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<h1>Publications</h1>
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<div class="center">
<h2>Preprints</h2>
</div>
<p><li>Apostolides M, Choi B, Navickas A, Saberi A, Soto LM, <strong>Goodarzi H</strong>✝, and Najafabadi HS✝ (2024). Accurate isoform quantification by joint short- and long-read RNA-sequencing. ✝ Co-corresponding authors <a href="https://www.biorxiv.org/content/10.1101/2024.07.11.603067v1"><i class="ai ai-biorxiv"></i></a></li></p>
<p><li>Wang J, Suh JM, Navickas A, Garcia K, Yin K, Fish L, Cavazos T, Hänisch B, Markett D, Hirst G, Brown-Swigart L, Esserman LJ, van ‘t Veer LJ, and <strong>Goodarzi H</strong> (2024). Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers. <a href="https://www.biorxiv.org/content/10.1101/2024.03.19.585748v1"><i class="ai ai-biorxiv"></i></a></li></p>
<p><li>Connell W, Garcia K, <strong>Goodarzi H</strong>, Keiser MJ (2023). Learning chemical sensitivity reveals mechanisms of cellular response. <a href="https://www.biorxiv.org/content/10.1101/2023.08.26.554851v1"><i class="ai ai-biorxiv"></i></a></li></p>
<p><li>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></li></p>
<p><li>Woo BJ, Moussavi-Baygi M, Karner H, Karimzadeh M, Garcia K, Joshi T, Yin K, Navickas A, Gilbert LA, Wang B, Asgharian H✝, Feng FY✝, <strong>Goodarzi H</strong>✝ (2023). Integrative identification of non-coding regulatory regions driving metastatic prostate cancer. ✝ Co-corresponding authors <a href="https://www.biorxiv.org/content/10.1101/2023.04.14.535921v1"><i class="ai ai-biorxiv"></i></a></li></p>
<p><li>Samuel RM, Navickas A, Maynard A, Gaylord EA, Garcia K, Chat S, Majd H Richter MN, Elder N, Le D, Nguyen P, Shibata B, Llabata ML, Selleri L, Laird SJ, Darmanis S, <strong>Goodarzi H</strong>✝, and Faranak Fattahi✝ (2023). Generation of Schwann cell derived melanocytes from hPSCs identifies pro-metastatic factors in melanoma. *Contributed equally; ✝ Co-corresponding authors <a href="https://www.biorxiv.org/content/10.1101/2023.03.06.531220v1"><i class="ai ai-biorxiv"></i></a></li></p>
<p><li>Ge A*, Arab A*, Navickas A, Fish L, Garcia K, Asgharian H, <strong>Goodarzi H</strong>✝, Gilbert L✝ (2022). A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation. *Contributed equally; ✝ Co-corresponding authors <a href="https://www.biorxiv.org/content/10.1101/2022.12.14.518457v1"><i class="ai ai-biorxiv"></i></a></li></p>
</br></br>
<div class="center">
<h2>2024</h2>
</div>
<p><li>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, Mardakheh FK✝, Kulakovskiy I✝, <strong>Goodarzi H</strong>✝ (2024). Systematic Identification of Post-Transcriptional Regulatory Modules. <strong><em>Nature Comm</em></strong> in press *Contributed equally ✝ Co-corresponding authors <a href="https://www.biorxiv.org/content/10.1101/2023.02.27.530345v1"><i class="ai ai-biorxiv"></i></a></li></p>
<p><li>Khoroshkin MS, Asarnow D, Navickas A, Winters A, Yu J, Zhou SK, Zhou S, Palka C, Fish LC, Ansel M, Cheng Y, Gilbert L, <strong>Goodarzi H</strong> (2024). A systematic search for RNA structural switches across the human transcriptome. <strong><em>Nature Methods</em></strong> in press <a href="https://www.biorxiv.org/content/10.1101/2023.03.11.532161v1"><i class="ai ai-biorxiv"></i></a></li></p>
<p><li>Zirak B, Naghipourfar M, Saberi A, Pouyabahar D, Zarezadeh A, Fish L, Luo L, Huh D, Navickas A✝, Sharifi-Zarchi A✝, <strong>Goodarzi H</strong>✝ (2023). Revealing the Grammar of Small RNA Secretion Using Interpretable Machine Learning. <strong><em>Cell Genomics</em></strong> 4, 100522 ✝ Co-corresponding authors <a href="https://www.cell.com/cell-genomics/fulltext/S2666-979X(24)00064-8"><i class="fa fa-chrome"></i></a> <a href="https://www.biorxiv.org/content/10.1101/2023.04.04.535452v1"><i class="ai ai-biorxiv"></i></a></li></p>
<p><li>Arshadi AK*, Salem M*, Karner H*, Garcia K, Arab A, Yuan JS, <strong>Goodarzi H</strong> (2024). Functional microRNA-Targeting Drug Discovery by Graph-Based Deep Learning. <strong><em>Patterns</em></strong> 10.1016/j.patter.2023.100909 *Contributed equally; <a href="https://www.cell.com/patterns/fulltext/S2666-3899(23)00318-5"><i class="fa fa-chrome"></i></a> <a href="https://www.biorxiv.org/content/10.1101/2023.01.13.524005v1"><i class="ai ai-biorxiv"></i></a></li></p>
<p><li>Chen S, Navickas A✝, <strong>Goodarzi H</strong>✝ (2024). Translational adaptation in breast cancer metastasis and emerging therapeutic opportunities. <strong><em>Trends Pharmacol Sci</em></strong> https://doi.org/10.1016/j.tips.2024.02.002 ✝ Co-corresponding authors <a href="https://www.cell.com/trends/pharmacological-sciences/fulltext/S0165-6147(24)00029-4"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Nanda S*, Wu K*, Ostrowski MS, Clugston AS, Satpathy AS, Sweet-Cordero AE, <strong>Goodarzi H</strong>, Kasinathan S✝, Ramani V✝ (2022). Direct transposition of native DNA for sensitive multimodal single-molecule sequencing. <strong><em>Nature Genetics</em></strong> 56, pages1300–1309 <a href="https://www.nature.com/articles/s41588-024-01748-0"><i class="fa fa-chrome"></i></a> <a href="https://www.biorxiv.org/content/10.1101/2023.04.04.535452v1"><a href="https://www.biorxiv.org/content/10.1101/2022.08.07.502893v2"><i class="ai ai-biorxiv"></i></a></li></p>
</br></br>
<div class="center">
<h2>2023</h2>
</div>
<p><li>Wang S, Böhnert V, Joseph AJ, Sudaryo V, Swinderman J, Yu FB, Lyu X, Skariah G, Subramanyam V, Gilbert LA, <strong>Goodarzi H</strong>, and Lingyin L (2023). ENPP1 is an innate immune checkpoint of the anticancer cGAMP–STING pathway in breast cancer. <strong><em>PNAS</em></strong> 120 (52) e2313693120 <a href="https://www.pnas.org/doi/10.1073/pnas.2313693120"><i class="fa fa-chrome"></i></a> <a href="https://www.biorxiv.org/content/10.1101/2023.06.01.543353v1"><i class="ai ai-biorxiv"></i></a></li></p>
<p><li>Culbertson B*, Garcia K*, Markett D, Asgharian H, Chen L, Fish L, Navickas A, Yu J, Woo B, Nanda S, Rabinowitz J, and <strong>Goodarzi H</strong> (2023). A sense-antisense RNA interaction promotes breast cancer metastasis via regulation of NQO1 expression. <strong><em>Nature Cancer</em></strong> 4, 682–698 *Contributed equally <a href="https://www.nature.com/articles/s43018-023-00554-7"><i class="fa fa-chrome"></i></a> <a href="https://www.biorxiv.org/content/10.1101/2021.10.08.463652v1"><i class="ai ai-biorxiv"></i></a></li></p>
<p><li>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></li></p>
<p><li>Raths F*, Karimzadeh M*, Ing N, Martinez A, Qu Y, Lee T, Mulligan B, Devkota S, Wang B, Giuliano AE, Bose S, <strong>Goodarzi H</strong>✝, Ray EC✝, Cui X✝, Knott SRV✝ (2023). The molecular consequences of androgen activity in the human breast. <strong><em>Cell Genomics</em></strong> 3(3):100272 *Contributed equally; ✝ Co-corresponding authors <a href="https://www.cell.com/cell-genomics/fulltext/S2666-979X(23)00032-0"><i class="fa fa-chrome"></i></a> <a href="https://www.biorxiv.org/content/10.1101/2022.04.22.489095v1"><i class="ai ai-biorxiv"></i></a></li></p>
<p><li>Perez-Pepe M, Desotell AW, Li H, Li W, Han B, Lin Q, Klein DE, Liu Y, <strong>Goodarzi H</strong>, Alarcón CR (2023). 7SK methylation by METTL3 promotes transcriptional activity. <strong><em>Sci Adv</em></strong> 9(19):10.1126/sciadv.ade7500 <a href="https://www.science.org/doi/full/10.1126/sciadv.ade7500"></a></li></p>
<p><li>Linares GR, Li Y, Chang WH, Rubin-Sigler J, Mendonca S, Hong S, Eoh Y, Guo W, Huang YH, Chang J, Tu S, Dorjsuren N, Santana M, Hung ST, Yu J, Perez J, Chickering M, Cheng TY, Huang CC, Lee SJ, Deng HJ, Bach KT, Gray K, Subramanyam V, Rosenfeld J, Alworth SV, <strong>Goodarzi H</strong>, Ichida JK (2023). SYF2 suppression mitigates neurodegeneration in models of diverse forms of ALS. <strong><em>Cell Stem Cell</em></strong> 30(2):171-187.e14 <a href="https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(23)00005-X"></a></li></p>
</br></br>
<div class="center">
<h2>2022</h2>
</div>
<p><li>Earnest-Noble LB, Hsu D, Chen S, Asgharian H, Nandan M, Passarelli MC, <strong>Goodarzi H</strong>✝, Tavazoie SF✝ (2022). Two isoleucyl tRNAs that decode synonymous codons divergently regulate breast cancer metastatic growth by controlling translation of proliferation-regulating genes. <strong><em>Nature Cancer</em></strong> https://doi.org/10.1038/s43018-022-00469-9. ✝ Co-corresponding authors <a href="https://www.nature.com/articles/s43018-022-00469-9"><i class="fa fa-chrome"></i></a> <a href="https://www.biorxiv.org/content/10.1101/2021.04.22.440519v1.full"><i class="ai ai-biorxiv"></i></a></li></p>
<p><li>Furuya H, Sasaki Y, Chen R, Peres R, Hokutan K, Murakami K, Kim N, Chan OTM, Pagano I, Dyrskjøt L, Jensen JB, Malmstrom PU, Segersten U, Sun Y, Arab A, <strong>Goodarzi H</strong>, Goodison S, Rosser CJ. (2022). PAI-1 is a potential transcriptional silencer that supports bladder cancer cell activity. <strong><em>Sci Rep</em></strong> 12(1):12186. <a href="https://www.nature.com/articles/s41598-022-16518-3"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Argouarch AR, Schultz N, Yang AC, Jang Y, Garcia K, Cosme CG, Corrales CI, Nana AL, Karydas AM, Spina S, Grinberg LT, Miller B, Wyss-Coray T, Abyzov A, <strong>Goodarzi H</strong>, Seeley WW, Kao AW (2022). Postmortem Human Dura Mater Cells Exhibit Phenotypic, Transcriptomic and Genetic Abnormalities that Impact their Use for Disease Modeling. <strong><em>Stem Cell Rev Rep</em></strong> 18(8):3050-3065. <a href="https://link.springer.com/article/10.1007/s12015-022-10416-x"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Xiao J, McGill JR, Nasir A, Lekan A, Johnson B, Wilkins DJ, Pearson GW, Tanner K, <strong>Goodarzi H</strong>, Glasgow E, Schlegel R, Agarwal S (2022). Identifying drivers of breast cancer metastasis in progressively invasive subpopulations of zebrafish-xenografted MDA-MB-231. <strong><em>Mol Biomed</em></strong> 3(1):16. <a href="https://link.springer.com/content/pdf/10.1186/s43556-022-00080-5.pdf"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Passarelli MC, Pinzaru AM, Asgharian H, Liberti MV, Heissel S, Molina H, <strong>Goodarzi H</strong>✝, Tavazoie SF✝ (2022). Leucyl-tRNA synthetase is a tumour suppressor in breast cancer and regulates codon-dependent translation dynamics. <strong><em>Nature Cell Biol</em></strong> 13(1):167. ✝ Co-corresponding authors <a href="https://www.nature.com/articles/s41556-022-00856-5"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Navickas A, <strong>Goodarzi H</strong> (2022). A Wnt twist in FTO's role in cancer progression. <strong><em>Nat Cancer</em></strong> 2(6):579-580. <a href="https://www.nature.com/articles/s43018-021-00224-6"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Liu XZ, Rulina A, Choi MH, Pedersen L, Lepland J, Takle ST, Madeleine N, Peters SD, Wogsland CE, Grøndal SM, Lorens JB, <strong>Goodarzi H</strong>, Lønning PE, Knappskog S, Molven A, Halberg N (2022). C/EBPB-dependent adaptation to palmitic acid promotes tumor formation in hormone receptor negative breast cancer. <strong><em>Nat Commun</em></strong> 13(1):69. <a href="https://www.nature.com/articles/s41467-021-27734-2"><i class="fa fa-chrome"></i></a></li></p>
</br></br>
<div class="center">
<h2>2021</h2>
</div>
<p><li>Yogodzinski C, Arab A, Pritchard JR, <strong>Goodarzi H</strong>, Gilbert LA (2021). A global cancer data integrator reveals principles of synthetic lethality, sex disparity and immunotherapy. <strong><em>Genome Med</em></strong> 13(1):167 <a href="https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-00987-8">
<i class="fa fa-chrome"></i></a></li></p>
<p><li>Xu Y, Huangyang P, Wang Y, Xue L, Devericks E, Nguyen HG, Yu X, Oses-Prieto JA, Burlingame AL, Miglani S, <strong>Goodarzi H</strong>, and Ruggero D (2021). ERα is an RNA-binding protein sustaining tumor cell survival and drug resistance. <strong><em>Cell</em></strong> 184(20):5215-5229 <a href="https://www.sciencedirect.com/science/article/pii/S0092867421010473"><i class="fa fa-chrome"> </i></a></li></p>
<p><li>Chen WC, To MD, Westcott PMK, Delrosario R, Kim IJ, Philips M, Tran Q, Bollam SR, <strong>Goodarzi H</strong>, Bayani N, Mirzoeva O, Balmain A (2021). Targeting KRAS4A splicing through the RBM39/DCAF15 pathway inhibits cancer stem cells. <strong><em>Nat Communications</em></strong> 12(1):4288 <a href="https://www.nature.com/articles/s41467-021-24498-7"><i class="fa fa-chrome"> </i></a></li></p>
<p><li>Kuzuoglu-Ozturk D, Hu Z, Rama M, Devericks E, Weiss J, Chiang GG, Worland ST, Brenner SE, <strong>Goodarzi H</strong>, Gilbert LA, Ruggero D. (2021). Revealing molecular pathways for cancer cell fitness through a genetic screen of the cancer translatome. <strong><em>Cell Rep</em></strong> 35(13):109321 <a href="https://www.sciencedirect.com/science/article/pii/S2211124721006975"><i class="fa fa-chrome"> </i></a></li></p>
<p><li>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></li></p>
<p><li>Huh D, Passarelli MC, Gao J, Dusmatova SN, Goin C, Fish L, Pinzaru AM, Molina H, Ren Z, McMillan EA, Asgharian H, <strong>Goodarzi H</strong>, Tavazoie SF (2021). A stress-induced tyrosine-tRNA depletion response mediates codon-based translational repression and growth suppression.<strong><em>The EMBO Journal</em></strong> 40(2):e106696 <a href="https://www.embopress.org/doi/full/10.15252/embj.2020106696"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Zhu XG, Chudnovskiy A, Baudrier L, Prizer B, Liu Y, Ostendorf BN, Yamaguchi N, Arab A, Tavora B, Timson R, Heissel S, de Stanchina E, Molina H, Victora GD, <strong>Goodarzi H</strong>, Birsoy K (2021). Functional Genomics In Vivo Reveal Metabolic Dependencies of Pancreatic Cancer Cells. <strong><em>Cell Metabolism</em></strong> 33(1):211-221.e6 <a href="https://www.sciencedirect.com/science/article/pii/S1550413120305507"><i class="fa fa-chrome"></i></a></li></p>
</br></br>
<div class="center">
<h2>2016 - 2020</h2>
</div>
<p><li>Samuel RM, Majd H, Richter M, et al, Ott M, <strong>Goodarzi H</strong>✝, Fattahi F✝ (2020). Androgen Signaling Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men. <strong><em>Cell Stem Cell</em></strong> 27:876-889. ✝ Co-corresponding authors <a href="https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(20)30547-6"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Zhu, X.G., Chudnovskiy, A., Baudrier, L. et al, <strong>Goodarzi H</strong>, and Birsoy K (2020). Functional Genomics In Vivo Reveal Metabolic Dependencies of Pancreatic Cancer Cells. <strong><em>Cell Metab</em></strong> doi.org/10.1016/j.cmet.2020.10.017 <a href="https://www.sciencedirect.com/science/article/pii/S1550413120305507"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Tavora, B., Mederer, T., Wessel, K.J. et al, <strong>Goodarzi H</strong>, and Tavazoie SF (2020). Tumoural activation of TLR3–SLIT2 axis in endothelium drives metastasis. <strong><em>Nature</em></strong> 586:299-304. <a href="https://www.nature.com/articles/s41586-020-2774-y"><i class="fa fa-chrome"></i></a></li></p>
<p><li>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> 10:1410–23 <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></li></p>
<p><li>Fish L, Navickas A, Culbertson B, Xu Y, Nguyen HCB, Zhang S, Hochman M, Okimoto R, Dill BD, Molina H, Najafabadi HS, Alarcon C, Ruggero D, and <strong>Goodarzi H</strong> (2019). Nuclear TARBP2 Drives Oncogenic Dysregulation of RNA Splicing and Decay. <strong><em>Mol Cell</em></strong> 75(5), 967-81. <a href="https://doi.org/10.1101/389213"><i class="ai ai-biorxiv"></i></a> <a href="https://www.cell.com/molecular-cell/fulltext/S1097-2765(19)30434-4"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Litterman AJ, Kageyama R, Le Tonqueze O, Zhao W, Gagnon JD, <strong>Goodarzi H</strong>, Erle D, and Ansel M (2019). A massively parallel 3′ UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization. <strong><em>Genome Res</em></strong> doi:10.1101/gr.242552.118. <a href="https://genome.cshlp.org/content/early/2019/05/31/gr.242552.118"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Mauer J, Sindelar M, Despic V, Guez T, Hawley BR, Vasseur J, Rentmeister A, Gross S, Pellizzoni L, Debart F, <strong>Goodarzi H</strong>, Jaffrey S (2019). FTO controls reversible m6Am RNA methylation during snRNA biogenesis. <strong><em>Nature Chem Biol</em></strong> 15, 340–347. <a href="https://www.nature.com/articles/s41589-019-0231-8"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Fish L, Zhang S, Yu J, Culbertson B, Zhou A, Goga A, <strong>Goodarzi H</strong> (2018). Cancer cells exploit an orphan RNA to drive metastatic progression. <strong><em>Nature Med</em></strong> 24, 1743-51. <a href="https://www.nature.com/articles/s41591-018-0230-4"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Knott SRV, Wagenblast E, Khan S, et al., <strong>Goodarzi H</strong>, Poulogiannis G, Hannon G (2018). Asparagine bioavailability governs metastasis in a model of breast cancer. <strong><em>Nature</em></strong> 554:378–381. <a href="https://www.nature.com/articles/nature25465"><i class="fa fa-chrome"></i></a></li></p>
<p><li>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></li></p>
<p><li><strong>Goodarzi H</strong> (2017). Charting the “unknown unknowns” of cancer progression. <strong><em>Sci Transl Med</em></strong> 9 (400), eaao0959. <a href="http://stm.sciencemag.org/content/9/400/eaao0959.full?ijkey=l3dBm/4zTI6A6&keytype=ref&siteid=scitransmed"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Kingham PT, Nguyen CB, Zheng J, Konstantinidis IT, Sadot E, Shia J, Kuk D, Zhang S, Saltz L, D’Angelica M, Jarnagin WR, <strong>Goodarzi H</strong>✝, Tavazoie SF✝ (2016). MicroRNA-203 predicts human survival after resection of colorectal liver metastasis. <strong><em>Oncotarget</em></strong> 8:18821-31. ✝ Co-corresponding authors <a href="http://www.impactjournals.com/oncotarget/misc/linkedout.php?pii=13816"><i class="fa fa-chrome"></i></a></li></p>
<p><li><strong>Goodarzi H</strong>*✝, Nguyen HCB, Zhang S, Dill BD, Molina H, Tavazoie SF✝ (2016). Modulated expression of specific tRNAs drives gene expression and cancer progression. <strong><em>Cell</em></strong> 165, 1416-1427. *Contributed equally; ✝ Co-corresponding authors <a href="http://www.cell.com/cell/fulltext/S0092-8674(16)30649-3"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Lee H, <strong>Goodarzi H</strong>, Tavazoie SF, Alarcon CR (2016). TMEM2 Is a SOX4-Regulated Gene That Mediates Metastatic Migration and Invasion in Breast Cancer. <strong><em>Cancer Res</em></strong> 76(17):4994-5005.<a href="http://cancerres.aacrjournals.org/cgi/pmidlookup?view=long&pmid=27328729"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Hwang HW, Park CY, <strong>Goodarzi H</strong>, Fak JJ, Mele A, Moore MJ, Saito Y, Darnell RB (2016). PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A) Site Usage. <strong><em>Cell Rep</em></strong> 15(2):423-435.<a href="http://www.sciencedirect.com/science/article/pii/S2211124716302649"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Nguyen A, Yoshida M, <strong>Goodarzi H</strong>, Tavazoie SF (2016). Highly variable cancer subpopulations that exhibit enhanced transcriptome variability and metastatic fitness. <strong><em>Nature Comm</em></strong> 7: 11246.<a href="http://www.nature.com/ncomms/2016/160503/ncomms11246/full/ncomms11246.html"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Fish L, Pencheva N*, <strong>Goodarzi H</strong>*, Tran H, Yoshida M, Tavazoie SF (2016). Muscleblind-like 1 suppresses breast cancer metastatic colonization and stabilizes metastasis suppressor transcripts. <strong><em>Genes & Dev</em></strong> 30: 386-398. *Contributed equally <a href="http://genesdev.cshlp.org/content/30/4/386.short"><i class="fa fa-chrome"></i></a></li></p>
</br></br>
<div class="center">
<h2>2012 - 2015</h2>
</div>
<p><li>Alarcon C, <strong>Goodarzi H</strong>, Lee H, Liu X, Tavazoie S, Tavazoie SF (2015). HNRNPA2B1 Is a Mediator of m6A-Dependent Nuclear RNA Processing Events. <strong><em>Cell</em></strong> 162: 1299-1308. <a href="http://www.cell.com/cell/abstract/S0092-8674(15)01024-7"><i class="fa fa-chrome"></i></a></li></p>
<p><li><strong>Goodarzi H</strong>, Liu X, Nguyen HCB, Fish L, Tavazoie SF (2015). Endogenous tRNA-Derived Fragments Suppress Breast Cancer Progression via YBX1 Displacement. <strong><em>Cell</em></strong> 161: 790-802. <a href="http://www.cell.com/cell/abstract/S0092-8674(15)00318-9"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Furlow PW, Zhang S, Soong ST, Halberg N, <strong>Goodarzi H</strong>, Mangrum C, Wu G, Elemento O, Tavazoie S (2015). Mechanosensitive pannexin-1 channels mediate microvascular metastatic cell survival. <strong><em>Nature Cell Bio</em></strong> 17, 943-952. <a href="http://www.nature.com/ncb/journal/v17/n7/abs/ncb3194.html"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Alarcon CR, Lee H*, <strong>Goodarzi H</strong>*, Halberg N, Tavazoie S (2015). N<sup>6</sup>-methyladenosine marks primary microRNAs for processing. <strong><em>Nature</em></strong> 519, 482-485. *Contributed equally <a href="http://www.nature.com/nature/journal/v519/n7544/full/nature14281.html?WT.ec_id=NATURE-20150326"><i class="fa fa-chrome"></i></a></li></p>
<p><li><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></li></p>
<p><li>Oikonomou P*, <strong>Goodarzi H</strong>*, Tavazoie S (2014). Systematic Identification of Regulatory Elements in Conserved 3? UTRs of Human Transcripts. <strong><em>Cell Reports</em></strong> 7(1): 281-292. *Contributed equally <a href="http://www.cell.com/cell-reports/fulltext/S2211-1247(14)00159-4"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Freddolino PL*, <strong>Goodarzi H</strong>*, Tavazoie S (2013). Revealing the genetic basis of natural bacterial phenotypic divergence. <strong><em>J. Bacteriol.</em></strong> doi:10.1128/JB.01039-13 *Contributed equally <a href="http://jb.asm.org/content/early/2013/12/04/JB.01039-13"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Chiu IM, Morimoto ETA, <strong>Goodarzi H</strong>, et al., Tavazoie S, Myers RM, Maniatis T (2013). A Neurodegeneration-Specific Gene-Expression Signature of Acutely Isolated Microglia from an Amyotrophic Lateral Sclerosis Mouse Model. <strong><em>Cell Reports</em></strong> 4(2): 385-401 <a href="http://www.cell.com/cell-reports/fulltext/S2211-1247(13)00296-9"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Freddolino PL*, <strong>Goodarzi H</strong>*, Tavazoie S (2012). Fitness landscape transformation through a single amino acid change in the Rho terminator. <strong><em>PLoS Genetics</em></strong> Vol. 8, e1002744. *Contributed equally <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002744"><i class="fa fa-chrome"></i></a></li></p>
<p><li><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></li></p>
</br></br>
<div class="center">
<h2>2007 - 2011</h2>
</div>
<p><li> Korpal M, Ell BJ, Buffa FM, Ibrahim T, Blanco MA, Celia-Terrassa T, Mercatali L, Khan Z, <strong>Goodarzi H</strong>, et al. (2011). Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization. <strong><em>Nature Med</em></strong> 17(9):1048-9. <a href="http://www.nature.com/nm/journal/vaop/ncurrent/full/nm.2401.html"><i class="fa fa-chrome"></i></a></li></p>
<p><li><strong>Goodarzi H</strong>, Bennet BD, et al. (2010). Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in <em>E. coli</em>. <strong><em>Mol Syst Biol</em></strong> 6:278. <a href="http://www.nature.com/msb/journal/v6/n1/full/msb201033.html"><i class="fa fa-chrome"></i></a></li></p>
<p><li><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></li></p>
<p><li>Najafabadi HS*, <strong>Goodarzi H</strong>*, Salavati R (2009). Universal function-specificity of codon usage. <strong><em>Nucl Acids Res</em></strong> 37(21):7014-7023. *contributed equally <a href="http://nar.oxfordjournals.org/cgi/content/full/gkp792"><i class="fa fa-chrome"></i></a></li></p>
<p><li><strong>Goodarzi H</strong>, Hottes AK, Tavazoie S (2009). Global discovery of adaptive mutations. <strong><em>Nat Methods</em></strong> 6(8):581-3. <a href="http://www.nature.com/nmeth/journal/v6/n8/abs/nmeth.1352.html"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Amini S, <strong>Goodarzi H</strong>, Tavazoie S (2009). Genetic dissection of an exogenously induced biofilm in laboratory and clinical isolates of <em>E. coli</em>. <strong><em>PLoS Pathogens</em></strong> 5:e1000432. <a href="http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1000432"><i class="fa fa-chrome"></i></a></li></p>
<p><li><strong>Goodarzi H</strong>, Torabi N, Najafabadi HS, Archetti M (2008). Amino acid and codon usage profiles: adaptive changes in the frequency of amino acids and codons. <strong><em>Gene</em></strong> 407(1-2):30-41. <a href="https://www.sciencedirect.com/science/article/pii/S0378111907004982"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Elahi E, Shafaghati Y, Asadi S, Absalan F, <strong>Goodarzi H</strong>, et al. (2007). Intragenic SNP haplotypes associated with 84dup18 mutation in TNFRSF11A in four FEO pedigrees suggest three independent origins for this mutation. <strong><em>J Bone Miner Metab</em></strong> 25(3):159-64. <a href="http://www.springerlink.com/content/68w0g65743860562/"><i class="fa fa-chrome"></i></a></li></p>
<p><li><strong>Goodarzi H</strong>, Katanforoush A, Torabi N, Najafabadi HS (2007). Solvent accessibility, residue charge and residue volume, the three ingredients of a robust amino acid substitution matrix. <strong><em>J Theor Biol</em></strong> 245(4):715-25. <a href="https://www.sciencedirect.com/science/article/pii/S002251930600573X"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Torabi N, <strong>Goodarzi H</strong>, Shateri Najafabadi H. (2007). The case for an error minimizing set of coding amino acids. <strong><em>J Theor Biol</em></strong> 244(4):737-44. <a href="https://www.sciencedirect.com/science/article/pii/S0022519306004310"><i class="fa fa-chrome"></i></a></li></p>
</br></br>
<div class="center">
<h2>2004 - 2006</h2>
</div>
<p><li>Najafabadi HS, <strong>Goodarzi H</strong>, Torabi N, Banihosseini SS.(2006). Applying a neural network to predict the thermodynamic parameters for an expanded nearest-neighbor model. <strong><em>J Theor Biol</em></strong> 238(3):657-65. <a href="https://www.sciencedirect.com/science/article/pii/S0022519305002729"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Marashi SA, <strong>Goodarzi H</strong>, Sadeghi M, Eslahchi C, Pezeshk H (2006). Importance of RNA secondary structure information for yeast donor and acceptor splice site predictions by neural networks. <strong><em>Comput Biol Chem</em></strong> 30(1):50-7. <a href="https://www.sciencedirect.com/science/article/pii/S1476927105001106"><i class="fa fa-chrome"></i></a></li></p>
<p><li><strong>Goodarzi H</strong>, Shateri Najafabadi H, Torabi N (2005). On the coevolution of genes and genetic code. <strong><em>Gene</em></strong> 362:133-40. <a href="https://www.sciencedirect.com/science/article/pii/S0378111905005020"><i class="fa fa-chrome"></i></a></li></p>
<p><li>Najafabadi HS, <strong>Goodarzi H</strong>, Torabi N (2005). Optimality of codon usage in Escherichia coli due to load minimization. <strong><em>J Theor Biol</em></strong> 237(2):203-9. <a href="https://www.sciencedirect.com/science/article/pii/S0022519305001621"><i class="fa fa-chrome"></i></a></li></p>
<p><li><strong>Goodarzi H</strong>, Najafabadi HS, Hassani K, Nejad HA, Torabi N (2005). On the optimality of the genetic code, with the consideration of coevolution theory by comparison of prominent cost measure matrices. <strong><em>J Theor Biol</em></strong> 235(3):318-25. <a href="https://www.sciencedirect.com/science/article/pii/S0022519305000378"><i class="fa fa-chrome"></i></a></li></p>
<p><li><strong>Goodarzi H</strong>, Shateri Najafabadi H, Torabi N (2005). Designing a neural network for the constraint optimization of the fitness functions devised based on the load minimization of the genetic code. <strong><em>Biosystems</em></strong> 81(2):91-100. <a href="https://www.sciencedirect.com/science/article/pii/S0303264705000080"><i class="fa fa-chrome"></i></a></li></p>
<p><li><strong>Goodarzi H</strong>, Nejad HA, Torabi N (2005). On the optimality of the genetic code, with the consideration of termination codons. <strong><em>Biosystems</em></strong> 77(1-3):163-73. <a href="https://www.sciencedirect.com/science/article/pii/S0303264704000942"><i class="fa fa-chrome"></i></a></li></p>
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