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Recent technologies have made it cost-effective to collect diverse types of genome-wide data. Computational methods are needed to combine these data to create a comprehensive view of a given disease or a biological process. Similarity network fusion (SNF) solves this problem by constructing networks of samples (e.g., patients) for each available data type(More)
High-throughput RNA sequencing (RNA-seq) promises to revolutionize our understanding of genes and their role in human disease by characterizing the RNA content of tissues and cells. The realization of this promise, however, is conditional on the development of effective computational methods for the identification and quantification of transcripts from(More)
Rheumatoid arthritis (RA) affects millions world-wide. While anti-TNF treatment is widely used to reduce disease progression, treatment fails in ∼one-third of patients. No biomarker currently exists that identifies non-responders before treatment. A rigorous community-based assessment of the utility of SNP data for predicting anti-TNF treatment efficacy in(More)
High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data exploration and analysis capabilities. Although most existing tools for HTS data analysis are developed for either automated (e.g. genotyping) or visualization (e.g. genome browsing) purposes, such(More)
Identifying microRNA signatures for the different types and subtypes of cancer can result in improved detection, characterization and understanding of cancer and move us towards more personalized treatment strategies. However, using microRNA's differential expression (tumour versus normal) to determine these signatures may lead to inaccurate predictions and(More)
Articles nAture methods | ADVANCE ONLINE PUBLICATION | and focusing only on common patterns can miss valuable complementary information. One recent machine-learning approach, iCluster 7 , uses a joint latent variable model for integrative clustering. Though powerful, iCluster and related machine-learning approaches 4 do not scale to the full spectrum of(More)
in the author list. This has now been corrected in the HTML; the PDF version of the paper was correct from the time of publication. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise(More)
Identifying genes associated with complex human diseases is one of the main challenges of human genetics and computational medicine. To answer this question, millions of genetic variants get screened to identify a few of importance. To increase the power of identifying genes associated with diseases and to account for other potential sources of protein(More)
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