If you are here for the supplementary materials from our paper 'Identifying conserved protein complexes between species by constructing interolog networks' (BMC Bioinformatics 2013, 14(Suppl 16):S8), please visit the COCIN website. Have a nice day!
NEW!! Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer (2015):
Srihari S, Singla J, Wong L, Ragan MA (2015). Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer. Biology Direct, to appear.
NEW!! An up-to-date survey of protein complex prediction methods (2015):
Srihari S, Yong CH, Patil A, Wong L (2015). Methods for protein complex prediction and their contributions towards understanding the organisation, function and dynamics of complexes, FEBS Letters doi:10.1016/j.febslet.2015.04.026. [PDF] with slides!
Sriganesh Srihari1,*, Kang Ning3,* and Hon Wai Leong2
1Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia.
2Department of Computer Science, National University of Singapore, Singapore 117590.
3Qingdao Institute, Chinese Academy of Sciences, Qingdao 266101, China.
* This work was done when SS was with the Department of Computer Science, National University of Singapore, Singapore, and KN was with the Department of Pathology, University of Michigan, Ann Arbor USA.
Source codes and datasets for MCL-CAw are available for here
What can MCL-CAw do?
Input: A weighted PPI network, MCL clusters extracted from the network
Output: Core-attachment based refinement of MCL clusters listing the 'cores' and 'attachments' in each cluster.
Read about cores and attachments here or here.
Srihari S, Ning K, Leong HW (2010). MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure, BMC Bioinformatics, 11:504.
Srihari S, Leong HW (2013). A survey of computational methods for protein complex prediction from protein interaction networks, J Bioinf Comp Biol, 11:1230002. [Link to the paper]Acknowledgements: Funding from NUS -- ARF grant R252-000-361-112.