Systems biology tools

Current limitations and future visions of this emerging field are discussed, with the conclusion that combining knowledge from biological pathways and high-throughput omics data will move clinical medicine one step further to individualize medical diagnosis and treatment.

Abstract Systems biology aims to understand the nonlinear interactions of multiple biomolecular components that characterize a living organism. Publication types Research Support, Non-U. Gov't Review. Gaggle, genome browser, tiling arrays, ChIP-chip Visualization Genome Fingerprints Genome fingerprints enable ultrafast comparison of personal genomes.

Analysis Software Computation, Genomics, Analysis, Privacy Genotype Fingerprints Genotype fingerprints enable fast and private comparison of genetic testing results for research and direct-to-consumer applications. Analysis Software Database Kojak Database search algorithm to identify cross-linked peptides from tandem mass spectra. This data set includes the values of multiple genetic markers.

Information Resource Database, Proteomics, Public Resource, SRM, Transitions PeptideAtlas PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. PeptideProphet is now a core part of the Trans-Proteomic Pipeline software distrubtion. We denote these consistently observed peptides to be proteotypic peptides. A comprehensive map of the mTOR signaling network.

Kaizu, K. A comprehensive molecular interaction map of the budding yeast cell cycle. Kanehisa, M. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. Joshi-Tope, G. Reactome: a knowledgebase of biological pathways.

Mi, H. Cerami, E. Pathway Commons, a web resource for biological pathway data. Karp, P. Hucka, M. The systems biology markup language SBML : a medium for representation and exchange of biochemical network models.

Bioinformatics 19 , — An original paper on SBML that triggered various standardization efforts in systems biology. Demir, E. The BioPAX community standard for pathway data sharing.

Le Novere, N. The Systems Biology Graphical Notation. Using process diagrams for the graphical representation of biological networks. Klipp, E. Systems biology standards — the community speaks. Sauro, H. OMICS 7 , — Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics 9 , Shannon, P. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Bauer-Mehren, A. Pathway databases and tools for their exploitation: benefits, current limitations and challenges.

Calzone, L. Thiele, I. Reconstruction annotation jamborees: a community approach to systems biology. This paper discusses issues regarding community efforts to reconstruct comprehensive metabolic networks. A protocol for generating a high-quality genome-scale metabolic reconstruction. Feist, A. Reconstruction of biochemical networks in microorganisms. A review on the current state-of-the-art in data-driven genome-wide network reconstruction.

Herrgard, M. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Wu, G. A comprehensive molecular interaction map for rheumatoid arthritis. Matsuoka, Y. Payao: a community platform for SBML pathway model curation. Bioinformatics 26 , — Pico, A. WikiPathways: pathway editing for the people. Wierling, C. Resources, standards and tools for systems biology. A text book with examples of modelling and computational analysis.

Google Scholar. Lopez-Aviles, S. Irreversibility of mitotic exit is the consequence of systems-level feedback. McAdams, H. Stochastic mechanisms in gene expression. Ozbudak, E. Regulation of noise in the expression of a single gene. Arkin, A. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells.

Genetics , — Emonet, T. AgentCell: a digital single-cell assay for bacterial chemotaxis. Bioinformatics 21 , — Hofestadt, R. Quantitative modeling of biochemical networks.

Health Technol. Blinov, M. BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Swainston, N. Enzyme kinetics informatics: from instrument to browser. FEBS J. Waltemath, D. Dada, J. SBRML: a markup language for associating systems biology data with models.

Hoops, S. Haefner, J. Kauffman, S. Metabolic stability and epigenesis in randomly constructed genetic nets. Zheng, J. SimBoolNet — a Cytoscape plugin for dynamic simulation of signaling networks. Iglesias, P. An excellent collection of introductory articles on how control theory can be applied to systems biology analysis.

Chen, Q. Genetic basis and molecular mechanism for idiopathic ventricular fibrillation. Noble, D. Modeling the heart — from genes to cells to the whole organ. Nomura, T. Towards integration of biological and physiological functions at multiple levels. Gleeson, P. NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail.

Asai, Y. Specifications of insilicoML 1. Plewczynski, D. Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database. Englebienne, P. Docking ligands into flexible and solvated macromolecules. Swertz, M. Beyond standardization: dynamic software infrastructures for systems biology. Kemper, B. PathText: a text mining integrator for biological pathway visualizations.

Bioinformatics 26 , i—i Maier, H. LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts. Huss, J. The Gene Wiki: community intelligence applied to human gene annotation. Callaway, E. No rest for the bio-wikis.