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
• 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/
• 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

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

• 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/

• 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

• 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

• 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/

• 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/

• 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

• 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

Mathematical tools

• NetLogo: a cross-platform multi-agent programmable modeling environment: http://ccl.northwestern.edu/netlogo/
• tnet - analysis of weighted, two-mode and longitudinal networks: http://opsahl.co.uk/tnet/content/view/15/27/
• BisoGenet - http://bio.cigb.edu.cu/bisogenet - Bioinformatic tool for searching, visualizing and analizing molecular interactions information around a set of genes/proteins.
• BIANA - http://sbi.imim.es/web/BIANA.php - a software framework for compiling biological interactions and analyzing networks
• TULIP: Graph visualization software, http://tulip.labri.fr/TulipDrupal/
• Complex system modelling program: http://education.mit.edu/starlogo/
• Cytospace: Cytoscape is 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/
• Fast overlapping module explorer programs: http://www.angel.elte.hu/clustering
• Differential equation solvers:
  http://www.berkeleymadonna.com
  http://www.math.pitt.edu/~bard/xpp/whatis.html
• network map construction:
  http://discover.nci.nih.gov/kohnk/interaction_maps.html
  http://vlado.fmf.uni-lj.si/pub/networks/pajek
  http://paup.csit.fsu.edu
  http://www.yworks.com/en/products_yed_about.htm?gclid=CP-8taC365wCFQYTzAodEn-UiA
• Arena 3d: visualizes datas in layers in 3D: http://arena3d.org/
• VisANT: a three-tier enterprise system designed specifically for the integrative visual data-mining of multi-scale Bio-Network/Pathways http://visant.bu.edu/
• digital organism development programs: http://physis.sourceforge.net
• R-statistics: http://www.r-project.org
• image analysis software: http://rsb.info.nih.gov/nih-image/Default.html
• simulation of stochastic processes: http://info.anat.cam.ac.uk/groups/comp-cell/StochSim.html
• conformational spread hypothesis: an interesting example of Boolean behavior: http://info.anat.cam.ac.uk/groups/comp-cell/ConfSpread.html
• Osprey is a software platform for visuaization of complex interaction networks: http://biodata.mshri.on.ca/osprey/servlet/Index
• Gephi: visualization and exploration platform for networks and complex systems http://gephi.org/
• Dynamic multi-level network analysis http://www.dynanets.org/
• R statistical computing and graphics http://www.r-project.org/
• Text mining www.textrend.org
• Network Workbench: A Large-Scale Network Analysis, Modeling and Visualization Toolkit for Biomedical, Social Science and Physics Research. http://nwb.slis.indiana.edu/
• Social network analysis software http://en.wikipedia.org/wiki/Social_network_analysis_software

Network datasets

• Network time series datasources http://www.stanford.edu/group/sonia/dataSources/index.html