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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...

An integrated map of HIV-human protein complexes that facilitate viral infection. PDF available through Get Fulltext Research

Emig-Agius, Dorothea Olivieri, Kevin Pache, Lars Shih, Hsin Ling Pustovalova, Olga Bessarabova, Marina Young, John A T Chanda, Sumit K Ideker, Trey

Published in PloS one

Recent proteomic and genetic studies have aimed to identify a complete network of interactions between HIV and human proteins and genes. This HIV-human interaction network provides invaluable information as to how HIV exploits the host machinery and can be used as a starting point for further functional analyses. We integrated this network with com...

Development of ultra-high-density screening tools for microbial "omics". PDF available through Get Fulltext Research

Bean, Gordon J Jaeger, Philipp A Bahr, Sondra Ideker, Trey

Published in PloS one

High-throughput genetic screens in model microbial organisms are a primary means of interrogating biological systems. In numerous cases, such screens have identified the genes that underlie a particular phenotype or a set of gene-gene, gene-environment or protein-protein interactions, which are then used to construct highly informative network maps...

Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer... PDF available through Get Fulltext Research

Gross, Andrew M Kreisberg, Jason F Ideker, Trey

Published in PloS one

To identify the transcriptional regulatory changes that are most widespread in solid tumors, we performed a pan-cancer analysis using over 600 pairs of tumors and adjacent normal tissues profiled in The Cancer Genome Atlas (TCGA). Frequency of upregulation was calculated across mRNA expression levels, microRNA expression levels and CpG methylation ...

Rac2 controls tumor growth, metastasis and M1-M2 macrophage differentiation in vivo. PDF available through Get Fulltext Research

Joshi, Shweta Singh, Alok R Zulcic, Muamera Bao, Lei Messer, Karen Ideker, Trey Dutkowski, Janusz Durden, Donald L

Published in PloS one

Although it is well-established that the macrophage M1 to M2 transition plays a role in tumor progression, the molecular basis for this process remains incompletely understood. Herein, we demonstrate that the small GTPase, Rac2 controls macrophage M1 to M2 differentiation and the metastatic phenotype in vivo. Using a genetic approach, combined with...

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