1. This page lists various projects I have worked on during the years. In some I have led their development (like the WASP, AS-DB, or SNAP), in others I wrote/designed specific modules (like libB and ScoreGene). For each project you can find a short description and a link to the relevant website.

  2. BulletWASP: Website for Alternative Splicing Prediction
    A webtool for prediction and analysis of condition specific alternative splicing.
    WASP is a web application that predicts whether or not an exon is alternatively spliced, and if so, how its splicing depends on different cellular conditions, such as tissue type. Users can click on the above tabs to view curated exons that were also profiled using microarray data, or view de novo predictions for additional exons for which experimental data is not available. The application also maps putative regulatory elements in primary transcript sequence that is nearby regulated exons. It can be used to scan specific genes or exons of interest (eg, an exon that has been linked with a specific phenotype) in search of regulatory elements, and to perform genome-wide scans to identify exons with common regulatory patterns (eg, exons regulated in embryonic tissues).

  3. BulletAS-DB:
    A shared database for alternative splicing data.
    We have build a web interface for an underlying database, aimed to facilitate and coordinate our research efforts in alternative splicing. We aim to have information like genomic sequences, micro array reads, sequencing reads, motif predictions etc. all linked for ease of use. We are currently working to expand the underlying DB and add more useful features to its web interface, to make this a highly useful tool not just for us but for the research community at large.

  4. BulletSNAP: SequeNce Analysis Platform
    A generic platform to carry out sequence analysis tasks
    We have build a web interface for a set of tools for sequence analysis, commonly used in our lab. Using an underlying DB like the AS DB described above, it enables users to share resources while managing their own accounts. A user can manage his own resources by uploading/downloading/deleting data and can run the various analysis tools like motif finding or mapping. A user can also use one algorithm’s output as input for another, creating a pipeline. The tool set was already applied successfully by members of the Blencowe lab (see for example here). A subset of the tools are also currently utilized by Prof. Bejerano’s lab in Stanford in an on going collaboration. We plan to make SNAP a useful tool for the research community by turning it into a package that other labs can install.

  5. BulletScoreGene
    A gene expression data analysis toolkit
    ScoreGenes is a data analysis toolkit designed for large sets of gene expressions over various experiments. ScoreGenes includes methods for evaluating data sets, discovering informative genes that are differentially expressed across the classes, classifying the experiments using supervised learning algorithms, and clustering the genes using semi-supervised learning method. This toolkit efficiently handles large data sets.

  6. BulletLibB
    Probabilistic Graphical models library.
    LibB is a huge C++ library implementing algorithms for learning probabilistic graphical models. It was developed in Prof. Friedman’s lab, where I did my PhD.