Research Summary

Cancer, fundamentally, is a disease of disordered gene expression. Cancer cells rely on deregulated expression of oncogenic and tumor suppressive pathways to initiate and maintain the transformation process. Thus, delineating how cancer cells achieve such pathologic gene expression states is a crucial step towards understanding and ultimately treating cancer as a disease. Towards achieving this goal, my laboratory employs a systems biological and multidisciplinary approach that integrates computational and experimental strategies to identify and characterize key regulatory programs that underlie cancer progression. The systems-level frameworks implemented in our lab ensure a truly unbiased and systematic approach to studying this key biological challenge. Such bottom-up and agnostic approaches are crucial for discovering pathways that fall outside of our prior knowledge of regulatory interactions and would otherwise remain hidden in a top-down reductionist framework.

Lab website: http://goodarzilab.ucsf.edu

Research Funding

  • July 1, 2021 - June 30, 2026 - The RNA structural code underlying pathological regulation of RNA splicing in metastasis , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01CA244634
  • July 1, 2019 - June 30, 2024 - An antisense RNA-mediated regulatory program that drives cancer metastasis , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01CA240984
  • September 1, 2017 - August 31, 2022 - Targeted regulation of transcript stability through RNA methylation and intron retention , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01GM123977
  • May 1, 2016 - April 30, 2020 - Systematic dissection of an aberrant splicing program driving cancer metastasis , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R00CA194077
  • July 21, 2015 - April 30, 2016 - Structural RNA elements and their roles in post-transcriptional regulation , Principal Investigator . Sponsor: NIH, Sponsor Award ID: K99CA194077

Education

University of Tehran, B.S., 2006, Biotechnology
Princeton University, Ph.D., 2010, Molecular Biology
Princeton University, Postdoctoral Associate, 2012, Systems Biology
Rockefeller University, Postdoctoral Fellow, 2016, Cancer Systems Biology

Honors & Awards

  • 2022
    CZ Biohub Investigator
  • 2022
    Vilcek Prize for Creative Promise in Biomedical Sciences
  • 2021
    Mark Foundation ASPIRE Award
  • 2020 
    AACR-MPM Oncology Foundation Transformative Cancer Research
  • 2017
    AAAS Martin and Rose Wachtel Cancer Research Award
  • 2015
    Blavatnik Regional Awards for Young Scientists
  • 2015
    NIH K99/R00 Pathway to Independence Award
  • 2015
    Tri-Institutional Breakout Prize for Junior Investigators
  • 2014
    Ruth L. Kirschstein National Research Service Award (T32CA009673)
  • 2014
    RUCCTS/CDDS/SCBN Pilot Project Award
  • 2012
    Anderson Cancer Center Postdoctoral Fellowship at Rockefeller University
  • 2006
    William G. Bowen Merit Fellowship
  • 2005
    Top undergraduate student in the Department of Biotechnology (University of Tehran)
  • 2002
    University of Tehran fellowship for IBO medalists
  • 2002
    Silver medal in the 13th International Biology Olympiad in Riga, Latvia
  • 2001
    Gold medal in the 4th National Biology Olympiad in Tehran, Iran
  • 2001
    Member, Young Scholar’s Club (Tehran, Iran)

Selected Publications

  1. Jesse Stone Handler, Zijie Li, Rachel Dveirin, Jessica Lin, Weixiang Fang, James Forsmo, Hani Goodarzi, Elana J. Fertig, Reza Kalhor. Effect of clonal competition model of PDAC liver metastasis on a pan-carcinoma gene signature of metastatic potential. Journal of Clinical Oncology. 2025 Jun 1; 43(16_suppl).  View on PubMed
  2. Momen-Roknabadi A, Karimzadeh M, Chen NC, Cavazos TB, Wang J, Ku J, Degtiar A, Krishnan A, Hernandez M, Gebala M, Huang A, Chen S, Nguyen D, Lam T, Hanna R, Fish L, Smith AJ, Sekhon S, Yen J, Gregg J, Li H, Hormozdiari F, Behsaz B, Hartwig A, Goodarzi H, Schwartzberg L, Alipanahi B. Detection of Early-Stage Colorectal Cancer Using Cell-Free oncRNA Biomarkers and Artificial Intelligence. Clin Cancer Res. 2025 May 14.  View on PubMed
  3. Deniz Guney Olgun, Simai Wang, Saeid Parast, Ali Shilatifard, Hani Goodarzi, Vijay Ramani. Abstract 5035: Barcode-free demultiplexing of HiFi reads using natural genetic variation. Cancer Research. 2025 Apr 21; 85(8_Supplement_1):5035-5035.  View on PubMed
  4. Cui H, Tejada-Lapuerta A, Brbic M, Saez-Rodriguez J, Cristea S, Goodarzi H, Lotfollahi M, Theis FJ, Wang B. Towards multimodal foundation models in molecular cell biology. Nature. 2025 Apr; 640(8059):623-633.  View on PubMed
  5. Moussavi-Baygi R, Ryan MJ, Sim W, Hoelscher SB, Luga V, Chandrakumar AA, Hoes L, Cha J, Lee YS, Herm K, Doron B, Ding CKC, Stohr BA, Jin P, Nadkarni T, Fang X, Haryono M, Nguyen A, Karthaus WR, Sawyers C, Feng FY, Goodarzi H, Bose R. Stochastically Emergent Tumors offer in vivo whole genome interrogation of cancer evolution from non-malignant precursors. bioRxiv. 2025 Mar 18.  View on PubMed
  6. Micaela E. Consens, Cameron Dufault, Michael Wainberg, Duncan Forster, Mehran Karimzadeh, Hani Goodarzi, Fabian J. Theis, Alan Moses, Bo Wang. Transformers and genome language models. Nature Machine Intelligence. 2025 Mar 1; 7(3):346-362.  View on PubMed
  7. Kovalski JR, Sarioglu G, Subramanyam V, Hernandez G, Rademaker G, Oses-Prieto JA, Slota M, Mohan N, Yiakis K, Liu I, Wen KW, Kim GE, Miglani S, Burlingame AL, Goodarzi H, Perera RM, Ruggero D. Functional screen identifies RBM42 as a mediator of oncogenic mRNA translation specificity. Nat Cell Biol. 2025 Mar; 27(3):518-529.  View on PubMed
  8. Nakagawa R, Beardsley A, Durney S, Hayward MK, Subramanyam V, Meyer NP, Wismer H, Goodarzi H, Weaver VM, Van de Mark D, Goga A. Tumor Cell Spatial Organization Directs EGFR/RAS/RAF Pathway Primary Therapy Resistance through YAP Signaling. bioRxiv. 2025 Jan 31.  View on PubMed
  9. Yang MG, Richter HJ, Wang S, McNally CP, Harris N, Dhillon S, Maresca M, de Wit E, Willenbring H, Maher J, Goodarzi H, Ramani V. Pervasive and programmed nucleosome distortion patterns on single mammalian chromatin fibers. bioRxiv. 2025 Jan 22.  View on PubMed
  10. Crawford KD, Khan AG, Lopez SC, Goodarzi H, Shipman SL. High throughput variant libraries and machine learning yield design rules for retron gene editors. Nucleic Acids Res. 2025 Jan 11; 53(2).  View on PubMed
  11. Khoroshkin M, Zinkevich A, Aristova E, Yousefi H, Lee SB, Mittmann T, Manegold K, Penzar D, Raleigh DR, Kulakovskiy IV, Goodarzi H. A generative framework for enhanced cell-type specificity in rationally designed mRNAs. bioRxiv. 2024 Dec 31.  View on PubMed
  12. McKeever PM, Sababi AM, Sharma R, Xu Z, Xiao S, McGoldrick P, Ketela T, Sato C, Moreno D, Visanji N, Kovacs GG, Keith J, Zinman L, Rogaeva E, Goodarzi H, Bader GD, Robertson J. Single-nucleus transcriptome atlas of orbitofrontal cortex in amyotrophic lateral sclerosis with a deep learning-based decoding of alternative polyadenylation mechanisms. bioRxiv. 2024 Dec 16.  View on PubMed
  13. Karimzadeh M, Momen-Roknabadi A, Cavazos TB, Fang Y, Chen NC, Multhaup M, Yen J, Ku J, Wang J, Zhao X, Murzynowski P, Wang K, Hanna R, Huang A, Corti D, Nguyen D, Lam T, Kilinc S, Arensdorf P, Chau KH, Hartwig A, Fish L, Li H, Behsaz B, Elemento O, Zou J, Hormozdiari F, Alipanahi B, Goodarzi H. Deep generative AI models analyzing circulating orphan non-coding RNAs enable detection of early-stage lung cancer. Nat Commun. 2024 11 21; 15(1):10090.  View on PubMed
  14. Ostrowski MS, Yang MG, McNally CP, Abdulhay NJ, Wang S, Renduchintala K, Irkliyenko I, Biran A, Chew BTL, Midha AD, Wong EV, Sandoval J, Jain IH, Groth A, Nora EP, Goodarzi H, Ramani V. The single-molecule accessibility landscape of newly replicated mammalian chromatin. Cell. 2025 Jan 09; 188(1):237-252.e19.  View on PubMed
  15. Hani Goodarzi. Abstract I004: Systematic Discovery and Annotation of Cancer Emergent Orphan non-coding RNAs in human Cancers. Molecular Cancer Therapeutics. 2024 Nov 14; 23(11_Supplement):i004-i004.  View on PubMed
  16. Ge AY, Arab A, Dai R, Navickas A, Fish L, Garcia K, Asgharian H, Goudreau J, Lee S, Keenan K, Pappalardi MB, McCabe MT, Przybyla L, Goodarzi H, Gilbert LA. A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation. Sci Rep. 2024 10 29; 14(1):25940.  View on PubMed
  17. Khoroshkin M, Buyan A, Dodel M, Navickas A, Yu J, Trejo F, Doty A, Baratam R, Zhou S, Lee SB, Joshi T, Garcia K, Choi B, Miglani S, Subramanyam V, Modi H, Carpenter C, Markett D, Corces MR, Mardakheh FK, Kulakovskiy IV, Goodarzi H. Author Correction: Systematic identification of post-transcriptional regulatory modules. Nat Commun. 2024 Oct 28; 15(1):9277.  View on PubMed
  18. Naghipourfar M, Chen S, Howard MK, Macdonald CB, Saberi A, Hagen T, Mofrad MRK, Coyote-Maestas W, Goodarzi H. A Suite of Foundation Models Captures the Contextual Interplay Between Codons. bioRxiv. 2024 Oct 13.  View on PubMed
  19. Kovalski JR, Sarioglu G, Subramanyam V, Hernandez G, Rademaker G, Oses-Prieto JA, Slota M, Mohan N, Yiakis K, Liu I, Wen KW, Kim GE, Miglani S, Burlingame AL, Goodarzi H, Perera RM, Ruggero D. Functional screen for mediators of onco-mRNA translation specificity. bioRxiv. 2024 Oct 11.  View on PubMed
  20. S. Wang, V. Böhnert, A. Joseph, V. Sudaryo, G. Skariah, J. Swinderman, F. Yu, V. Subramanyam, D. Wolf, X. Lyu, L. Gilbert, L. van’t Veer, H. Goodarzi, L. Li. 261 (PB249): ENPP1 is an innate immune checkpoint of the anticancer cGAMPSTING pathway in breast cancer. European Journal of Cancer. 2024 Oct 1; 211:114778.  View on PubMed

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