yoshiko version 2.0
We have released yoshiko
version 2.0, a mature version of our cluster editing algorithm. It has been implemented mostly by Emanuel Laude and contains a lot of helpful redcution rules from fixed parameter algorithmics and a powerful heuristic for large data sets.
24 Aug 2011
natalie version 2.0
We have released natalie
version 2.0, a mature version of our network alignment algorithm.
27 Jun 2011
side chain placement
is a package that contains our code for exact side chain placement as used in a recent paper in Optimization Letters.
5 Mar 2010
heinz and BioNet
now works together with the BioNet
17 Dec 2008
code is now online. The tool solves the cluster editing problem as well as its directed "cousin", the transitivity editing problem, to provable optimality.
1 Sep 2008
planet lisa moves to Amsterdam
The planet lisa project is now based at the Centre for Mathematics and Computer Science (CWI)
in Amsterdam, The Netherlands.
20 Jul 2008
Our paper Identifying Functional Modules in Protein-Protein Interaction Data: An Integrated Exact Approach
has won the oustanding paper award
at ISMB 2008
in Toronto, Canada. See the heinz
section for more information on our software to discover optimal subnetworks with respect to our signal-based scoring scheme of p-values.
We will give a presentation at ISMB 2008 on Identifying Functional Modules in Protein-Protein Interaction Data: An Integrated Exact Approach
. Our software is available as the heinz
Algorithmic Operations Research
Our theoretical lara paper has been accepted for publication in Algorithmic Operations Research.
27 Jul 07
describing the lara
program has been accepted for publication in BMC Bioinformatics
28 Jun 07
4SALE support for lara
has been integrated into the RNA alignment and editing framework 4SALE
. Get the latest lara
version that is compatible with 4SALE