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, Proteome, Systems biology, Gene
Papers published on a yearly basis
Papers
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TL;DR: The genome of the halophilic archaeon Halobacterium sp.
Abstract: The genome of the halophilic archaeon Halobacterium sp. NRC-1 and predicted proteome have been analyzed by computational methods and reveal characteristics relevant to life in an extreme environment distinguished by hypersalinity and high solar radiation: (1) The proteome is highly acidic, with a median pI of 4.9 and mostly lacking basic proteins. This characteristic correlates with high surface negative charge, determined through homology modeling, as the major adaptive mechanism of halophilic proteins to function in nearly saturating salinity. (2) Codon usage displays the expected GC bias in the wobble position and is consistent with a highly acidic proteome. (3) Distinct genomic domains of NRC-1 with bacterial character are apparent by whole proteome BLAST analysis, including two gene clusters coding for a bacterial-type aerobic respiratory chain. This result indicates that the capacity of halophiles for aerobic respiration may have been acquired through lateral gene transfer. (4) Two regions of the large chromosome were found with relatively lower GC composition and overrepresentation of IS elements, similar to the minichromosomes. These IS-element-rich regions of the genome may serve to exchange DNA between the three replicons and promote genome evolution. (5) GC-skew analysis showed evidence for the existence of two replication origins in the large chromosome. This finding and the occurrence of multiple chromosomes indicate a dynamic genome organization with eukaryotic character.
318 citations
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TL;DR: In this article, the authors show that immunoglobulin (Ig)G2a and 2b autoantibodies are the pathogenic isotypes by recruiting FcγRIV expressing macrophages.
Abstract: Loss of tolerance in systemic lupus erythematosus (SLE) leads to the generation of autoantibodies, which accumulate in end-organs where they induce disease. Here we show that immunoglobulin (Ig)G2a and 2b autoantibodies are the pathogenic isotypes by recruiting FcγRIV expressing macrophages. Class switching, but not development, of IgM anti-self B cells to these pathogenic subclasses requires the innate immune receptor Toll-like receptor (TLR)9 and MyD88 signaling. In their absence, switching of autoreactive B cells to the IgG2a and 2b subclasses is blocked, resulting in reduced pathology and mortality. In contrast, switching of anti-self B cells to IgG1 is not perturbed and generation of nonautoreactive IgG2a and 2b antibodies is not impaired in TLR9-deficient mice. Thus, the TLR9 pathway is a potential target for therapeutic intervention in SLE.
317 citations
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TL;DR: It is shown that the metabolic system acts as a low-pass filter that reliably responds to a slowly changing environment, while effectively ignoring fast fluctuations, which suggests that although certain characteristics of the complex networks may differ when probed in a static environment, the system has been optimized for a robust response to a dynamically changing environment.
Abstract: Natural selection dictates that cells constantly adapt to dynamically changing environments in a context-dependent manner. Gene-regulatory networks often mediate the cellular response to perturbation, and an understanding of cellular adaptation will require experimental approaches aimed at subjecting cells to a dynamic environment that mimics their natural habitat. Here we monitor the response of Saccharomyces cerevisiae metabolic gene regulation to periodic changes in the external carbon source by using a microfluidic platform that allows precise, dynamic control over environmental conditions. We show that the metabolic system acts as a low-pass filter that reliably responds to a slowly changing environment, while effectively ignoring fast fluctuations. The sensitive low-frequency response was significantly faster than in predictions arising from our computational modelling, and this discrepancy was resolved by the discovery that two key galactose transcripts possess half-lives that depend on the carbon source. Finally, to explore how induction characteristics affect frequency response, we compare two S. cerevisiae strains and show that they have the same frequency response despite having markedly different induction properties. This suggests that although certain characteristics of the complex networks may differ when probed in a static environment, the system has been optimized for a robust response to a dynamically changing environment.
314 citations
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TL;DR: The observations that IL-10 has an unexpected negative effect on Aβ proteostasis and cognition in APP mouse models demonstrate the complex interplay between innate immunity and protestasis in neurodegenerative diseases, an interaction the authors call immunoproteostasis.
314 citations
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University of Pennsylvania1, Roswell Park Cancer Institute2, National Institutes of Health3, J. Craig Venter Institute4, Cedars-Sinai Medical Center5, Fred Hutchinson Cancer Research Center6, California Institute of Technology7, University of California, San Francisco8, Stanford University9, Harvard University10, University of Washington11, Case Western Reserve University12, Los Alamos National Laboratory13, Lawrence Berkeley National Laboratory14, Children's Hospital Oakland Research Institute15, Institute for Systems Biology16, Boston Children's Hospital17, University of California, Santa Cruz18
TL;DR: This resource represents the first comprehensive integration of cytogenetic, radiation hybrid, linkage and sequence maps of the human genome and provides an independent validation of the sequence map and framework for contig order and orientation.
Abstract: We have placed 7,600 cytogenetically defined landmarks on the draft sequence of the human genome to help with the characterization of genes altered by gross chromosomal aberrations that cause human disease. The landmarks are large-insert clones mapped to chromosome bands by fluorescence in situ hybridization. Each clone contains a sequence tag that is positioned on the genomic sequence. This genome-wide set of sequence-anchored clones allows structural and functional analyses of the genome. This resource represents the first comprehensive integration of cytogenetic, radiation hybrid, linkage and sequence maps of the human genome; provides an independent validation of the sequence map and framework for contig order and orientation; surveys the genome for large-scale duplications, which are likely to require special attention during sequence assembly; and allows a stringent assessment of sequence differences between the dark and light bands of chromosomes. It also provides insight into large-scale chromatin structure and the evolution of chromosomes and gene families and will accelerate our understanding of the molecular bases of human disease and cancer.
314 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 |