Institution
Institute for Systems Biology
Nonprofit•Seattle, Washington, United States•
About: Institute for Systems Biology is a nonprofit organization based out in Seattle, Washington, United States. It is known for research contribution in the topics: Population & Proteomics. The organization has 1277 authors who have published 2777 publications receiving 353165 citations.
Topics: Population, Proteomics, Gene, Proteome, Systems biology
Papers published on a yearly basis
Papers
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TL;DR: Using global gene expression data from macrophages stimulated with a variety of Toll-like receptor agonists, it is found that macrophage dynamics are indeed critical, providing the most compelling evidence to date for this general principle of dynamics in biological systems.
Abstract: Cells are dynamical systems of biomolecular interactions that process information from their environment to mount diverse yet specific responses. A key property of many self-organized systems is that of criticality: a state of a system in which, on average, perturbations are neither dampened nor amplified, but are propagated over long temporal or spatial scales. Criticality enables the coordination of complex macroscopic behaviors that strike an optimal balance between stability and adaptability. It has long been hypothesized that biological systems are critical. Here, we address this hypothesis experimentally for system-wide gene expression dynamics in the macrophage. To this end, we have developed a method, based on algorithmic information theory, to assess macrophage criticality, and we have validated the method on networks with known properties. Using global gene expression data from macrophages stimulated with a variety of Toll-like receptor agonists, we found that macrophage dynamics are indeed critical, providing the most compelling evidence to date for this general principle of dynamics in biological systems.
224 citations
Baylor College of Medicine1, University of Texas at San Antonio2, University of Bari3, Agency for Science, Technology and Research4, Louisiana State University5, Comenius University in Bratislava6, University of Wisconsin-Madison7, Saint Louis University8, Indiana University9, University of Illinois at Urbana–Champaign10, Children's Hospital Oakland Research Institute11, University of Washington12, Wellcome Trust Sanger Institute13, University of Geneva14, Boehringer Ingelheim15, University of Houston16, Harvard University17, University College London18, Institute for Systems Biology19, Massachusetts Institute of Technology20, University of Utah21, University of Oviedo22, Pompeu Fabra University23, Novartis24, University of California, Santa Cruz25, Howard Hughes Medical Institute26, Wayne State University27, Rutgers University28, Swiss Institute of Bioinformatics29, Imperial College London30
TL;DR: The whole-genome sequence of the common marmoset enables increased power for comparative analyses among available primate genomes and facilitates biomedical research application.
Abstract: Kim Worley and colleagues report the whole-genome sequence of the common marmoset, Callithrix jacchus, the first New World monkey to be sequenced.
222 citations
TL;DR: A molecular link between thymoma and the autoimmune disease myasthenia gravis is identified, characterized by tumoral overexpression of muscle autoantigens, and increased aneuploidy.
222 citations
TL;DR: This work explored the immediate changes in gene expression in response to activation of a mitogen-activated protein kinase pathway in yeast by mating pheromone and found that analysis of transcript level, albeit extremely important, is insufficient by itself to describe completely the phenotypes of cells under different conditions.
222 citations
TL;DR: It is argued that DNA-centered network modeling, separate descriptions of network organization and network behavior, and support for network documentation and annotation are essential requirements for computational modeling of developmental GRNs.
222 citations
Authors
Showing all 1292 results
| Name | H-index | Papers | Citations |
|---|---|---|---|
| Younan Xia | 216 | 943 | 175757 |
| Ruedi Aebersold | 182 | 879 | 141881 |
| David Haussler | 172 | 488 | 224960 |
| Steven P. Gygi | 172 | 704 | 129173 |
| Nahum Sonenberg | 167 | 647 | 104053 |
| Leroy Hood | 158 | 853 | 128452 |
| Mark H. Ellisman | 117 | 637 | 55289 |
| Wei Zhang | 112 | 1189 | 93641 |
| John Ralph | 109 | 442 | 39238 |
| Eric H. Davidson | 106 | 454 | 47058 |
| James R. Heath | 103 | 425 | 58548 |
| Alan Aderem | 99 | 246 | 46682 |
| Anne-Claude Gingras | 97 | 336 | 40714 |
| Trey Ideker | 97 | 306 | 72276 |
| Michael H. Gelb | 94 | 506 | 34714 |