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.

pyPAGE: Pathway Analysis of Gene Expression in Python

A python package for efficient and powered gene-set enrichment analysis.

Related publications:

Bakulin A, Teyssier NM, Kampmann M, Khoroshkin M✝, Goodarzi H✝ (2023). Addressing biases in gene-set enrichment analysis: a case study of Alzheimer's Disease. ✝ Co-corresponding authors RBP-Browser: RNA-binding protein map

A shiny app for exploration of our RBP post-transcriptional regulatory modules.

Related publications:

Khoroshkin MS*, Buyan A*, Dodel M*, Navickas A, Yu J, Trejo F, Doty A, Baratam R, Zhou S, Joshi T, Miglani S, Choi MH, Subramanyam V, Modi H, Corces R, Markett D, Kulakovskiy I, Mardakheh FK, Goodarzi H (2023). Systematic Identification of Post-Transcriptional Regulatory Modules. *Contributed equally; APAlog: Statistical framework for analysis of differential poly-adenylation

Analysis of altenative poly-A site selection and processing using 3'-end RNA sequencing.

Related publications:

Navickas A*, Asgharian H*, Winkler J, Fish L, Garcia K, Markett D, Dodel M, Culbertson B, Miglani S, Joshi T, Nguyen P, Zhang S, Stevers N, Hwang H, Mardakheh F, Goga A, and Goodarzi H (2023). An mRNA processing pathway suppresses metastasis by governing translational control from the nucleus. Nature Cell Bio10.1038/s41556-023-01141-9 *Contributed equally Ribolog: Statistical framework for Ribo-seq data analysis

Ribosome footprinting pre-processing, QC, and analysis.

Related publications:

Navickas A*, Asgharian H*, Winkler J, Fish L, Garcia K, Markett D, Dodel M, Culbertson B, Miglani S, Joshi T, Nguyen P, Zhang S, Stevers N, Hwang H, Mardakheh F, Goga A, and Goodarzi H (2023). An mRNA processing pathway suppresses metastasis by governing translational control from the nucleus. Nature Cell Bio10.1038/s41556-023-01141-9 *Contributed equally pyTEISER: Modular implementation of TEISER in Python

Discovery of RNA structural elements using in silico and hybrid RNA SHAPE strategies.

Related publications:

Fish L, Khoroshkin M, Navickas A, Garcia K, Culbertson B, Hänisch B, Zhang S, Nguyen HCB, Soto L, Dermit M, Mardakheh FK, Molina H, Alarcón C, Najafabadi HS, and Goodarzi H (2021). A pro-metastatic splicing program regulated by SNRPA1 interactions with structured RNA elements. Science 372 (6543) eabc7531 PRADA: Prioritization of Regulatory Pathways based on Analysis of RNA Dynamics Alterations

Systematic nomination of RNA-binding proteins that govern gene expression alterations in health and disease.

Related publications:

Yu J, Naviskas A, Asgharian H, Culbertson B, Fish L, Garcia K, Olegario JP, Dermit M, Dodel M, Hanisch B, Liu Y, Weinberg EM, Dienstmann R, Warren RS, Mardakheh F, and Goodarzi H (2020). RBMS1 suppresses colon cancer metastasis through targeted stabilization of its mRNA regulon. Cancer Disc 10.1158/2159-8290.CD-19-1375 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 package 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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