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1 News 161 Publications 32 Members

Evolutionarily conserved herpesviral protein interaction networks.

Fossum, E Friedel, Cc Rajagopala, Sv Titz, B Baiker, A Schmidt, T Kraus, T Stellberger, T Rutenberg, C Suthram, S ...

Published in PLoS Pathogens

Herpesviruses constitute a family of large DNA viruses widely spread in vertebrates and causing a variety of different diseases. They possess dsDNA genomes ranging from 120 to 240 kbp encoding between 70 to 170 open reading frames. We previously reported the protein interaction networks of two herpesviruses, varicella-zoster virus (VZV) and Kaposi ...

Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling.

Hustedt, N Seeber, A Sack, R Tsai-Pflugfelder, M Bhullar, B Vlaming, H Van Leeuwen, F Guénolé, A Van Attikum, H Srivas, R ...

Published in Molecular Cell

Mec1-Ddc2 (ATR-ATRIP) controls the DNA damage checkpoint and shows differential cell-cycle regulation in yeast. To find regulators of Mec1-Ddc2, we exploited a mec1 mutant that retains catalytic activity in G2 and recruitment to stalled replication forks, but which is compromised for the intra-S phase checkpoint. Two screens, one for spontaneous su...

NDEx, the Network Data Exchange.

Pratt, D Jing Chen David Welker Rivas, R Rudolf T. Pillich Vladimir Rynkov Keiichiro Ono Miello, C Hicks, L Szalma, S ...

Published in Cell Systems

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....

Improving breast cancer survival analysis through competition-based multidimensional modeling.

Bilal, E Dutkowski, J Guinney, J Jang, Is Logsdon, Ba Pandey, G Sauerwine, Ba Shimoni, Y Moen Vollan, Hk Mecham, Bh ...

Published in PLoS Computational Biology

Breast cancer is the most common malignancy in women and is responsible for hundreds of thousands of deaths annually. As with most cancers, it is a heterogeneous disease and different breast cancer subtypes are treated differently. Understanding the difference in prognosis for breast cancer based on its molecular and phenotypic features is one aven...

Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression.

Chuang, Hy Rassenti, L Salcedo, M Kate Licon Kohlmann, A Haferlach, T Foà, R Trey Ideker Kipps, Tj

Published in Blood

The clinical course of patients with chronic lymphocytic leukemia (CLL) is heterogeneous. Several prognostic factors have been identified that can stratify patients into groups that differ in their relative tendency for disease progression and/or survival. Here, we pursued a subnetwork-based analysis of gene expression profiles to discriminate betw...

Systems biology 101—what you need to know.

Trey Ideker

Published in Nature Biotechnology

Global architecture of genetic interactions on the protein network.

Ozier, O Amin, N Trey Ideker

Published in Nature Biotechnology

ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer.

Choueiri, Mb John Paul Y.C. Shen Gross, Am Justin Huang Trey Ideker Fanta, P

Published in PLoS ONE

In patients with metastatic colon cancer, response to first line chemotherapy is a strong predictor of overall survival (OS). Currently, oncologists lack diagnostic tests to determine which chemotherapy regimen offers the greatest chance for response in an individual patient. Here we present the results of gene expression analysis for two genes, ER...

NeXO Web: the NeXO ontology database and visualization platform.

Dutkowski, J Keiichiro Ono Michael Kramer Michael Yu Pratt, D Barry Demchak Trey Ideker

Published in Nucleic Acids Research

The Network-extracted Ontology (NeXO) is a gene ontology inferred directly from large-scale molecular networks. While most ontologies are constructed through manual expert curation, NeXO uses a principled computational approach which integrates evidence from hundreds of thousands of individual gene and protein interactions to construct a global hie...

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