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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...

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 ...

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...

Boosting signal-to-noise in complex biology: prior knowledge is power. PDF available through Get Fulltext Research

Ideker, Trey Dutkowski, Janusz Hood, Leroy

Published in Cell

A major difficulty in the analysis of complex biological systems is dealing with the low signal-to-noise inherent to nearly all large biological datasets. We discuss powerful bioinformatic concepts for boosting signal-to-noise through external knowledge incorporated in processing units we call filters and integrators. These concepts are illustrated...

PiNGO: a Cytoscape plugin to find candidate genes in biological networks.

M, Smoot K, Ono T, Ideker S, Maere

Published in Bioinformatics

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