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.

Increasing coverage of transcription factor position weight matrices through domain-level homology.

Transcription factor-DNA interactions, central to cellular regulation and control, are commonly described by position weight matrices (PWMs). These matrices are frequently used to predict transcription factor binding sites in regulatory regions of DNA to complement and guide further experimental investigation. The DNA sequence preferences of transcription factors, encoded in PWMs, are dictated primarily by select residues within the DNA binding domain(s) that interact directly with DNA.

EPEPT: a web service for enhanced P-value estimation in permutation tests.

Background: In computational biology, permutation tests have become a widely used tool to assess the statistical significance of an event under investigation. However, the common way of computing the P-value, which expresses the statistical significance, requires a very large number of permutations when small (and thus interesting) P-values are to be accurately estimated. This is computationally expensive and often infeasible.

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments.

Background: High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires.

Results: Existing software solutions provide static and well-established algorithms in a restrictive package.

Complicated bronchiolitis: another use for your bedside ultrasound in the emergency department.

Diaphragmatic eventration or diaphragmatic herniations are congenital defect that involve abnormal development of the diaphragm and stretching of the muscular fibers leading to protrusion of abdominal organs into the thoracic cavity. Left sided defects will lead to stomach contents into the chest cavity while, right sided defects will have bowel or liver in the thoracic cavity. Infants with Congenital diaphragmatic hernia often present with respiratory distress that can be life-threatening unless treated appropriately.