Tools

This page contains the tools and software packages we have developed here at UCSF or previously at other institutions. Please visit our GitHub page for our latest releases.

REMBRANDTS: Differential analysis of RNA stability

Computational estimation of changes in RNA stability from RNA-seq data.

Related publications:

Alkallas R, Fish L, Goodarzi H, Najafabadi HS (2017). Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer’s disease. Nature Comm 8: 909. TEISER: Discovery of structural elements in RNA

A software packge for systematic discovery of functional structural elements in RNA.

Related publications:

Goodarzi H, Zhang S, Buss CG, Fish L, Tavazoie S, Tavazoie SF (2014). Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins. Nature 513, 255-260
Goodarzi H, Najafabadi HS, Oikonomou P, Greco TM, Fish L, Salavati R, Cristea IM, Tavazoie S (2012). Systematic discovery of structural elements governing stability of mammalian messenger RNAs. Nature 485, 264-268. iPAGE: Pathway-level analysis of gene expression

A suite of mutual information-based tools for module-level analysis of gene expression.

Related publications:

Goodarzi H, Najafabadi HS, Oikonomou P, Greco TM, Fish L, Salavati R, Cristea IM, Tavazoie S (2012). Systematic discovery of structural elements governing stability of mammalian messenger RNAs. Nature 485, 264-268.
Goodarzi H*, Elemento O*, Tavazoie S (2009). Revealing Global Regulatory Perturbations across Human Cancers. Mol Cell 36:900-11. *contributed equally FIRE: Finding informative regulatory elements

A motif discovery and characterization program based on mutual information.

Related publications:

Goodarzi H*, Elemento O*, Tavazoie S (2009). Revealing Global Regulatory Perturbations across Human Cancers. Mol Cell 36:900-11. *contributed equally
Elemento O*, Slonim N*, Tavazoie S (2007). A universal framework for regulatory element discovery across all genomes and data-types. Mol Cell 28:337-50. *contributed equally iGET: Integrated Genomics Exploration Tools

Web portal to a suite of tools for exploring biological pathways and DNA/RNA/protein regulatory elements associated with large-scale gene expression and protein behavior dynamics hosted by the Tavazoie lab at Columbia University.

Related publications:

Goodarzi H, Najafabadi HS, Oikonomou P, Greco TM, Fish L, Salavati R, Cristea IM, Tavazoie S (2012). Systematic discovery of structural elements governing stability of mammalian messenger RNAs. Nature 485, 264-268.
Goodarzi H*, Elemento O*, Tavazoie S (2009). Revealing Global Regulatory Perturbations across Human Cancers. Mol Cell 36:900-11. *contributed equally
Elemento O*, Slonim N*, Tavazoie S (2007). A universal framework for regulatory element discovery across all genomes and data-types. Mol Cell 28:337-50. *contributed equally


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