A new set of links has been added to our link-compendium

August 2010

Our suggestion of interesting links has been expanded by aging databases, links on complex system evolution, on network analysis, on network datasets, on network visualization and on several important mathematical tools. Our link-compendium is open for further amendments. If you want to suggest us your interesting, network-related link to include, please write us to info@linkgroup.hu or send a note here.

The ModuLand overlapping modularization method family has been published in PLoS ONE

August 2010

Our paper introducing the novel concept of ModuLand has been accepted in PLoS ONE. Moduland is an integrative method family determining overlapping network modules as hills of an influence function-based, centrality-type community landscape, and including several widely used modularization methods as special cases. As various adaptations of the method family, we developed several algorithms, which provide an efficient analysis of weighted and directed networks, and (1) determine pervasively overlapping modules with high resolution; (2) uncover a detailed hierarchical network structure allowing an efficient, zoom-in analysis of large networks; (3) allow the determination of key network nodes and (4) help to predict network dynamics. Published version: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012528; Supporting website with all downloadable algorithms: http://www.linkgroup.hu/modules.php

Our paper on an extended concept of induced-fit and conformational selection will be the cover story of the October issue of the Trends in Biochemical Sciences

June 2010

In collaboration with Ruth Nussinov we described an extended conformational selection model, which embraces a repertoire of selection and adjustment processes. Induced fit can be viewed as a subset of this repertoire, whose contribution is affected by the bond-types stabilizing the interaction and the differences between the interacting partners. We argue that protein segments whose dynamics are distinct from the rest of the protein (‘discrete breathers’) can govern conformational transitions and allosteric propagation that accompany binding processes, and as such may be more sensitive to mutational events. Additionally, we highlight the dynamic complexity of binding scenarios as they relate to events such as aggregation and signalling, and the crowded cellular environment. The paper can be viewed here and its pdf file can be downloaded from here.

The SignaLink database has been published in Bioinformatics

June 2010

SignaLink is a manually curated signalling network, which contains 1554 protein components and 1461 interactions of eight major signalling pathways from the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and humans. Unlike worms and flies, all the eight human signalling pathways have the potential to cross-talk with all other pathways. The utilisation of these cross-talks is tissue-specific. We predicted 271 novel signalling proteins in the three species from which all of the six novel C. elegans Notch components were verified experimentally. 40 novel drug target candidates were identified. Posters on the project were awarded both at the March (Tamás Korcsmáros) and September (Illés Farkas) FEBS signaling conferences. Manuscript, supporting website: http://signalink.org.

The updated, paperback version of the Weak Links book has been released

May 2009

The updated, paperback version of the successful 2006 book on Weak Links, i.e. low affinity, low intensity network contacts has been released in May 30th 2009 and can be ordered here. The book summarizes the stabilizing role of weak links in ALL complex systems, and offers novel chapters on network modules and on the creative elements of networks. The extensive coverage, the easy language and the 832 original references make this book a very good companion to anyone interested in networks between age 14 (or before) and 114 (or later).

The recent Link-Group paper showing that aging is a price of cooperation and complexity became a highlight of BioEssays

Apr 2009

The LINK-Group paper showing that aging can be perceived as a price of cooperation and the development of complexity of the self-organizing matter became a highlight of the June issue of BioEssays. The paper shows that the emergence of hierarchical complexity needs cooperation. This leads to the ageing (i.e. gradual deterioration) of the constituent networks. A stable environment develops cooperation leading to over-optimization, and forming an ‘always-old’ network, which accumulates damage, and dies in an apoptosis-like process. A rapidly changing environment develops competition forming a 'forever-young' network, which may suffer an occasional over-perturbation exhausting system-resources, and causing death in a necrosis-like process. The paper summarizes how various forms of cooperation and consequent ageing emerge as key elements in all major steps of evolution from the formation of protocells to the establishment of the globalized, modern human society.

The SignaLink database received the best poster award of the 2009 FEBS SysBio Conference

March 2009

Tamás Korcsmáros and co-authors presented the SignaLink signaling and protein-protein interaction database at the FEBS SysBio Conference (7-13 March 2009, Alpbach, Austria) and received the best poster award of the meeting. The database and results will be available soon here.

The ModuLand modularization program received a silver medal on a Hungarian National Competition

Feb 2009

Máté Szalay, Robin Palotai and István Kovács received a silver medal on the Hungarian National Science Competition of Undergraduate Students for the ModuLand method determining the overlapping modules of complex networks. A preliminary version of the method can be found here as a patent application. The full description of the method, results and all algorithms, programs and source codes will be available soon here.

The Journal of Biology LINK-Group paper on network-based drug-target prediction became a "highly accessed" paper

Aug 2008

The LINK-Group paper summarizing a number of recent drug-target network papers in leading journals and suggesting novel methods for the network-based prediction of novel drug targets as well as a better network-based assessment of drug candidate efficiency and side effects became a "Highly accessed" paper of the Journal of Biology, the premier biology journal of BioMed Central. An extended version of the paper containing a more detailed description of network-based methods to assess drug-effects on cellular robustness can be found here

Peter Csermely published a Nature Journal Club paper, and its background info in Trends in Biochem. Sci. on creative elements

July 2008

LINK-Group member, Péter Csermely published a Nature Journal Club paper on the active centers of enzymes and proposed that the protein structure network elements forming these active centers, called creative elements, can be found in all evolved networks and play a key role in the development, inheritance and regulation of evolvability. The detailed description of creative elements appeared as a cover story in Trends in Biochem. Sci. and can be found here.Download it!