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ISMB 2013 Learning Subgroup-Specific Regulatory Interactions and Regulator Independence with PARADIGM

Paper Abstract

Supplementary Data Files

ISMB 2010 PAthway Representation and Analysis by Direct Inference on Graphical Models

Paper Abstract

This code is provided for research purposes to scientists at non-profit organizations. All other use is strictly prohibited. For further details please contact University of California, Santa Cruz or Five3 Genomics, LLC ( Get the code on github


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Accurately assessing the state of a patient's genome is one of the most powerful tools in the emerging field of personalized medicine. Let Five3 Genomics apply its leading genomic analyses to rapidly discover variants in a patient's raw genomics data using sequencing and chip-based technologies.

We annotate all variants against a knowledge database comprising all known and probable disease-associated genes to rank the genomic alterations that have the highest clinical relevance. When applied to cancer tumor/normal samples, our analysis is capable of quickly identifying genomic alterations that could lead to tumorigenesis for a fraction of the cost of conventional approaches.

Mutation & SNP Discovery
Highly-accurate Bayesian approach to identify germline and somatic variants.
Variant Annotation
Identify variants causing alterations in proteins and if they've been seen before in other cancers.
Structural Variants
Find rearrangements causing fusions or explain copy number alterations.


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Data transfer is one of the largest challenges associated with the analysis of sequencing data. Our high speed transfer client Transporter is capable of transferring at blazing speeds while encrypting data on-the-fly using military-grade algorithms.

Transfers at line speed
Capable of transfering as fast as your connection to the internet.
Fully encrypted
Uses the same encryption as the US Military for Top Secret documents.
Streamlined annotation process
Our annotation wizard makes processing your sequencing data simple and intuitive.