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: A remarkably high UV-radiation resistance in the extremely halophilic archaeon Halobacterium NRC-1 withstanding up to 110 J/m2 with no loss of viability is reported.
Abstract: We report a remarkably high UV-radiation resistance in the extremely halophilic archaeon Halobacterium NRC-1 withstanding up to 110 J/m2 with no loss of viability. Gene knockout analysis in two putative photolyase-like genes (phr1 and phr2) implicated only phr2 in photoreactivation. The UV-response was further characterized by analyzing simultaneously, along with gene function and protein interactions inferred through comparative genomics approaches, mRNA changes for all 2400 genes during light and dark repair. In addition to photoreactivation, three other putative repair mechanisms were identified including d(CTAG) methylation-directed mismatch repair, four oxidative damage repair enzymes, and two proteases for eliminating damaged proteins. Moreover, a UV-induced down-regulation of many important metabolic functions was observed during light repair and seems to be a phenomenon shared by all three domains of life. The systems analysis has facilitated the assignment of putative functions to 26 of 33 key proteins in the UV response through sequence-based methods and/or similarities of their predicted three-dimensional structures to known structures in the PDB. Finally, the systems analysis has raised, through the integration of experimentally determined and computationally inferred data, many experimentally testable hypotheses that describe the metabolic and regulatory networks of Halobacterium NRC-1.
145 citations
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European Bioinformatics Institute1, Protein Sciences2, Chongqing University of Posts and Telecommunications3, University of Michigan4, Australian National University5, University of California, San Diego6, Institute for Systems Biology7, University of Manitoba8, University of Cambridge9, University of Oxford10, University of California, Los Angeles11
TL;DR: Yasset Perez-Riverola,*, Mingze Baia,b,c,†, Felipe da Veiga Leprevostd, Silvano Squizzatoa, Young Mi Parka, Kenneth Hauga, Adam J. Carrolle, Dylan Spaldinga, Justin Paschalla, Mingxun Wangf, Noemi del-Toroa, Tobias Ternenta, Peng Zhangd,g, Nicola Busoa, Nuno Bandeiraf
Abstract: This work has been supported by the US NIH BD2K
grant U54 GM114833 and a National Natural Science
Foundation of China grant (61501071). A.I.N. is
supported by US National Institute of Health grant
(R01-GM-094231). Y.P.-R. is supported by BBSRC
‘PROCESS’ grant (BB/K01997X/1). M.B. is supported
by Projects of International Cooperation and
Exchanges grant (2014DFB30010). M.W. is supported
by an NIH grant (5P41GM103484-07). J.A.V. and
N.d.-T. are supported by the Wellcome Trust (grant
WT101477MA). T.T. is supported by the BBSRC
‘ProteoGenomics’ grant (BB/L024225/1). E.W.D. and
D.S.C. are supported in part by grant (U24 AI117966-
02S1). S.-A.S. is supported in part by US NIH BD2K
grant (1U24AI117966-01). M.W. and N.Bandeira were supported by NIH grant (5P41GM103484-07).
N.Bandeira was also partially supported as an Alfred
P. Sloan Fellow. S.Subramaniam is supported by NIH
grants U01 DK097430 and U01 CA198941
145 citations
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TL;DR: This is the first report demonstrating the ability of ATF3 to enhance breast cancer-initiating cell features and to feedback on TGFβ, and the functional significance of twist in ATF3 action.
Abstract: The activating transcription factor 3 (ATF3) gene is induced by a variety of signals, including many of those encountered by cancer cells. We present evidence that ATF3 is induced by TGFβ in the MCF10CA1a breast cancer cells and plays an integral role for TGFβ to upregulate its target genes snail, slug and twist, and to enhance cell motility. Furthermore, ATF3 upregulates the expression of the TGFb gene itself, forming a positive-feedback loop for TGFβ signaling. Functionally, ectopic expression of ATF3 leads to morphological changes and alterations of markers consistent with epithelial-to-mesenchymal transition (EMT). It also leads to features associated with breast-cancer-initiating cells: increased CD24low–CD44high population of cells, mammosphere formation and tumorigenesis. Conversely, knockdown of ATF3 reduces EMT, CD24low–CD44high cells and mammosphere formation. Importantly, knocking down twist, a downstream target, reduces the ability of ATF3 to enhance mammosphere formation, indicating the functional significance of twist in ATF3 action. To our knowledge, this is the first report demonstrating the ability of ATF3 to enhance breast cancer-initiating cell features and to feedback on TGFβ. Because ATF3 is an adaptive-response gene and is induced by various stromal signals, these findings have significant implications for how the tumor microenvironment might affect cancer development.
143 citations
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TL;DR: This review summarizes technical and conceptual advances in quantitative subproteome profiling based on tandem mass spectrometry and chemical probes and describes how such projects typically combine the use of chemical probes that are specific for a targeted group of proteins and may contain stable isotope signatures for accurate quantification.
143 citations
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TL;DR: It is shown that the MLL2 complex associates with the hematopoietic activator NF-E2 in erythroid cells and is important for H3K4 trimethylation and maximal levels of transcription at the beta-globin locus.
142 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 |