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Article
Open AccessSIX1 and EWS/FLI1 co-regulate an anti-metastatic gene network in Ewing Sarcoma
Ewing sarcoma (ES), which is characterized by the presence of oncogenic fusion proteins such as EWS/FLI1, is an aggressive pediatric malignancy with a high rate of early dissemination and poor outcome after di...
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Article
Open AccessA harmonized resource of integrated prostate cancer clinical, -omic, and signature features
Genomic and transcriptomic data have been generated across a wide range of prostate cancer (PCa) study cohorts. These data can be used to better characterize the molecular features associated with clinical out...
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Article
Open AccessInhibition of the CCL2 receptor, CCR2, enhances tumor response to immune checkpoint therapy
Immunotherapies targeting the PD-1/PD-L1 axis are now a mainstay in the clinical management of multiple cancer types, however, many tumors still fail to respond. CCL2 is highly expressed in various cancer type...
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Article
Open AccessTrisomy 21 activates the kynurenine pathway via increased dosage of interferon receptors
Trisomy 21 (T21) causes Down syndrome (DS), affecting immune and neurological function by ill-defined mechanisms. Here we report a large metabolomics study of plasma and cerebrospinal fluid, showing in indepen...
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Article
Open AccessSimulating heterogeneous populations using Boolean models
Certain biological processes, such as the development of cancer and immune activation, can be controlled by rare cellular events that are difficult to capture computationally through simulations of individual ...
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Article
Crowdsourcing biomedical research: leveraging communities as innovation engines
Crowdsourcing is emerging as a novel framework to tackle scientific problems.
A variant of crowdsourcing, s...
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Article
A community effort to assess and improve drug sensitivity prediction algorithms
A community of researchers report the lessons learned from applying 44 algorithms to predict drug sensitivity in cancer cell lines using genomic, epigenetic and proteomic datasets
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Article
A community computational challenge to predict the activity of pairs of compounds
A community computational challenge generates algorithms to predict activity of drug combinations.
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Article
International progress: from cytology to genomics
The past decade has seen many notable contributions to bladder cancer research. Here, we highlight the international efforts in the field, with findings from Europe, USA and China, as well as papers resulting ...
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Article
Correction: Corrigendum: Oncogenic NRAS signaling differentially regulates survival and proliferation in melanoma
Nat. Med. 18, 1503–1510 (2012); published online 16 September 2012; corrected after print 20 November 2012 In the version of this article initially published, the formula to calculate the mutual information ma...
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Article
Oncogenic NRAS signaling differentially regulates survival and proliferation in melanoma
NRAS-driven melanomas have limited therapeutic options. Combining genetically engineered models and oncogenic signaling inhibitors with rational systems-biology approaches, the authors compare the effects of g...
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Article
Wisdom of crowds for robust gene network inference
This analysis comprehensively compares methods for gene regulatory network inference submitted through the DREAM5 challenge. It demonstrates that integration of predictions from multiple methods shows the most...
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Article
Open AccessGene networks in Drosophila melanogaster: integrating experimental data to predict gene function
Discovering the functions of all genes is a central goal of contemporary biomedical research. Despite considerable effort, we are still far from achieving this goal in any metazoan organism. Collectively, the ...
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Chapter and Conference Paper
Limitations of Pseudogenes in Identifying Gene Losses
The loss of previously established genes has been proposed as a major force in evolutionary change. While the sequencing of many new species offers the opportunity to identify cases of gene loss, the best meth...
