans. Comput. Biology Bioinform
. 2013, 10(1): 151-160.
6. Li J, Roebuck P,Gruenewald S, Liang H. SurvNet: a web server for identifying network-based biomarkers that most correlate with patient survival data. Nucleic Acids Res
. 2012, 40: W123-126.
7. Grunewald S, Koolen J, Moulton V, Wu T. The size of 3-compatible, weakly compatible split systems. J Appl Math Comput
. 2012, 40: 249-259.
8. Grunewald S. Slim sets of binary trees. J Comb Theory A
. 2012, 119(2): 323-330.
9. Yang J, Li J, Dong L,Gruenewald S. A heuristic algorithm to align protein interaction networks. J Biomath. 2011, 26(3): 569-575. 10. Ding Y,Gruenewald S, Humphries J. On agreement forests. J Comb Theory A
. 2011, 118(7): 2059-2065.
11. Yang J, Li J, Dong L,Gruenewald S. Analysis on the reconstruction accuracy of the Fitch method for inferring ancestral states. BMC Bioinformatics
. 2011, 12:18.
12. Grunewald S, Moulton V, Spillner A. Consistency of the QNet algorithm for generating planar split networks from weighted quartets. Discrete Appl Math
. 2009, 157(10): 2325-2334.
13. Andreas WM Dress, Christoph Flamm, Guido Fritzsch, Stefan Gruenewald, Matthias Kruspe, Sonja J Prohaska and Peter F Stadler. Noisy: Identification of Problematic Columns in Multiple Sequence Alignments. Algorithms for Molecular Biology
, 2008,3:7
14. Stefan Gruenewald, Peter J. Humphries and Charles Semple. Quartet Compatibility and the Quartet Graph. The Electronic Journal of Combinatorics
, 2008,15:R103
15. Stefan Gruenewald, Kristoffer Forslund, Andreas Dress and Vincent Moulton. QNet: An Agglomerative Method for the Construction of Phylogenetic Networks from Weighted Quartets. Molecular Biology and Evolution, 2007,24(2):532-538