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<!DOCTYPE html>
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<h2>Tools</h2>
<p class="lead">This page contains the tools and software packages we have developed here at UCSF or previously at other institutions. Please visit our <a href="https://github.com/goodarzilab">GitHub page</a> for our latest releases.</p>
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<a class="btn btn-primary btn-block btn-lg" href='https://github.com/goodarzilab/pypage'><strong>pyPAGE</strong>: Pathway Analysis of Gene Expression in Python</a>
<h2>A python package for efficient and powered gene-set enrichment analysis.</h2>
<h3>Related publications:</h3>
Bakulin A, Teyssier NM, Kampmann M, Khoroshkin M✝, <strong>Goodarzi H</strong>✝ (2023). Addressing biases in gene-set enrichment analysis: a case study of Alzheimer's Disease. ✝ Co-corresponding authors <a href="https://www.biorxiv.org/content/10.1101/2023.08.13.553133v1"><i class="ai ai-biorxiv"></i></a>
<a class="btn btn-primary btn-block btn-lg" href='https://goodarzilab.shinyapps.io/RBP-Browser'><strong>RBP-Browser</strong>: RNA-binding protein map</a>
<h2>A shiny app for exploration of our RBP post-transcriptional regulatory modules.</h2>
<h3>Related publications:</h3>
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, <strong>Goodarzi H</strong> (2023). Systematic Identification of Post-Transcriptional Regulatory Modules. *Contributed equally; <a href="https://www.biorxiv.org/content/10.1101/2023.02.27.530345v1"><i class="ai ai-biorxiv"></i></a>
<a class="btn btn-primary btn-block btn-lg" href='https://github.com/goodarzilab/APAlog'><strong>APAlog</strong>: Statistical framework for analysis of differential poly-adenylation</a>
<h2>Analysis of altenative poly-A site selection and processing using 3'-end RNA sequencing.</h2>
<h3>Related publications:</h3>
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 <strong>Goodarzi H</strong> (2023). An mRNA processing pathway suppresses metastasis by governing translational control from the nucleus. <strong><em>Nature Cell Bio</em></strong>10.1038/s41556-023-01141-9 *Contributed equally <a href="https://www.nature.com/articles/s41556-023-01141-9"><i class="fa fa-chrome"></i></a><a href="https://www.biorxiv.org/content/10.1101/2021.10.04.463118v1"><i class="ai ai-biorxiv"></i></a>
<a class="btn btn-primary btn-block btn-lg" href='https://github.com/goodarzilab/Ribolog'><strong>Ribolog</strong>: Statistical framework for Ribo-seq data analysis</a>
<h2>Ribosome footprinting pre-processing, QC, and analysis.</h2>
<h3>Related publications:</h3>
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 <strong>Goodarzi H</strong> (2023). An mRNA processing pathway suppresses metastasis by governing translational control from the nucleus. <strong><em>Nature Cell Bio</em></strong>10.1038/s41556-023-01141-9 *Contributed equally <a href="https://www.nature.com/articles/s41556-023-01141-9"><i class="fa fa-chrome"></i></a><a href="https://www.biorxiv.org/content/10.1101/2021.10.04.463118v1"><i class="ai ai-biorxiv"></i></a>
<a class="btn btn-primary btn-block btn-lg" href='https://github.com/goodarzilab/pyTEISER'><strong>pyTEISER</strong>: Modular implementation of TEISER in Python</a>
<h2>Discovery of RNA structural elements using in silico and hybrid RNA SHAPE strategies.</h2>
<h3>Related publications:</h3>
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 <strong>Goodarzi H</strong> (2021). A pro-metastatic splicing program regulated by SNRPA1 interactions with structured RNA elements. <strong><em>Science</em></strong> 372 (6543) eabc7531 <a href="https://science.sciencemag.org/content/372/6543/eabc7531"><i class="fa fa-chrome"></i></a>
<a class="btn btn-primary btn-block btn-lg" href='https://github.com/goodarzilab/PRADA'><strong>PRADA</strong>: Prioritization of Regulatory Pathways based on Analysis of RNA Dynamics Alterations</a>
<h2>Systematic nomination of RNA-binding proteins that govern gene expression alterations in health and disease.</h2>
<h3>Related publications:</h3>
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 <strong>Goodarzi H</strong> (2020). RBMS1 suppresses colon cancer metastasis through targeted stabilization of its mRNA regulon. <strong><em>Cancer Disc</em></strong> 10.1158/2159-8290.CD-19-1375 <a href="https://www.biorxiv.org/content/10.1101/2020.01.22.916205v1"><i class="ai ai-biorxiv"></i></a> <a href="https://cancerdiscovery.aacrjournals.org/content/early/2020/06/06/2159-8290.CD-19-1375"><i class="fa fa-chrome"></i></a>
<a class="btn btn-primary btn-block btn-lg" href='https://github.com/csglab/REMBRANDTS'><strong>REMBRANDTS</strong>: Differential analysis of RNA stability</a>
<h2>Computational estimation of changes in RNA stability from RNA-seq data.</h2>
<h3>Related publications:</h3>
Alkallas R, Fish L, <strong>Goodarzi H</strong>, Najafabadi HS (2017). Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer’s disease. <strong><em>Nature Comm</em></strong> 8: 909. <a href="https://www.nature.com/articles/s41467-017-00867-z"><i class="fa fa-chrome"></i></a>
<a class="btn btn-primary btn-block btn-lg" href='https://github.com/goodarzilab/TEISER'><strong>TEISER</strong>: Discovery of structural elements in RNA</a>
<h2>A software package for systematic discovery of functional structural elements in RNA.</h2>
<h3>Related publications:</h3>
<strong>Goodarzi H</strong>, Zhang S, Buss CG, Fish L, Tavazoie S, Tavazoie SF (2014). Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins. <strong><em>Nature</em></strong> 513, 255-260 <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13466.html"><i class="fa fa-chrome"></i></a><br />
<strong>Goodarzi H</strong>, 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. <strong><em>Nature</em></strong> 485, 264-268. <a href="http://www.nature.com/nature/journal/v485/n7397/full/nature11013.html"><i class="fa fa-chrome"></i></a>
<a class="btn btn-primary btn-block btn-lg" href='https://github.com/goodarzilab/PAGE'><strong>iPAGE</strong>: Pathway-level analysis of gene expression</a>
<h2>A suite of mutual information-based tools for module-level analysis of gene expression.</h2>
<h3>Related publications:</h3>
<strong>Goodarzi H</strong>, 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. <strong><em>Nature</em></strong> 485, 264-268. <a href="http://www.nature.com/nature/journal/v485/n7397/full/nature11013.html"><i class="fa fa-chrome"></i></a><br />
<strong>Goodarzi H</strong>*, Elemento O*, Tavazoie S (2009). Revealing Global Regulatory Perturbations across Human Cancers. <strong><em>Mol Cell</em></strong> 36:900-11. *contributed equally <a href="http://www.cell.com/molecular-cell/fulltext/S1097-2765(09)00857-0"><i class="fa fa-chrome"></i></a>
<a class="btn btn-primary btn-block btn-lg" href='https://github.com/goodarzilab/FIRE'><strong>FIRE</strong>: Finding informative regulatory elements</a>
<h2>A motif discovery and characterization program based on mutual information.</h2>
<h3>Related publications:</h3>
<strong>Goodarzi H</strong>*, Elemento O*, Tavazoie S (2009). Revealing Global Regulatory Perturbations across Human Cancers. <strong><em>Mol Cell</em></strong> 36:900-11. *contributed equally <a href="http://www.cell.com/molecular-cell/fulltext/S1097-2765(09)00857-0"><i class="fa fa-chrome"></i></a><br />
Elemento O*, Slonim N*, Tavazoie S (2007). A universal framework for regulatory element discovery across all genomes and data-types. <strong><em>Mol Cell</em></strong> 28:337-50. *contributed equally <a href="https://www.sciencedirect.com/science/article/pii/S1097276507006661"><i class="fa fa-chrome"></i></a>
<a class="btn btn-primary btn-block btn-lg" href='https://iget.c2b2.columbia.edu'><strong>iGET</strong>: Integrated Genomics Exploration Tools</a>
<h2>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.</h2>
<h3>Related publications:</h3>
<strong>Goodarzi H</strong>, 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. <strong><em>Nature</em></strong> 485, 264-268. <a href="http://www.nature.com/nature/journal/v485/n7397/full/nature11013.html"><i class="fa fa-chrome"></i></a><br />
<strong>Goodarzi H</strong>*, Elemento O*, Tavazoie S (2009). Revealing Global Regulatory Perturbations across Human Cancers. <strong><em>Mol Cell</em></strong> 36:900-11. *contributed equally <a href="http://www.cell.com/molecular-cell/fulltext/S1097-2765(09)00857-0"><i class="fa fa-chrome"></i></a><br />
Elemento O*, Slonim N*, Tavazoie S (2007). A universal framework for regulatory element discovery across all genomes and data-types. <strong><em>Mol Cell</em></strong> 28:337-50. *contributed equally <a href="https://www.sciencedirect.com/science/article/pii/S1097276507006661"><i class="fa fa-chrome"></i></a>
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