Contact Links Find US IT Service Chinese Version


Combinatorics Seminar

Biology Seminars

Toponomics Seminars

Fund Apply

Research Event

PICB Mini Symposium Combinatorial Problems arising in Computational Biology

February 6,2007

     Mini Symposium Combinatorial Problems arising in
     Computational Biology


Morning Session

Vincent Moulton,
University of East Anglia ,
Norwich, UK

9:00 Visualising collections of trees using split networks
Martin Lott,
University of East Anglia,
9:45 An algorithm to reconstruct reticulate evolution in polyploid species
  10:30-10:45 Coffee Break
Jacobus Koolen,
Pohang University of Science and Technology, Pohang, South Korea
10:45PM Lopsided sets: An Important Class of Subsets of the Hypercube
Yaokun WU,
Shanghai Jiaotong Uni- versity,Shanghai, China
11:30AM Split decomposition theory and the mod2 cohomology of finite simplicial complexes
  12:15-13:30 Lunch Break

Afternoon Session

William H.Chen,
Nankai University, Tianjin,

13:30 Detecting Community Structures of Networks by Linear Programming
Rudolf Fleischer
Fudan University, Shang- hai,China
14:15 Die Another Day
  15:00-15:15 Coffee Break
Simon Rayner,
Wuhan Institute of Viro- logy, Chinese Academy of Sciences
15:15 Doing Something useful with all the biological databases: Traditional vs Trendy
Stefan Gruenewald
PICB Shanghai, China
16:00 On the Simplicial Complex of compatible line Arrangements
  16:45-17:00 Coffee Break
Andreas Dress,(moderator) 17:00 Round Table Discrete and Combi- natorial Optimization as a Topic of Research and Teaching in CHina


Martin Lott,
University of East Anglia,
An algorithm to reconstruct reticulate evolution in polyploid species
A new algorithm is presented which creates phylogenetic networks for poly- ploid species starting from a multi-labelled tree. This acts as a fast and ea-  sy alternative for creating networks that are usually inferred using ad hoc       arguments. To illustrate the applicability of our algorithm, we present some examples of networks for plant allopolyploids. The algorithm has been imple- mented in our PADRE software package which is freely available for use from http://www.uea.ac.uk/a043878/padre.html. This is joint work with Katharina Huber,Vincent Moulton and Bengt Oxelman


Vincent Moulton,
University of East Anglia,
Visualising collections of trees using split networks
Many Phylogenetic methods produce large collections of trees as opposed to a single tree, which allows the exploration of support for various evolutionary hypotheses. However, to be useful, the information contained in collections of trees usually needs to be summarized; frequently this is achieved by constructing a consensus tree. Consensus trees display only those signals that are present in a large proportion of the trees. However, by their very nature consensus trees require that any conflicts between the trees are necessarily disregarded. We review a method that extends the nothion of consensus trees to allow the visualization of conflicting hypotheses in a consensus network. In addition, we describe some extensions of this method that can be applied to construction of whole genome phylogenies.


Rudolf Fleischer,
Fudan University,Shang- hai, China
Die Another Day
The Hydra was a many-headed monster from Greek mythology that would immediately replace a head that was cut off by one or two new heads. It was the second task of Hercules to kill this monster. In an abstract sense, a Hydra can be modeled as a tree where the leaves are the heads, and when a head is cut off some subtrees get duplicated. Different Hydra species differ by which subtress can be duplicated in which multiplicity. Using some deep mathematics, it had been shown that two classes of Hydra species must always die, independent of the order in which heads are cut off. In this talk we identify three properties for a Hydra that are necessary and sufficient to make it immortal or force it to die. We also give a simple combinatorial proof for this classification. Now, if Hercules had known this...

All are welcome




320 Yue Yang Road,Shanghai, China, Fax:86-21-54920451,Email:icb@sibs.ac.cn