Groups working on networks and complex systems

• Luigi F. Agnati:
  http://www.cibiotech.it/asp/dtglresponsabile.asp?ID_socio=77
• Reka Albert:
  http://www.phys.psu.edu/~ralbert/
• László A. Barabási:
  www.BarabasiLab.com
• Adam P. Arkin:
  http://gobi.lbl.gov/~aparkin/People/TheBoss.html
• György Buzsáki:
  http://osiris.rutgers.edu/frontmid/indexmid.html
• Cambridge Networks Network
  http://www.cnn.group.cam.ac.uk/
• Gerald M. Edelman:
  http://www.nsi.edu/public/scientists/index.php
• Murray Gell-Mann:
  http://www.santafe.edu/sfi/People/mgm/
• Mark Granovetter:
  http://www.stanford.edu/
  dept/soc/people/faculty/granovetter/granovet.html
• Balázs Gulyás:
  http://www.cns.ki.se/en/research/
  balazs_gulyas/balazs_gulyas/description.html
• Stuart A. Kaufmann:
  http://www.santafe.edu/sfi/People/kauffman/
• Jose Fernando Mendes, GNET:  http://www2.fis.ua.pt/grupoteorico/gteorico.htm
• Mark J. Newman:
  http://www.santafe.edu/~mark/
• Csaba Pléh:
  http://www.itm.bme.hu/ktk/csaba/
• Sándor Pongor:
  http://www.icgeb.trieste.it/RESEARCH/TS/Pongor.htm
• Ricard V. Solé:
  http://complex.upf.es/~ricard/
• Steven H. Strogatz:
  http://tam.cornell.edu/Strogatz.html
• Eörs Szathmáry:
  http://www.colbud.hu/main/FellowSection/permanentfellows.html
• Tamás Vicsek:
  http://angel.elte.hu/~vicsek/
  http://www.angel.elte.hu/clustering
• Duncan J. Watts:
  http://smallworld.columbia.edu/watts.html
• Peter Wolynes:
  http://www-chem.ucsd.edu/Faculty/bios/wolynes.html
• EmergeNet Group
  http://www.emergenet.org
  
• Cellular Network Biology Group:
  http://www.linkgroup.hu/links.php

Groups working with signaling networks

• Marc Vidal
  interactome modeling, molecular networks (C. elegans, Human)
  http://vidal.dfci.harvard.edu/
• Mark Gerstein
  tYNA Network Analyzer, literature-derived networks, predicting protein-protein interactions
  http://networks.gersteinlab.org/
• Sarah Teichmann
  organisation of protein domains in genome sequences, in metabolic pathways and in protein-protein interactions
  http://www.mrc-lmb.cam.ac.uk/genomes/Sarah/
• Tony Pawson
  mechanisms that underlie intracellular signal transduction, modular protein domains, synthetic biology
  http://pawsonlab.mshri.on.ca/
• Jason A. Papin
  signaling networks, cell-cell signaling, pathogen-host interactions
  http://www.bme.virginia.edu/csbl/
• Ravi Iyengar
  cellular signaling, heterotrimeric G proteins, dynamics of network topology
  http://www.mssm.edu/labs/iyengar/
• Harel Weinstein
  biomedicine, multidisciplinary approach, systems biology
  http://icb.med.cornell.edu/index.xml
• Trey G. Ideker
  comparative network science, DNA damage
  http://chianti.ucsd.edu/idekerlab/
  
• Hiroaki Kitano
  robustness of biological systems, metabolic pathways, protein-protein interactions
  http://www.symbio.jst.go.jp/symbio2/index.html http://www.systems-biology.org/
• Edda Klipp
  signal transduction, stress, yeast, systems biology
  http://www.molgen.mpg.de/~ag_klipp/
• Andre Levchenko
  bioinformatics, systems modelling
  http://www.icm.jhu.edu/
• Boris N. Kholodenko
  systems biology of cellular signaling, metabolic and gene networks
  http://cellnetworks.org/
• Upinder Bhalla
  quantitative cellular signaling, programing signaling pathways (MAPK)
  http://www.ncbs.res.in
• Bernhard O. Palsson
  metabolic and signaling networks, mathematical analysis
  http://gcrg.ucsd.edu/
• Wendell Lim
  protein-protein recognition, protein switches and networks, network evolution, synthetic biology
  http://www.ucsf.edu/limlab/
  
• Cellular Network Biology Group:
  http://www.linkgroup.hu/links.php

Biological science links

Aging databases

• AgeID: aging genes database http://uwaging.org/genesdb/index.php
• AnAge: Animal aging and longevity database http://genomics.senescence.info/species/
• GenAge: aging genes database http://genomics.senescence.info/genes/
• MatrixDB: extracellular aging-related PPI network http://matrixdb.ibcp.fr/
• NetAge: gene sets and microRNA-regulated PPI networks for longevity www.netage-project.org

Gene databases, List of E. coli gene database resources

• The yeast genome database: http://www.yeastgenome.org/
• The C. elegans knowledgebase: http://www.wormbase.org
• The Drosophila knowledgebase: http://www.flybase.org
• The database of selected eukaryotic genomes: http://www.ensembl.org

Genetic networks

• Gene interactions and pathways (genetic networks): http://www.biocarta.com/genes/allpathways.asp
  http://www.csa.ru/Inst/gorb_dep/inbios/genet/genet.htm
  http://www.its.caltech.edu/~mirsky/endomes.htm
  http://www.cifn.unam.mx/Computational_Genomics/regulondb
  http://strc.herts.ac.uk/bio/maria/NetBuilder/
  http://www.genome.jp/kegg/
• Genetic Interaction Predictor for C. elegans: http://tenaya.caltech.edu:8000/predict/
• Yeast sporulation network http://cmgm.stanford.edu/pbrown/sporulation
• Gene expression databases:
  http://www.ncbi.nlm.nih.gov/geo/
  http://www.mged.org/
  http://expression.gnf.org/
  http://genome-www5.stanford.edu/
• OpenStemCellWiki, a Differentially Expressed Connected Subnetwork (DECS) found to be active in human embryonic stem cells: http://www.openstemcellwiki.org

Protein databases

• BioGrid http://thebiogrid.org/
• IntAct experimentally verified, curated data  http://www.ebi.ac.uk/intact/main.xhtml
• MINT experimentally verified, curated data  http://160.80.34.4/mint/Welcome.do 
• STRING http://string-db.org/
• NetAge: Protein identifiers across multiple source databases, http://netage-project.org/
• http://www.ebi.ac.uk/Tools/picr/
• Yeast: http://www.proteome.com/YPDhome.html
• Human: http://www.hprd.org/
• Universal Protein Resource (UniProt): http://www.ebi.uniprot.org

Protein structure tools and networks

• Prediction of protein binding regions in disordered proteins http://anchor.enzim.hu
• Prediction of intrinsically unstructured proteins http://iupred.enzim.hu/
• RING is a web server that can be used to derive protein residue interaction networks, i.e. different physical/chemical interactions at atomic level, to be visualized with Cytoscape http://protein.bio.unipd.it/ring/

Protein networks

• Information about the microRNA-regulated protein-protein interaction networks
• Yeast:
  http://yeast.cellzome.com
  http://www.bind.ca
  http://dip.doe-mbi.ucla.edu/
  http://vidal.dfci.harvard.edu/fyi/
• C. elegans: http://vidal.dfci.harvard.edu/interactomedb/i-View/interactomeCurrent.pl
• Drosophila: http://proteome.wayne.edu/PIMdb.html
• Human: http://www.hprd.org/
• Filtered high throughput database of yeast, worm, fly and human PIN: http://helix.protein.osaka-u.ac.jp/htp/htp.php
  Mitochondrial interactome: http://mitointeractome.kobic.kr

Text search engines for extracting information on bionetwork

• Text mining: www.textrend.org
• iHOP provides the network of genes and proteins as a natural way of accessing the millions of abstracts in PubMed. By employing genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed becomes bound together into one navigable resource. : http://www.ihop-net.org/UniPub/iHOP/
• Arrowsmith: a tool for identifying links between two sets of Medline articles: http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/start.cgi
• Connect-Molecules Query: will attempt to find a sequence of interactions that connect two or more given molecules: http://cmap.nci.nih.gov/PW/Connect
• A Compendium of Free, Public Biomedical Text Mining Tools Available on the Web: http://arrowsmith.psych.uic.edu/arrowsmith_uic/tools.html
• Textpresso: http://www.textpresso.org/
• GoPubMed - Ontology based literature search: http://www.gopubmed.org/

Datamining sites for network buildings

• A rich collection of different pathway websites: http://www.pathguide.org
• MultiParanoid A database of multi-species clusters of orthologs: http://multiparanoid.cgb.ki.se
• MINT database for functional interactions between biological molecules (proteins, RNA, DNA): http://mint.bio.uniroma2.it/mint/Welcome.do
• pSTIING: knowledgebase about protein-protein, ligand-receptor interactions, receptor-cell type information and signal transduction pathways: http://pstiing.licr.org/
• BioGRID
  a database of physical and genetic interactions for model organisms including Homo sapiens, Saccharomyces cerevisiae, Mus musculus, C. elegans, and Drosophila melanogaster: http://www.thebiogrid.org/
• List of databases of interactions: http://www.biodirectory.com/directory/
  Molecular_interactions/Databases_of_interactions_394.html
• Functional annotation site: http://david.abcc.ncifcrf.gov/

Chemical reactions, metabolic networks

• modeling of biochemical reactions: http://www.gepasi.org/
• whole cell simulation:
  http://www.e-cell.org/
  http://www.nrcam.uchc.edu/
• metabolic networks (yeast): http://systemsbiology.ucsd.edu/organisms/yeast.html
  metabolic networks (E. coli): http://gcrg.ucsd.edu/organisms/ecoli.html
• red blood cell: http://systemsbiology.ucsd.edu/organisms/rbc.html

Signaling pathway analyzer tools

• Ingenuity Pathway Analyser: https://analysis.ingenuity.com/
• Hippron: Dynamic Signaling Maps: http://www.hippron.com/hippron/
• Biological Networks: http://brak.sdsc.edu/pub/BiologicalNetworks/reg.php
• SiTNA: http://www.eco.ethz.ch/SITNA/

Social networks

• Social network analysis software: http://en.wikipedia.org/wiki/Social_network_analysis_software
• Menopause and Black Cohosh Information center
• small world home

Complex system evolution

• NetLogo: a cross-platform multi-agent programmable modeling environment: http://ccl.northwestern.edu/netlogo/
• Physis - software tool for studying the evolution of self-replcating  machine-code  computer programs: http://physis.sourceforge.net
• Starlogo: Complex system modelling program: http://education.mit.edu/starlogo/

Network analysis

• BIANA - http://sbi.imim.es/web/BIANA.php - a software framework for compiling biological interactions and analyzing networks
• BisoGenet - http://bio.cigb.edu.cu/bisogenet - Bioinformatic tool for searching, visualizing and analyzing molecular interactions information around a set of genes/proteins
• Boolean Network Modeling - http://code.google.com/p/booleannet/ - Intuitive and accessible tools for simulating biological regulatory networks in a boolean formalism. Using this simulator biologist and bioinformaticians can specify their system in a simple textual language then explore various dynamic behaviors via a web interface or an application programming interface (API).
• Conan: a platform for complex network analysis (network reverse engineering, topological entropy, fractal dimension, modularization, etc.) http://github.com/rhz/conan/
• Cytoscape: an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data, http://www.cytoscape.org/
• CerebraL: it uses subcellular localization annotation to create a layered view of a cell, a Cytospace plugin http://www.pathogenomics.ca/cerebral/
• Dynamic multi-level network analysis http://www.dynanets.org/
• Gephi: visualization and exploration platform for networks and complex systems http://gephi.org/
• GraphCrunch 2 - http://bio-nets.doc.ic.ac.uk/graphcrunch2 - An open source, multi-platform (Windows and Linux) software tool for network modeling, alignment and clustering that parallelizes computationally intensive tasks.
• GUESS, a network visualization and analysis tool, http://graphexploration.cond.org/index.html
• Network modularization tools
• Agarwal method http://www-scf.usc.edu/~gaurava/
• Caflish method http://www.biochem-caflisch.uzh.ch/public/5/network-clusterization-algorithm.html
• CFinder for overlapping modules http://cfinder.org
• Clauset algorithms http://cs.unm.edu/~aaron/research/fastmodularity.htm http://tuvalu.santafe.edu/~aaronc/hierarchy/
• Gregory’s methods like CONGA http://www.cs.bris.ac.uk/~steve/networks/index.html
• Jerarca hierarchical clustering method, http://jerarca.sourceforge.net/
• Latapy-Pons Walktrap http://www-rp.lip6.fr/~latapy/PP/walktrap.html
• Louvain method http://sites.google.com/site/findcommunities/
• Lumped Markov-chain community finding method (http://home.dei.polimi.it/piccardi/FTNCbyLMC.html)
• MCL, Markov Cluster Algorithm http://www.micans.org/mcl/
• ModuLand for pervasively overlapping modules www.linkgroup.hu/modules.php
• Nepusz method for overlapping modules http://www.cs.rhul.ac.uk/home/tamas/assets/files/fuzzyclust-static.tar.gz
• Radicchi method http://filrad.homelinux.org/Data/
• Rosvall – Bergstom Infomap http://www.tp.umu.se/~rosvall/code.html 
• Wakita method http://ken-wakita.net/research/en/community-structure-analysis/
• Wiggins methods http://www.columbia.edu/~chw2/code.html
• Network Workbench: A Large-Scale Network Analysis, Modeling and Visualization Toolkit for Biomedical, Social Science and Physics Research. http://nwb.slis.indiana.edu/
• RINalyzer - http://www.rinalyzer.de/ - A Cytoscape plugin to link Cytoscape with UCSF Chimera and thus to analyze and visualize residue interaction networks (RINs).
• RING - http://protein.bio.unipd.it/ring/ - RING is a web server that can be used to derive protein residue interaction networks, i.e. different physical/chemical interactions at atomic level, to be visualized with Cytoscape.
• Social network analysis software http://en.wikipedia.org/wiki/Social_network_analysis_software
• tnet - analysis of weighted, two-mode and longitudinal networks: http://opsahl.co.uk/tnet/content/view/15/27/
• UCSF Chimera - http://www.cgl.ucsf.edu/chimera/ - UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.
• VisANT: a three-tier enterprise system designed specifically for the integrative visual data-mining of multi-scale Bio-Network/Pathways http://visant.bu.edu/
• Wordom - http://wordom.sf.net - Wordom is a command line utility for molecular structure and dynamics analysis. It is also able to manipulate and convert dcd, xtc, pdb, crd and xyz files and can be used in shell scripts or in custom modules.

Network datasets

• Alex Arenas datasets: http://deim.urv.cat/~aarenas/data/welcome.htm
• Barabasi network data: http://www.barabasilab.com/rs-netdb.php http://www.nd.edu/~networks/resources.htm
• Benchmark graphs of Santo Fortunato: http://sites.google.com/site/santofortunato/inthepress2
• Gephi datasets: http://wiki.gephi.org/index.php/Datasets
• Indiana University datasets: http://iv.slis.indiana.edu/db/index.html
• International network archive http://www.princeton.edu/~ina/data/index.html
• Mark Newman network data: http://www-personal.umich.edu/~mejn/netdata/
• Network time series data-sources http://www.stanford.edu/group/sonia/dataSources/index.html
• Pajek datasets: http://vlado.fmf.uni-lj.si/pub/networks/data/
• RINdata - http://rinalyzer.de/rindata.php - 3D protein structure dataset created with RINalyzer/RINerator from Protein Data Bank.
• RING - http://protein.bio.unipd.it/ring/ - RING is a web server that can be used to derive protein residue interaction networks, i.e. different physical/chemical interactions at atomic level, to be visualized with Cytoscape.
• Social network datasets: http://datamob.org/datasets/tag/social-networks
• Stanford large network datasets: http://snap.stanford.edu/data/
• Thesaurus of synonym words:
  http://www.visualthesaurus.com/landing/?ad=cdo&utm_medium=default
  &utm_campaign=VT&utm_source=cdo&word=functionality
• Trust network datasets: http://www.trustlet.org/wiki/Trust_network_datasets
• UciNet datasets: http://vlado.fmf.uni-lj.si/pub/networks/data/UciNet/UciData.htm

Network visualization

• Arena 3D: visualizes biological networks in 3D: http://arena3d.org/
• A Chopin nocturne in a network sense: http://www.youtube.com/watch?v=asDXpfFMKNA
• Cytoscape: an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data, http://www.cytoscape.org/
• Gephi: visualization and exploration platform for networks and complex systems http://gephi.org/
• GUESS, a network visualization and analysis tool, http://graphexploration.cond.org/index.html
• Network Workbench: A Large-Scale Network Analysis, Modeling and Visualization Toolkit for Biomedical, Social Science and Physics Research. http://nwb.slis.indiana.edu/
• Osprey is a software platform for visualization of complex interaction networks: http://biodata.mshri.on.ca/osprey/servlet/Index
• Pajek: http://pajek.imfm.si/doku.php
• Paup for phylogenetic trees: http://paup.csit.fsu.edu
• RING - http://protein.bio.unipd.it/ring/ - RING is a web server that can be used to derive protein residue interaction networks, i.e. different physical/chemical interactions at atomic level, to be visualized with Cytoscape.
• Text visual representation: http://www.textarc.org/
• UCSF StructureViz - http://www.cgl.ucsf.edu/cytoscape/structureViz/ - UCSF structureViz is a Cytoscape plugin that links visualization of biological networks in Cytoscape with visualization and analysis of molecular structures in UCSF Chimera.
• VisANT: a three-tier enterprise system designed specifically for the integrative visual data-mining of multi-scale Bio-Network/Pathways http://visant.bu.edu/
• Web-site graphs: http://www.aharef.info/2006/05/websites_as_graphs.htm http://www.aharef.info/static/htmlgraph/
• yFiles: http://www.yworks.com/en/index.html

Other mathematical tools

• The database of useful biological numbers: http://bionumbers.hms.harvard.edu/default.aspx
• Differential equation solvers:
  http://www.berkeleymadonna.com
  http://www.math.pitt.edu/~bard/xpp/whatis.html

• NIH-Image, an image analysis software: http://rsb.info.nih.gov/nih-image/Default.html
• R statistical computing and graphics http://www.r-project.org/
• StochSim: stochastical simulation of biochemical reactions: http://www.ebi.ac.uk/~lenov/stochsim.html
• Text mining www.textrend.org

Related organizations

• Hungarian Cell Stress Society
  (an affiliate of Cell Stress Society International)
  • Annual report 2005.
  • Annual report 2006.
  • Annual report 2007.
  • Annual report 2008.
  • Annual report 2009.
  • Annual report 2010.