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1.  Fastbreak: a tool for analysis and visualization of structural variations in genomic data 
Genomic studies are now being undertaken on thousands of samples requiring new computational tools that can rapidly analyze data to identify clinically important features. Inferring structural variations in cancer genomes from mate-paired reads is a combinatorially difficult problem. We introduce Fastbreak, a fast and scalable toolkit that enables the analysis and visualization of large amounts of data from projects such as The Cancer Genome Atlas.
PMCID: PMC3605143  PMID: 23046488
Cancer genomics; Structural variation; Translocation
2.  Inference of Boolean Networks Using Sensitivity Regularization 
The inference of genetic regulatory networks from global measurements of gene expressions is an important problem in computational biology. Recent studies suggest that such dynamical molecular systems are poised at a critical phase transition between an ordered and a disordered phase, affording the ability to balance stability and adaptability while coordinating complex macroscopic behavior. We investigate whether incorporating this dynamical system-wide property as an assumption in the inference process is beneficial in terms of reducing the inference error of the designed network. Using Boolean networks, for which there are well-defined notions of ordered, critical, and chaotic dynamical regimes as well as well-studied inference procedures, we analyze the expected inference error relative to deviations in the networks' dynamical regimes from the assumption of criticality. We demonstrate that taking criticality into account via a penalty term in the inference procedure improves the accuracy of prediction both in terms of state transitions and network wiring, particularly for small sample sizes.
PMCID: PMC3171400  PMID: 18604289

Results 1-2 (2)