Welcome to the website of the LINK-Group!

Description of NetworGame 2.0, a program package to simulate spatial games on model and real world networks with individual starting strategies of any nodes was published as a preprint

May 2013

The NetworGame program package is a cross-platform, multi-threaded, generic tool to simulate repeated spatial games. NetworGame accommodates any model or real-world networks and is able to set individual starting strategies to any nodes. The NetworGame program package is a console application augmented with a Graphical User Interface, and a data mining tool, which helps extracting and storing data in comma-separated value (csv) format. You may see a more detailed characterization of the program and download its Linux- or Windows-compatible packages, and detailed instructions here. The preprint describing the results obtained by NetworGame can be accessed here: http://arxiv.org/abs/1304.3796

Description of Turbine 1.4, an extensive tool for the analysis of network perturbations and dynamics was published as a pre-print

May 2013

Turbine 1.4 is an open-source network analysis package for simulating network dynamics. It is particularly suited for experiments involving perturbations (i.e.: observing the effects of outside stimulations on a target network). Turbine is written in C++, and is currently available for Windows and Linux systems. Turbine is able to accommodate any model or real world networks, single, multiple, or continuous perturbations with custom-made delay or dissipation dynamics. You may see a more detailed characterization of the program and download all its components, source code, and detailed instructions here. The preprint describing the results obtained by Turbine can be accessed here: http://arxiv.org/abs/1305.2496

Our comprehensive review on the use of networks in drug design was published in Pharmacology & Therapeutics

May 2013

A comprehensive review on the topology and dynamics of networks was published in Pharmacology & Therapeutics. In the review we cited 1270 references, and gave extensive examples on the use of network approach in drug design. Several novel concepts were formulated, including the concept of the "central hit strategy", which selectively targets central node/edges of the flexible networks of infectious agents or cancer cells to kill them. On the contrary, the "network influence strategy" works against other diseases, where an efficient reconfiguration of rigid networks needs to be achieved. The review can be downloaded from here.

Peter Csermely was elected as a member of the Hungarian Academy of Sciences

May 2013

The LINK-member, Peter Csermely was elected as a member of the Hungarian Academy of Sciences. The Academy was established in 1825, covers all areas of science and the number of its members younger than 70 years can not be higher than 200.

Our extended signal transduction network and database, SignaLinK 2.0 was highlighted by Science Signaling

March 2013

SignaLink 2.0, the recently published extension of our former signaling network and database was highlighted in the March issue of Science Signaling. SignaLink 2.0 is the second network resource from our lab, after ModuLand featured by Science Signaling and included to their selected list of bioinformatics resources.

A network analysis of chromatin networks was published in Cell Reports

November 2012

As a joint work with Singaporean colleagues a detailed analysis of the interaction network of trancriptionally active, RNA-polymerase II-related DNA segments was published in Cell Reports. The paper successfully applied the ModuLand method of the LINK-Group and showed the existence of functional modules of the transcriptionally active chromatin.

The LINK-Group member Tamás Korcsmáros received the Prima Junior Award

October 2012

Tamás Korcsmáros has received the prestigeous Prima Junior Award recognizing excellent Hungarian young scientists.

Peter Csermely was elected as a member of Academia Europaea and as president of the European Council for High Ability

September 2012

LINK-Group member, Peter Csermely was elected at the Bergen-meeting of the Academia Europaea as a member of the academy.

He was also elected as the president of the European Council for High Ability between 2012 and 2016. The Council promotes network building of talent support acitvities in all European countries. This work is supported by the Budapest Centre of Talent Support established in the spring of 2012.

A significantly updated version of our signaling database, SignaLink 2.0 has been published

September 2012

In cooperation with the Cellular Network Biology Group in the Eötvös University an update of our signaling database Signalink 2.0 was published.

The updated version contains pathway regulators (e.g., scaffold and endocytotic proteins) and modifier enzymes (e.g., phosphatases, ubiquitin ligases) as well as the transcriptional and post-transcriptional regulators (transcription factors and micro-RNAs) besides signaling pathway components.

A Cytoscape plug-in of the ModuLand modularization program was published in Bioinformatics

August 2012

An updated version of the user-friendly, platform independent implementation of the LinkLand method of the ModuLand method family published earlier in PLoS ONE became available as a plug-in for the widely used Cytoscape program. The paper introducing the plug-in was published in Bioinformatics and can be accessed here. The introducing paper demonstrates the usefulness of the method

1. to identify an extensively overlapping modular structure;
2. to define a modular core and hierarchy allowing an easier functional annotation;
3. to identify key nodes of high community centrality, modular overlap or bridgeness in protein structure, protein-protein interaction and metabolic networks.

The program file and its User Guide can be downloaded from here.

We assembled ComPPI, a integrative protein-protein interaction database containing subcellular localizations

July 2012

ComPPI offers

1. an integrated dataset of 19 databases covering four species (S. cerevisiae, C. elegans, D. melanogaster, H. sapiens);
2. a hierarchic structure of subcellular localizations using >1500 GO cellular component terms;
3. a confidence score characterizing data-quality and interactome-consensus of subcellular localizations;
4. direct and advanced search options for individual proteins, interacting protein pairs, or interaction lists;
5. download options of whole-proteome, organelle-specific, or sub-organelle interactomes.

ComPPI searches can be initiated and subcellular organelle, or sub-organelle specific interactomes can be downloaded from here: http://linkgroup.hu/comppi/

A joint paper with Ruth Nussinov on the new drug-design paradigm of allo-network drugs was published as the cover story of the December issue of Trends in Pharmacological Sciences

November 2011

The paper proposed that the concept of allosteric drugs can be broadened to allo-network drugs, whose effects can propagate either within a protein, or across several proteins, to enhance or inhibit specific interactions along a pathway. Allo-network drugs can achieve specific, limited changes at the systems level, and in this way can achieve fewer side effects and lower toxicity. The paper summarized possible methods to identify allo-network drug targets and sites. The concept outlined a new paradigm in systems-based drug design. The paper, which was published as the cover story of the December issue of Trends in Pharmacological Sciences, can be downloaded from here.

Ágoston Mihalik's paper showing a partial desintegration of the yeast interactome as a general model of systems level adatptation processes has been published in PLoS Computational Biology

July 2011

The paper described that heat shock induces a marked decrease in the overlap of the communities (modules) of the yeast interactome. Our results indicated that heat shock induces a partial disintegration of the protein-protein interaction network. The residual inter-modular bridges, maintaining the integrity of the interactome after stress, were key proteins of stress-survival. The changes observed may be rather general occurring at the initial phase of crises in many complex systems, such as proteins in physical stretch, ecosystems in abrupt environmental changes or social networks in economic crisis. De-coupling and re-wiring of modules emerges as a general model of adaptation and learning. The paper and its Supplement, which were published in PLoS Computational Biology, can be downloaded from here.

Peter Csermely became a network and systems biology editor of (Nature) Scientific Reports

Peter Csermely became an editor of (Nature) Scientific Reports. The newly started journal publishes articles of all fields.

The Hungarian version of the book Weak Links was voted to the best 500 Hungarian books

June 2011

A wide panel of experts has recently determined the “Márai-list”, which is a list of the top 500 Hungarian books (including the top 250 non-fiction books) among a competing 8,000 books recommended to all Hungarian libraries. The Hungarian version of the book Weak Links (a 2009 Springer book on networks, which is downloadable from here or at Google) has been included to this selection of the top 250 non-fiction Hungarian books.

A summary paper of our results appeared in Science Signaling: Network-based tools in the identification of novel drug-targets

May 2011

A summary paper and an accompanying slide show of our work appeared in the May 2011 issue of Science Signaling. Slides were updated from the opening presentation at the International Conference on Systems Biology of Human Disease (SBHD) in Boston, Massachusetts, 16 to 18 June 2010. The paper contains several novel ideas on network dynamics and drug design, a summary of our very recent results as well as a brief description of a few ongoing projects. The paper is available here and the accompanying slideshow is downloadable from here.

A hypothesis on protein signal transduction mechanism and a comprehensive review on disordered proteins

February 2011

A LINK-Group paper has been accepted in the special issue of Current Protein and Peptide Science on disordered proteins (edited by Vladimir Uversky). The paper gives a comprehensive review on A.) the network descriptions of disordered proteins, B.) the consequences of network disorder on protein structure and dynamics; and C.) the functional consequences of protein disorder in cellular networks. Besides these the paper formulates two hypotheses: I.) on a novel classification of proteins to stratus- and cumulus-type classes describing the two ways of intramolecular signal transduction in these networks, and II.) suggesting that disorder plays a major role to reach hidden, rarely visited protein conformations important e.g. in cellular signaling. The paper can be downloaded from here.

The ModuLand method has been featured in Science Signaling

February 2011

The February 2011 issue of Science Signaling highlighted the ModuLand method as one of the two network modeling tools of its ST Netwatch section. The method has been published earlier in PLoS ONE and we currently develop its user-friendly application as well as its sequel(s). The free computer program package with User Guide, algorithms and background can be downloaded from here.