Mahmoud Ghandi

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Recent studies have revealed that ARID1A, encoding AT-rich interactive domain 1A (SWI-like), is frequently mutated across a variety of human cancers and also has bona fide tumor suppressor properties. Consequently, identification of vulnerabilities conferred by ARID1A mutation would have major relevance for human cancer. Here, using a broad screening(More)
Oligomers of length k, or k-mers, are convenient and widely used features for modeling the properties and functions of DNA and protein sequences. However, k-mers suffer from the inherent limitation that if the parameter k is increased to resolve longer features, the probability of observing any specific k-mer becomes very small, and k-mer counts approach a(More)
UNLABELLED We present a new R package for training gapped-kmer SVM classifiers for DNA and protein sequences. We describe an improved algorithm for kernel matrix calculation that speeds run time by about 2 to 5-fold over our original gkmSVM algorithm. This package supports several sequence kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard(More)
Jun 2012-present • Developing state-of-the-art computational methods for integrative analysis of large-scale biological data including next generation sequencing (DNA, RNAseq), proteomics (RPPA, TK-Luminex, Mass Spec), Metabolomics and Epigenetic data. Applying these methods to predict sensitivities to drug treatment and shRNA gene knockdown, find new(More)
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