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Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication.

R, König Y, Zhou D, Elleder Tl, Diamond Gm, Bonamy Jt, Irelan Cy, Chiang Bp, Tu Pd, De Jesus Ce, Lilley ...

Published in Cell

Human Immunodeficiency Viruses (HIV-1 and HIV-2) rely upon host-encoded proteins to facilitate their replication. Here, we combined genome-wide siRNA analyses with interrogation of human interactome databases to assemble a host-pathogen biochemical network containing 213 confirmed host cellular factors and 11 HIV-1-encoded proteins. Protein complex...

Integrated genomic characterization of papillary thyroid carcinoma.

Cancer Genome Atlas Research, Network

Published in Cell

Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. Here, we describe the genomic landscape of 496 PTCs. We observed a low frequency of somatic alterations (relative to other carcinomas) and extended the set of known PTC driver alterations to include EIF1AX, PPM1D, and CHEK2 and diverse gene fusions. These discoveries reduc...

PKCε promotes oncogenic functions of ATF2 in the nucleus while blocking its apoptotic function at mitochondria.

Lau, E Kluger, H Varsano, T Lee, K Scheffler, I Rimm, Dl Trey Ideker Ronai, Za

Published in Cell

The transcription factor ATF2 elicits oncogenic activities in melanoma and tumor suppressor activities in nonmalignant skin cancer. Here, we identify that ATF2 tumor suppressor function is determined by its ability to localize at the mitochondria, where it alters membrane permeability following genotoxic stress. The ability of ATF2 to reach the mit...

Forging new ties between E. coli genes.

T, Ideker

Published in Cell

A recent study in Nature (Isalan et al., 2008) has examined the effects of systematically adding new transcriptional interactions in the bacterium Escherichia coli. Surprisingly, the majority of the engineered connections have no effect on growth, and in some cases the new connections enhance fitness. These findings reveal insights into the robustn...

Modeling transcriptome dynamics in a complex world.

Philipp Jaeger Doherty, C Trey Ideker

Published in Cell

An accurate prediction of how extrinsic stimuli influence changes in gene expression has been challenging. In this issue, Nagano and colleagues successfully model genome-wide mRNA expression changes under variable environmental conditions in rice, raising hopes that scientists will soon be able to predict genome-wide transcriptional responses in a ...

An atlas of combinatorial transcriptional regulation in mouse and man.

Ravasi, T Suzuki, H Cannistraci, Cv Katayama, S Bajic, Vb Tan, K Akalin, A Schmeier, S Kanamori-Katayama, M Bertin, N ...

Published in Cell

Combinatorial interactions among transcription factors are critical to directing tissue-specific gene expression. To build a global atlas of these combinations, we have screened for physical interactions among the majority of human and mouse DNA-binding transcription factors (TFs). The complete networks contain 762 human and 877 mouse interactions....

Boosting signal-to-noise in complex biology: prior knowledge is power.

Trey Ideker Dutkowski, J Hood, L

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...

Siri of the cell: what biology could learn from the iPhone.

Anne-Ruxandra Carvunis Trey Ideker

Published in Cell

Modern genomics is very efficient at mapping genes and gene networks, but how to transform these maps into predictive models of the cell remains unclear. Recent progress in computer science, embodied by intelligent agents such as Siri, inspires an approach for moving from networks to multiscale models able to predict a range of cellular phenotypes ...

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