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