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Checkpoint kinases regulate a global network of transcription factors in response to DNA damage. PDF available through Get Fulltext Research

Jaehnig, Eric J Kuo, Dwight Hombauer, Hans Ideker, Trey G Kolodner, Richard D

Published in Cell reports

DNA damage activates checkpoint kinases that induce several downstream events, including widespread changes in transcription. However, the specific connections between the checkpoint kinases and downstream transcription factors (TFs) are not well understood. Here, we integrate kinase mutant expression profiles, transcriptional regulatory interactio...

Landscape of protein-protein interactions in Drosophila immune deficiency signaling during bacterial challenge.

H, Fukuyama Y, Verdier Y, Guan C, Makino-Okamura V, Shilova X, Liu E, Maksoud J, Matsubayashi I, Haddad K, Spirohn ...

Published in Proceedings of the National Academy of Sciences

The Drosophila defense against pathogens largely relies on the activation of two signaling pathways: immune deficiency (IMD) and Toll. The IMD pathway is triggered mainly by Gram-negative bacteria, whereas the Toll pathway responds predominantly to Gram-positive bacteria and fungi. The activation of these pathways leads to the rapid induction of nu...

Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. PDF available through Get Fulltext Research

Chang, Katherine Noelani Zhong, Shan Weirauch, Matthew T Hon, Gary Pelizzola, Mattia Li, Hai Huang, Shao-Shan Carol Schmitz, Robert J Urich, Mark A Kuo, Dwight ...

Published in eLife

The gaseous plant hormone ethylene regulates a multitude of growth and developmental processes. How the numerous growth control pathways are coordinated by the ethylene transcriptional response remains elusive. We characterized the dynamic ethylene transcriptional response by identifying targets of the master regulator of the ethylene signaling pat...

Dissection of DNA damage responses using multiconditional genetic interaction maps. PDF available through Get Fulltext Research

Guénolé, Aude Srivas, Rohith Vreeken, Kees Wang, Ze Zhong Wang, Shuyi Krogan, Nevan J Ideker, Trey van Attikum, Haico

Published in Molecular cell

To protect the genome, cells have evolved a diverse set of pathways designed to sense, signal, and repair multiple types of DNA damage. To assess the degree of coordination and crosstalk among these pathways, we systematically mapped changes in the cell's genetic network across a panel of different DNA-damaging agents, resulting in ~1,800,000 diffe...

Genome-wide methylation profiles reveal quantitative views of human aging rates. PDF available through Get Fulltext Research

Hannum, Gregory Guinney, Justin Zhao, Ling Zhang, Li Hughes, Guy Sadda, SriniVas Klotzle, Brandy Bibikova, Marina Fan, Jian-Bing Gao, Yuan ...

Published in Molecular cell

The ability to measure human aging from molecular profiles has practical implications in many fields, including disease prevention and treatment, forensics, and extension of life. Although chronological age has been linked to changes in DNA methylation, the methylome has not yet been used to measure and compare human aging rates. Here, we build a q...

A travel guide to Cytoscape plugins.

Saito, Rintaro Smoot, Michael E Ono, Keiichiro Ruscheinski, Johannes Wang, Peng-Liang Lotia, Samad Pico, Alexander R Bader, Gary D Ideker, Trey

Published in Nature methods

Cytoscape is open-source software for integration, visualization and analysis of biological networks. It can be extended through Cytoscape plugins, enabling a broad community of scientists to contribute useful features. This growth has occurred organically through the independent efforts of diverse authors, yielding a powerful but heterogeneous set...

DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1. PDF available through Get Fulltext Research

Travesa, Anna Kuo, Dwight de Bruin, Robertus A M Kalashnikova, Tatyana I Guaderrama, Marisela Thai, Kevin Aslanian, Aaron Smolka, Marcus B Yates, John R 3rd Ideker, Trey ...

Published in The EMBO journal

MBF and SBF transcription factors regulate a large family of coordinately expressed G1/S genes required for early cell-cycle functions including DNA replication and repair. SBF is inactivated upon S-phase entry by Clb/CDK whereas MBF targets are repressed by the co-repressor, Nrm1. Using genome-wide expression analysis of cells treated with methyl ...

Differential network biology. PDF available through Get Fulltext Research

Ideker, Trey Krogan, Nevan J

Published in Molecular systems biology

Protein and genetic interaction maps can reveal the overall physical and functional landscape of a biological system. To date, these interaction maps have typically been generated under a single condition, even though biological systems undergo differential change that is dependent on environment, tissue type, disease state, development or speciati...

The protein architecture of human secretory vesicles reveals differential regulation of signaling molecule secretion by ... PDF available through Get Fulltext Research

Bark, Steven J Wegrzyn, Jill Taupenot, Laurent Ziegler, Michael O'Connor, Daniel T Ma, Qi Smoot, Michael Ideker, Trey Hook, Vivian

Published in PloS one

Secretory vesicles are required for release of chemical messengers to mediate intercellular signaling among human biological systems. It is necessary to define the organization of the protein architecture of the 'human' dense core secretory vesicles (DCSV) to understand mechanisms for secretion of signaling molecules essential for cellular regulato...

Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic pro... PDF available through Get Fulltext Research

Mercer, Elinore M Lin, Yin C Benner, Christopher Jhunjhunwala, Suchit Dutkowski, Janusz Flores, Martha Sigvardsson, Mikael Ideker, Trey Glass, Christopher K Murre, Cornelis ...

Published in Immunity

Recent studies have documented genome-wide binding patterns of transcriptional regulators and their associated epigenetic marks in hematopoietic cell lineages. In order to determine how epigenetic marks are established and maintained during developmental progression, we have generated long-term cultures of hematopoietic progenitors by enforcing the...

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